From 9c83f923ace6d1fd338c7c83daa605ccd65643ee Mon Sep 17 00:00:00 2001 From: sn248 Date: Sun, 10 Nov 2024 16:34:21 -0500 Subject: [PATCH] code refactoring Just just code cleaning after fixing abstolerance --- DESCRIPTION | 2 +- R/RcppExports.R | 2 +- docs/.nojekyll | 1 + docs/404.html | 127 ++-- docs/LICENSE-text.html | 121 +--- docs/articles/index.html | 123 +--- docs/articles/my-vignette.html | 656 ++++++++++++++++++ .../figure-html/unnamed-chunk-4-1.png | Bin 85662 -> 45396 bytes .../header-attrs-2.1/header-attrs.js | 12 - docs/authors.html | 167 ++--- docs/index.html | 189 +++++ docs/pkgdown.css | 87 ++- docs/pkgdown.js | 4 +- docs/pkgdown.yml | 7 +- docs/reference/cvode.html | 324 ++++----- docs/reference/cvodes.html | 344 ++++----- docs/reference/cvsolve.html | 274 +++----- docs/reference/ida.html | 213 ++---- docs/reference/index.html | 162 +---- docs/sitemap.xml | 14 + inst/include/cvodes/cvodes.h | 3 +- inst/include/nvector/nvector_parallel.h | 6 +- inst/include/nvector/nvector_serial.h | 6 +- .../sundials/sundials_adaptcontroller.h | 4 + inst/include/sundials/sundials_config.in | 3 +- .../sundials/sundials_hip_policies.hpp | 6 +- inst/include/sunlinsol/sunlinsol_ginkgo.hpp | 8 + .../sunlinsol/sunlinsol_kokkosdense.hpp | 4 +- .../sunmatrix/sunmatrix_kokkosdense.hpp | 6 +- man/cvodes.Rd | 2 +- src/Makevars | 4 +- src/cvode.cpp | 293 ++++---- src/cvodes.cpp | 248 +++---- src/cvsolve.cpp | 16 +- src/ida.cpp | 183 +++-- src/sundials/cvode/cvode.c | 30 +- src/sundials/cvode/cvode_bandpre.c | 9 +- src/sundials/cvode/cvode_bbdpre.c | 16 +- src/sundials/cvode/cvode_diag.c | 27 +- src/sundials/cvode/cvode_fused_stubs.c | 10 +- src/sundials/cvode/cvode_impl.h | 31 +- src/sundials/cvode/cvode_io.c | 4 + src/sundials/cvode/cvode_ls.c | 5 +- src/sundials/cvode/cvode_nls.c | 6 - 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allowed values are Staggered (default)", "STG" (for Staggered) or "SIM" (for Simultaneous) +#'@param SensType Sensitivity Type - allowed values are "STG" (for Staggered, default) or "SIM" (for Simultaneous) #'@param ErrCon Error Control - allowed values are TRUE or FALSE (default) #'@returns A data frame. First column is the time-vector, the next y * p columns are sensitivities of y1 w.r.t all parameters, then y2 w.r.t all parameters etc. y is the state vector, p is the parameter vector #'@example /inst/examples/cvs_Roberts_dns.r diff --git a/docs/.nojekyll b/docs/.nojekyll new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/docs/.nojekyll @@ -0,0 +1 @@ + diff --git a/docs/404.html b/docs/404.html index 8338231..58ac873 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,66 +1,27 @@ - - - - + + + + - Page not found (404) • sundialr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + - - - -
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All vignettes

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sundialr - An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers
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sundialr - An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers
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+
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-

Developed by Satyaprakash Nayak.

+
+

Developed by Satyaprakash Nayak.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 2.1.1.

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+ + - - - + diff --git a/docs/articles/my-vignette.html b/docs/articles/my-vignette.html new file mode 100644 index 0000000..79d0ab5 --- /dev/null +++ b/docs/articles/my-vignette.html @@ -0,0 +1,656 @@ + + + + + + + +sundialr - An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers • sundialr + + + + + + + + + + + +
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+

sundialr - An Interface to ‘SUNDIALS’ Ordinary +Differential Equation (ODE) Solvers

+

Satyaprakash +Nayak

+ +

2024-11-10

+ + Source: vignettes/my-vignette.Rmd + + +
+ + + +
+

Introduction +

+

Ordinary Differential Equations (ODEs) describe the rate of change of +dependent variables with respect to a single independent variable and +are used in many fields to model behavior of the system. There are many +good C libraries available to solve (i.e., integrate +systems of ODEs) and SUNDIALS +available from the Lawrence Livermore National Laboratory is a one of +the most popular and well-respected C library for solving +non-stiff and stiff systems of ODEs.

+

Currently, this package provides an interface to the +CVODE and CVODES function (serial version) in +the library which is used to solve ODEs (or Initial Value Problems) and +calculate sensitivities.

+

The four exported functions from the package are:

+
    +

  • cvode - An interface to the CVODE +function in SUNDIALS to solve a system of ODEs.

    • +

  • cvodes - An interface to the CVODES +function in SUNDIALS to calculate forward sensitivites with +respect to parameters of the ODE system.

    • +

  • ida - An interface to the IDA function +in SUNDIALS to solve a system of Differential-Algebraic +Equations (DAEs).

    • +

  • cvsolve - A convenient interface to solve a system +of ODEs with discontinuities in solution.

    • +
+

In future, we plan to provide interface for the other solvers (i.e., +IDA/IDAS and ARCODE in the library also. Right +now, this package serves as a test case for providing an interface to +the SUNDIALS library for R users.

+

One of the advantage of using this package is that all the source +code of the SUNDIALS library is bundled with the package +itself, so it does not require the SUNDIALS library to be +installed on the machine separately (which is sometimes non trivial on a +Windows machine).

+
+
+

System of ODEs +

+

As described in the link above, the problem is from chemical +kinetics, and consists of the following three rate equations:

+

dy1dt=−.04×y1+104×y2×y3dy2dt=.04×y1−104×y2×y3−3×107×y22dy3dt=3×107×y22 +\begin{aligned} +\frac{dy_1}{dt} &= -.04 \times y_1 + 10^4 \times y_2 \times y_3 \\ +\frac{dy_2}{dt} &= .04 \times y_1 - 10^4 \times y_2 \times y_3 - 3 \times 10^7 \times y_2^2 \\ +\frac{dy_3}{dt} &= 3 \times 10^7 \times y_2^2 +\end{aligned} +

+

with time interval from +t=0.0t = 0.0 +to +t=4×1010t = 4 \times 10^{10} +and initial conditions: +y1=1.0,y2=y3=0 y_1 = 1.0 , ~y_2 = y_3 = 0

+

The problem is stiff.

+

The original example , While integrating the system, also uses the +rootfinding feature to find the points at which

+

y1=1×10−4 y_1 = 1 \times 10^{-4} +or at which +y3=0.01 y_3 = 0.01 +but currently root-finding is not supported in this version. As in the +original example, this package also solves the problem with the +BDF method, Newton iteration with the SUNDENSE +dense linear solver, however, without a user-supplied Jacobian routine +(unlike the original example). The future versions may include an +ability to provide Jacobian calculated analytically or via automatic +differentiation. CVODE uses a scalar relative tolerance and +a vector absolute tolerance (which can be provided as an input). Output +is printed in decades from +t=0.4t = 0.4 +to +t=4×1010t = 4 \times 10^{10} +in this example.

+
+
+

Writing the Differential Equations +

+
+

Using R +

+

Differential equations can be written as an R function +or as an Rcpp function. Differential equations function +must be written as

+
+function(t, y, p){
+  # code to write differential equations
+  # using parameter vector (p) and state/entity vector (y)
+  # should return `ydot`, the vector representing
+  # rate of change of entities in `y`
+  # length of `ydot` must be equal to `y1
+}
+

where t represents time, y is the vector +describing the values of states/entities of the ODE system at time +t and p is the vector of parameters used to +define the ODEs. The output of this function is a vector of rate of +change of entities of y.

+

The key aspect to keep in mind is that the signature of the function +must be function(t,y,p). As an example, we try to solve the +cv_Roberts_dns.c problem described above, the original code +can be found here. +An example of an R function is as follows:

+
+ODE_R <- function(t, y, p){
+
+   ## initialize the derivative vector
+   ydot <- vector(mode = "numeric", length = length(y))
+   
+   ## p (parameter vector input) is  [-0.04 1e04 3e07]
+   
+   ydot[1] = p[1]*y[1] + p[2]*y[2]*y[3]
+   ydot[2] = -p[1]*y[1] - p[2]*y[2]*y[3] - p[3]*y[2]*y[2]
+   ydot[3] = p[3]*y[2]*y[2]
+
+   ydot      ## return ydot
+}
+

where p is a parameter vector with the values +[-0.04 1e04 3e07].

+
+
+

Using Rcpp +

+

Also, since this package using Rcpp to bundle the C +code, we can use the notation used in Rcpp to describe the +system of ODEs. The cv_Roberts_dns problem describe above +can be described in an Rcpp function as follows (indices in +C++ start from 0, functions need to declare +their return type, here NumericVector and every expression +ends in a semicolon, ;) :

+
#include <Rcpp.h>
+using namespace Rcpp;
+
+// [[Rcpp::export]]
+NumericVector ODE_Rcpp (double t, NumericVector y){
+
+  // Initialize ydot filled with zeros
+  NumericVector ydot(y.length());
+
+  // p (parameter vector) is [-0.04 1e04 3e07]
+  ydot[0] = p[0] * y[0] + p[1] * y[1] * y[2];
+  ydot[1] = -p[0]*y[0] - p[1]*y[1]*y[2] - p[2]*y[1]*y[1]
+  ydot[2] = p[2] * y[1] * y[1];
+
+  return ydot;
+
+}
+

The above is a re-write of the cvRoberts_dns.c example +in the documentation of CVODE.

+
+
+

Putting everything together +

+

The entire R file to create right hand side of ODE +function (which calculates rates of change) is as follows (also found here):

+
+# ODEs described by an R function
+ODE_R <- function(t, y, p){
+
+   ## initialize the derivative vector
+   ydot <- vector(mode = "numeric", length = length(y))
+   
+   ## p (parameter vector) is  [-0.04 1e04 3e07]
+   
+   ydot[1] = p[1]*y[1] + p[2]*y[2]*y[3]
+   ydot[2] = -p[1]*y[1] - p[2]*y[2]*y[3] - p[3]*y[2]*y[2]
+   ydot[3] = p[3]*y[2]*y[2]
+
+   ydot      ## return ydot
+}
+
+# ODEs can also be described using Rcpp
+Rcpp::sourceCpp(code = '
+
+#include <Rcpp.h>
+using namespace Rcpp;
+
+// [[Rcpp::export]]
+NumericVector ODE_Rcpp (double t, NumericVector y){
+
+  // Initialize ydot filled with zeros
+  NumericVector ydot(y.length());
+
+  // p (parameter vector) is [-0.04 1e04 3e07]
+  ydot[0] = p[0] * y[0] + p[1] * y[1] * y[2];
+  ydot[1] = -p[0]*y[0] - p[1]*y[1]*y[2] - p[2]*y[1]*y[1]
+  ydot[2] = p[2] * y[1] * y[1];
+
+  return ydot;
+
+}')
+
+# Generate time vector, IC and call cvode to solve the equations
+# R code to genrate time vector, IC and solve the equations
+time_vec <- c(0.0, 0.4, 4.0, 40.0, 4E2, 4E3, 4E4, 4E5, 4E6, 4E7, 4E8, 4E9, 4E10)
+IC <- c(1,0,0)
+params <- c(0.04, 10000, 30000000)
+reltol <- 1e-04
+abstol <- c(1e-8,1e-14,1e-6)
+
+## Solving the ODEs using cvode function
+df1 <- cvode(time_vec, IC, ODE_R , params, reltol, abstol)           ## using R
+df2 <- cvode(time_vec, IC, ODE_Rcpp , params, reltol, abstol)        ## using Rcpp
+
+## Check that both solutions are identical
+# identical(df1, df2)
+

The final output is the df1 matrix in which first column +is time, second, third and fourth column are the values of +y1, y2 and y3 respectively.

+
> df1
+       [,1]         [,2]         [,3]       [,4]
+ [1,] 0e+00 1.000000e+00 0.000000e+00 0.00000000
+ [2,] 4e-01 9.851641e-01 3.386242e-05 0.01480205
+ [3,] 4e+00 9.055097e-01 2.240338e-05 0.09446793
+ [4,] 4e+01 7.158016e-01 9.185043e-06 0.28418924
+ [5,] 4e+02 4.505209e-01 3.222826e-06 0.54947590
+ [6,] 4e+03 1.832217e-01 8.943516e-07 0.81677741
+ [7,] 4e+04 3.898091e-02 1.621669e-07 0.96101893
+ [8,] 4e+05 4.936971e-03 1.984450e-08 0.99506301
+ [9,] 4e+06 5.170103e-04 2.069098e-09 0.99948299
+[10,] 4e+07 5.204927e-05 2.082078e-10 0.99994795
+[11,] 4e+08 5.184946e-06 2.073989e-11 0.99999482
+[12,] 4e+09 5.246212e-07 2.098486e-12 0.99999948
+[13,] 4e+10 6.043000e-08 2.417200e-13 0.99999994
+
+
+
+

Solving a system of Differential-Algebraic Equations +

+

An interface to the IDA solver is also provided to solve +a system of Differential-Algebraic equations. A system of +differential-algebraic equations is a system of equations containing +both differential and algebraic equations and can be written as +F(ẋ(t),x(t),t)=0 +F(\dot{x}(t), x(t), t) = 0 + The equations for such a system are +written in terms of residuals and require both the value of +x0x_0 +and +ẋ0\dot{x}_0 +as the initial conditions. Writing the previously solved equations as a +system of DAEs, we have, +ẏ1=−p1y1+p2y2y3ẏ2=p1y1−p2y2y3−p3y221=y1+y2+y3 +\begin{aligned} +\dot{y}_1 &= -p_1y_1 + p_2y_2y_3 \\ +\dot{y}_2 &= p_1y_1 - p_2y_2y_3 - p_3y_2^2 \\ +1 &= y_1 + y_2 + y_3 +\end{aligned} + The above system of DAEs can be written +in terms of residuals as

+

res1=−p1y1+p2y2y3−ẏ1res2=p1y1−p2y2y3−p3y22−ẏ2res3=y1+y2+y3−1 +\begin{aligned} +res_1 &= -p_1y_1 + p_2y_2y_3 - \dot{y}_1 \\ +res_2 &= p_1y_1 - p_2y_2y_3 - p_3y_2^2 - \dot{y}_2\\ +res_3 &= y_1 + y_2 + y_3 - 1 +\end{aligned} + Here is the complete code for solving +this system of DAEs,

+
+DAE_R <- function(t, y, ydot, p){
+
+  # vector containing the residuals
+  res = vector(mode = "numeric", length = length(y))
+
+  # R indices start from 1
+  res[1] <- -0.04 * y[1] + 10000 * y[2] * y[3] - ydot[1]
+  res[2] <- -res[1] - 30000000 * y[2] * y[2] - ydot[2]
+  res[3] <- y[1] + y[2] + y[3] - 1.0
+
+  res
+}
+
+# R code to genrate time vector, IC and solve the equations
+time_vec <- c(0.0, 0.4, 4.0, 40.0, 4E2, 4E3, 4E4, 4E5, 4E6, 4E7, 4E8, 4E9, 4E10)
+IC <- c(1,0,0)                  # Initial value of y
+IRes <- c(-0.4, 0.4, 0)         # Initial value of ydot
+params <- c(0.04, 10000, 30000000)
+reltol <- 1e-04
+abstol <- c(1e-8,1e-14,1e-6)
+
+## Solving the DAEs using the ida function
+df1 <- sundialr::ida(time_vec, IC, IRes, DAE_R , params, reltol, abstol)
+
+
+

Solving an ODE system with discontinuties in solution +

+

The cvsolve function defined in sundialr +package provides a convenience interface to solve ODEs with one or more +discontinuities in solution. An example of such a system of ODEs would +be pharmacokinetics of a drug with repeated bolus administration. Let’s +look at a simple example of multiple doses of a drug with a first-order +degradation administered intravenously. The ODE system for the drug is +dCdt=−kel*C +\frac{dC}{dt} = -k_{el} * C + where +CC +is the concentration of the drug and +kelk_{el} +is the elimination rate of the drug. The +RR +code for such a system is

+
+ODErepeated_R <- function(t, y, p){
+
+  # vector containing the right hand side gradients
+  ydot = vector(mode = "numeric", length = length(y))
+
+  # R indices start from 1
+  ydot[1] = -p[1]*y[1]
+
+  ydot
+
+}
+

We also need to define when the multiple doses are given and the +state to which they are to be applied (here to be applied to the only +state in the model, +CC). +This is provided via the +EventsEvents +dataframe (here, +TDOSETDOSE +or the dosing dataframe).

+
+TDOSE <- data.frame(ID = 1, TIMES = c(0, 10, 20, 30, 40, 50), VAL = 100)
+TDOSE
+#>   ID TIMES VAL
+#> 1  1     0 100
+#> 2  1    10 100
+#> 3  1    20 100
+#> 4  1    30 100
+#> 5  1    40 100
+#> 6  1    50 100
+

TDOSE is a data frame with the index of the state to +which discontinuity is to be applied (represented by ID), +the times at which the discontinuity is to be applied (represented by +TIMES) at the value to be added to the +value of the state at that time-point. A typical example would be +addition of the dose amount to the value of the concentration at the +specified times, e.g., the TDOSE data frame says that a +value of 100 is to be added to the concentration of the 1st +state (the only state in this system) at the times specified by the +TIMES column. In summary,

+
    +

  • ID represents the index of the state with +discontinuity

    • +

  • TIMES represents the times at which discontinutiy is +applied

    • +

  • VAL represents the value added to +the value of the state at specified times.

    • +
+

The complete code for simulating such a system is

+
+# Example of solving a set of ODEs with multiple discontinuities using cvsolve
+# A simple One dimensional equation, y = -0.1 * y
+# ODEs described by an R function
+ODE_R <- function(t, y, p){
+
+  # vector containing the right hand side gradients
+  ydot = vector(mode = "numeric", length = length(y))
+
+  # R indices start from 1
+  ydot[1] = -p[1]*y[1]
+
+  ydot
+
+}
+
+# R code to generate time vector, IC and solve the equations
+TSAMP <- seq(from = 0, to = 100, by = 0.1)      # sampling time points
+IC <- c(1)
+params <- c(0.1)
+
+# A dataset describing the dosing at times at which additions to y[1] are to be done
+# Names of the columns don't matter, but they MUST be in the order of state index,
+# times and Values at discontinuity.
+TDOSE <- data.frame(ID = 1, TIMES = c(0, 10, 20, 30, 40, 50), VAL = 100)
+
+df1 <- sundialr::cvsolve(TSAMP, c(1), ODE_R, params)         # solving without any discontinuity
+df2 <- sundialr::cvsolve(TSAMP, c(1), ODE_R, params, TDOSE)  # solving with discontinuity
+
+## Plot the solution with discontinuities
+## first column is time, second column is the state
+time <- df2[,1]
+y1 <- df2[,2]
+plot(time, y1, type = "l", lty = 1, main = "An ODE system with discontinuties", frame.plot = F)
+

+

Note that in the example above, TSAMP is the sampling +time at which the solution is desired. Also, even though an Initial +Value of +y1y_1 +of 1 is provided by the IC parameter, it is overwritten by +the value of 100 provided in the TDOSE data frame. In +general, the values in the initial conditions are overwritten by values +in the Events input.

+
+
+

System of ODEs for Parameter Sensitivities +

+

Sensitivity with respect to the parameters of the ODE system can be +calculated using CVODES function. This package implements +Forward Sensitivity Analysis from CVODES function (see the +example cvRoberts_FSA_dns.c from the link here). +Briefly, given the ODE system as described below

+

dy1dt=−p1y1+p2y2y3dy2dt=p1y1−p2y2y3−p3y22dy3dt=p3y22 +\begin{aligned} +\frac{dy_1}{dt} &= -p_1y_1 + p_2y_2y_3 \\ +\frac{dy_2}{dt} &= p_1y_1 - p_2y_2y_3 - p_3y_2^2 \\ +\frac{dy_3}{dt} &= p_3y_2^2 +\end{aligned} + with the same initial conditions as +above (i.e., +y1=0,y2=y3=0y_1 = 0, y_2 = y_3 = 0) +and +p1=0.04,p2=104,p3=3×107p_1 = 0.04, \quad p_2 = 10^4, \quad p_3 = 3\times10^7. +The system of Sensitivity equations (taken from +cvs_guide.pdf) that is solved can be given by +dsdt=[−p1p2y3p2y2p1−p2y3−2p3y2−p2y202p3y20]si+∂f∂pi,si(t0)=[000],i=1,2,3 +\begin{aligned} +\frac{ds}{dt} = +\left[\begin{array} +{ccc} +-p_1 & p_2y_3 & p_2y_2 \\ +p_1 & -p_2y_3-2p_3y_2 & -p_2y_2 \\ +0 & 2p_3y_2 & 0 +\end{array}\right]s_i + \frac{\partial f}{\partial p_i}, +\quad s_i(t_0) = +\left[\begin{array} {c} 0 \\ 0 \\ 0 \end{array}\right], \quad i = 1, 2, 3 +\end{aligned} + where +∂f∂p1=[−y1y10],∂f∂p2=[y2y3−y2y30],∂f∂p3=[0−y22y22] +\frac{\partial f}{\partial p_1} = \left[\begin{array} {c} -y_1 \\ y_1 \\ 0 \end{array}\right], +\quad \frac{\partial f}{\partial p_2} = \left[\begin{array} {c} y_2y_3 \\ -y_2y_3 \\ 0 \end{array}\right], +\quad +\frac{\partial f}{\partial p_3} = \left[\begin{array} {c} 0 \\ -y_2^2 \\ y_2^2 \end{array}\right] + In the original CVODES +interface from SUNDIALS, the sensitivity equations can +either be provided by the user or can be calculated using numerical +interpolation by the solver. Here, I have only included the numerical +interpolation version and currently the user cannot specify the +sensitivity equations. However, in the future versions I will provide an +ability to specify user-defined Jacobian as well as user-defined +sensitivity equations.

+

Also, currently, forward sensitivities are calculated with respect to +all parameters of the system. I plan to provide in future, an ability to +specify specific particular parameters for which sensitivity is desired. +Currently, SIMULATENOUS and STAGGERED methods +of sensitivity calculations from the SUNDIALS library are +supported in this package.

+
+
+

Calculation of Sensitivities using CVODES +

+

Once, the system of ODEs has been defined using the instructions +provided above, sensitivities can be easily calculated using the +cvodes function using the function call below (the entire +code can be found at this link)

+
+df1 <- cvodes(time_vec, IC, ODE_R , params, reltol, abstol,"STG",F)  ## using R
+df2 <- cvodes(time_vec, IC, ODE_Rcpp , params, reltol, abstol,"STG",F)  ## using Rcpp
+

The additional arguments in cvodes specify the +senstivity calculation method to be used (STG for +STAGGERED or SIM for +SIMULATENOUS) and flag for error control (either +T or F).

+

The output of cvodes is a matrix with number of rows +equal to the length of the time vector (time_vec) and the +number of columns being equal to length of (y +×\timesp + 1). The first columns is for time. Currently, the +sensitivity of every enitity is calculated with respect to every +parameter in model. For example, for the current model with +3 entities (ODEs) and 3 parameters, a total of +9 sensitivities are calculated at each output time, +i.e. y1 w.r.t p1, p2, +p3, y2 w.r.t. p1, +p2, p3 and so on. The first 3 +(length(y)) columns give sensitivity w.r.t the first +parameter, the next 3 (length(y)) columns give sensitivity +w.r.t the second parameter and so on.

+

In the Sensitivity Matrix output for the systems of equations +described above, the first column gives output time, the next +3 columns provide sensitivity of y1, +y2 and y3 w.r.t first parameter (say +p1), the next three columns provide sensitivity of +y1, y2 and y3 w.r.t. the second +parameter (p2) and so on. The output Sensitivity Matrix is +given below. The sensitivity values match with the values provided in +the CVODES documentation.

+
> df1
+       [,1]          [,2]          [,3]         [,4]         [,5]          [,6]          [,7]          [,8]          [,9]        [,10]
+ [1,] 0e+00  0.000000e+00  0.000000e+00 0.000000e+00 0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00 0.000000e+00
+ [2,] 4e-01 -3.561085e-01  3.902252e-04 3.557183e-01 9.483149e-08 -2.132509e-10 -9.461823e-08 -1.573297e-11 -5.289692e-13 1.626194e-11
+ [3,] 4e+00 -1.876130e+00  1.792229e-04 1.875951e+00 2.961233e-06 -5.830758e-10 -2.960650e-06 -4.932970e-10 -2.762408e-13 4.935732e-10
+ [4,] 4e+01 -4.247395e+00  4.592812e-05 4.247349e+00 1.372964e-05 -2.357270e-10 -1.372941e-05 -2.288274e-09 -1.138015e-13 2.288387e-09
+ [5,] 4e+02 -5.958192e+00  3.545986e-06 5.958189e+00 2.273754e-05 -2.260807e-11 -2.273752e-05 -3.789554e-09 -4.994795e-14 3.789604e-09
+ [6,] 4e+03 -4.750132e+00 -5.991971e-06 4.750138e+00 1.880937e-05  2.312156e-11 -1.880939e-05 -3.134824e-09 -1.875976e-14 3.134843e-09
+ [7,] 4e+04 -1.574902e+00 -2.761679e-06 1.574905e+00 6.288404e-06  1.100645e-11 -6.288415e-06 -1.047876e-09 -4.536508e-15 1.047881e-09
+ [8,] 4e+05 -2.363168e-01 -4.584043e-07 2.363173e-01 9.450741e-07  1.832930e-12 -9.450760e-07 -1.574929e-10 -6.362045e-16 1.574935e-10
+ [9,] 4e+06 -2.566355e-02 -5.105587e-08 2.566361e-02 1.026491e-07  2.042044e-13 -1.026493e-07 -1.711080e-11 -6.851356e-17 1.711087e-11
+[10,] 4e+07 -2.597859e-03 -5.190342e-09 2.597864e-03 1.039134e-08  2.076100e-14 -1.039136e-08 -1.732552e-12 -6.930923e-18 1.732559e-12
+[11,] 4e+08 -2.601996e-04 -5.199259e-10 2.602002e-04 1.040802e-09  2.079717e-15 -1.040804e-09 -1.737821e-13 -6.951356e-19 1.737828e-13
+[12,] 4e+09 -2.648142e-05 -5.616896e-11 2.648147e-05 1.059193e-10  2.246502e-16 -1.059195e-10 -1.804535e-14 -7.218146e-20 1.804542e-14
+[13,] 4e+10 -2.899376e-06 -7.759920e-12 2.899383e-06 1.159764e-11  3.104024e-17 -1.159768e-11 -1.727574e-15 -6.910296e-21 1.727581e-15
+

In future, I intend to provide options to select specific entities +and parameters with respect to which sensitivities are to be computed as +the sensitivity matrix can get very large for medium to large +models.

+
+
+

Summary +

+
    +

  • The package sundialr provides a way to interface +with the famous SUNDIALS C library (provided by Lawerence +Livermore National Security) to solver initial value problems.

    • +

  • The package allows the system of differential equations to be +written in R or using Rcpp. Function +cvode is used to solve initial value problems with a single +initialization, but problems with multiple discontinuities in the +solution can be solved using the cvsolve +interface.

    • +

  • For sensitivities, currently, calculation of forward +sensitivities for all entities with respect to all the parameters in the +model is implemented in the cvodes function. An ability to +select specific entities and parameters for which sensitivities is to be +calculated will be added soon.

    • +

  • To solve a system of differential algebraic systems, the +ida function is provided which is an interface to the +IDA function in SUNDIALS.

    • +
+

As a note, since this package is under active development, the +interfaces of both CVODE and CVODES (i.e., the +function signatures) may change in the future versions. Please keep this +mind if you intend to use sundialr in your applications. In +near future, interface for other solvers from the C library +such asIDAS and ARKODE may also be added.

+
+
+ + + +
+ + + +
+

+

Developed by Satyaprakash Nayak.

+
+ +
+

+

Site built with pkgdown 2.1.1.

+
+ +
+
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+ + - - - + diff --git a/docs/reference/ida.html b/docs/reference/ida.html index 1dde5ce..0f8dc7f 100644 --- a/docs/reference/ida.html +++ b/docs/reference/ida.html @@ -1,67 +1,12 @@ - - - - - - - -ida — ida • sundialr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ida — ida • sundialr - - + - -
-
- - -
-
+

ida

- Source: R/RcppExports.R + Source: R/RcppExports.R
@@ -129,75 +59,76 @@

ida

IDA solver to solve stiff DAEs

- 
ida(
-  time_vector,
-  IC,
-  IRes,
-  input_function,
-  Parameters,
-  reltolerance = 1e-04,
-  abstolerance = 1e-04
-)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
time_vector

time vector

IC

Initial Value of y

IRes

Inital Value of ydot

input_function

Right Hand Side function of DAEs

Parameters

Parameters input to ODEs

reltolerance

Relative Tolerance (a scalar, default value = 1e-04)

abstolerance

Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)

+
+ 
ida(
+  time_vector,
+  IC,
+  IRes,
+  input_function,
+  Parameters,
+  reltolerance = 1e-04,
+  abstolerance = 1e-04
+)
+
+ +
+

Arguments

+ + +
time_vector
+

time vector

+ + +
IC
+

Initial Value of y

+ + +
IRes
+

Inital Value of ydot

+ +
input_function
+

Right Hand Side function of DAEs

+ + +
Parameters
+

Parameters input to ODEs

+ + +
reltolerance
+

Relative Tolerance (a scalar, default value = 1e-04)

+ + +
abstolerance
+

Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)

+ +
+
+

Value

+

A data frame. First column is the time-vector, the other columns are values of y in order they are provided.

+
+
-
-
-

Developed by Satyaprakash Nayak.

+
+

Developed by Satyaprakash Nayak.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 2.1.1.

-
-
+
-
-
-
+
-
-

Authors

+
+
+

Authors and Citation

+
+ + +
  • +

    Satyaprakash Nayak. Author, maintainer, copyright holder. +

    +
    • +
  • +

    Lawrence Livermore National Security. Copyright holder. +

    +
    • +
  • +

    Southern Methodist University. Copyright holder. +

    +
    • +
+
+
+

Citation

+ Source: inst/CITATION
+
+ -
    -
  • -

    Satyaprakash Nayak. Author, maintainer, copyright holder. -

    -
    • -
  • -

    Lawrence Livermore National Security. Copyright holder. -

    -
    • -
  • -

    Southern Methodist University. Copyright holder. -

    -
    • -
+

Satyaprakash Nayak (2023) The sundialr package: An Interface to 'SUNDIALS' + Ordinary Differential Equation (ODE) Solvers. https://doi.org/10.5281/zenodo.5501631/

+ 
@Misc{,
+  title = {The sundialr package: An Interface to 'SUNDIALS' Ordinary Differential Equation (ODE) Solvers},
+  year = {2023},
+  author = {Satyaprakash Nayak},
+  doi = {10.5281/zenodo.5501631},
+  url = {https://github.com/sn248/sundialr/},
+}
@@ -143,22 +92,20 @@

Authors

-
-
-

Developed by Satyaprakash Nayak.

+
+

Developed by Satyaprakash Nayak.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 2.1.1.

-
-
+
+ + - - - + diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..53d00ff --- /dev/null +++ b/docs/index.html @@ -0,0 +1,189 @@ + + + + + + + +An Interface to SUNDIALS Ordinary Differential Equation (ODE) Solvers • sundialr + + + + + + + + + + + + +
+
+ + + + +
+
+
+

sundialr +

+ + + +
+

sundialr +

+

sundialr is a wrapper around a few of the solvers in the SUNDIALS ODE solving C library produced by the Lawrence Livermore National Laboratory and Southern Methodist University. More information about SUNDIALS can be found here. SUNDIALS is one of the most popular and well-respected ODE solving libraries available and sundialr provides a way to interface some of the SUNDIALS solvers in R.

+

Currently sundialr provides an interface to the serial versions of cvode (for solving ODES), cvodes (for solving ODE with sensitivity equations) and ida (for solving differential-algebraic equations) using the Linear Solver (dense version).

+

A convenience function cvsolve is provided which allows solving a system of equations with multiple discontinutities in solution. An application of such a system of equations would be to simulate the effect of multiple bolus doses of a drug in clinical pharmacokinetics. See the vignette for more details.

+
+
+

What’s new? +

+
+

Release 0.1.4.1 +

+
    +
  • Fixed the linking bug due to multiple defined symbols. No other change.
    • +
+
+
+

Release 0.1.4 +

+
    +
  • This version has version 5.2.0 of SUNDIALS (released in March 2020) at the back end.
    • +
  • A new function cvsolve is added. It allows solving ODEs with multiple discontinuities in the solution. See a complete use case in the vignette.
    • +
  • A pkgdown create site of the package is added.
    • +
  • A hex sticker for the package is released!
    • +
+
+
+

Release 0.1.3 +

+
    +
  • This version has version 4.0.1 of SUNDIALS (released in Dec 2018) at the back end.
    • +
  • An interface to CVODES is added. It calculates forward sensitivities w.r.t all parameters of the ODE system.
    • +
  • Parameters can now be defined as an input parameter to the ODE function. This will allow performing parameter optimization via numerical optimizers.
    • +
+
+
+
+
+ + +
+ + +
+

+

Developed by Satyaprakash Nayak.

+
+ +
+

+

Site built with pkgdown 2.1.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index c01e592..80ea5b8 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -56,8 +56,10 @@ img.icon { float: right; } -img { +/* Ensure in-page images don't run outside their container */ +.contents img { max-width: 100%; + height: auto; } /* Fix bug in bootstrap (only seen in firefox) */ @@ -78,11 +80,10 @@ dd { /* Section anchors ---------------------------------*/ a.anchor { - margin-left: -30px; - display:inline-block; - width: 30px; - height: 30px; - visibility: hidden; + display: none; + margin-left: 5px; + width: 20px; + height: 20px; background-image: url(./link.svg); background-repeat: no-repeat; @@ -90,17 +91,15 @@ a.anchor { background-position: center center; } -.hasAnchor:hover a.anchor { - visibility: visible; -} - -@media (max-width: 767px) { - .hasAnchor:hover a.anchor { - visibility: hidden; - } +h1:hover .anchor, +h2:hover .anchor, +h3:hover .anchor, +h4:hover .anchor, +h5:hover .anchor, +h6:hover .anchor { + display: inline-block; } - /* Fixes for fixed navbar --------------------------*/ .contents h1, .contents h2, .contents h3, .contents h4 { @@ -244,14 +243,14 @@ nav[data-toggle='toc'] .nav .nav > .active:focus > a { .ref-index th {font-weight: normal;} -.ref-index td {vertical-align: top;} +.ref-index td {vertical-align: top; min-width: 100px} .ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} .ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} .ref-arguments .name {width: 20%;} .ref-arguments .desc {width: 80%;} @@ -264,31 +263,26 @@ table { /* Syntax highlighting ---------------------------------------------------- */ -pre { - word-wrap: normal; - word-break: normal; - border: 1px solid #eee; -} - -pre, code { +pre, code, pre code { background-color: #f8f8f8; color: #333; } +pre, pre code { + white-space: pre-wrap; + word-break: break-all; + overflow-wrap: break-word; +} -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; +pre { + border: 1px solid #eee; } -pre .img { +pre .img, pre .r-plt { margin: 5px 0; } -pre .img img { +pre .img img, pre .r-plt img { background-color: #fff; - display: block; - height: auto; } code a, pre a { @@ -305,9 +299,8 @@ a.sourceLine:hover { .kw {color: #264D66;} /* keyword */ .co {color: #888888;} /* comment */ -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} +.error {font-weight: bolder;} +.warning {font-weight: bolder;} /* Clipboard --------------------------*/ @@ -365,3 +358,27 @@ mark { content: ""; } } + +/* Section anchors --------------------------------- + Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71 +*/ + +div.csl-bib-body { } +div.csl-entry { + clear: both; +} +.hanging-indent div.csl-entry { + margin-left:2em; + text-indent:-2em; +} +div.csl-left-margin { + min-width:2em; + float:left; +} +div.csl-right-inline { + margin-left:2em; + padding-left:1em; +} +div.csl-indent { + margin-left: 2em; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 7e7048f..6f0eee4 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -80,7 +80,7 @@ $(document).ready(function() { var copyButton = ""; - $(".examples, div.sourceCode").addClass("hasCopyButton"); + $("div.sourceCode").addClass("hasCopyButton"); // Insert copy buttons: $(copyButton).prependTo(".hasCopyButton"); @@ -91,7 +91,7 @@ // Initialize clipboard: var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { - return trigger.parentNode.textContent; + return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 17645ac..6e32b98 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,7 +1,6 @@ -pandoc: 2.9.2.1 -pkgdown: 1.5.1 +pandoc: '3.2' +pkgdown: 2.1.1 pkgdown_sha: ~ articles: my-vignette: my-vignette.html -last_built: 2020-05-31T18:50Z - +last_built: 2024-11-10T21:17Z diff --git a/docs/reference/cvode.html b/docs/reference/cvode.html index 565609d..99110cd 100644 --- a/docs/reference/cvode.html +++ b/docs/reference/cvode.html @@ -1,67 +1,12 @@ - - - - - - - -cvode — cvode • sundialr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cvode — cvode • sundialr - - + - -
-
- - -
-
+

cvode

- Source: R/RcppExports.R + Source: R/RcppExports.R
@@ -129,127 +59,131 @@

cvode

CVODE solver to solve stiff ODEs

- 
cvode(
-  time_vector,
-  IC,
-  input_function,
-  Parameters,
-  reltolerance = 1e-04,
-  abstolerance = 1e-04
-)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - -
time_vector

time vector

IC

Initial Conditions

input_function

Right Hand Side function of ODEs

Parameters

Parameters input to ODEs

reltolerance

Relative Tolerance (a scalar, default value = 1e-04)

abstolerance

Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)

- - -

Examples

- 
# Example of solving a set of ODEs with cvode function
-# ODEs described by an R function
-ODE_R <- function(t, y, p){
-
-  # vector containing the right hand side gradients
-  ydot = vector(mode = "numeric", length = length(y))
-
-  # R indices start from 1
-  ydot[1] = -p[1]*y[1] + p[2]*y[2]*y[3]
-  ydot[2] = p[1]*y[1] - p[2]*y[2]*y[3] - p[3]*y[2]*y[2]
-  ydot[3] = p[3]*y[2]*y[2]
-
-  # ydot[1] = -0.04 * y[1] + 10000 * y[2] * y[3]
-  # ydot[3] = 30000000 * y[2] * y[2]
-  # ydot[2] = -ydot[1] - ydot[3]
-
-  ydot
-
-}
-
-# ODEs can also be described using Rcpp
-Rcpp::sourceCpp(code = '
-
-                #include <Rcpp.h>
-                using namespace Rcpp;
-
-                // ODE functions defined using Rcpp
-                // [[Rcpp::export]]
-                NumericVector ODE_Rcpp (double t, NumericVector y, NumericVector p){
-
-                // Initialize ydot filled with zeros
-                NumericVector ydot(y.length());
-
-                ydot[0] = -p[0]*y[0] + p[1]*y[1]*y[2];
-                ydot[1] = p[0]*y[0] - p[1]*y[1]*y[2] - p[2]*y[1]*y[1];
-                ydot[2] = p[2]*y[1]*y[1];
-
-                return ydot;
-
-                }')
-
-
-
-# R code to genrate time vector, IC and solve the equations
-time_vec <- c(0.0, 0.4, 4.0, 40.0, 4E2, 4E3, 4E4, 4E5, 4E6, 4E7, 4E8, 4E9, 4E10)
-IC <- c(1,0,0)
-params <- c(0.04, 10000, 30000000)
-reltol <- 1e-04
-abstol <- c(1e-8,1e-14,1e-6)
-
-## Solving the ODEs using cvode function
-df1 <- cvode(time_vec, IC, ODE_R , params, reltol, abstol)           ## using R
-df2 <- cvode(time_vec, IC, ODE_Rcpp , params, reltol, abstol)        ## using Rcpp
-
-## Check that both solutions are identical
-# identical(df1, df2)
+
+ 
cvode(
+  time_vector,
+  IC,
+  input_function,
+  Parameters,
+  reltolerance = 1e-04,
+  abstolerance = 1e-04
+)
+
+ +
+

Arguments

+ + +
time_vector
+

time vector

+ + +
IC
+

Initial Conditions

+ + +
input_function
+

Right Hand Side function of ODEs

+ + +
Parameters
+

Parameters input to ODEs

+ + +
reltolerance
+

Relative Tolerance (a scalar, default value = 1e-04)

+ + +
abstolerance
+

Absolute Tolerance (a scalar or vector with length equal to ydot (dy/dx), default = 1e-04)

+ +
+
+

Value

+

A data frame. First column is the time-vector, the other columns are values of y in order they are provided.

+
+ +
+

Examples

+ 
# Example of solving a set of ODEs with cvode function
+# ODEs described by an R function
+ODE_R <- function(t, y, p){
+
+  # vector containing the right hand side gradients
+  ydot = vector(mode = "numeric", length = length(y))
+
+  # R indices start from 1
+  ydot[1] = -p[1]*y[1] + p[2]*y[2]*y[3]
+  ydot[2] = p[1]*y[1] - p[2]*y[2]*y[3] - p[3]*y[2]*y[2]
+  ydot[3] = p[3]*y[2]*y[2]
+
+  # ydot[1] = -0.04 * y[1] + 10000 * y[2] * y[3]
+  # ydot[3] = 30000000 * y[2] * y[2]
+  # ydot[2] = -ydot[1] - ydot[3]
+
+  ydot
+
+}
+
+# ODEs can also be described using Rcpp
+Rcpp::sourceCpp(code = '
+
+                #include <Rcpp.h>
+                using namespace Rcpp;
+
+                // ODE functions defined using Rcpp
+                // [[Rcpp::export]]
+                NumericVector ODE_Rcpp (double t, NumericVector y, NumericVector p){
+
+                // Initialize ydot filled with zeros
+                NumericVector ydot(y.length());
+
+                ydot[0] = -p[0]*y[0] + p[1]*y[1]*y[2];
+                ydot[1] = p[0]*y[0] - p[1]*y[1]*y[2] - p[2]*y[1]*y[1];
+                ydot[2] = p[2]*y[1]*y[1];
+
+                return ydot;
+
+                }')
+
+
+
+# R code to genrate time vector, IC and solve the equations
+time_vec <- c(0.0, 0.4, 4.0, 40.0, 4E2, 4E3, 4E4, 4E5, 4E6, 4E7, 4E8, 4E9, 4E10)
+IC <- c(1,0,0)
+params <- c(0.04, 10000, 30000000)
+reltol <- 1e-04
+abstol <- c(1e-8,1e-14,1e-6)
+
+## Solving the ODEs using cvode function
+df1 <- cvode(time_vec, IC, ODE_R , params, reltol, abstol)           ## using R
+df2 <- cvode(time_vec, IC, ODE_Rcpp , params, reltol, abstol)        ## using Rcpp
+
+## Check that both solutions are identical
+# identical(df1, df2)
+
+
+
-
-
-

Developed by Satyaprakash Nayak.

+
+

Developed by Satyaprakash Nayak.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 2.1.1.

-
-
+
+ + - - - + diff --git a/docs/reference/cvodes.html b/docs/reference/cvodes.html index c476440..78ffc32 100644 --- a/docs/reference/cvodes.html +++ b/docs/reference/cvodes.html @@ -1,67 +1,12 @@ - - - - - - - -cvodes — cvodes • sundialr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cvodes — cvodes • sundialr - + - - -
-
- - -
-
+

cvodes

- Source: R/RcppExports.R + Source: R/RcppExports.R
@@ -129,137 +59,141 @@

cvodes

CVODES solver to solve ODEs and calculate sensitivities

- 
cvodes(
-  time_vector,
-  IC,
-  input_function,
-  Parameters,
-  reltolerance = 1e-04,
-  abstolerance = 1e-04,
-  SensType = "STG",
-  ErrCon = "F"
-)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
time_vector

time vector

IC

Initial Conditions

input_function

Right Hand Side function of ODEs

Parameters

Parameters input to ODEs

reltolerance

Relative Tolerance (a scalar, default value = 1e-04)

abstolerance

Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)

SensType

Sensitivity Type - allowed values are Staggered (default)", "STG" (for Staggered) or "SIM" (for Simultaneous)

ErrCon

Error Control - allowed values are TRUE or FALSE (default)

- - -

Examples

- 
# Example of solving a set sensitivity equations for ODEs with cvodes function
-# ODEs described by an R function
-ODE_R <- function(t, y, p){
-
-  # vector containing the right hand side gradients
-  ydot = vector(mode = "numeric", length = length(y))
-
-  # R indices start from 1
-  ydot[1] = -p[1]*y[1] + p[2]*y[2]*y[3]
-  ydot[2] = p[1]*y[1] - p[2]*y[2]*y[3] - p[3]*y[2]*y[2]
-  ydot[3] = p[3]*y[2]*y[2]
-
-  # ydot[1] = -0.04 * y[1] + 10000 * y[2] * y[3]
-  # ydot[3] = 30000000 * y[2] * y[2]
-  # ydot[2] = -ydot[1] - ydot[3]
-
-  ydot
-
-}
-
-# ODEs can also be described using Rcpp
-Rcpp::sourceCpp(code = '
-
-                #include <Rcpp.h>
-                using namespace Rcpp;
-
-                // ODE functions defined using Rcpp
-                // [[Rcpp::export]]
-                NumericVector ODE_Rcpp (double t, NumericVector y, NumericVector p){
-
-                // Initialize ydot filled with zeros
-                NumericVector ydot(y.length());
-
-                ydot[0] = -p[0]*y[0] + p[1]*y[1]*y[2];
-                ydot[1] = p[0]*y[0] - p[1]*y[1]*y[2] - p[2]*y[1]*y[1];
-                ydot[2] = p[2]*y[1]*y[1];
-
-                return ydot;
-
-                }')
-
-
-
-# R code to genrate time vector, IC and solve the equations
-time_vec <- c(0.0, 0.4, 4.0, 40.0, 4E2, 4E3, 4E4, 4E5, 4E6, 4E7, 4E8, 4E9, 4E10)
-IC <- c(1,0,0)
-params <- c(0.04, 10000, 30000000)
-reltol <- 1e-04
-abstol <- c(1e-8,1e-14,1e-6)
-
-## Solving the ODEs and Sensitivities using cvodes function
-df1 <- cvodes(time_vec, IC, ODE_R , params, reltol, abstol,"STG",FALSE)           ## using R
-df2 <- cvodes(time_vec, IC, ODE_Rcpp , params, reltol, abstol,"STG",FALSE)        ## using Rcpp
-
-## Check that both solutions are identical
-# identical(df1, df2)
+
+ 
cvodes(
+  time_vector,
+  IC,
+  input_function,
+  Parameters,
+  reltolerance = 1e-04,
+  abstolerance = 1e-04,
+  SensType = "STG",
+  ErrCon = "F"
+)
+
+ +
+

Arguments

+ + +
time_vector
+

time vector

+ + +
IC
+

Initial Conditions

+ + +
input_function
+

Right Hand Side function of ODEs

+ + +
Parameters
+

Parameters input to ODEs

+ + +
reltolerance
+

Relative Tolerance (a scalar, default value = 1e-04)

+ + +
abstolerance
+

Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)

+ + +
SensType
+

Sensitivity Type - allowed values are "STG" (for Staggered, default) or "SIM" (for Simultaneous)

+ + +
ErrCon
+

Error Control - allowed values are TRUE or FALSE (default)

+ +
+
+

Value

+

A data frame. First column is the time-vector, the next y * p columns are sensitivities of y1 w.r.t all parameters, then y2 w.r.t all parameters etc. y is the state vector, p is the parameter vector

+
+ +
+

Examples

+ 
# Example of solving a set sensitivity equations for ODEs with cvodes function
+# ODEs described by an R function
+ODE_R <- function(t, y, p){
+
+  # vector containing the right hand side gradients
+  ydot = vector(mode = "numeric", length = length(y))
+
+  # R indices start from 1
+  ydot[1] = -p[1]*y[1] + p[2]*y[2]*y[3]
+  ydot[2] = p[1]*y[1] - p[2]*y[2]*y[3] - p[3]*y[2]*y[2]
+  ydot[3] = p[3]*y[2]*y[2]
+
+  # ydot[1] = -0.04 * y[1] + 10000 * y[2] * y[3]
+  # ydot[3] = 30000000 * y[2] * y[2]
+  # ydot[2] = -ydot[1] - ydot[3]
+
+  ydot
+
+}
+
+# ODEs can also be described using Rcpp
+Rcpp::sourceCpp(code = '
+
+                #include <Rcpp.h>
+                using namespace Rcpp;
+
+                // ODE functions defined using Rcpp
+                // [[Rcpp::export]]
+                NumericVector ODE_Rcpp (double t, NumericVector y, NumericVector p){
+
+                // Initialize ydot filled with zeros
+                NumericVector ydot(y.length());
+
+                ydot[0] = -p[0]*y[0] + p[1]*y[1]*y[2];
+                ydot[1] = p[0]*y[0] - p[1]*y[1]*y[2] - p[2]*y[1]*y[1];
+                ydot[2] = p[2]*y[1]*y[1];
+
+                return ydot;
+
+                }')
+
+
+
+# R code to genrate time vector, IC and solve the equations
+time_vec <- c(0.0, 0.4, 4.0, 40.0, 4E2, 4E3, 4E4, 4E5, 4E6, 4E7, 4E8, 4E9, 4E10)
+IC <- c(1,0,0)
+params <- c(0.04, 10000, 30000000)
+reltol <- 1e-04
+abstol <- c(1e-8,1e-14,1e-6)
+
+## Solving the ODEs and Sensitivities using cvodes function
+df1 <- cvodes(time_vec, IC, ODE_R , params, reltol, abstol,"STG",FALSE)           ## using R
+df2 <- cvodes(time_vec, IC, ODE_Rcpp , params, reltol, abstol,"STG",FALSE)        ## using Rcpp
+
+## Check that both solutions are identical
+# identical(df1, df2)
+
+
+
-
-
-

Developed by Satyaprakash Nayak.

+
+

Developed by Satyaprakash Nayak.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 2.1.1.

-
-
+
+ + - - - + diff --git a/docs/reference/cvsolve.html b/docs/reference/cvsolve.html index 25ad7e7..c9b9cc1 100644 --- a/docs/reference/cvsolve.html +++ b/docs/reference/cvsolve.html @@ -1,67 +1,12 @@ - - - - - - - -cvsolve — cvsolve • sundialr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cvsolve — cvsolve • sundialr + - - - -
-
- - -
-
+

cvsolve

- Source: R/RcppExports.R + Source: R/RcppExports.R
@@ -129,102 +59,106 @@

cvsolve

CVSOLVE solver to solve stiff ODEs with discontinuties

- 
cvsolve(
-  time_vector,
-  IC,
-  input_function,
-  Parameters,
-  Events = NULL,
-  reltolerance = 1e-04,
-  abstolerance = 1e-04
-)
- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
time_vector

time vector

IC

Initial Conditions

input_function

Right Hand Side function of ODEs

Parameters

Parameters input to ODEs

Events

Discontinuities in the solution (a DataFrame, default value is NULL)

reltolerance

Relative Tolerance (a scalar, default value = 1e-04)

abstolerance

Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)

- - -

Examples

- 
# Example of solving a set of ODEs with multiple discontinuities using cvsolve
-# A simple One dimensional equation, y = -0.1 * y
-# ODEs described by an R function
-ODE_R <- function(t, y, p){
-
-  # vector containing the right hand side gradients
-  ydot = vector(mode = "numeric", length = length(y))
-
-  # R indices start from 1
-  ydot[1] = -p[1]*y[1]
-
-  ydot
-
-}
-
-# R code to generate time vector, IC and solve the equations
-TSAMP <- seq(from = 0, to = 100, by = 0.1)      # sampling time points
-IC <- c(1)
-params <- c(0.1)
-
-# A dataset describing the dosing at times at which additions to y[1] are to be done
-# Names of the columns don't matter, but they MUST be in the order of state index,
-# times and Values at discontinuity.
-TDOSE <- data.frame(ID = 1, TIMES = c(0, 10, 20, 30, 40, 50), VAL = 100)
-df1 <- cvsolve(TSAMP, c(1), ODE_R, params)         # solving without any discontinuity
-df2 <- cvsolve(TSAMP, c(1), ODE_R, params, TDOSE)  # solving with discontinuity
+
+ 
cvsolve(
+  time_vector,
+  IC,
+  input_function,
+  Parameters,
+  Events = NULL,
+  reltolerance = 1e-04,
+  abstolerance = 1e-04
+)
+
+ +
+

Arguments

+ + +
time_vector
+

time vector

+ + +
IC
+

Initial Conditions

+ + +
input_function
+

Right Hand Side function of ODEs

+ + +
Parameters
+

Parameters input to ODEs

+ + +
Events
+

Discontinuities in the solution (a DataFrame, default value is NULL)

+ + +
reltolerance
+

Relative Tolerance (a scalar, default value = 1e-04)

+ + +
abstolerance
+

Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)

+ +
+
+

Value

+

A data frame. First column is the time-vector, the other columns are values of y in order they are provided.

+
+ +
+

Examples

+ 
# Example of solving a set of ODEs with multiple discontinuities using cvsolve
+# A simple One dimensional equation, y = -0.1 * y
+# ODEs described by an R function
+ODE_R <- function(t, y, p){
+
+  # vector containing the right hand side gradients
+  ydot = vector(mode = "numeric", length = length(y))
+
+  # R indices start from 1
+  ydot[1] = -p[1]*y[1]
+
+  ydot
+
+}
+
+# R code to generate time vector, IC and solve the equations
+TSAMP <- seq(from = 0, to = 100, by = 0.1)      # sampling time points
+IC <- c(1)
+params <- c(0.1)
+
+# A dataset describing the dosing at times at which additions to y[1] are to be done
+# Names of the columns don't matter, but they MUST be in the order of state index,
+# times and Values at discontinuity.
+TDOSE <- data.frame(ID = 1, TIMES = c(0, 10, 20, 30, 40, 50), VAL = 100)
+df1 <- cvsolve(TSAMP, c(1), ODE_R, params)         # solving without any discontinuity
+df2 <- cvsolve(TSAMP, c(1), ODE_R, params, TDOSE)  # solving with discontinuity
+
+
+
-
-
-

Developed by Satyaprakash Nayak.

+
+

Developed by Satyaprakash Nayak.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 2.1.1.

-
-
+
+ + - - - + diff --git a/docs/reference/index.html b/docs/reference/index.html index 9ac5094..62701e0 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,66 +1,12 @@ - - - - - - - -Function reference • sundialr - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Package index • sundialr + - - - -
-
- - -
-
+

Reference

- - - - - - - - - - -
-

All functions

+ - - - - - - - - - - - - - - - - - - - - -
+

All functions

+

cvode()

cvode

+

cvodes()

cvodes

+

cvsolve()

cvsolve

+

ida()

ida

- +
+
-
-
-

Developed by Satyaprakash Nayak.

+
+

Developed by Satyaprakash Nayak.

-

Site built with pkgdown 1.5.1.

+

Site built with pkgdown 2.1.1.

-
-
+
+ + - - - + diff --git a/docs/sitemap.xml b/docs/sitemap.xml new file mode 100644 index 0000000..2c72a3f --- /dev/null +++ b/docs/sitemap.xml @@ -0,0 +1,14 @@ + +/404.html +/LICENSE-text.html +/articles/index.html +/articles/my-vignette.html +/authors.html +/index.html +/reference/cvode.html +/reference/cvodes.html +/reference/cvsolve.html +/reference/ida.html +/reference/index.html + + diff --git a/inst/include/cvodes/cvodes.h b/inst/include/cvodes/cvodes.h index 813ded3..8af98fc 100644 --- a/inst/include/cvodes/cvodes.h +++ b/inst/include/cvodes/cvodes.h @@ -579,7 +579,8 @@ SUNDIALS_EXPORT int CVodeGetAdjCheckPointsInfo(void* cvode_mem, CVadjCheckPointRec* ckpnt); /* CVLS interface function that depends on CVRhsFn */ -int CVodeSetJacTimesRhsFnB(void* cvode_mem, int which, CVRhsFn jtimesRhsFn); +SUNDIALS_EXPORT int CVodeSetJacTimesRhsFnB(void* cvode_mem, int which, + CVRhsFn jtimesRhsFn); /* Undocumented Optional Output Functions For Backward Problems */ diff --git a/inst/include/nvector/nvector_parallel.h b/inst/include/nvector/nvector_parallel.h index e05e4c7..385ca52 100644 --- a/inst/include/nvector/nvector_parallel.h +++ b/inst/include/nvector/nvector_parallel.h @@ -117,10 +117,8 @@ void N_VPrint_Parallel(N_Vector v); SUNDIALS_EXPORT void N_VPrintFile_Parallel(N_Vector v, FILE* outfile); -static inline N_Vector_ID N_VGetVectorID_Parallel(N_Vector v) -{ - return SUNDIALS_NVEC_PARALLEL; -} +SUNDIALS_EXPORT +N_Vector_ID N_VGetVectorID_Parallel(N_Vector v); SUNDIALS_EXPORT N_Vector N_VCloneEmpty_Parallel(N_Vector w); diff --git a/inst/include/nvector/nvector_serial.h b/inst/include/nvector/nvector_serial.h index bcbc995..988e090 100644 --- a/inst/include/nvector/nvector_serial.h +++ b/inst/include/nvector/nvector_serial.h @@ -102,10 +102,8 @@ void N_VPrint_Serial(N_Vector v); SUNDIALS_EXPORT void N_VPrintFile_Serial(N_Vector v, FILE* outfile); -static inline N_Vector_ID N_VGetVectorID_Serial(N_Vector v) -{ - return SUNDIALS_NVEC_SERIAL; -} +SUNDIALS_EXPORT +N_Vector_ID N_VGetVectorID_Serial(N_Vector v); SUNDIALS_EXPORT N_Vector N_VCloneEmpty_Serial(N_Vector w); diff --git a/inst/include/sundials/sundials_adaptcontroller.h b/inst/include/sundials/sundials_adaptcontroller.h index 9cde03b..b27d7c7 100644 --- a/inst/include/sundials/sundials_adaptcontroller.h +++ b/inst/include/sundials/sundials_adaptcontroller.h @@ -91,6 +91,10 @@ struct _generic_SUNAdaptController SUNDIALS_EXPORT SUNAdaptController SUNAdaptController_NewEmpty(SUNContext sunctx); +/* Function to free a generic SUNAdaptController (assumes content is already empty) */ +SUNDIALS_EXPORT +void SUNAdaptController_DestroyEmpty(SUNAdaptController C); + /* Function to report the type of a SUNAdaptController object. */ SUNDIALS_EXPORT SUNAdaptController_Type SUNAdaptController_GetType(SUNAdaptController C); diff --git a/inst/include/sundials/sundials_config.in b/inst/include/sundials/sundials_config.in index b56ae8f..def1a87 100644 --- a/inst/include/sundials/sundials_config.in +++ b/inst/include/sundials/sundials_config.in @@ -60,6 +60,7 @@ #cmakedefine SUNDIALS_C_COMPILER_HAS_ATTRIBUTE_ASSUME #cmakedefine SUNDIALS_C_COMPILER_HAS_BUILTIN_ASSUME #cmakedefine SUNDIALS_C_COMPILER_HAS_ASSUME +#cmakedefine SUNDIALS_C_COMPILER_HAS_ATTRIBUTE_UNUSED /* Define precision of SUNDIALS data type 'sunrealtype' * Depending on the precision level, one of the following @@ -220,7 +221,7 @@ #cmakedefine SUNDIALS_GINKGO_BACKENDS_HIP #cmakedefine SUNDIALS_GINKGO_BACKENDS_OMP #cmakedefine SUNDIALS_GINKGO_BACKENDS_REF -#cmakedefine SUNDIALS_GINKGO_BACKENDS_DPCPP +#cmakedefine SUNDIALS_GINKGO_BACKENDS_SYCL /* MAGMA backends */ #cmakedefine SUNDIALS_MAGMA_BACKENDS_CUDA diff --git a/inst/include/sundials/sundials_hip_policies.hpp b/inst/include/sundials/sundials_hip_policies.hpp index d5592ae..f7950f8 100644 --- a/inst/include/sundials/sundials_hip_policies.hpp +++ b/inst/include/sundials/sundials_hip_policies.hpp @@ -27,10 +27,12 @@ namespace sundials { namespace hip { -#if defined(__HIP_PLATFORM_HCC__) +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) constexpr const sunindextype WARP_SIZE = 64; -#elif defined(__HIP_PLATFORM_NVCC__) +#elif defined(__HIP_PLATFORM_NVCC__) || defined(__HIP_PLATFORM_NVDIA__) constexpr const sunindextype WARP_SIZE = 32; +#else +#error "Unknown HIP_PLATFORM, report to github.com/LLNL/sundials/issues" #endif constexpr const sunindextype MAX_BLOCK_SIZE = 1024; constexpr const sunindextype MAX_WARPS = MAX_BLOCK_SIZE / WARP_SIZE; diff --git a/inst/include/sunlinsol/sunlinsol_ginkgo.hpp b/inst/include/sunlinsol/sunlinsol_ginkgo.hpp index d801cb1..2817d42 100644 --- a/inst/include/sunlinsol/sunlinsol_ginkgo.hpp +++ b/inst/include/sunlinsol/sunlinsol_ginkgo.hpp @@ -332,11 +332,19 @@ class LinearSolver : public ConvertibleTo } iter_count_ = static_cast(logger->get_num_iterations()); +#if (GKO_VERSION_MAJOR == 1) && (GKO_VERSION_MINOR < 6) GkoExec()->get_master()->copy_from(gko::lend(GkoExec()), 1, gko::as( logger->get_residual_norm()) ->get_const_values(), &res_norm_); +#else + GkoExec()->get_master()->copy_from(GkoExec(), 1, + gko::as( + logger->get_residual_norm()) + ->get_const_values(), + &res_norm_); +#endif return result; } diff --git a/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp b/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp index ba109bb..2fbda95 100644 --- a/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp +++ b/inst/include/sunlinsol/sunlinsol_kokkosdense.hpp @@ -40,12 +40,12 @@ class DenseLinearSolver; namespace impl { -SUNLinearSolver_Type SUNLinSolGetType_KokkosDense(SUNLinearSolver S) +static SUNLinearSolver_Type SUNLinSolGetType_KokkosDense(SUNLinearSolver S) { return SUNLINEARSOLVER_DIRECT; } -SUNLinearSolver_ID SUNLinSolGetID_KokkosDense(SUNLinearSolver S) +static SUNLinearSolver_ID SUNLinSolGetID_KokkosDense(SUNLinearSolver S) { return SUNLINEARSOLVER_KOKKOSDENSE; } diff --git a/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp b/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp index b2b82ad..15bf696 100644 --- a/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp +++ b/inst/include/sunmatrix/sunmatrix_kokkosdense.hpp @@ -46,7 +46,7 @@ inline MatrixType* GetDenseMat(SUNMatrix A) namespace impl { -SUNMatrix_ID SUNMatGetID_KokkosDense(SUNMatrix A) +static SUNMatrix_ID SUNMatGetID_KokkosDense(SUNMatrix A) { return SUNMATRIX_KOKKOSDENSE; } @@ -210,7 +210,11 @@ SUNErrCode SUNMatMatvec_KokkosDense(SUNMatrix A, N_Vector x, N_Vector y) Kokkos::subview(y_data, Kokkos::pair(idx * rows, (idx + 1) * rows)); +#if KOKKOSKERNELS_VERSION_MAJOR > 3 + KokkosBlas::TeamVectorGemv< +#else KokkosBatched::TeamVectorGemv< +#endif member_type, KokkosBatched::Trans::NoTranspose, KokkosBatched::Algo::Gemv::Unblocked>::invoke(team_member, SUN_RCONST(1.0), diff --git a/man/cvodes.Rd b/man/cvodes.Rd index ed9be88..16ec095 100644 --- a/man/cvodes.Rd +++ b/man/cvodes.Rd @@ -28,7 +28,7 @@ cvodes( \item{abstolerance}{Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04)} -\item{SensType}{Sensitivity Type - allowed values are Staggered (default)", "STG" (for Staggered) or "SIM" (for Simultaneous)} +\item{SensType}{Sensitivity Type - allowed values are "STG" (for Staggered, default) or "SIM" (for Simultaneous)} \item{ErrCon}{Error Control - allowed values are TRUE or FALSE (default)} } diff --git a/src/Makevars b/src/Makevars index 080e23b..34a4a8b 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,6 +1,6 @@ CXX=clang++ -PKG_CPPFLAGS= -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX11 -I./sundials/sundials -#CXX_STD = CXX11 +PKG_CPPFLAGS= -I../inst/include/ -I./inst/ -DHAVE_CONFIG_H -DARMA_USE_CXX17 -I./sundials/sundials +CXX_STD = CXX17 PKG_LIBS= $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -L../inst/ -lsundials_all LIBS=-L./ -L../inst/ diff --git a/src/cvode.cpp b/src/cvode.cpp index 3b9d752..e5cfd37 100644 --- a/src/cvode.cpp +++ b/src/cvode.cpp @@ -57,154 +57,149 @@ using namespace Rcpp; //'@returns A data frame. First column is the time-vector, the other columns are values of y in order they are provided. //'@example /inst/examples/cv_Roberts_dns.r // [[Rcpp::export]] -NumericMatrix cvode(NumericVector time_vector, NumericVector IC, SEXP input_function, - NumericVector Parameters, - double reltolerance = 0.0001, NumericVector abstolerance = 0.0001){ - - int flag; - - int time_vec_len = time_vector.length(); - double time; - int NOUT = time_vec_len; - sunrealtype T0 = SUN_RCONST(time_vector[0]); //RCONST(0.0); // Initial Time - - // Initial Conditions - int y_len = IC.length(); - - // Relative tolerance - sunrealtype reltol = reltolerance; - - // Absolute tolerance - int abstol_len = abstolerance.length(); - - // absolute tolerance is either length == 1 or equal to length of IC - // If abstol is not equal to 1 and abstol is not equal to IC, then stop - if(abstol_len != 1 && abstol_len != y_len){ - stop("Absolute tolerance must be a scalar or a vector of same length as IC \n"); - } - - // Set the vector absolute tolerance ----------------------------------------- - // abstol must be same length as IC - SUNContext sunctx; - SUNContext_Create(SUN_COMM_NULL, &sunctx); - N_Vector abstol = N_VNew_Serial(y_len, sunctx); - sunrealtype *abstol_ptr = N_VGetArrayPointer(abstol); - if(abstol_len == 1){ - // if a scalar is provided - use it to make a vector with same values - for (int i = 0; i >(Parameters), - reltolerance, abstolerance}; - - // setting the user_data in rhs function - flag = CVodeSetUserData(cvode_mem, (void*)&my_rhs_function); - if (check_retval(&flag, "CVodeSetUserData", 1)) { stop("Stopping cvodes, something went wrong in setting user data!"); } - - /* Allocate space for CVODES */ - flag = CVodeInit(cvode_mem, rhs_function_sens, T0, y0); - if (check_retval(&flag, "CVodeInit", 1)) { stop("Stopping cvodes, something went wrong in allocating space for CVODES!"); } - - /* Use private function to compute error weights */ - flag = CVodeWFtolerances(cvode_mem, ewt); - if (check_retval(&flag, "CVodeSetEwtFn", 1)) { stop("Stopping cvodes, something went wrong in computing error weights!"); } - - /* Create dense SUNMatrix */ - sunindextype y_len_M = y_len; - SUNMatrix SM = SUNDenseMatrix(y_len_M, y_len_M, sunctx); - if (check_retval((void *)SM, "SUNDenseMatrix", 0)) { stop("Stopping cvodes, something went wrong in setting SUNDenseMatrix!"); } - - /* Create dense SUNLinearSolver */ - SUNLinearSolver LS = SUNLinSol_Dense(y0, SM, sunctx); - if (check_retval((void *)LS, "SUNLinSol_Dense", 0)) { stop("Stopping cvodes, something went wrong in setting Linear Solver!"); } - - /* Attach the matrix and linear solver */ - flag = CVodeSetLinearSolver(cvode_mem, LS, SM); - if (check_retval(&flag, "CVodeSetLinearSolver", 1)) { stop("Stopping cvodes, something went wrong in attaching SUNDenseMatrix and Linear Solver!"); } - - if (check_retval((void *)yS, "N_VCloneVectorArray", 0)) { stop("Stopping cvodes, something went wrong in setting Sensitivity Array!"); } - for (int is=0;isparams[0]); - flag = CVodeSetSensParams(cvode_mem, (my_rhs_function.params).begin(), Parameters.begin(), NULL); // double *y = x.begin() - if (check_retval(&flag, "CVodeSetSensParams", 1)) { stop("Stopping cvodes, something went wrong in setting Sensitivity Parameters!"); } - - // First row for initial conditions, First column is for time - int y_len_1 = y_len + 1; - NumericMatrix soln(Dimension(time_vec_len,y_len_1)); - - // fill the first row of soln matrix with Initial Conditions - soln(0,0) = time_vector[0]; // get the first time value - for(int i = 0; i >(Parameters), + reltolerance, abstolerance}; + + // setting the user_data in rhs function + flag = CVodeSetUserData(cvode_mem, (void*)&my_rhs_function); + if (check_retval(&flag, "CVodeSetUserData", 1)) { stop("Stopping cvodes, something went wrong in setting user data!"); } + + /* Allocate space for CVODES */ + flag = CVodeInit(cvode_mem, rhs_function_sens, T0, y0); + if (check_retval(&flag, "CVodeInit", 1)) { stop("Stopping cvodes, something went wrong in allocating space for CVODES!"); } + + /* Use private function to compute error weights */ + flag = CVodeWFtolerances(cvode_mem, ewt); + if (check_retval(&flag, "CVodeSetEwtFn", 1)) { stop("Stopping cvodes, something went wrong in computing error weights!"); } + + /* Create dense SUNMatrix */ + sunindextype y_len_M = y_len; + SUNMatrix SM = SUNDenseMatrix(y_len_M, y_len_M, sunctx); + if (check_retval((void *)SM, "SUNDenseMatrix", 0)) { stop("Stopping cvodes, something went wrong in setting SUNDenseMatrix!"); } + + /* Create dense SUNLinearSolver */ + SUNLinearSolver LS = SUNLinSol_Dense(y0, SM, sunctx); + if (check_retval((void *)LS, "SUNLinSol_Dense", 0)) { stop("Stopping cvodes, something went wrong in setting Linear Solver!"); } + + /* Attach the matrix and linear solver */ + flag = CVodeSetLinearSolver(cvode_mem, LS, SM); + if (check_retval(&flag, "CVodeSetLinearSolver", 1)) { stop("Stopping cvodes, something went wrong in attaching SUNDenseMatrix and Linear Solver!"); } + + if (check_retval((void *)yS, "N_VCloneVectorArray", 0)) { stop("Stopping cvodes, something went wrong in setting Sensitivity Array!"); } + for (int is=0;isparams[0]); + flag = CVodeSetSensParams(cvode_mem, (my_rhs_function.params).begin(), Parameters.begin(), NULL); // double *y = x.begin() + if (check_retval(&flag, "CVodeSetSensParams", 1)) { stop("Stopping cvodes, something went wrong in setting Sensitivity Parameters!"); } + + // First row for initial conditions, First column is for time + int y_len_1 = y_len + 1; + NumericMatrix soln(Dimension(time_vec_len,y_len_1)); + + // fill the first row of soln matrix with Initial Conditions + soln(0,0) = time_vector[0]; // get the first time value + for(int i = 0; i y_len) { + stop("The state intex in first column of Events dataframe cannot be higher than number of states"); + } + + // Check that the highest event time is less than or equal to the last time point + Rcpp::NumericVector EventsDF_time_col = Events_DF[1]; + if(Rcpp::max(EventsDF_time_col) > Rcpp::max(time_vector)) { + stop("Event cannot happen after the last time point. See the third column of the Events dataframe."); + } + + // Sort the Event DataFrame to combine discontinuities and sampling data points TCOMB = sorted_times(Events_DF, time_vector, NSTATES); // get the sorted Combined time matrix // Decrease State index by 1 to convert R state index to internal cpp index, all sampling times get state index of -1 for(int i = 0; i < TCOMB.nrow(); i++){ diff --git a/src/ida.cpp b/src/ida.cpp index fb8db36..f929c4a 100644 --- a/src/ida.cpp +++ b/src/ida.cpp @@ -48,7 +48,6 @@ struct res_func{ NumericVector params; }; - // function called by IDAInit if user inputs R function int res_function(sunrealtype t, N_Vector yy, N_Vector yp, N_Vector rr, void* user_data){ @@ -56,7 +55,7 @@ int res_function(sunrealtype t, N_Vector yy, N_Vector yp, N_Vector rr, void* use int yy_len = NV_LENGTH_S(yy); // NumericVector analog of yy - NumericVector yy1(yy_len); // filled with zeros + NumericVector yy1(yy_len); // filled with zeros sunrealtype *yy_ptr = N_VGetArrayPointer(yy); for (int i = 0; i < yy_len; i++){ yy1[i] = yy_ptr[i]; // Ith(y,i+1); @@ -67,12 +66,12 @@ int res_function(sunrealtype t, N_Vector yy, N_Vector yp, N_Vector rr, void* use NumericVector yp1(yp_len); // filled with zeros sunrealtype *yp_ptr = N_VGetArrayPointer(yp); for (int i = 0; i < yp_len; i++){ - yp1[i] = yp_ptr[i]; // Ith(y,i+1); + yp1[i] = yp_ptr[i]; // Ith(y,i+1); } // NumericVector analog of rr int rr_len = NV_LENGTH_S(rr); - NumericVector rr1(rr_len); // filled with zeros + NumericVector rr1(rr_len); // filled with zeros if(!user_data){ stop("Something went wrong, stopping!"); @@ -91,11 +90,11 @@ int res_function(sunrealtype t, N_Vector yy, N_Vector yp, N_Vector rr, void* use rr1 = res_fun(t, yy1, yp1, p_values); } else{ - stop("Something went wrong, stopping!"); + stop("Something went wrong in evaluating the residual function, stopping!"); } } else { - stop("Something went wrong, stopping!"); + stop("Something went wrong in accessing the residual function, stopping!"); } // convert NumericVector rr1 to N_Vector rr @@ -122,19 +121,18 @@ int res_function(sunrealtype t, N_Vector yy, N_Vector yp, N_Vector rr, void* use //'@param abstolerance Absolute Tolerance (a scalar or vector with length equal to ydot, default = 1e-04) //'@returns A data frame. First column is the time-vector, the other columns are values of y in order they are provided. // [[Rcpp::export]] -NumericMatrix ida(NumericVector time_vector, NumericVector IC, NumericVector IRes, SEXP input_function, +NumericMatrix ida(NumericVector time_vector, NumericVector IC, + NumericVector IRes, SEXP input_function, NumericVector Parameters, - double reltolerance = 0.0001, NumericVector abstolerance = 0.0001){ - + double reltolerance = 0.0001, + NumericVector abstolerance = 0.0001){ int time_vec_len = time_vector.length(); int y_len = IC.length(); SUNContext sunctx; SUNContext_Create(SUN_COMM_NULL, &sunctx); - if(y_len != IRes.length()){ - stop("IC and IRes should be of same length"); - } + if(y_len != IRes.length()){ stop("IC (Initial Conditions) and IRes (Residuals) should be of same length"); } int abstol_len = abstolerance.length(); // absolute tolerance is either length == 1 or equal to length of IC @@ -166,6 +164,7 @@ NumericMatrix ida(NumericVector time_vector, NumericVector IC, NumericVector IRe abstol_ptr[i] = abstolerance[i]; } } + //---------------------------------------------------------------------------- // // Set the initial values of y ----------------------------------------------- N_Vector yy0 = N_VNew_Serial(y_len, sunctx); // declared as yy0 to be consistent with example C code @@ -188,124 +187,110 @@ NumericMatrix ida(NumericVector time_vector, NumericVector IC, NumericVector IRe /* Call IDACreate and IDAInit to initialize IDA memory */ ida_mem = IDACreate(sunctx); - if(check_retval((void *)ida_mem, "IDACreate", 0)) { - stop("Stopping IDA, something went wrong in allocating memory!"); - } + if(check_retval((void *)ida_mem, "IDACreate", 0)) { stop("Stopping IDA, something went wrong in allocating memory!"); } // -- assign user input to the struct based on SEXP type of input_function - if(!input_function){ - stop("Something is wrong with the input function, stopping!"); - } - - switch(TYPEOF(input_function)){ + if(!input_function){ stop("Something is wrong with the input function, stopping!"); } - case CLOSXP:{ + if(TYPEOF(input_function) != CLOSXP) { stop("Incorrect input function type - input function can be an R or Rcpp function"); } - struct res_func my_res_function = {input_function, Parameters}; + struct res_func my_res_function = {input_function, Parameters}; - // setting the user data in the rhs residual function - flag = IDASetUserData(ida_mem, (void*)&my_res_function); - if (check_retval(&flag, "CVodeSetUserData", 1)) { stop("Stopping IDA, something went wrong in setting user data!"); } + // setting the user data in the rhs residual function + flag = IDASetUserData(ida_mem, (void*)&my_res_function); + if (check_retval(&flag, "CVodeSetUserData", 1)) { stop("Stopping IDA, something went wrong in setting user data!"); } - flag = IDAInit(ida_mem, res_function, T0, yy0, yp0); - if(check_retval(&flag, "IDAInit", 1)) { stop("Stopping, something went wrong in initializing IDA!"); }; + flag = IDAInit(ida_mem, res_function, T0, yy0, yp0); + if(check_retval(&flag, "IDAInit", 1)) { stop("Stopping, something went wrong in initializing IDA!"); }; - /* Call IDASVtolerances to set tolerances */ - flag = IDASVtolerances(ida_mem, reltol, abstol); - if(check_retval(&flag, "IDASVtolerances", 1)) { stop("Stopping, something went wrong in setting tolerances!"); }; + /* Call IDASVtolerances to set tolerances */ + flag = IDASVtolerances(ida_mem, reltol, abstol); + if(check_retval(&flag, "IDASVtolerances", 1)) { stop("Stopping, something went wrong in setting tolerances!"); }; - /* Call IDARootInit to specify the root function grob with 2 components */ - // retval = IDARootInit(mem, 2, grob); - // if (check_retval(&retval, "IDARootInit", 1)) return(1); + /* Call IDARootInit to specify the root function grob with 2 components */ + // retval = IDARootInit(mem, 2, grob); + // if (check_retval(&retval, "IDARootInit", 1)) return(1); - /* Create dense SUNMatrix for use in linear solves */ - sunindextype y_len_M = y_len; - SUNMatrix SM = SUNDenseMatrix(y_len_M, y_len_M, sunctx); - if(check_retval((void *)SM, "SUNDenseMatrix", 0)) { stop("Stopping IDA, something went wrong in setting the dense matrix!"); } + /* Create dense SUNMatrix for use in linear solves */ + sunindextype y_len_M = y_len; + SUNMatrix SM = SUNDenseMatrix(y_len_M, y_len_M, sunctx); + if(check_retval((void *)SM, "SUNDenseMatrix", 0)) { stop("Stopping IDA, something went wrong in setting the dense matrix!"); } - // Create dense SUNLinearSolver object for use by IDA - SUNLinearSolver LS = SUNLinSol_Dense(yy0, SM, sunctx); - if(check_retval((void *)LS, "SUNLinSol_Dense", 0)) { stop("Stopping IDA, something went wrong in setting the linear solver!"); } + // Create dense SUNLinearSolver object for use by IDA + SUNLinearSolver LS = SUNLinSol_Dense(yy0, SM, sunctx); + if(check_retval((void *)LS, "SUNLinSol_Dense", 0)) { stop("Stopping IDA, something went wrong in setting the linear solver!"); } - /* Attach the matrix and linear solver */ - flag = IDASetLinearSolver(ida_mem, LS, SM); - if(check_retval(&flag, "IDASetLinearSolver", 1)) return(1); + /* Attach the matrix and linear solver */ + flag = IDASetLinearSolver(ida_mem, LS, SM); + if(check_retval(&flag, "IDASetLinearSolver", 1)) { stop("Stopping IDA, something went wrong in setting the linear solver!"); } - // /* Set the user-supplied Jacobian routine */ - // retval = IDASetJacFn(mem, jacrob); - // if(check_retval(&retval, "IDASetJacFn", 1)) return(1); + // /* Set the user-supplied Jacobian routine */ + // retval = IDASetJacFn(mem, jacrob); + // if(check_retval(&retval, "IDASetJacFn", 1)) return(1); - /* Create Newton SUNNonlinearSolver object. IDA uses a - * Newton SUNNonlinearSolver by default, so it is unecessary - * to create it and attach it. */ - SUNNonlinearSolver NLS = SUNNonlinSol_Newton(yy0, sunctx); - if(check_retval((void *)NLS, "SUNNonlinSol_Newton", 0)) return(1); + /* Create Newton SUNNonlinearSolver object. IDA uses a + * Newton SUNNonlinearSolver by default, so it is unecessary + * to create it and attach it. */ + SUNNonlinearSolver NLS = SUNNonlinSol_Newton(yy0, sunctx); + if(check_retval((void *)NLS, "SUNNonlinSol_Newton", 0)) { stop("Stopping IDA, something went wrong in creating the Non-linear Solver in IDA!"); } - /* Attach the nonlinear solver */ - flag = IDASetNonlinearSolver(ida_mem, NLS); - if(check_retval(&flag, "IDASetNonlinearSolver", 1)) return(1); + /* Attach the nonlinear solver */ + flag = IDASetNonlinearSolver(ida_mem, NLS); + if(check_retval(&flag, "IDASetNonlinearSolver", 1)) { stop("Stopping IDA, something went wrong in attaching the Non-linear Solver in IDA!"); } - /* In loop, call IDASolve, print results, and test for error. - Break out of loop when NOUT preset output times have been reached. */ + /* In loop, call IDASolve, print results, and test for error. + Break out of loop when NOUT preset output times have been reached. */ - sunrealtype tout; // For output times + sunrealtype tout; // For output times - int y_len_1 = y_len + 1; // remove later - NumericMatrix soln(Dimension(time_vec_len,y_len_1)); // remove later + int y_len_1 = y_len + 1; // remove later + NumericMatrix soln(Dimension(time_vec_len,y_len_1)); // remove later - // nothing to do with Events - single initialization of the ODE system - // First row for initial conditions, First column is for time - // int y_len_1 = y_len + 1; - // NumericMatrix soln(Dimension(time_vec_len,y_len_1)); + // nothing to do with Events - single initialization of the ODE system + // First row for initial conditions, First column is for time + // int y_len_1 = y_len + 1; + // NumericMatrix soln(Dimension(time_vec_len,y_len_1)); - // fill the first row of soln matrix with Initial Conditions - soln(0,0) = time_vector[0]; // get the first time value - for(int i = 0; icv_zn[0], CV_LOGGER->debug_fp); #endif } @@ -4824,15 +4809,20 @@ static int cvEwtSetSV(CVodeMem cv_mem, N_Vector ycur, N_Vector weight) void cvProcessError(CVodeMem cv_mem, int error_code, int line, const char* func, const char* file, const char* msgfmt, ...) { - /* Initialize the argument pointer variable + /* We initialize the argument pointer variable before each vsnprintf call to avoid undefined behavior (msgfmt is the last required argument to cvProcessError) */ va_list ap; - va_start(ap, msgfmt); /* Compose the message */ + va_start(ap, msgfmt); size_t msglen = vsnprintf(NULL, 0, msgfmt, ap) + 1; - char* msg = (char*)malloc(msglen); + va_end(ap); + + char* msg = (char*)malloc(msglen); + + va_start(ap, msgfmt); vsnprintf(msg, msglen, msgfmt, ap); + va_end(ap); do { if (cv_mem == NULL) @@ -4860,8 +4850,6 @@ void cvProcessError(CVodeMem cv_mem, int error_code, int line, const char* func, } while (0); - /* Finalize argument processing */ - va_end(ap); free(msg); return; diff --git a/src/sundials/cvode/cvode_bandpre.c b/src/sundials/cvode/cvode_bandpre.c index f421257..b19c32e 100644 --- a/src/sundials/cvode/cvode_bandpre.c +++ b/src/sundials/cvode/cvode_bandpre.c @@ -435,9 +435,12 @@ static int CVBandPrecSetup(sunrealtype t, N_Vector y, N_Vector fy, The value returned by the CVBandPrecSolve function is always 0, indicating success. -----------------------------------------------------------------*/ -static int CVBandPrecSolve(sunrealtype t, N_Vector y, N_Vector fy, N_Vector r, - N_Vector z, sunrealtype gamma, sunrealtype delta, - int lr, void* bp_data) +static int CVBandPrecSolve(SUNDIALS_MAYBE_UNUSED sunrealtype t, + SUNDIALS_MAYBE_UNUSED N_Vector y, + SUNDIALS_MAYBE_UNUSED N_Vector fy, N_Vector r, + N_Vector z, SUNDIALS_MAYBE_UNUSED sunrealtype gamma, + SUNDIALS_MAYBE_UNUSED sunrealtype delta, + SUNDIALS_MAYBE_UNUSED int lr, void* bp_data) { CVBandPrecData pdata; int retval; diff --git a/src/sundials/cvode/cvode_bbdpre.c b/src/sundials/cvode/cvode_bbdpre.c index 6c8a284..4cdefc1 100644 --- a/src/sundials/cvode/cvode_bbdpre.c +++ b/src/sundials/cvode/cvode_bbdpre.c @@ -467,9 +467,10 @@ int CVBBDPrecGetNumGfnEvals(void* cvode_mem, long int* ngevalsBBDP) 0 if successful, 1 for a recoverable error (step will be retried). -----------------------------------------------------------------*/ -static int CVBBDPrecSetup(sunrealtype t, N_Vector y, N_Vector fy, - sunbooleantype jok, sunbooleantype* jcurPtr, - sunrealtype gamma, void* bbd_data) +static int CVBBDPrecSetup(sunrealtype t, N_Vector y, + SUNDIALS_MAYBE_UNUSED N_Vector fy, sunbooleantype jok, + sunbooleantype* jcurPtr, sunrealtype gamma, + void* bbd_data) { CVBBDPrecData pdata; CVodeMem cv_mem; @@ -556,9 +557,12 @@ static int CVBBDPrecSetup(sunrealtype t, N_Vector y, N_Vector fy, The value returned by the CVBBDPrecSolve function is always 0, indicating success. -----------------------------------------------------------------*/ -static int CVBBDPrecSolve(sunrealtype t, N_Vector y, N_Vector fy, N_Vector r, - N_Vector z, sunrealtype gamma, sunrealtype delta, - int lr, void* bbd_data) +static int CVBBDPrecSolve(SUNDIALS_MAYBE_UNUSED sunrealtype t, + SUNDIALS_MAYBE_UNUSED N_Vector y, + SUNDIALS_MAYBE_UNUSED N_Vector fy, N_Vector r, + N_Vector z, SUNDIALS_MAYBE_UNUSED sunrealtype gamma, + SUNDIALS_MAYBE_UNUSED sunrealtype delta, + SUNDIALS_MAYBE_UNUSED int lr, void* bbd_data) { int retval; CVBBDPrecData pdata; diff --git a/src/sundials/cvode/cvode_diag.c b/src/sundials/cvode/cvode_diag.c index e24592c..25af67f 100644 --- a/src/sundials/cvode/cvode_diag.c +++ b/src/sundials/cvode/cvode_diag.c @@ -23,20 +23,6 @@ #include "cvode_diag_impl.h" #include "cvode_impl.h" -#ifdef SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS -extern int cvDiagSetup_formY(const sunrealtype h, const sunrealtype r, - const N_Vector fpred, const N_Vector zn1, - const N_Vector ypred, N_Vector ftemp, N_Vector y); - -extern int cvDiagSetup_buildM(const sunrealtype fract, const sunrealtype uround, - const sunrealtype h, const N_Vector ftemp, - const N_Vector fpred, const N_Vector ewt, - N_Vector bit, N_Vector bitcomp, N_Vector y, - N_Vector M); - -int cvDiagSolve_updateM(const sunrealtype r, N_Vector M); -#endif - /* Other Constants */ #define FRACT SUN_RCONST(0.1) @@ -334,9 +320,10 @@ static int CVDiagInit(CVodeMem cv_mem) * ----------------------------------------------------------------- */ -static int CVDiagSetup(CVodeMem cv_mem, int convfail, N_Vector ypred, - N_Vector fpred, sunbooleantype* jcurPtr, N_Vector vtemp1, - N_Vector vtemp2, N_Vector vtemp3) +static int CVDiagSetup(CVodeMem cv_mem, SUNDIALS_MAYBE_UNUSED int convfail, + N_Vector ypred, N_Vector fpred, sunbooleantype* jcurPtr, + N_Vector vtemp1, N_Vector vtemp2, + SUNDIALS_MAYBE_UNUSED N_Vector vtemp3) { sunrealtype r; N_Vector ftemp, y; @@ -426,8 +413,10 @@ static int CVDiagSetup(CVodeMem cv_mem, int convfail, N_Vector ypred, * ----------------------------------------------------------------- */ -static int CVDiagSolve(CVodeMem cv_mem, N_Vector b, N_Vector weight, - N_Vector ycur, N_Vector fcur) +static int CVDiagSolve(CVodeMem cv_mem, N_Vector b, + SUNDIALS_MAYBE_UNUSED N_Vector weight, + SUNDIALS_MAYBE_UNUSED N_Vector ycur, + SUNDIALS_MAYBE_UNUSED N_Vector fcur) { sunbooleantype invOK; sunrealtype r; diff --git a/src/sundials/cvode/cvode_fused_stubs.c b/src/sundials/cvode/cvode_fused_stubs.c index cd7aa6a..7bc41c5 100644 --- a/src/sundials/cvode/cvode_fused_stubs.c +++ b/src/sundials/cvode/cvode_fused_stubs.c @@ -18,6 +18,7 @@ #include "cvode_diag_impl.h" #include "cvode_impl.h" +#include "sundials_macros.h" #define ZERO SUN_RCONST(0.0) #define PT1 SUN_RCONST(0.1) @@ -121,10 +122,11 @@ int cvDiagSetup_formY(const sunrealtype h, const sunrealtype r, * ----------------------------------------------------------------- */ -int cvDiagSetup_buildM(const sunrealtype fract, const sunrealtype uround, - const sunrealtype h, const N_Vector ftemp, - const N_Vector fpred, const N_Vector ewt, N_Vector bit, - N_Vector bitcomp, N_Vector y, N_Vector M) +int cvDiagSetup_buildM(SUNDIALS_MAYBE_UNUSED const sunrealtype fract, + const sunrealtype uround, const sunrealtype h, + const N_Vector ftemp, const N_Vector fpred, + const N_Vector ewt, N_Vector bit, N_Vector bitcomp, + N_Vector y, N_Vector M) { N_VLinearSum(ONE, M, -ONE, fpred, M); N_VLinearSum(FRACT, ftemp, -h, M, M); diff --git a/src/sundials/cvode/cvode_impl.h b/src/sundials/cvode/cvode_impl.h index d7d9d08..e2f3a36 100644 --- a/src/sundials/cvode/cvode_impl.h +++ b/src/sundials/cvode/cvode_impl.h @@ -22,10 +22,11 @@ #include #include #include +#include #include "cvode_proj_impl.h" -#include "sundials/sundials_math.h" #include "sundials_logger_impl.h" +#include "sundials_macros.h" #ifdef __cplusplus /* wrapper to enable C++ usage */ extern "C" { @@ -634,6 +635,34 @@ void cvRestore(CVodeMem cv_mem, sunrealtype saved_t); void cvRescale(CVodeMem cv_mem); +#ifdef SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS +int cvEwtSetSS_fused(const sunbooleantype atolmin0, const sunrealtype reltol, + const sunrealtype Sabstol, const N_Vector ycur, + N_Vector tempv, N_Vector weight); + +int cvEwtSetSV_fused(const sunbooleantype atolmin0, const sunrealtype reltol, + const N_Vector Vabstol, const N_Vector ycur, + N_Vector tempv, N_Vector weight); + +int cvCheckConstraints_fused(const N_Vector c, const N_Vector ewt, + const N_Vector y, const N_Vector mm, N_Vector tempv); + +int cvNlsResid_fused(const sunrealtype rl1, const sunrealtype ngamma, + const N_Vector zn1, const N_Vector ycor, + const N_Vector ftemp, N_Vector res); + +int cvDiagSetup_formY(const sunrealtype h, const sunrealtype r, + const N_Vector fpred, const N_Vector zn1, + const N_Vector ypred, N_Vector ftemp, N_Vector y); + +int cvDiagSetup_buildM(const sunrealtype fract, const sunrealtype uround, + const sunrealtype h, const N_Vector ftemp, + const N_Vector fpred, const N_Vector ewt, N_Vector bit, + N_Vector bitcomp, N_Vector y, N_Vector M); + +int cvDiagSolve_updateM(const sunrealtype r, N_Vector M); +#endif + /* * ================================================================= * E R R O R M E S S A G E S diff --git a/src/sundials/cvode/cvode_io.c b/src/sundials/cvode/cvode_io.c index 1a545a0..1f23b85 100644 --- a/src/sundials/cvode/cvode_io.c +++ b/src/sundials/cvode/cvode_io.c @@ -104,6 +104,8 @@ int CVodeSetMonitorFn(void* cvode_mem, CVMonitorFn fn) cv_mem->cv_monitorfun = fn; return (CV_SUCCESS); #else + /* silence warnings when monitoring is disabled */ + ((void)fn); cvProcessError(cv_mem, CV_ILL_INPUT, __LINE__, __func__, __FILE__, "SUNDIALS was not built with monitoring enabled."); return (CV_ILL_INPUT); @@ -1023,6 +1025,8 @@ int CVodeSetUseIntegratorFusedKernels(void* cvode_mem, sunbooleantype onoff) cv_mem->cv_usefused = onoff; return (CV_SUCCESS); #else + /* silence warnings when fused kernels are disabled */ + ((void)onoff); cvProcessError(cv_mem, CV_ILL_INPUT, __LINE__, __func__, __FILE__, "CVODE was not built with fused integrator kernels enabled"); return (CV_ILL_INPUT); diff --git a/src/sundials/cvode/cvode_ls.c b/src/sundials/cvode/cvode_ls.c index a51ef16..50c60c6 100644 --- a/src/sundials/cvode/cvode_ls.c +++ b/src/sundials/cvode/cvode_ls.c @@ -977,7 +977,8 @@ int cvLsPSolve(void* cvode_mem, N_Vector r, N_Vector z, sunrealtype tol, int lr) approximation routines. ---------------------------------------------------------------*/ int cvLsDQJac(sunrealtype t, N_Vector y, N_Vector fy, SUNMatrix Jac, - void* cvode_mem, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) + void* cvode_mem, N_Vector tmp1, N_Vector tmp2, + SUNDIALS_MAYBE_UNUSED N_Vector tmp3) { CVodeMem cv_mem; int retval; @@ -1213,7 +1214,7 @@ int cvLsBandDQJac(sunrealtype t, N_Vector y, N_Vector fy, SUNMatrix Jac, } /* Evaluate f with incremented y */ - retval = cv_mem->cv_f(cv_mem->cv_tn, ytemp, ftemp, cv_mem->cv_user_data); + retval = cv_mem->cv_f(t, ytemp, ftemp, cv_mem->cv_user_data); cvls_mem->nfeDQ++; if (retval != 0) { break; } diff --git a/src/sundials/cvode/cvode_nls.c b/src/sundials/cvode/cvode_nls.c index ade248a..7821bd9 100644 --- a/src/sundials/cvode/cvode_nls.c +++ b/src/sundials/cvode/cvode_nls.c @@ -40,12 +40,6 @@ static int cvNlsLSolve(N_Vector delta, void* cvode_mem); static int cvNlsConvTest(SUNNonlinearSolver NLS, N_Vector ycor, N_Vector del, sunrealtype tol, N_Vector ewt, void* cvode_mem); -#ifdef SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS -int cvNlsResid_fused(const sunrealtype rl1, const sunrealtype ngamma, - const N_Vector zn1, const N_Vector ycor, - const N_Vector ftemp, N_Vector res); -#endif - /* ----------------------------------------------------------------------------- * Exported functions * ---------------------------------------------------------------------------*/ diff --git a/src/sundials/cvodes/cvodea.c b/src/sundials/cvodes/cvodea.c index fd4ae06..2df97cf 100644 --- a/src/sundials/cvodes/cvodea.c +++ b/src/sundials/cvodes/cvodea.c @@ -1793,7 +1793,7 @@ static CVckpntMem CVAckpntInit(CVodeMem cv_mem) ck_mem->ck_t0 = cv_mem->cv_tn; ck_mem->ck_nst = 0; ck_mem->ck_q = 1; - ck_mem->ck_h = 0.0; + ck_mem->ck_h = ZERO; /* Do we need to carry quadratures */ ck_mem->ck_quadr = cv_mem->cv_quadr && cv_mem->cv_errconQ; diff --git a/src/sundials/cvodes/cvodes.c b/src/sundials/cvodes/cvodes.c index d1e994f..55399d7 100644 --- a/src/sundials/cvodes/cvodes.c +++ b/src/sundials/cvodes/cvodes.c @@ -2057,7 +2057,7 @@ int CVodeSensReInit(void* cvode_mem, int ism, N_Vector* yS0) * CVodeSensSVtolerances specifies scalar relative tolerance and a vector * absolute tolerance for each sensitivity vector (a potentially different * absolute tolerance for each vector component). - * CVodeEEtolerances specifies that tolerances for sensitivity variables + * CVodeSensEEtolerances specifies that tolerances for sensitivity variables * should be estimated from those provided for the state variables. */ @@ -6531,7 +6531,7 @@ static void cvPredict(CVodeMem cv_mem) #ifdef SUNDIALS_LOGGING_EXTRA_DEBUG SUNLogger_QueueMsg(CV_LOGGER, SUN_LOGLEVEL_DEBUG, "CVODES::cvPredict", - "forward", "predictor =", ""); + "forward", "zn_0(:) =", ""); N_VPrintFile(cv_mem->cv_zn[0], CV_LOGGER->debug_fp); #endif @@ -6548,7 +6548,7 @@ static void cvPredict(CVodeMem cv_mem) #ifdef SUNDIALS_LOGGING_EXTRA_DEBUG SUNLogger_QueueMsg(CV_LOGGER, SUN_LOGLEVEL_DEBUG, "CVODES::cvPredict", - "quad", "predictor =", ""); + "quad", "znQ_0(:) =", ""); N_VPrintFile(cv_mem->cv_znQ[0], CV_LOGGER->debug_fp); #endif } @@ -6566,7 +6566,7 @@ static void cvPredict(CVodeMem cv_mem) for (i = 0; i < cv_mem->cv_Ns; i++) { SUNLogger_QueueMsg(CV_LOGGER, SUN_LOGLEVEL_DEBUG, "CVODES::cvPredict", - "sensi", " i = %d, predictor_i = ", i); + "sensi", " i = %d, znS_i(:) = ", i); N_VPrintFile(cv_mem->cv_znS[0][i], CV_LOGGER->debug_fp); } #endif @@ -6587,7 +6587,7 @@ static void cvPredict(CVodeMem cv_mem) for (i = 0; i < cv_mem->cv_Ns; i++) { SUNLogger_QueueMsg(CV_LOGGER, SUN_LOGLEVEL_DEBUG, "CVODES::cvPredict", - "quad-sensi", " i = %d, predictor_i = ", i); + "quad-sensi", " i = %d, znQS_i(:) = ", i); N_VPrintFile(cv_mem->cv_znQS[0][i], CV_LOGGER->debug_fp); } #endif @@ -9402,8 +9402,8 @@ static int cvQuadSensEwtSetSV(CVodeMem cv_mem, N_Vector* yQScur, * Updates the norm old_nrm to account for all quadratures. */ -static sunrealtype cvQuadUpdateNorm(CVodeMem cv_mem, sunrealtype old_nrm, - N_Vector xQ, N_Vector wQ) +static sunrealtype cvQuadUpdateNorm(SUNDIALS_MAYBE_UNUSED CVodeMem cv_mem, + sunrealtype old_nrm, N_Vector xQ, N_Vector wQ) { sunrealtype qnrm; @@ -9620,9 +9620,9 @@ int cvSensRhsInternalDQ(int Ns, sunrealtype t, N_Vector y, N_Vector ydot, * non-zero return value from f(). */ -int cvSensRhs1InternalDQ(int Ns, sunrealtype t, N_Vector y, N_Vector ydot, - int is, N_Vector yS, N_Vector ySdot, void* cvode_mem, - N_Vector ytemp, N_Vector ftemp) +int cvSensRhs1InternalDQ(SUNDIALS_MAYBE_UNUSED int Ns, sunrealtype t, N_Vector y, + N_Vector ydot, int is, N_Vector yS, N_Vector ySdot, + void* cvode_mem, N_Vector ytemp, N_Vector ftemp) { CVodeMem cv_mem; int retval, method; @@ -9908,15 +9908,20 @@ static int cvQuadSensRhs1InternalDQ(CVodeMem cv_mem, int is, sunrealtype t, void cvProcessError(CVodeMem cv_mem, int error_code, int line, const char* func, const char* file, const char* msgfmt, ...) { - /* Initialize the argument pointer variable + /* We initialize the argument pointer variable before each vsnprintf call to avoid undefined behavior (msgfmt is the last required argument to cvProcessError) */ va_list ap; - va_start(ap, msgfmt); /* Compose the message */ + va_start(ap, msgfmt); size_t msglen = vsnprintf(NULL, 0, msgfmt, ap) + 1; - char* msg = (char*)malloc(msglen); + va_end(ap); + + char* msg = (char*)malloc(msglen); + + va_start(ap, msgfmt); vsnprintf(msg, msglen, msgfmt, ap); + va_end(ap); do { if (cv_mem == NULL) @@ -9944,8 +9949,6 @@ void cvProcessError(CVodeMem cv_mem, int error_code, int line, const char* func, } while (0); - /* Finalize argument processing */ - va_end(ap); free(msg); return; diff --git a/src/sundials/cvodes/cvodes_bandpre.c b/src/sundials/cvodes/cvodes_bandpre.c index 98a9308..55dbe1a 100644 --- a/src/sundials/cvodes/cvodes_bandpre.c +++ b/src/sundials/cvodes/cvodes_bandpre.c @@ -438,9 +438,12 @@ static int cvBandPrecSetup(sunrealtype t, N_Vector y, N_Vector fy, The value returned by the cvBandPrecSolve function is always 0, indicating success. -----------------------------------------------------------------*/ -static int cvBandPrecSolve(sunrealtype t, N_Vector y, N_Vector fy, N_Vector r, - N_Vector z, sunrealtype gamma, sunrealtype delta, - int lr, void* bp_data) +static int cvBandPrecSolve(SUNDIALS_MAYBE_UNUSED sunrealtype t, + SUNDIALS_MAYBE_UNUSED N_Vector y, + SUNDIALS_MAYBE_UNUSED N_Vector fy, N_Vector r, + N_Vector z, SUNDIALS_MAYBE_UNUSED sunrealtype gamma, + SUNDIALS_MAYBE_UNUSED sunrealtype delta, + SUNDIALS_MAYBE_UNUSED int lr, void* bp_data) { CVBandPrecData pdata; int retval; diff --git a/src/sundials/cvodes/cvodes_bbdpre.c b/src/sundials/cvodes/cvodes_bbdpre.c index af9cba7..12eb1b7 100644 --- a/src/sundials/cvodes/cvodes_bbdpre.c +++ b/src/sundials/cvodes/cvodes_bbdpre.c @@ -479,9 +479,10 @@ int CVBBDPrecGetNumGfnEvals(void* cvode_mem, long int* ngevalsBBDP) 0 if successful, 1 for a recoverable error (step will be retried). -----------------------------------------------------------------*/ -static int cvBBDPrecSetup(sunrealtype t, N_Vector y, N_Vector fy, - sunbooleantype jok, sunbooleantype* jcurPtr, - sunrealtype gamma, void* bbd_data) +static int cvBBDPrecSetup(sunrealtype t, N_Vector y, + SUNDIALS_MAYBE_UNUSED N_Vector fy, sunbooleantype jok, + sunbooleantype* jcurPtr, sunrealtype gamma, + void* bbd_data) { CVBBDPrecData pdata; CVodeMem cv_mem; @@ -568,9 +569,12 @@ static int cvBBDPrecSetup(sunrealtype t, N_Vector y, N_Vector fy, The value returned by the cvBBDPrecSolve function is always 0, indicating success. -----------------------------------------------------------------*/ -static int cvBBDPrecSolve(sunrealtype t, N_Vector y, N_Vector fy, N_Vector r, - N_Vector z, sunrealtype gamma, sunrealtype delta, - int lr, void* bbd_data) +static int cvBBDPrecSolve(SUNDIALS_MAYBE_UNUSED sunrealtype t, + SUNDIALS_MAYBE_UNUSED N_Vector y, + SUNDIALS_MAYBE_UNUSED N_Vector fy, N_Vector r, + N_Vector z, SUNDIALS_MAYBE_UNUSED sunrealtype gamma, + SUNDIALS_MAYBE_UNUSED sunrealtype delta, + SUNDIALS_MAYBE_UNUSED int lr, void* bbd_data) { int retval; CVBBDPrecData pdata; diff --git a/src/sundials/cvodes/cvodes_diag.c b/src/sundials/cvodes/cvodes_diag.c index b1db687..857a81b 100644 --- a/src/sundials/cvodes/cvodes_diag.c +++ b/src/sundials/cvodes/cvodes_diag.c @@ -326,9 +326,10 @@ static int CVDiagInit(CVodeMem cv_mem) * ----------------------------------------------------------------- */ -static int CVDiagSetup(CVodeMem cv_mem, int convfail, N_Vector ypred, - N_Vector fpred, sunbooleantype* jcurPtr, N_Vector vtemp1, - N_Vector vtemp2, N_Vector vtemp3) +static int CVDiagSetup(CVodeMem cv_mem, SUNDIALS_MAYBE_UNUSED int convfail, + N_Vector ypred, N_Vector fpred, sunbooleantype* jcurPtr, + N_Vector vtemp1, N_Vector vtemp2, + SUNDIALS_MAYBE_UNUSED N_Vector vtemp3) { sunrealtype r; N_Vector ftemp, y; @@ -400,8 +401,10 @@ static int CVDiagSetup(CVodeMem cv_mem, int convfail, N_Vector ypred, * ----------------------------------------------------------------- */ -static int CVDiagSolve(CVodeMem cv_mem, N_Vector b, N_Vector weight, - N_Vector ycur, N_Vector fcur) +static int CVDiagSolve(CVodeMem cv_mem, N_Vector b, + SUNDIALS_MAYBE_UNUSED N_Vector weight, + SUNDIALS_MAYBE_UNUSED N_Vector ycur, + SUNDIALS_MAYBE_UNUSED N_Vector fcur) { sunbooleantype invOK; sunrealtype r; diff --git a/src/sundials/cvodes/cvodes_impl.h b/src/sundials/cvodes/cvodes_impl.h index e98b88b..c22d166 100644 --- a/src/sundials/cvodes/cvodes_impl.h +++ b/src/sundials/cvodes/cvodes_impl.h @@ -18,12 +18,14 @@ #define _CVODES_IMPL_H #include + +#include #include +#include -#include "cvodes/cvodes.h" #include "cvodes_proj_impl.h" -#include "sundials/sundials_math.h" #include "sundials_logger_impl.h" +#include "sundials_macros.h" #ifdef __cplusplus /* wrapper to enable C++ usage */ extern "C" { diff --git a/src/sundials/cvodes/cvodes_io.c b/src/sundials/cvodes/cvodes_io.c index 4114259..e4599bd 100644 --- a/src/sundials/cvodes/cvodes_io.c +++ b/src/sundials/cvodes/cvodes_io.c @@ -104,6 +104,8 @@ int CVodeSetMonitorFn(void* cvode_mem, CVMonitorFn fn) cv_mem->cv_monitorfun = fn; return (CV_SUCCESS); #else + /* silence warnings when monitoring is disabled */ + ((void)fn); cvProcessError(cv_mem, CV_ILL_INPUT, __LINE__, __func__, __FILE__, "SUNDIALS was not built with monitoring enabled."); return (CV_ILL_INPUT); diff --git a/src/sundials/cvodes/cvodes_ls.c b/src/sundials/cvodes/cvodes_ls.c index 6c7362d..539a69a 100644 --- a/src/sundials/cvodes/cvodes_ls.c +++ b/src/sundials/cvodes/cvodes_ls.c @@ -1055,7 +1055,8 @@ int cvLsPSolve(void* cvode_mem, N_Vector r, N_Vector z, sunrealtype tol, int lr) approximation routines. ---------------------------------------------------------------*/ int cvLsDQJac(sunrealtype t, N_Vector y, N_Vector fy, SUNMatrix Jac, - void* cvode_mem, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) + void* cvode_mem, N_Vector tmp1, N_Vector tmp2, + SUNDIALS_MAYBE_UNUSED N_Vector tmp3) { CVodeMem cv_mem; int retval; @@ -1291,7 +1292,7 @@ int cvLsBandDQJac(sunrealtype t, N_Vector y, N_Vector fy, SUNMatrix Jac, } /* Evaluate f with incremented y */ - retval = cv_mem->cv_f(cv_mem->cv_tn, ytemp, ftemp, cv_mem->cv_user_data); + retval = cv_mem->cv_f(t, ytemp, ftemp, cv_mem->cv_user_data); cvls_mem->nfeDQ++; if (retval != 0) { break; } @@ -2884,7 +2885,7 @@ int cvLs_AccessLMemBCur(void* cvode_mem, const char* fname, CVodeMem* cv_mem, /* access CVodeMem structure */ if (cvode_mem == NULL) { - cvProcessError(NULL, CVLS_MEM_NULL, __LINE__, __func__, __FILE__, + cvProcessError(NULL, CVLS_MEM_NULL, __LINE__, fname, __FILE__, MSG_LS_CVMEM_NULL); return (CVLS_MEM_NULL); } @@ -2893,7 +2894,7 @@ int cvLs_AccessLMemBCur(void* cvode_mem, const char* fname, CVodeMem* cv_mem, /* access CVadjMem structure */ if ((*cv_mem)->cv_adjMallocDone == SUNFALSE) { - cvProcessError(*cv_mem, CVLS_NO_ADJ, __LINE__, __func__, __FILE__, + cvProcessError(*cv_mem, CVLS_NO_ADJ, __LINE__, fname, __FILE__, MSG_LS_NO_ADJ); return (CVLS_NO_ADJ); } @@ -2902,7 +2903,7 @@ int cvLs_AccessLMemBCur(void* cvode_mem, const char* fname, CVodeMem* cv_mem, /* get current backward problem */ if ((*ca_mem)->ca_bckpbCrt == NULL) { - cvProcessError(*cv_mem, CVLS_LMEMB_NULL, __LINE__, __func__, __FILE__, + cvProcessError(*cv_mem, CVLS_LMEMB_NULL, __LINE__, fname, __FILE__, MSG_LS_LMEMB_NULL); return (CVLS_LMEMB_NULL); } @@ -2911,7 +2912,7 @@ int cvLs_AccessLMemBCur(void* cvode_mem, const char* fname, CVodeMem* cv_mem, /* access CVLsMemB structure */ if ((*cvB_mem)->cv_lmem == NULL) { - cvProcessError(*cv_mem, CVLS_LMEMB_NULL, __LINE__, __func__, __FILE__, + cvProcessError(*cv_mem, CVLS_LMEMB_NULL, __LINE__, fname, __FILE__, MSG_LS_LMEMB_NULL); return (CVLS_LMEMB_NULL); } diff --git a/src/sundials/cvodes/cvodes_nls_stg1.c b/src/sundials/cvodes/cvodes_nls_stg1.c index a1b4fdc..c292572 100644 --- a/src/sundials/cvodes/cvodes_nls_stg1.c +++ b/src/sundials/cvodes/cvodes_nls_stg1.c @@ -258,7 +258,8 @@ static int cvNlsLSolveSensStg1(N_Vector delta, void* cvode_mem) return (CV_SUCCESS); } -static int cvNlsConvTestSensStg1(SUNNonlinearSolver NLS, N_Vector ycor, +static int cvNlsConvTestSensStg1(SUNNonlinearSolver NLS, + SUNDIALS_MAYBE_UNUSED N_Vector ycor, N_Vector delta, sunrealtype tol, N_Vector ewt, void* cvode_mem) { diff --git a/src/sundials/ida/ida.c b/src/sundials/ida/ida.c index 5236754..ea06a7a 100644 --- a/src/sundials/ida/ida.c +++ b/src/sundials/ida/ida.c @@ -3992,15 +3992,20 @@ static int IDARootfind(IDAMem IDA_mem) void IDAProcessError(IDAMem IDA_mem, int error_code, int line, const char* func, const char* file, const char* msgfmt, ...) { - /* Initialize the argument pointer variable + /* We initialize the argument pointer variable before each vsnprintf call to avoid undefined behavior (msgfmt is the last required argument to IDAProcessError) */ va_list ap; - va_start(ap, msgfmt); /* Compose the message */ + va_start(ap, msgfmt); size_t msglen = vsnprintf(NULL, 0, msgfmt, ap) + 1; - char* msg = (char*)malloc(msglen); + va_end(ap); + + char* msg = (char*)malloc(msglen); + + va_start(ap, msgfmt); vsnprintf(msg, msglen, msgfmt, ap); + va_end(ap); do { if (IDA_mem == NULL) @@ -4028,8 +4033,6 @@ void IDAProcessError(IDAMem IDA_mem, int error_code, int line, const char* func, } while (0); - /* Finalize argument processing */ - va_end(ap); free(msg); return; diff --git a/src/sundials/ida/ida_bbdpre.c b/src/sundials/ida/ida_bbdpre.c index 2352ff3..8bce33e 100644 --- a/src/sundials/ida/ida_bbdpre.c +++ b/src/sundials/ida/ida_bbdpre.c @@ -455,7 +455,8 @@ int IDABBDPrecGetNumGfnEvals(void* ida_mem, long int* ngevalsBBDP) < 0 for a nonrecoverable error (step fails). ----------------------------------------------------------------*/ static int IDABBDPrecSetup(sunrealtype tt, N_Vector yy, N_Vector yp, - N_Vector rr, sunrealtype c_j, void* bbd_data) + SUNDIALS_MAYBE_UNUSED N_Vector rr, sunrealtype c_j, + void* bbd_data) { IBBDPrecData pdata; IDAMem IDA_mem; @@ -502,9 +503,13 @@ static int IDABBDPrecSetup(sunrealtype tt, N_Vector yy, N_Vector yp, IDABBDPrecSolve returns the value returned from the linear solver object. ---------------------------------------------------------------*/ -static int IDABBDPrecSolve(sunrealtype tt, N_Vector yy, N_Vector yp, - N_Vector rr, N_Vector rvec, N_Vector zvec, - sunrealtype c_j, sunrealtype delta, void* bbd_data) +static int IDABBDPrecSolve(SUNDIALS_MAYBE_UNUSED sunrealtype tt, + SUNDIALS_MAYBE_UNUSED N_Vector yy, + SUNDIALS_MAYBE_UNUSED N_Vector yp, + SUNDIALS_MAYBE_UNUSED N_Vector rr, N_Vector rvec, + N_Vector zvec, SUNDIALS_MAYBE_UNUSED sunrealtype c_j, + SUNDIALS_MAYBE_UNUSED sunrealtype delta, + void* bbd_data) { IBBDPrecData pdata; int retval; diff --git a/src/sundials/ida/ida_ic.c b/src/sundials/ida/ida_ic.c index f1a0dac..2d44eab 100644 --- a/src/sundials/ida/ida_ic.c +++ b/src/sundials/ida/ida_ic.c @@ -58,8 +58,6 @@ */ extern int IDAInitialSetup(IDAMem IDA_mem); -extern sunrealtype IDAWrmsNorm(IDAMem IDA_mem, N_Vector x, N_Vector w, - sunbooleantype mask); static int IDAnlsIC(IDAMem IDA_mem); static int IDANewtonIC(IDAMem IDA_mem); diff --git a/src/sundials/ida/ida_impl.h b/src/sundials/ida/ida_impl.h index b68debb..f61a793 100644 --- a/src/sundials/ida/ida_impl.h +++ b/src/sundials/ida/ida_impl.h @@ -20,10 +20,12 @@ #define _IDA_IMPL_H #include + +#include #include -#include "ida/ida.h" #include "sundials_logger_impl.h" +#include "sundials_macros.h" #ifdef __cplusplus /* wrapper to enable C++ usage */ extern "C" { diff --git a/src/sundials/ida/ida_ls.c b/src/sundials/ida/ida_ls.c index c0a0c73..a8e2707 100644 --- a/src/sundials/ida/ida_ls.c +++ b/src/sundials/ida/ida_ls.c @@ -860,7 +860,8 @@ int idaLsPSetup(void* ida_mem) is the only case in which the user's psolve routine is allowed to be NULL. ---------------------------------------------------------------*/ -int idaLsPSolve(void* ida_mem, N_Vector r, N_Vector z, sunrealtype tol, int lr) +int idaLsPSolve(void* ida_mem, N_Vector r, N_Vector z, sunrealtype tol, + SUNDIALS_MAYBE_UNUSED int lr) { IDAMem IDA_mem; IDALsMem idals_mem; @@ -1138,7 +1139,7 @@ int idaLsBandDQJac(sunrealtype tt, sunrealtype c_j, N_Vector yy, N_Vector yp, /* Increment yj and ypj. */ ytemp_data[j] += inc; - yptemp_data[j] += IDA_mem->ida_cj * inc; + yptemp_data[j] += c_j * inc; } /* Call res routine with incremented arguments. */ diff --git a/src/sundials/ida/ida_nls.c b/src/sundials/ida/ida_nls.c index 8873023..160b817 100644 --- a/src/sundials/ida/ida_nls.c +++ b/src/sundials/ida/ida_nls.c @@ -233,7 +233,8 @@ int idaNlsInit(IDAMem IDA_mem) return (IDA_SUCCESS); } -static int idaNlsLSetup(sunbooleantype jbad, sunbooleantype* jcur, void* ida_mem) +static int idaNlsLSetup(SUNDIALS_MAYBE_UNUSED sunbooleantype jbad, + sunbooleantype* jcur, void* ida_mem) { IDAMem IDA_mem; int retval; @@ -318,7 +319,8 @@ static int idaNlsResidual(N_Vector ycor, N_Vector res, void* ida_mem) return (IDA_SUCCESS); } -static int idaNlsConvTest(SUNNonlinearSolver NLS, N_Vector ycor, N_Vector del, +static int idaNlsConvTest(SUNNonlinearSolver NLS, + SUNDIALS_MAYBE_UNUSED N_Vector ycor, N_Vector del, sunrealtype tol, N_Vector ewt, void* ida_mem) { IDAMem IDA_mem; diff --git a/src/sundials/idas/idas.c b/src/sundials/idas/idas.c index d42aeba..3174660 100644 --- a/src/sundials/idas/idas.c +++ b/src/sundials/idas/idas.c @@ -7836,8 +7836,9 @@ static sunrealtype IDAQuadSensWrmsNorm(IDAMem IDA_mem, N_Vector* xQS, * Updates the norm old_nrm to account for all quadratures. */ -static sunrealtype IDAQuadWrmsNormUpdate(IDAMem IDA_mem, sunrealtype old_nrm, - N_Vector xQ, N_Vector wQ) +static sunrealtype IDAQuadWrmsNormUpdate(SUNDIALS_MAYBE_UNUSED IDAMem IDA_mem, + sunrealtype old_nrm, N_Vector xQ, + N_Vector wQ) { sunrealtype qnrm; @@ -8441,10 +8442,10 @@ int IDASensResDQ(int Ns, sunrealtype t, N_Vector yy, N_Vector yp, * (<0 if res fails unrecoverably, >0 if res has a recoverable error). */ -static int IDASensRes1DQ(int Ns, sunrealtype t, N_Vector yy, N_Vector yp, - N_Vector resval, int is, N_Vector yyS, N_Vector ypS, - N_Vector resvalS, void* user_dataS, N_Vector ytemp, - N_Vector yptemp, N_Vector restemp) +static int IDASensRes1DQ(SUNDIALS_MAYBE_UNUSED int Ns, sunrealtype t, N_Vector yy, + N_Vector yp, N_Vector resval, int is, N_Vector yyS, + N_Vector ypS, N_Vector resvalS, void* user_dataS, + N_Vector ytemp, N_Vector yptemp, N_Vector restemp) { IDAMem IDA_mem; int method; @@ -8756,15 +8757,20 @@ static int IDAQuadSensRhs1InternalDQ(IDAMem IDA_mem, int is, sunrealtype t, void IDAProcessError(IDAMem IDA_mem, int error_code, int line, const char* func, const char* file, const char* msgfmt, ...) { - /* Initialize the argument pointer variable + /* We initialize the argument pointer variable before each vsnprintf call to avoid undefined behavior (msgfmt is the last required argument to IDAProcessError) */ va_list ap; - va_start(ap, msgfmt); /* Compose the message */ + va_start(ap, msgfmt); size_t msglen = vsnprintf(NULL, 0, msgfmt, ap) + 1; - char* msg = (char*)malloc(msglen); + va_end(ap); + + char* msg = (char*)malloc(msglen); + + va_start(ap, msgfmt); vsnprintf(msg, msglen, msgfmt, ap); + va_end(ap); do { if (IDA_mem == NULL) @@ -8792,8 +8798,6 @@ void IDAProcessError(IDAMem IDA_mem, int error_code, int line, const char* func, } while (0); - /* Finalize argument processing */ - va_end(ap); free(msg); return; diff --git a/src/sundials/idas/idas_bbdpre.c b/src/sundials/idas/idas_bbdpre.c index a584499..25521a9 100644 --- a/src/sundials/idas/idas_bbdpre.c +++ b/src/sundials/idas/idas_bbdpre.c @@ -469,7 +469,8 @@ int IDABBDPrecGetNumGfnEvals(void* ida_mem, long int* ngevalsBBDP) < 0 for a nonrecoverable error (step fails). ----------------------------------------------------------------*/ static int IDABBDPrecSetup(sunrealtype tt, N_Vector yy, N_Vector yp, - N_Vector rr, sunrealtype c_j, void* bbd_data) + SUNDIALS_MAYBE_UNUSED N_Vector rr, sunrealtype c_j, + void* bbd_data) { IBBDPrecData pdata; IDAMem IDA_mem; @@ -516,9 +517,13 @@ static int IDABBDPrecSetup(sunrealtype tt, N_Vector yy, N_Vector yp, IDABBDPrecSolve returns the value returned from the linear solver object. ---------------------------------------------------------------*/ -static int IDABBDPrecSolve(sunrealtype tt, N_Vector yy, N_Vector yp, - N_Vector rr, N_Vector rvec, N_Vector zvec, - sunrealtype c_j, sunrealtype delta, void* bbd_data) +static int IDABBDPrecSolve(SUNDIALS_MAYBE_UNUSED sunrealtype tt, + SUNDIALS_MAYBE_UNUSED N_Vector yy, + SUNDIALS_MAYBE_UNUSED N_Vector yp, + SUNDIALS_MAYBE_UNUSED N_Vector rr, N_Vector rvec, + N_Vector zvec, SUNDIALS_MAYBE_UNUSED sunrealtype c_j, + SUNDIALS_MAYBE_UNUSED sunrealtype delta, + void* bbd_data) { IBBDPrecData pdata; int retval; diff --git a/src/sundials/idas/idas_ic.c b/src/sundials/idas/idas_ic.c index 783a75a..c2f4d03 100644 --- a/src/sundials/idas/idas_ic.c +++ b/src/sundials/idas/idas_ic.c @@ -58,13 +58,6 @@ */ extern int IDAInitialSetup(IDAMem IDA_mem); -extern sunrealtype IDAWrmsNorm(IDAMem IDA_mem, N_Vector x, N_Vector w, - sunbooleantype mask); -extern sunrealtype IDASensWrmsNorm(IDAMem IDA_mem, N_Vector* xS, N_Vector* wS, - sunbooleantype mask); -extern sunrealtype IDASensWrmsNormUpdate(IDAMem IDA_mem, sunrealtype old_nrm, - N_Vector* xS, N_Vector* wS, - sunbooleantype mask); extern int IDASensEwtSet(IDAMem IDA_mem, N_Vector* yScur, N_Vector* weightS); diff --git a/src/sundials/idas/idas_impl.h b/src/sundials/idas/idas_impl.h index 90abcbc..e54b593 100644 --- a/src/sundials/idas/idas_impl.h +++ b/src/sundials/idas/idas_impl.h @@ -19,10 +19,12 @@ #define _IDAS_IMPL_H #include + +#include #include -#include "idas/idas.h" #include "sundials_logger_impl.h" +#include "sundials_macros.h" #ifdef __cplusplus /* wrapper to enable C++ usage */ extern "C" { diff --git a/src/sundials/idas/idas_ls.c b/src/sundials/idas/idas_ls.c index dc0c0ba..088bcbb 100644 --- a/src/sundials/idas/idas_ls.c +++ b/src/sundials/idas/idas_ls.c @@ -901,7 +901,8 @@ int idaLsPSetup(void* ida_mem) is the only case in which the user's psolve routine is allowed to be NULL. ---------------------------------------------------------------*/ -int idaLsPSolve(void* ida_mem, N_Vector r, N_Vector z, sunrealtype tol, int lr) +int idaLsPSolve(void* ida_mem, N_Vector r, N_Vector z, sunrealtype tol, + SUNDIALS_MAYBE_UNUSED int lr) { IDAMem IDA_mem; IDALsMem idals_mem; @@ -1179,7 +1180,7 @@ int idaLsBandDQJac(sunrealtype tt, sunrealtype c_j, N_Vector yy, N_Vector yp, /* Increment yj and ypj. */ ytemp_data[j] += inc; - yptemp_data[j] += IDA_mem->ida_cj * inc; + yptemp_data[j] += c_j * inc; } /* Call res routine with incremented arguments. */ diff --git a/src/sundials/idas/idas_nls.c b/src/sundials/idas/idas_nls.c index 034f2c3..17ba1e6 100644 --- a/src/sundials/idas/idas_nls.c +++ b/src/sundials/idas/idas_nls.c @@ -233,7 +233,8 @@ int idaNlsInit(IDAMem IDA_mem) return (IDA_SUCCESS); } -static int idaNlsLSetup(sunbooleantype jbad, sunbooleantype* jcur, void* ida_mem) +static int idaNlsLSetup(SUNDIALS_MAYBE_UNUSED sunbooleantype jbad, + sunbooleantype* jcur, void* ida_mem) { IDAMem IDA_mem; int retval; @@ -321,7 +322,8 @@ static int idaNlsResidual(N_Vector ycor, N_Vector res, void* ida_mem) return (IDA_SUCCESS); } -static int idaNlsConvTest(SUNNonlinearSolver NLS, N_Vector ycor, N_Vector del, +static int idaNlsConvTest(SUNNonlinearSolver NLS, + SUNDIALS_MAYBE_UNUSED N_Vector ycor, N_Vector del, sunrealtype tol, N_Vector ewt, void* ida_mem) { IDAMem IDA_mem; diff --git a/src/sundials/idas/idas_nls_sim.c b/src/sundials/idas/idas_nls_sim.c index d23a6c2..d527189 100644 --- a/src/sundials/idas/idas_nls_sim.c +++ b/src/sundials/idas/idas_nls_sim.c @@ -277,8 +277,8 @@ int idaNlsInitSensSim(IDAMem IDA_mem) return (IDA_SUCCESS); } -static int idaNlsLSetupSensSim(sunbooleantype jbad, sunbooleantype* jcur, - void* ida_mem) +static int idaNlsLSetupSensSim(SUNDIALS_MAYBE_UNUSED sunbooleantype jbad, + sunbooleantype* jcur, void* ida_mem) { IDAMem IDA_mem; int retval; @@ -415,7 +415,8 @@ static int idaNlsResidualSensSim(N_Vector ycorSim, N_Vector resSim, void* ida_me return (IDA_SUCCESS); } -static int idaNlsConvTestSensSim(SUNNonlinearSolver NLS, N_Vector ycor, +static int idaNlsConvTestSensSim(SUNNonlinearSolver NLS, + SUNDIALS_MAYBE_UNUSED N_Vector ycor, N_Vector del, sunrealtype tol, N_Vector ewt, void* ida_mem) { diff --git a/src/sundials/idas/idas_nls_stg.c b/src/sundials/idas/idas_nls_stg.c index 6311cf6..3e1590c 100644 --- a/src/sundials/idas/idas_nls_stg.c +++ b/src/sundials/idas/idas_nls_stg.c @@ -232,8 +232,8 @@ int idaNlsInitSensStg(IDAMem IDA_mem) return (IDA_SUCCESS); } -static int idaNlsLSetupSensStg(sunbooleantype jbad, sunbooleantype* jcur, - void* ida_mem) +static int idaNlsLSetupSensStg(SUNDIALS_MAYBE_UNUSED sunbooleantype jbad, + sunbooleantype* jcur, void* ida_mem) { IDAMem IDA_mem; int retval; @@ -326,7 +326,8 @@ static int idaNlsResidualSensStg(N_Vector ycorStg, N_Vector resStg, void* ida_me return (IDA_SUCCESS); } -static int idaNlsConvTestSensStg(SUNNonlinearSolver NLS, N_Vector ycor, +static int idaNlsConvTestSensStg(SUNNonlinearSolver NLS, + SUNDIALS_MAYBE_UNUSED N_Vector ycor, N_Vector del, sunrealtype tol, N_Vector ewt, void* ida_mem) { diff --git a/src/sundials/kinsol/kinsol.c b/src/sundials/kinsol/kinsol.c index 205ffbc..acfe65f 100644 --- a/src/sundials/kinsol/kinsol.c +++ b/src/sundials/kinsol/kinsol.c @@ -2491,8 +2491,10 @@ static sunrealtype KINScSNorm(KINMem kin_mem, N_Vector v, N_Vector u) * passes it to the info handler function. */ -void KINPrintInfo(KINMem kin_mem, int info_code, const char* module, - const char* fname, const char* msgfmt, ...) +void KINPrintInfo(SUNDIALS_MAYBE_UNUSED KINMem kin_mem, int info_code, + SUNDIALS_MAYBE_UNUSED const char* module, + SUNDIALS_MAYBE_UNUSED const char* fname, const char* msgfmt, + ...) { va_list ap; char msg[256], msg1[40]; @@ -2540,7 +2542,7 @@ void KINPrintInfo(KINMem kin_mem, int info_code, const char* module, { /* Compose the message */ - vsprintf(msg, msgfmt, ap); + vsnprintf(msg, sizeof msg, msgfmt, ap); } #if SUNDIALS_LOGGING_LEVEL >= SUNDIALS_LOGGING_INFO @@ -2563,15 +2565,20 @@ void KINPrintInfo(KINMem kin_mem, int info_code, const char* module, void KINProcessError(KINMem kin_mem, int error_code, int line, const char* func, const char* file, const char* msgfmt, ...) { - /* Initialize the argument pointer variable + /* We initialize the argument pointer variable before each vsnprintf call to avoid undefined behavior (msgfmt is the last required argument to KINProcessError) */ va_list ap; - va_start(ap, msgfmt); /* Compose the message */ + va_start(ap, msgfmt); size_t msglen = vsnprintf(NULL, 0, msgfmt, ap) + 1; - char* msg = (char*)malloc(msglen); + va_end(ap); + + char* msg = (char*)malloc(msglen); + + va_start(ap, msgfmt); vsnprintf(msg, msglen, msgfmt, ap); + va_end(ap); do { if (kin_mem == NULL) @@ -2599,8 +2606,6 @@ void KINProcessError(KINMem kin_mem, int error_code, int line, const char* func, } while (0); - /* Finalize argument processing */ - va_end(ap); free(msg); return; @@ -2837,7 +2842,7 @@ static int KINFP(KINMem kin_mem) #ifdef SUNDIALS_LOGGING_EXTRA_DEBUG SUNLogger_QueueMsg(KIN_LOGGER, SUN_LOGLEVEL_DEBUG, "KINSOL::KINFP", "begin", - "%s", "u_0:"); + "%s", "u_0(:) ="); N_VPrintFile(kin_mem->kin_uu, KIN_LOGGER->debug_fp); #endif @@ -2857,7 +2862,7 @@ static int KINFP(KINMem kin_mem) #ifdef SUNDIALS_LOGGING_EXTRA_DEBUG SUNLogger_QueueMsg(KIN_LOGGER, SUN_LOGLEVEL_DEBUG, "KINSOL::KINFP", "while-loop-before-compute-new", - "G_%ld:", kin_mem->kin_nni - 1); + "G_%ld(:) =", kin_mem->kin_nni - 1); N_VPrintFile(kin_mem->kin_fval, KIN_LOGGER->debug_fp); #endif @@ -2912,8 +2917,8 @@ static int KINFP(KINMem kin_mem) #ifdef SUNDIALS_LOGGING_EXTRA_DEBUG SUNLogger_QueueMsg(KIN_LOGGER, SUN_LOGLEVEL_DEBUG, "KINSOL::KINFP", - "while-loop-after-compute-new", "u_%ld:\n", - kin_mem->kin_nni); + "while-loop-after-compute-new", + "u_%ld(:) =", kin_mem->kin_nni); N_VPrintFile(kin_mem->kin_unew, KIN_LOGGER->debug_fp); #endif diff --git a/src/sundials/kinsol/kinsol_bbdpre.c b/src/sundials/kinsol/kinsol_bbdpre.c index 3cd8b78..7025f38 100644 --- a/src/sundials/kinsol/kinsol_bbdpre.c +++ b/src/sundials/kinsol/kinsol_bbdpre.c @@ -399,8 +399,9 @@ int KINBBDPrecGetNumGfnEvals(void* kinmem, long int* ngevalsBBDP) 0 if successful, > 0 for a recoverable error - step will be retried. ------------------------------------------------------------------*/ -static int KINBBDPrecSetup(N_Vector uu, N_Vector uscale, N_Vector fval, - N_Vector fscale, void* bbd_data) +static int KINBBDPrecSetup(N_Vector uu, N_Vector uscale, + SUNDIALS_MAYBE_UNUSED N_Vector fval, + SUNDIALS_MAYBE_UNUSED N_Vector fscale, void* bbd_data) { KBBDPrecData pdata; KINMem kin_mem; @@ -463,8 +464,11 @@ static int KINBBDPrecSetup(N_Vector uu, N_Vector uscale, N_Vector fval, flag returned from the lienar solver object. ------------------------------------------------------------------*/ -static int KINBBDPrecSolve(N_Vector uu, N_Vector uscale, N_Vector fval, - N_Vector fscale, N_Vector vv, void* bbd_data) +static int KINBBDPrecSolve(SUNDIALS_MAYBE_UNUSED N_Vector uu, + SUNDIALS_MAYBE_UNUSED N_Vector uscale, + SUNDIALS_MAYBE_UNUSED N_Vector fval, + SUNDIALS_MAYBE_UNUSED N_Vector fscale, N_Vector vv, + void* bbd_data) { KBBDPrecData pdata; sunrealtype* vd; diff --git a/src/sundials/kinsol/kinsol_impl.h b/src/sundials/kinsol/kinsol_impl.h index 7122c07..117bf00 100644 --- a/src/sundials/kinsol/kinsol_impl.h +++ b/src/sundials/kinsol/kinsol_impl.h @@ -20,12 +20,14 @@ #ifndef _KINSOL_IMPL_H #define _KINSOL_IMPL_H -#include #include + +#include #include #include "sundials_iterative_impl.h" #include "sundials_logger_impl.h" +#include "sundials_macros.h" #ifdef __cplusplus /* wrapper to enable C++ usage */ extern "C" { diff --git a/src/sundials/kinsol/kinsol_ls.c b/src/sundials/kinsol/kinsol_ls.c index 684995a..37c706e 100644 --- a/src/sundials/kinsol/kinsol_ls.c +++ b/src/sundials/kinsol/kinsol_ls.c @@ -678,7 +678,9 @@ int kinLsPSetup(void* kinmem) in the case in which preconditioning is not done. This is the only case in which the user's psolve routine is allowed to be NULL. ------------------------------------------------------------------*/ -int kinLsPSolve(void* kinmem, N_Vector r, N_Vector z, sunrealtype tol, int lr) +int kinLsPSolve(void* kinmem, N_Vector r, N_Vector z, + SUNDIALS_MAYBE_UNUSED sunrealtype tol, + SUNDIALS_MAYBE_UNUSED int lr) { KINMem kin_mem; KINLsMem kinls_mem; @@ -941,8 +943,8 @@ int kinLsBandDQJac(N_Vector u, N_Vector fu, SUNMatrix Jac, KINMem kin_mem, a recovery may still be possible even if the system function fails (recoverably). ------------------------------------------------------------------*/ -int kinLsDQJtimes(N_Vector v, N_Vector Jv, N_Vector u, sunbooleantype* new_u, - void* kinmem) +int kinLsDQJtimes(N_Vector v, N_Vector Jv, N_Vector u, + SUNDIALS_MAYBE_UNUSED sunbooleantype* new_u, void* kinmem) { sunrealtype sigma, sigma_inv, sutsv, sq1norm, sign, vtv; KINMem kin_mem; diff --git a/src/sundials/nvector/serial/nvector_serial.c b/src/sundials/nvector/serial/nvector_serial.c index a4a1bff..255aca3 100644 --- a/src/sundials/nvector/serial/nvector_serial.c +++ b/src/sundials/nvector/serial/nvector_serial.c @@ -16,14 +16,16 @@ * of the NVECTOR package. * -----------------------------------------------------------------*/ -#include #include #include + +#include #include #include #include +#include -#include "sundials/sundials_errors.h" +#include "sundials_macros.h" #define ZERO SUN_RCONST(0.0) #define HALF SUN_RCONST(0.5) @@ -217,6 +219,15 @@ N_Vector N_VMake_Serial(sunindextype length, sunrealtype* v_data, return (v); } +/* ---------------------------------------------------------------- + * Returns vector type ID. Used to identify vector implementation + * from abstract N_Vector interface. + */ +N_Vector_ID N_VGetVectorID_Serial(SUNDIALS_MAYBE_UNUSED N_Vector v) +{ + return SUNDIALS_NVEC_SERIAL; +} + /* ---------------------------------------------------------------------------- * Function to return number of vector elements */ diff --git a/src/sundials/sundials/priv/sundials_context_impl.h b/src/sundials/sundials/priv/sundials_context_impl.h new file mode 100644 index 0000000..1281333 --- /dev/null +++ b/src/sundials/sundials/priv/sundials_context_impl.h @@ -0,0 +1,45 @@ +/* ----------------------------------------------------------------- + * Programmer(s): Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + * This is a 'private' header file and should not be used in user + * code. It is subject to change without warning. + * !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + * ----------------------------------------------------------------- + * SUNDIALS context class implementation. + * ----------------------------------------------------------------*/ + +#ifndef _SUNDIALS_CONTEXT_IMPL_H +#define _SUNDIALS_CONTEXT_IMPL_H + +#include + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +extern "C" { +#endif + +struct SUNContext_ +{ + SUNProfiler profiler; + sunbooleantype own_profiler; + SUNLogger logger; + sunbooleantype own_logger; + SUNErrCode last_err; + SUNErrHandler err_handler; + SUNComm comm; +}; + +#ifdef __cplusplus +} +#endif +#endif diff --git a/src/sundials/sundials/priv/sundials_errors_impl.h b/src/sundials/sundials/priv/sundials_errors_impl.h new file mode 100644 index 0000000..115b5ee --- /dev/null +++ b/src/sundials/sundials/priv/sundials_errors_impl.h @@ -0,0 +1,557 @@ +/* ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + * This is a 'private' header file and should not be used in user + * code. It is subject to change without warning. + * !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + * ----------------------------------------------------------------- + * Contains all error checking macros and private error handling API. + * -----------------------------------------------------------------*/ + +#ifndef _SUNDIALS_ERRORS_IMPL_H +#define _SUNDIALS_ERRORS_IMPL_H + +#include + +#include "sundials/sundials_config.h" +#include "sundials/sundials_context.h" +#include "sundials/sundials_export.h" +#include "sundials/sundials_logger.h" +#include "sundials/sundials_types.h" + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +extern "C" { +#endif + +/* ---------------------------------------------------------------------------- + * Macros used in error handling + * ---------------------------------------------------------------------------*/ + +/* ------------------------------------------------------------------ + * SUNDIALS __builtin_expect related macros. + * These macros provide hints to the compiler that the condition + * is typically false (or true) which may allow the compiler to + * optimize. + * -----------------------------------------------------------------*/ + +/* Hint to the compiler that the branch is unlikely to be taken */ +#ifdef SUNDIALS_C_COMPILER_HAS_BUILTIN_EXPECT +#define SUNHintFalse(cond) __builtin_expect((cond), 0) +#else +#define SUNHintFalse(cond) (cond) +#endif + +/* Hint to the compiler that the branch is likely to be taken */ +#ifdef SUNDIALS_C_COMPILER_HAS_BUILTIN_EXPECT +#define SUNHintTrue(cond) __builtin_expect((cond), 1) +#else +#define SUNHintTrue(cond) (cond) +#endif + +/* ------------------------------------------------------------------ + * SUNAssume + * + * This macro tells the compiler that the condition should be assumed + * to be true. The consequence is that what happens if the assumption + * is violated is undefined. If there is not compiler support for + * assumptions, then we dont do anything as there is no reliable + * way to avoid the condition being executed in all cases (such as + * the condition being an opaque function call, which we have a lot of). + * -----------------------------------------------------------------*/ + +#if __cplusplus >= 202302L +#define SUNAssume(...) [[assume(__VA_ARGS__)]] +#elif defined(SUNDIALS_C_COMPILER_HAS_ATTRIBUTE_ASSUME) +#define SUNAssume(...) __attribute__((assume(__VA_ARGS__))) +#elif defined(SUNDIALS_C_COMPILER_HAS_BUILTIN_ASSUME) +#define SUNAssume(...) __builtin_assume(__VA_ARGS__) +#elif defined(SUNDIALS_C_COMPILER_HAS_ASSUME) +#define SUNAssume(...) __assume(__VA_ARGS__) +#else +#define SUNAssume(...) +#endif + +/* ---------------------------------------------------------------------------- + * SUNErrHandler_ definition. + * ---------------------------------------------------------------------------*/ + +struct SUNErrHandler_ +{ + SUNErrHandler previous; /* next error handler to call (singly linked-list) */ + SUNErrHandlerFn call; + void* data; +}; + +/* + This function creates a new SUNErrHandler object which is a node in a + singly linked-lis of error handlers. + + :param eh_fn: An error handler callback function + :param eh_data: A pointer that will be passed back to the error handler + callback function + :param eh_out: The new SUNErrHandler object + + :return: A SUNErrCode indicating success or failure +*/ +SUNDIALS_EXPORT +SUNErrCode SUNErrHandler_Create(SUNErrHandlerFn eh_fn, void* eh_data, + SUNErrHandler* eh_out); + +/* + This function destroys and frees the memory for the given SUNErrHandler + object. + + :param eh: A pointer to a SUNErrHandler object + + :return: void +*/ +SUNDIALS_EXPORT +void SUNErrHandler_Destroy(SUNErrHandler* eh); + +/* + This function will print an error out to stderr. It is used as a fallback + when the SUNContext is NULL or corrupt. It should not be used otherwise. + + :param line: the line number of the error + :param func: the function in which the error occurred + :param file: the file in which the error occurred + :param msg: a message associated with the error + :param args: the arguments to be provided to the format message + + :return: void +*/ +SUNDIALS_EXPORT +void SUNGlobalFallbackErrHandler(int line, const char* func, const char* file, + const char* msgfmt, SUNErrCode code, ...); + +/* + This function calls the error handlers registered with the SUNContext + with the provided message. + + :param line: the line number of the error + :param func: the function in which the error occurred + :param file: the file in which the error occurred + :param msgfmt: a message associated with the error with formatting + :param code: the SUNErrCode for the error + :param sunctx: a valid SUNContext object + + :return: void +*/ +static inline void SUNHandleErrWithMsg(int line, const char* func, + const char* file, const char* msg, + SUNErrCode code, SUNContext sunctx) +{ + if (!sunctx) { SUNGlobalFallbackErrHandler(line, func, file, msg, code); } + + sunctx->last_err = code; + SUNErrHandler eh = sunctx->err_handler; + while (eh != NULL) + { + eh->call(line, func, file, msg, code, eh->data, sunctx); + eh = eh->previous; + } +} + +/* + This function calls the error handlers registered with the SUNContext + with the provided format message. + + :param line: the line number of the error + :param func: the function in which the error occurred + :param file: the file in which the error occurred + :param msgfmt: a message associated with the error with formatting + :param code: the SUNErrCode for the error + :param sunctx: a valid SUNContext object + :param args: the arguments to be provided to the format message + + :return: void +*/ +static inline void SUNHandleErrWithFmtMsg(int line, const char* func, + const char* file, const char* msgfmt, + SUNErrCode code, SUNContext sunctx, ...) +{ + size_t msglen; + char* msg; + va_list values; + va_start(values, sunctx); + msglen = (size_t)vsnprintf(NULL, (size_t)0, msgfmt, values); /* determine size + of buffer + needed */ + msg = (char*)malloc(msglen + 1); + vsnprintf(msg, msglen + 1, msgfmt, values); + SUNHandleErrWithMsg(line, func, file, msg, code, sunctx); + va_end(values); + free(msg); +} + +/* + The SUNCTX_ macro expands to the name of the local SUNContext object + defined by SUNFunctionBegin. SUNCTX_ should be used to reference the + SUNContext inside of SUNDIALS functions. + */ +#define SUNCTX_ sunctx_local_scope_ + +/* + The SUNFunctionBegin macro is used to declare the local SUNContext object to + be used a function. It should be used at the start of every SUNDIALS + functions. + + :param sunctx: the SUNContext to set the local SUNContext variable to + */ +#define SUNFunctionBegin(sunctx) \ + SUNContext SUNCTX_ = sunctx; \ + (void)SUNCTX_ + +/* ---------------------------------------------------------------------------- + * SUNCheck* family of error checking macros + * + * We define several different versions of SUNCheck* macros to cover various + * programming scenarios. + * + * SUNCheckCall* macros are used to check SUNDIALS function calls that + * return a SUNErrCode. + * + * SUNCheckLastErr* macros are used to check SUNDIALS function calls that + * do not return a SUNErrCode. + * ---------------------------------------------------------------------------*/ + +/* + SUNCheck evaluates the given expression and calls the error handler if it is + false. It should be used to check expressions that do not imply stringent + assumptions. If the expression should be strictly assumed as true, then use + SUNAssert instead. + + Use SUNAssert macros to check for conditions that do not make sense e.g., + to check if malloc returned NULL. + + :param expr: an expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheck(expr, code) \ + do { \ + if (SUNHintFalse(!(expr))) \ + { \ + SUNHandleErrWithFmtMsg(__LINE__, __func__, __FILE__, "expected %s", \ + code, SUNCTX_, #expr); \ + return code; \ + } \ + } \ + while (0) +#else +#define SUNCheck(expr, code) +#endif + +/* + SUNCheckNoRet is the same as SUNCheck but *does not return from the caller*. + Use SUNAssert macros to check for conditions that do not make sense e.g., + to check if malloc returned NULL. + + :param expr: an expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ + +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckNoRet(expr, code) \ + do { \ + if (SUNHintFalse(!(expr))) \ + { \ + SUNHandleErrWithFmtMsg(__LINE__, __func__, __FILE__, "expected %s", \ + code, SUNCTX_, #expr); \ + } \ + } \ + while (0) +#else +#define SUNCheckNoRet(expr, code) +#endif + +/* + SUNCheckNull is the same as SUNCheck but *returns NULL from the caller*. + Use SUNAssert macros to check for conditions that do not make sense e.g., + to check if malloc returned NULL. + + :param expr: an expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ + +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckNull(expr, code) \ + do { \ + if (SUNHintFalse(!(expr))) \ + { \ + SUNHandleErrWithFmtMsg(__LINE__, __func__, __FILE__, "expected %s", \ + code, SUNCTX_, #expr); \ + return NULL; \ + } \ + } \ + while (0) +#else +#define SUNCheckNull(expr, code) +#endif + +/* + SUNCheckNull is the same as SUNCheck but *returns void from the caller*. + Use SUNAssert macros to check for conditions that do not make sense e.g., + to check if malloc returned NULL. + + :param expr: an expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ + +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckVoid(expr, code) \ + do { \ + if (SUNHintFalse(!(expr))) \ + { \ + SUNHandleErrWithFmtMsg(__LINE__, __func__, __FILE__, "expected %s", \ + code, SUNCTX_, #expr); \ + return; \ + } \ + } \ + while (0) +#else +#define SUNCheckVoid(expr, code) +#endif + +/* + SUNCheckCallMsg performs the SUNDIALS function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then return the error code**. + + :param call: the function call + :param msg: an error message +*/ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckCallMsg(call, msg) \ + do { \ + SUNErrCode sun_chk_call_err_code_ = call; \ + if (SUNHintFalse(sun_chk_call_err_code_ < 0)) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, \ + sun_chk_call_err_code_, SUNCTX_); \ + return sun_chk_call_err_code_; \ + } \ + } \ + while (0) +#else +#define SUNCheckCallMsg(call, msg) (void)call +#endif + +/* + SUNCheckCallNoRetMsg performs the SUNDIALS function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, and call the error handler. **It does not return**. + + :param call: the function call + :param msg: an error message +*/ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckCallNoRetMsg(call, msg) \ + do { \ + SUNErrCode sun_chk_call_err_code_ = call; \ + if (SUNHintFalse(sun_chk_call_err_code_ < 0)) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, \ + sun_chk_call_err_code_, SUNCTX_); \ + } \ + } \ + while (0) +#else +#define SUNCheckCallNoRetMsg(call, msg) (void)call +#endif + +/* + SUNCheckCallNullMsg performs the SUNDIALS function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then returns NULL**. + + :param call: the function call + :param msg: an error message +*/ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckCallNullMsg(call, msg) \ + do { \ + SUNErrCode sun_chk_call_err_code_ = call; \ + if (SUNHintFalse(sun_chk_call_err_code_ < 0)) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, \ + sun_chk_call_err_code_, SUNCTX_); \ + return NULL; \ + } \ + } \ + while (0) +#else +#define SUNCheckCallNullMsg(call, msg) (void)call +#endif + +/* + SUNCheckCallNullMsg performs the SUNDIALS function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then returns void**. + + :param call: the function call + :param msg: an error message +*/ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckCallVoidMsg(call, msg) \ + do { \ + SUNErrCode sun_chk_call_err_code_ = call; \ + if (SUNHintFalse(sun_chk_call_err_code_ < 0)) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, \ + sun_chk_call_err_code_, SUNCTX_); \ + return; \ + } \ + } \ + while (0) +#else +#define SUNCheckCallVoidMsg(call, msg) (void)call +#endif + +/* These versions of SUNCheckCall do not take a custom message so a + default message associated with the error code will be used. */ +#define SUNCheckCall(call) SUNCheckCallMsg(call, NULL) +#define SUNCheckCallNoRet(call) SUNCheckCallNoRetMsg(call, NULL) +#define SUNCheckCallNull(call) SUNCheckCallNullMsg(call, NULL) +#define SUNCheckCallVoid(call) SUNCheckCallVoidMsg(call, NULL) + +/* SUNCheckLastErrMsg checks the last_err value in the SUNContext. + If an error occured, then it will log the error, set the last_err + value, and call the error handler, **and then returns the code**. */ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckLastErrMsg(msg) \ + do { \ + SUNCheckCallMsg(SUNContext_PeekLastError(SUNCTX_), msg); \ + } \ + while (0) + +/* + SUNCheckLastErrNoRetMsg performs the SUNDIALS function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler. **It does not return.** + + :param msg: an error message +*/ +#define SUNCheckLastErrNoRetMsg(msg) \ + do { \ + SUNCheckCallNoRetMsg(SUNContext_PeekLastError(SUNCTX_), msg); \ + } \ + while (0) + +/* + SUNCheckLastErrNullMsg performs the SUNDIALS function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then returns NULL**. + + :param msg: an error message +*/ +#define SUNCheckLastErrNullMsg(msg) \ + do { \ + SUNCheckCallNullMsg(SUNContext_PeekLastError(SUNCTX_), msg); \ + } \ + while (0) + +/* + SUNCheckLastErrVoidMsg performs the SUNDIALS function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then returns void**. + + :param msg: an error message +*/ +#define SUNCheckLastErrVoidMsg(msg) \ + do { \ + SUNCheckCallVoidMsg(SUNContext_PeekLastError(SUNCTX_), msg); \ + } \ + while (0) +#else +#define SUNCheckLastErrNoRetMsg(msg) +#define SUNCheckLastErrMsg(msg) +#define SUNCheckLastErrVoidMsg(msg) +#define SUNCheckLastErrNullMsg(msg) +#endif + +/* These versions of SUNCheckLastErr do not take a custom message so the + default message associated with the error code will be used. */ +#define SUNCheckLastErr() SUNCheckLastErrMsg(NULL) +#define SUNCheckLastErrNoRet() SUNCheckLastErrNoRetMsg(NULL) +#define SUNCheckLastErrVoid() SUNCheckLastErrVoidMsg(NULL) +#define SUNCheckLastErrNull() SUNCheckLastErrNullMsg(NULL) + +/* + SUNAssert checks if an expression is true. It expands to SUNCheck in debug + builds othewrise we try to expand it to an assumption, if the compiler + supports assumptions, so that the compiler can make optimizations based on the + assumption. + + :param expr: a expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ + +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNAssert(expr, code) SUNCheck(expr, code) +#else +#define SUNAssert(expr, code) +#endif + +/* + SUNAssertNoRet is the same as SUNAssert but it does not return from the + caller. + + :param expr: a expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ + +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNAssertNoRet(expr, code) SUNCheckNoRet(expr, code) +#else +#define SUNAssertNoRet(expr, code) +#endif + +/* + SUNAssertNull is the same as SUNAssert but it *returns NULL from the caller*. + + :param expr: a expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ + +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNAssertNull(expr, code) SUNCheckNull(expr, code) +#else +#define SUNAssertNull(expr, code) +#endif + +/* + SUNAssertVoid is the same as SUNAssert but it *returns void from the caller*. + + :param expr: a expression to evaluate as true or false + :param code: the error code to pass to the error handler if the expression is + false +*/ + +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNAssertVoid(expr, code) SUNCheckVoid(expr, code) +#else +#define SUNAssertVoid(expr, code) +#endif + +#ifdef __cplusplus +} +#endif + +#endif /* _SUNDIALS_ERRORS_IMPL_H */ diff --git a/src/sundials/sundials/priv/sundials_mpi_errors_impl.h b/src/sundials/sundials/priv/sundials_mpi_errors_impl.h new file mode 100644 index 0000000..003cccf --- /dev/null +++ b/src/sundials/sundials/priv/sundials_mpi_errors_impl.h @@ -0,0 +1,137 @@ +/* ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + * This is a 'private' header file and should not be used in user + * code. It is subject to change without warning. + * !!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + * ----------------------------------------------------------------- + * Contains error checking macros and prototypes for MPI calls. + * -----------------------------------------------------------------*/ + +#ifndef _SUNDIALS_MPI_ERRORS_IMPL_H +#define _SUNDIALS_MPI_ERRORS_IMPL_H + +#include +#include +#include + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +extern "C" { +#endif + +/* + SUNCheckMPICallMsg performs the MPI function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then return SUN_ERR_MPI_FAIL**. + + :param call: the MPI function call + :param msg: an error message + */ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckMPICallMsg(call, msg) \ + do { \ + int sun_chk_mpi_call_err_code_ = call; \ + if (sun_chk_mpi_call_err_code_ != MPI_SUCCESS) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, SUN_ERR_MPI_FAIL, \ + SUNCTX_); \ + return SUN_ERR_MPI_FAIL; \ + } \ + } \ + while (0) +#else +#define SUNCheckMPICallMsg(call, msg) (void)call +#endif + +/* + SUNCheckMPICallNullMsg performs the MPI function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then return NULL**. + + :param call: the MPI function call + :param msg: an error message + */ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckMPICallNullMsg(call, msg) \ + do { \ + int sun_chk_mpi_call_err_code_ = call; \ + if (sun_chk_mpi_call_err_code_ != MPI_SUCCESS) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, SUN_ERR_MPI_FAIL, \ + SUNCTX_); \ + return NULL; \ + } \ + } \ + while (0) +#else +#define SUNCheckMPICallNullMsg(call, msg) (void)call +#endif + +/* + SUNCheckMPICallVoidMsg performs the MPI function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, call the error handler, **and then return void**. + + :param call: the MPI function call + :param msg: an error message + */ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckMPICallVoidMsg(call, msg) \ + do { \ + int sun_chk_mpi_call_err_code_ = call; \ + if (sun_chk_mpi_call_err_code_ != MPI_SUCCESS) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, SUN_ERR_MPI_FAIL, \ + SUNCTX_); \ + return; \ + } \ + } \ + while (0) +#else +#define SUNCheckMPICallVoidMsg(call, msg) (void)call +#endif + +/* + SUNCheckMPICallNoRetMsg performs the MPI function call, and checks the + returned error code. If an error occured, then it will log the error, set the + last_err value, and call the error handler. **It does not return**. + + :param call: the MPI function call + :param msg: an error message + */ +#if defined(SUNDIALS_ENABLE_ERROR_CHECKS) +#define SUNCheckMPICallNoRetMsg(call, msg) \ + do { \ + int sun_chk_mpi_call_err_code_ = call; \ + if (sun_chk_mpi_call_err_code_ != MPI_SUCCESS) \ + { \ + SUNHandleErrWithMsg(__LINE__, __func__, __FILE__, msg, SUN_ERR_MPI_FAIL, \ + SUNCTX_); \ + } \ + } \ + while (0) +#else +#define SUNCheckMPICallNoRetMsg(call, msg) (void)call +#endif + +/* These versions of SUNCheckMPICall do not take a custom message so a + default message associated with the error code will be used. */ +#define SUNCheckMPICall(call) SUNCheckMPICallMsg(call, NULL) +#define SUNCheckMPICallNoRet(call) SUNCheckMPICallNoRetMsg(call, NULL) +#define SUNCheckMPICallNull(call) SUNCheckMPICallNullMsg(call, NULL) +#define SUNCheckMPICallVoid(call) SUNCheckMPICallVoidMsg(call, NULL) + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +} +#endif + +#endif /* _SUNDIALS_MPI_ERRORS_IMPL_H */ diff --git a/src/sundials/sundials/sundials_adaptcontroller.c b/src/sundials/sundials/sundials_adaptcontroller.c new file mode 100644 index 0000000..39a5648 --- /dev/null +++ b/src/sundials/sundials/sundials_adaptcontroller.c @@ -0,0 +1,199 @@ +/* ----------------------------------------------------------------- + * Programmer(s): Daniel R. Reynolds @ SMU + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * This is the implementation file for a generic SUNAdaptController + * package. It contains the implementation of the SUNAdaptController + * operations listed in sundials_adaptcontroller.h + * -----------------------------------------------------------------*/ + +#include +#include + +#include "sundials/sundials_errors.h" + +/* ----------------------------------------------------------------- + * Create a new empty SUNAdaptController object + * ----------------------------------------------------------------- */ + +SUNAdaptController SUNAdaptController_NewEmpty(SUNContext sunctx) +{ + SUNAdaptController C; + SUNAdaptController_Ops ops; + + /* a context is required */ + if (sunctx == NULL) { return (NULL); } + + SUNFunctionBegin(sunctx); + + /* create controller object */ + C = NULL; + C = (SUNAdaptController)malloc(sizeof *C); + SUNAssertNull(C, SUN_ERR_MALLOC_FAIL); + + /* create matrix ops structure */ + ops = NULL; + ops = (SUNAdaptController_Ops)malloc(sizeof *ops); + SUNAssertNull(ops, SUN_ERR_MALLOC_FAIL); + + /* initialize operations to NULL */ + ops->gettype = NULL; + ops->destroy = NULL; + ops->reset = NULL; + ops->estimatestep = NULL; + ops->setdefaults = NULL; + ops->write = NULL; + ops->seterrorbias = NULL; + ops->updateh = NULL; + ops->space = NULL; + + /* attach ops and initialize content to NULL */ + C->ops = ops; + C->content = NULL; + C->sunctx = sunctx; + + return (C); +} + +/* ----------------------------------------------------------------- + * Free a generic SUNAdaptController (assumes content is already empty) + * ----------------------------------------------------------------- */ + +void SUNAdaptController_DestroyEmpty(SUNAdaptController C) +{ + if (C == NULL) { return; } + + /* free non-NULL ops structure */ + if (C->ops) { free(C->ops); } + C->ops = NULL; + + /* free overall SUNAdaptController object and return */ + free(C); + return; +} + +/* ----------------------------------------------------------------- + * Required functions in the 'ops' structure for non-NULL controller + * ----------------------------------------------------------------- */ + +SUNAdaptController_Type SUNAdaptController_GetType(SUNAdaptController C) +{ + if (C == NULL) { return SUN_ADAPTCONTROLLER_NONE; } + if (C->ops->gettype) { return C->ops->gettype(C); } + return SUN_ADAPTCONTROLLER_NONE; +} + +/* ----------------------------------------------------------------- + * Optional functions in the 'ops' structure + * ----------------------------------------------------------------- */ + +SUNErrCode SUNAdaptController_Destroy(SUNAdaptController C) +{ + if (C == NULL) { return (SUN_SUCCESS); } + + /* if the destroy operation exists use it */ + if (C->ops) + { + if (C->ops->destroy) { return (C->ops->destroy(C)); } + } + + /* if we reach this point, either ops == NULL or destroy == NULL, + try to cleanup by freeing the content, ops, and matrix */ + if (C->content) + { + free(C->content); + C->content = NULL; + } + if (C->ops) + { + free(C->ops); + C->ops = NULL; + } + free(C); + C = NULL; + + return (SUN_SUCCESS); +} + +SUNErrCode SUNAdaptController_EstimateStep(SUNAdaptController C, sunrealtype h, + int p, sunrealtype dsm, + sunrealtype* hnew) +{ + SUNErrCode ier = SUN_SUCCESS; + if (C == NULL) { return SUN_ERR_ARG_CORRUPT; } + SUNFunctionBegin(C->sunctx); + SUNAssert(hnew, SUN_ERR_ARG_CORRUPT); + *hnew = h; /* initialize output with identity */ + if (C->ops->estimatestep) { ier = C->ops->estimatestep(C, h, p, dsm, hnew); } + return (ier); +} + +SUNErrCode SUNAdaptController_Reset(SUNAdaptController C) +{ + SUNErrCode ier = SUN_SUCCESS; + if (C == NULL) { return SUN_ERR_ARG_CORRUPT; } + SUNFunctionBegin(C->sunctx); + if (C->ops->reset) { ier = C->ops->reset(C); } + return (ier); +} + +SUNErrCode SUNAdaptController_SetDefaults(SUNAdaptController C) +{ + SUNErrCode ier = SUN_SUCCESS; + if (C == NULL) { return SUN_ERR_ARG_CORRUPT; } + SUNFunctionBegin(C->sunctx); + if (C->ops->setdefaults) { ier = C->ops->setdefaults(C); } + return (ier); +} + +SUNErrCode SUNAdaptController_Write(SUNAdaptController C, FILE* fptr) +{ + SUNErrCode ier = SUN_SUCCESS; + if (C == NULL) { return SUN_ERR_ARG_CORRUPT; } + SUNFunctionBegin(C->sunctx); + SUNAssert(fptr, SUN_ERR_ARG_CORRUPT); + if (C->ops->write) { ier = C->ops->write(C, fptr); } + return (ier); +} + +SUNErrCode SUNAdaptController_SetErrorBias(SUNAdaptController C, sunrealtype bias) +{ + SUNErrCode ier = SUN_SUCCESS; + if (C == NULL) { return SUN_ERR_ARG_CORRUPT; } + SUNFunctionBegin(C->sunctx); + if (C->ops->seterrorbias) { ier = C->ops->seterrorbias(C, bias); } + return (ier); +} + +SUNErrCode SUNAdaptController_UpdateH(SUNAdaptController C, sunrealtype h, + sunrealtype dsm) +{ + SUNErrCode ier = SUN_SUCCESS; + if (C == NULL) { return SUN_ERR_ARG_CORRUPT; } + SUNFunctionBegin(C->sunctx); + if (C->ops->updateh) { ier = C->ops->updateh(C, h, dsm); } + return (ier); +} + +SUNErrCode SUNAdaptController_Space(SUNAdaptController C, long int* lenrw, + long int* leniw) +{ + SUNErrCode ier = SUN_SUCCESS; + if (C == NULL) { return SUN_ERR_ARG_CORRUPT; } + SUNFunctionBegin(C->sunctx); + SUNAssert(lenrw, SUN_ERR_ARG_CORRUPT); + SUNAssert(leniw, SUN_ERR_ARG_CORRUPT); + *lenrw = 0; /* initialize outputs with identity */ + *leniw = 0; + if (C->ops->space) { ier = C->ops->space(C, lenrw, leniw); } + return (ier); +} diff --git a/src/sundials/sundials/sundials_adiak_metadata.h b/src/sundials/sundials/sundials_adiak_metadata.h index 8013dbd..4e7e908 100644 --- a/src/sundials/sundials/sundials_adiak_metadata.h +++ b/src/sundials/sundials/sundials_adiak_metadata.h @@ -12,6 +12,9 @@ * SUNDIALS Copyright End * ----------------------------------------------------------------*/ +#ifndef _SUNDIALS_ADIAK_METADATA_H +#define _SUNDIALS_ADIAK_METADATA_H + #ifdef SUNDIALS_ADIAK_ENABLED #include @@ -142,3 +145,5 @@ static void sunAdiakCollectMetadata() #endif } #endif + +#endif diff --git a/src/sundials/sundials/sundials_band.c b/src/sundials/sundials/sundials_band.c index e8051d8..d5fbcbb 100644 --- a/src/sundials/sundials/sundials_band.c +++ b/src/sundials/sundials/sundials_band.c @@ -38,64 +38,33 @@ sunindextype SUNDlsMat_BandGBTRF(SUNDlsMat A, sunindextype* p) return (SUNDlsMat_bandGBTRF(A->cols, A->M, A->mu, A->ml, A->s_mu, p)); } -sunindextype BandGBTRF(SUNDlsMat A, sunindextype* p) -{ - return (SUNDlsMat_bandGBTRF(A->cols, A->M, A->mu, A->ml, A->s_mu, p)); -} - void SUNDlsMat_BandGBTRS(SUNDlsMat A, sunindextype* p, sunrealtype* b) { SUNDlsMat_bandGBTRS(A->cols, A->M, A->s_mu, A->ml, p, b); } -void BandGBTRS(SUNDlsMat A, sunindextype* p, sunrealtype* b) -{ - SUNDlsMat_bandGBTRS(A->cols, A->M, A->s_mu, A->ml, p, b); -} - void SUNDlsMat_BandCopy(SUNDlsMat A, SUNDlsMat B, sunindextype copymu, sunindextype copyml) { SUNDlsMat_bandCopy(A->cols, B->cols, A->M, A->s_mu, B->s_mu, copymu, copyml); } -void BandCopy(SUNDlsMat A, SUNDlsMat B, sunindextype copymu, sunindextype copyml) -{ - SUNDlsMat_bandCopy(A->cols, B->cols, A->M, A->s_mu, B->s_mu, copymu, copyml); -} - void SUNDlsMat_BandScale(sunrealtype c, SUNDlsMat A) { SUNDlsMat_bandScale(c, A->cols, A->M, A->mu, A->ml, A->s_mu); } -void BandScale(sunrealtype c, SUNDlsMat A) -{ - SUNDlsMat_bandScale(c, A->cols, A->M, A->mu, A->ml, A->s_mu); -} - void SUNDlsMat_BandMatvec(SUNDlsMat A, sunrealtype* x, sunrealtype* y) { SUNDlsMat_bandMatvec(A->cols, x, y, A->M, A->mu, A->ml, A->s_mu); } -void BandMatvec(SUNDlsMat A, sunrealtype* x, sunrealtype* y) -{ - SUNDlsMat_bandMatvec(A->cols, x, y, A->M, A->mu, A->ml, A->s_mu); -} - /* * ----------------------------------------------------- * Functions working on sunrealtype** * ----------------------------------------------------- */ -sunindextype bandGBTRF(sunrealtype** a, sunindextype n, sunindextype mu, - sunindextype ml, sunindextype smu, sunindextype* p) -{ - return (SUNDlsMat_bandGBTRF(a, n, mu, ml, smu, p)); -} - sunindextype SUNDlsMat_bandGBTRF(sunrealtype** a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu, sunindextype* p) @@ -212,12 +181,6 @@ sunindextype SUNDlsMat_bandGBTRF(sunrealtype** a, sunindextype n, return (0); } -void bandGBTRS(sunrealtype** a, sunindextype n, sunindextype smu, - sunindextype ml, sunindextype* p, sunrealtype* b) -{ - SUNDlsMat_bandGBTRS(a, n, smu, ml, p, b); -} - void SUNDlsMat_bandGBTRS(sunrealtype** a, sunindextype n, sunindextype smu, sunindextype ml, sunindextype* p, sunrealtype* b) { @@ -252,13 +215,6 @@ void SUNDlsMat_bandGBTRS(sunrealtype** a, sunindextype n, sunindextype smu, } } -void bandCopy(sunrealtype** a, sunrealtype** b, sunindextype n, - sunindextype a_smu, sunindextype b_smu, sunindextype copymu, - sunindextype copyml) -{ - SUNDlsMat_bandCopy(a, b, n, a_smu, b_smu, copymu, copyml); -} - void SUNDlsMat_bandCopy(sunrealtype** a, sunrealtype** b, sunindextype n, sunindextype a_smu, sunindextype b_smu, sunindextype copymu, sunindextype copyml) @@ -276,12 +232,6 @@ void SUNDlsMat_bandCopy(sunrealtype** a, sunrealtype** b, sunindextype n, } } -void bandScale(sunrealtype c, sunrealtype** a, sunindextype n, sunindextype mu, - sunindextype ml, sunindextype smu) -{ - SUNDlsMat_bandScale(c, a, n, mu, ml, smu); -} - void SUNDlsMat_bandScale(sunrealtype c, sunrealtype** a, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu) { @@ -297,11 +247,6 @@ void SUNDlsMat_bandScale(sunrealtype c, sunrealtype** a, sunindextype n, } } -void bandAddIdentity(sunrealtype** a, sunindextype n, sunindextype smu) -{ - SUNDlsMat_bandAddIdentity(a, n, smu); -} - void SUNDlsMat_bandAddIdentity(sunrealtype** a, sunindextype n, sunindextype smu) { sunindextype j; @@ -309,12 +254,6 @@ void SUNDlsMat_bandAddIdentity(sunrealtype** a, sunindextype n, sunindextype smu for (j = 0; j < n; j++) { a[j][smu] += ONE; } } -void bandMatvec(sunrealtype** a, sunrealtype* x, sunrealtype* y, sunindextype n, - sunindextype mu, sunindextype ml, sunindextype smu) -{ - SUNDlsMat_bandMatvec(a, x, y, n, mu, ml, smu); -} - void SUNDlsMat_bandMatvec(sunrealtype** a, sunrealtype* x, sunrealtype* y, sunindextype n, sunindextype mu, sunindextype ml, sunindextype smu) @@ -322,7 +261,7 @@ void SUNDlsMat_bandMatvec(sunrealtype** a, sunrealtype* x, sunrealtype* y, sunindextype i, j, is, ie; sunrealtype* col_j; - for (i = 0; i < n; i++) { y[i] = 0.0; } + for (i = 0; i < n; i++) { y[i] = ZERO; } for (j = 0; j < n; j++) { diff --git a/src/sundials/sundials/sundials_context.c b/src/sundials/sundials/sundials_context.c index f031dea..86b0a49 100644 --- a/src/sundials/sundials/sundials_context.c +++ b/src/sundials/sundials/sundials_context.c @@ -18,15 +18,17 @@ #include #include #include + #include #include #include +#include #include #include +#include -#include "sundials/sundials_errors.h" -#include "sundials/sundials_types.h" #include "sundials_adiak_metadata.h" +#include "sundials_macros.h" SUNErrCode SUNContext_Create(SUNComm comm, SUNContext* sunctx_out) { @@ -209,6 +211,9 @@ SUNErrCode SUNContext_SetProfiler(SUNContext sunctx, SUNProfiler profiler) /* set profiler */ sunctx->profiler = profiler; sunctx->own_profiler = SUNFALSE; +#else + /* silence warnings when profiling is disabled */ + ((void)profiler); #endif return SUN_SUCCESS; @@ -285,7 +290,7 @@ SUNErrCode SUNContext_Free(SUNContext* sunctx) SUNLogger_Destroy(&(*sunctx)->logger); } - SUNErrHandler_Destroy(&(*sunctx)->err_handler); + SUNContext_ClearErrHandlers(*sunctx); free(*sunctx); *sunctx = NULL; diff --git a/src/sundials/sundials/sundials_cuda.h b/src/sundials/sundials/sundials_cuda.h new file mode 100644 index 0000000..d0202ad --- /dev/null +++ b/src/sundials/sundials/sundials_cuda.h @@ -0,0 +1,79 @@ +/* + * ----------------------------------------------------------------- + * Programmer(s): Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * This header files defines internal utility functions and macros + * for working with CUDA. + * ----------------------------------------------------------------- + */ + +#include +#include +#include +#include + +#ifndef _SUNDIALS_CUDA_H +#define _SUNDIALS_CUDA_H + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +extern "C" { +#endif + +/* --------------------------------------------------------------------------- + * Utility macros + * ---------------------------------------------------------------------------*/ + +#define SUNDIALS_CUDA_VERIFY(cuerr) \ + SUNDIALS_CUDA_Assert(cuerr, __FILE__, __LINE__) + +#define SUNDIALS_KERNEL_NAME(...) __VA_ARGS__ +#ifndef SUNDIALS_DEBUG_CUDA_LASTERROR +#define SUNDIALS_LAUNCH_KERNEL(kernel, gridDim, blockDim, shMem, stream, ...) \ + { \ + kernel<<>>(__VA_ARGS__); \ + } +#else +#define SUNDIALS_LAUNCH_KERNEL(kernel, gridDim, blockDim, shMem, stream, ...) \ + { \ + kernel<<>>(__VA_ARGS__); \ + cudaDeviceSynchronize(); \ + SUNDIALS_CUDA_VERIFY(cudaGetLastError()); \ + } +#endif + +/* --------------------------------------------------------------------------- + * Utility functions + * ---------------------------------------------------------------------------*/ + +inline sunbooleantype SUNDIALS_CUDA_Assert(cudaError_t cuerr, const char* file, + int line) +{ + if (cuerr != cudaSuccess) + { +#ifdef SUNDIALS_DEBUG + fprintf(stderr, "ERROR in CUDA runtime operation: %s %s:%d\n", + cudaGetErrorString(cuerr), file, line); +#ifdef SUNDIALS_DEBUG_ASSERT + assert(false); +#endif +#endif + return SUNFALSE; /* Assert failed */ + } + return SUNTRUE; /* Assert OK */ +} + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +} +#endif + +#endif /* _SUNDIALS_CUDA_H */ diff --git a/src/sundials/sundials/sundials_cuda_kernels.cuh b/src/sundials/sundials/sundials_cuda_kernels.cuh new file mode 100644 index 0000000..529c344 --- /dev/null +++ b/src/sundials/sundials/sundials_cuda_kernels.cuh @@ -0,0 +1,448 @@ +/* + * ----------------------------------------------------------------- + * Programmer(s): Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + */ + +#ifndef _SUNDIALS_CUDA_KERNELS_CUH +#define _SUNDIALS_CUDA_KERNELS_CUH + +#define SUNDIALS_HOST_DEVICE __host__ __device__ +#define SUNDIALS_DEVICE_INLINE __forceinline__ +#include "sundials_reductions.hpp" + +#define GRID_STRIDE_XLOOP(type, iter, max) \ + for (type iter = blockDim.x * blockIdx.x + threadIdx.x; iter < max; \ + iter += blockDim.x * gridDim.x) + +#include "sundials_cuda.h" + +namespace sundials { +namespace cuda { +namespace impl { + +template +__forceinline__ __device__ T shfl_xor_sync(T var, int laneMask); + +template +__forceinline__ __device__ T shfl_sync(T var, int srcLane); + +template +__forceinline__ __device__ T shfl_down_sync(T var, int srcLane); + +template<> +__forceinline__ __device__ float shfl_xor_sync(float var, int laneMask) +{ + return ::__shfl_xor_sync(0xFFFFFFFF, var, laneMask); +} + +template<> +__forceinline__ __device__ double shfl_xor_sync(double var, int laneMask) +{ + return ::__shfl_xor_sync(0xFFFFFFFF, var, laneMask); +} + +template<> +__forceinline__ __device__ float shfl_sync(float var, int srcLane) +{ + return ::__shfl_sync(0xFFFFFFFF, var, srcLane); +} + +template<> +__forceinline__ __device__ double shfl_sync(double var, int srcLane) +{ + return ::__shfl_sync(0xFFFFFFFF, var, srcLane); +} + +template<> +__forceinline__ __device__ float shfl_down_sync(float val, int srcLane) +{ + return ::__shfl_down_sync(0xFFFFFFFF, val, srcLane); +} + +template<> +__forceinline__ __device__ double shfl_down_sync(double val, int srcLane) +{ + return ::__shfl_down_sync(0xFFFFFFFF, val, srcLane); +} + +/* The atomic functions below are implemented using the atomic compare and swap + function atomicCAS which performs an atomic version of + (*address == assumed) ? (assumed + val) : *address. Since *address could change + between when the value is loaded and the atomicCAS call the operation is repeated + until *address does not change between the read and the compare and swap operation. */ + +__forceinline__ __device__ double atomicAdd(double* address, double val) +{ +#if __CUDA_ARCH__ < 600 + unsigned long long int* address_as_ull = (unsigned long long int*)address; + unsigned long long int old = *address_as_ull, assumed; + + do { + assumed = old; + old = atomicCAS(address_as_ull, assumed, + __double_as_longlong(val + __longlong_as_double(assumed))); + // Note: uses integer comparison to avoid hang in case of NaN (since NaN != NaN) + } + while (assumed != old); + + return __longlong_as_double(old); +#else + return ::atomicAdd(address, val); +#endif +} + +__forceinline__ __device__ float atomicAdd(float* address, float val) +{ +#if __CUDA_ARCH__ < 600 + unsigned int* address_as_ull = (unsigned int*)address; + unsigned int old = *address_as_ull, assumed; + + do { + assumed = old; + old = atomicCAS(address_as_ull, assumed, + __float_as_int(val + __int_as_float(assumed))); + // Note: uses integer comparison to avoid hang in case of NaN (since NaN != NaN) + } + while (assumed != old); + + return __int_as_float(old); +#else + return ::atomicAdd(address, val); +#endif +} + +/* + * Compute the maximum of 2 double-precision floating point values using an atomic operation + * "address" is the address of the reference value which might get updated with the maximum + * "value" is the value that is compared to the reference in order to determine the maximum + */ +__forceinline__ __device__ void atomicMax(double* const address, + const double value) +{ + if (*address >= value) { return; } + + unsigned long long* const address_as_i = (unsigned long long*)address; + unsigned long long old = *address_as_i, assumed; + + do { + assumed = old; + if (__longlong_as_double(assumed) >= value) { break; } + old = atomicCAS(address_as_i, assumed, __double_as_longlong(value)); + } + while (assumed != old); +} + +/* + * Compute the maximum of 2 single-precision floating point values using an atomic operation + * "address" is the address of the reference value which might get updated with the maximum + * "value" is the value that is compared to the reference in order to determine the maximum + */ +__forceinline__ __device__ void atomicMax(float* const address, const float value) +{ + if (*address >= value) { return; } + + unsigned int* const address_as_i = (unsigned int*)address; + unsigned int old = *address_as_i, assumed; + + do { + assumed = old; + if (__int_as_float(assumed) >= value) { break; } + old = atomicCAS(address_as_i, assumed, __float_as_int(value)); + } + while (assumed != old); +} + +/* + * Compute the minimum of 2 double-precision floating point values using an atomic operation + * "address" is the address of the reference value which might get updated with the minimum + * "value" is the value that is compared to the reference in order to determine the minimum + */ +__forceinline__ __device__ void atomicMin(double* const address, + const double value) +{ + if (*address <= value) { return; } + + unsigned long long* const address_as_i = (unsigned long long*)address; + unsigned long long old = *address_as_i, assumed; + + do { + assumed = old; + if (__longlong_as_double(assumed) <= value) { break; } + old = atomicCAS(address_as_i, assumed, __double_as_longlong(value)); + } + while (assumed != old); +} + +/* + * Compute the minimum of 2 single-precision floating point values using an atomic operation + * "address" is the address of the reference value which might get updated with the minimum + * "value" is the value that is compared to the reference in order to determine the minimum + */ +__forceinline__ __device__ void atomicMin(float* const address, const float value) +{ + if (*address <= value) { return; } + + unsigned int* const address_as_i = (unsigned int*)address; + unsigned int old = *address_as_i, assumed; + + do { + assumed = old; + if (__int_as_float(assumed) <= value) { break; } + old = atomicCAS(address_as_i, assumed, __float_as_int(value)); + } + while (assumed != old); +} + +// +// Atomic specializations of sundials::reduction operators +// + +template +struct atomic; + +template +struct atomic> +{ + __device__ __forceinline__ void operator()(T* out, const T val) + { + atomicAdd(out, val); + } +}; + +template +struct atomic> +{ + __device__ __forceinline__ void operator()(T* out, const T val) + { + atomicMax(out, val); + } +}; + +template +struct atomic> +{ + __device__ __forceinline__ void operator()(T* out, const T val) + { + atomicMin(out, val); + } +}; + +/* + * Perform a reduce on the warp to get the operation result. + */ +template +__inline__ __device__ T warpReduceShflDown(T val) +{ + for (int offset = warpSize / 2; offset > 0; offset /= 2) + { + T rhs = shfl_down_sync(val, offset); + val = BinaryReductionOp{}(val, rhs); + } + return val; +} + +/* + * Reduce value across the thread block. + */ +template +__inline__ __device__ T blockReduceShflDown(T val, T identity) +{ + // Shared memory for the partial sums + static __shared__ T shared[MAX_WARPS]; + + int numThreads = blockDim.x * blockDim.y * blockDim.z; + + int threadId = threadIdx.x + blockDim.x * threadIdx.y + + (blockDim.x * blockDim.y) * threadIdx.z; + + int warpId = threadId / WARP_SIZE; + int warpLane = threadId % WARP_SIZE; + + // Each warp performs partial reduction + val = warpReduceShflDown(val); + + // Write reduced value from each warp to shared memory + if (warpLane == 0) shared[warpId] = val; + + // Wait for all partial reductions to complete + __syncthreads(); + + // Read per warp values from shared memory only if that warp existed + val = (threadId < numThreads / warpSize) ? shared[warpLane] : identity; + + // Final reduce within first warp + if (warpId == 0) val = warpReduceShflDown(val); + + return val; +} + +/* + * Warp reduce + block reduce using shfl instead of shfl_down. + */ +template +__inline__ __device__ T blockReduceShfl(T val, T identity) +{ + int numThreads = blockDim.x * blockDim.y * blockDim.z; + + int threadId = threadIdx.x + blockDim.x * threadIdx.y + + (blockDim.x * blockDim.y) * threadIdx.z; + + int warpId = threadId / WARP_SIZE; + int warpLane = threadId % WARP_SIZE; + + T temp = val; + + // Reduce each warp + if (numThreads % WARP_SIZE == 0) + { + for (int i = 1; i < WARP_SIZE; i *= 2) + { + T rhs = shfl_xor_sync(temp, i); + temp = BinaryReductionOp{}(temp, rhs); + } + } + else + { + for (int i = 1; i < WARP_SIZE; i *= 2) + { + int srcLane = threadId ^ i; + T rhs = shfl_sync(temp, srcLane); + // Only add from threads that exist to avoid double counting + if (srcLane < numThreads) temp = BinaryReductionOp{}(temp, rhs); + } + } + + // Reduce per warp values + if (numThreads > WARP_SIZE) + { + static_assert(MAX_WARPS <= WARP_SIZE, + "max warps must be <= warp size for this algorithm to work"); + + __shared__ T shared[MAX_WARPS]; + + // Write per warp values to shared memory + if (warpLane == 0) shared[warpId] = temp; + + __syncthreads(); + + if (warpId == 0) + { + // Read per warp values only if the warp existed + temp = (warpLane * WARP_SIZE < numThreads) ? shared[warpLane] : identity; + + // Final reduction + for (int i = 1; i < MAX_WARPS; i *= 2) + { + T rhs = shfl_xor_sync(temp, i); + temp = BinaryReductionOp{}(temp, rhs); + } + } + + __syncthreads(); + } + + return temp; +} + +/* + * Reduce values into thread 0 of the last running thread block. + * Output value is device_mem[0]. + */ +template +__device__ __forceinline__ void gridReduce(T val, T identity, T* device_mem, + unsigned int* device_count) +{ + int numBlocks = gridDim.x * gridDim.y * gridDim.z; + int numThreads = blockDim.x * blockDim.y * blockDim.z; + unsigned int wrap_around = numBlocks - 1; + + int blockId = blockIdx.x + gridDim.x * blockIdx.y + + (gridDim.x * gridDim.y) * blockIdx.z; + + int threadId = threadIdx.x + blockDim.x * threadIdx.y + + (blockDim.x * blockDim.y) * threadIdx.z; + + // Each block reduces a subset of the input + T temp = blockReduceShfl(val, identity); + + __shared__ bool isLastBlockDone; + if (threadId == 0) + { + // One thread per block stores the partial reductions to global memory + device_mem[blockId] = temp; + + // Ensure write visible to all threads + __threadfence(); + + // Increment counter, (wraps back to zero if old count == wrap_around) + unsigned int old_count = atomicInc(device_count, wrap_around); + isLastBlockDone = (old_count == wrap_around) ? 1 : 0; + } + + // Synchronize to ensure that each thread reads the + // correct value of isLastBlockDone. + __syncthreads(); + + // The last block reduces values in device_mem + if (isLastBlockDone) + { + // Reduce thread_i in each block into temp + temp = identity; + for (int i = threadId; i < numBlocks; i += numThreads) + temp = BinaryReductionOp{}(temp, device_mem[i]); + + // Compute the final block partial reductions + temp = blockReduceShfl(temp, identity); + + // One thread returns the final value + if (threadId == 0) device_mem[0] = temp; + } +} + +template +__device__ __forceinline__ void gridReduceAtomic(T val, T identity, T* device_mem) +{ + int threadId = threadIdx.x + blockDim.x * threadIdx.y + + (blockDim.x * blockDim.y) * threadIdx.z; + val = blockReduceShflDown(val, identity); + // Final reduction of all block values into the output device_mem + if (threadId == 0) atomic{}(device_mem, val); +} + +template +struct GridReducerLDS +{ + __device__ __forceinline__ void operator()(T val, T identity, T* device_mem, + unsigned int* device_count) + { + return gridReduce(val, identity, device_mem, + device_count); + } +}; + +template +struct GridReducerAtomic +{ + __device__ __forceinline__ void operator()(T val, T identity, T* device_mem, + unsigned int* device_count) + { + return gridReduceAtomic(val, identity, device_mem); + } +}; + +} // namespace impl +} // namespace cuda +} // namespace sundials + +#endif // _SUNDIALS_CUDA_KERNELS_CUH \ No newline at end of file diff --git a/src/sundials/sundials/sundials_cusolver.h b/src/sundials/sundials/sundials_cusolver.h new file mode 100644 index 0000000..87c9644 --- /dev/null +++ b/src/sundials/sundials/sundials_cusolver.h @@ -0,0 +1,66 @@ +/* + * ----------------------------------------------------------------- + * Programmer(s): Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * This header files defines internal utility functions and macros + * for working with CUDA. + * ----------------------------------------------------------------- + */ + +#include +#include +#include +#include +#include +#include + +#ifndef _SUNDIALS_CUSOLVER_H +#define _SUNDIALS_CUSOLVER_H + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +extern "C" { +#endif + +/* --------------------------------------------------------------------------- + * Utility macros + * ---------------------------------------------------------------------------*/ + +#define SUNDIALS_CUSOLVER_VERIFY(cuerr) \ + SUNDIALS_CUSOLVER_Assert(cuerr, __FILE__, __LINE__) + +/* --------------------------------------------------------------------------- + * Utility functions + * ---------------------------------------------------------------------------*/ + +inline sunbooleantype SUNDIALS_CUSOLVER_Assert(cusolverStatus_t status, + const char* file, int line) +{ + if (status != CUSOLVER_STATUS_SUCCESS) + { +#ifdef SUNDIALS_DEBUG + fprintf(stderr, "ERROR in cuSOLVER runtime operation: cusolverStatus_t = %d %s:%d\n", + status, file, line); +#ifdef SUNDIALS_DEBUG_ASSERT + assert(false); +#endif +#endif + return SUNFALSE; /* Assert failed */ + } + return SUNTRUE; /* Assert OK */ +} + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +} +#endif + +#endif /* _SUNDIALS_CUSOLVER_H */ diff --git a/src/sundials/sundials/sundials_cusparse.h b/src/sundials/sundials/sundials_cusparse.h new file mode 100644 index 0000000..c05f3e8 --- /dev/null +++ b/src/sundials/sundials/sundials_cusparse.h @@ -0,0 +1,65 @@ +/* + * ----------------------------------------------------------------- + * Programmer(s): Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * This header files defines internal utility functions and macros + * for working with CUDA. + * ----------------------------------------------------------------- + */ + +#include +#include +#include +#include +#include + +#ifndef _SUNDIALS_CUSPARSE_H +#define _SUNDIALS_CUSPARSE_H + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +extern "C" { +#endif + +/* --------------------------------------------------------------------------- + * Utility macros + * ---------------------------------------------------------------------------*/ + +#define SUNDIALS_CUSPARSE_VERIFY(cuerr) \ + SUNDIALS_CUSPARSE_Assert(cuerr, __FILE__, __LINE__) + +/* --------------------------------------------------------------------------- + * Utility functions + * ---------------------------------------------------------------------------*/ + +inline sunbooleantype SUNDIALS_CUSPARSE_Assert(cusparseStatus_t status, + const char* file, int line) +{ + if (status != CUSPARSE_STATUS_SUCCESS) + { +#ifdef SUNDIALS_DEBUG + fprintf(stderr, "ERROR in cuSPARSE runtime operation: cusparseStatus_t = %d %s:%d\n", + status, file, line); +#ifdef SUNDIALS_DEBUG_ASSERT + assert(false); +#endif +#endif + return SUNFALSE; /* Assert failed */ + } + return SUNTRUE; /* Assert OK */ +} + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +} +#endif + +#endif /* _SUNDIALS_CUSPARSE_H */ diff --git a/src/sundials/sundials/sundials_dense.c b/src/sundials/sundials/sundials_dense.c index f022212..ce420fc 100644 --- a/src/sundials/sundials/sundials_dense.c +++ b/src/sundials/sundials/sundials_dense.c @@ -38,99 +38,47 @@ sunindextype SUNDlsMat_DenseGETRF(SUNDlsMat A, sunindextype* p) return (SUNDlsMat_denseGETRF(A->cols, A->M, A->N, p)); } -sunindextype DenseGETRF(SUNDlsMat A, sunindextype* p) -{ - return (SUNDlsMat_denseGETRF(A->cols, A->M, A->N, p)); -} - void SUNDlsMat_DenseGETRS(SUNDlsMat A, sunindextype* p, sunrealtype* b) { SUNDlsMat_denseGETRS(A->cols, A->N, p, b); } -void DenseGETRS(SUNDlsMat A, sunindextype* p, sunrealtype* b) -{ - SUNDlsMat_denseGETRS(A->cols, A->N, p, b); -} - sunindextype SUNDlsMat_DensePOTRF(SUNDlsMat A) { return (SUNDlsMat_densePOTRF(A->cols, A->M)); } -sunindextype DensePOTRF(SUNDlsMat A) -{ - return (SUNDlsMat_densePOTRF(A->cols, A->M)); -} - void SUNDlsMat_DensePOTRS(SUNDlsMat A, sunrealtype* b) { SUNDlsMat_densePOTRS(A->cols, A->M, b); } -void DensePOTRS(SUNDlsMat A, sunrealtype* b) -{ - SUNDlsMat_densePOTRS(A->cols, A->M, b); -} - int SUNDlsMat_DenseGEQRF(SUNDlsMat A, sunrealtype* beta, sunrealtype* wrk) { return (SUNDlsMat_denseGEQRF(A->cols, A->M, A->N, beta, wrk)); } -int DenseGEQRF(SUNDlsMat A, sunrealtype* beta, sunrealtype* wrk) -{ - return (SUNDlsMat_denseGEQRF(A->cols, A->M, A->N, beta, wrk)); -} - int SUNDlsMat_DenseORMQR(SUNDlsMat A, sunrealtype* beta, sunrealtype* vn, sunrealtype* vm, sunrealtype* wrk) { return (SUNDlsMat_denseORMQR(A->cols, A->M, A->N, beta, vn, vm, wrk)); } -int DenseORMQR(SUNDlsMat A, sunrealtype* beta, sunrealtype* vn, sunrealtype* vm, - sunrealtype* wrk) -{ - return (SUNDlsMat_denseORMQR(A->cols, A->M, A->N, beta, vn, vm, wrk)); -} - void SUNDlsMat_DenseCopy(SUNDlsMat A, SUNDlsMat B) { SUNDlsMat_denseCopy(A->cols, B->cols, A->M, A->N); } -void DenseCopy(SUNDlsMat A, SUNDlsMat B) -{ - SUNDlsMat_denseCopy(A->cols, B->cols, A->M, A->N); -} - void SUNDlsMat_DenseScale(sunrealtype c, SUNDlsMat A) { SUNDlsMat_denseScale(c, A->cols, A->M, A->N); } -void DenseScale(sunrealtype c, SUNDlsMat A) -{ - SUNDlsMat_denseScale(c, A->cols, A->M, A->N); -} - void SUNDlsMat_DenseMatvec(SUNDlsMat A, sunrealtype* x, sunrealtype* y) { SUNDlsMat_denseMatvec(A->cols, x, y, A->M, A->N); } -void DenseMatvec(SUNDlsMat A, sunrealtype* x, sunrealtype* y) -{ - SUNDlsMat_denseMatvec(A->cols, x, y, A->M, A->N); -} - -sunindextype denseGETRF(sunrealtype** a, sunindextype m, sunindextype n, - sunindextype* p) -{ - return (SUNDlsMat_denseGETRF(a, m, n, p)); -} - sunindextype SUNDlsMat_denseGETRF(sunrealtype** a, sunindextype m, sunindextype n, sunindextype* p) { @@ -199,11 +147,6 @@ sunindextype SUNDlsMat_denseGETRF(sunrealtype** a, sunindextype m, return (0); } -void denseGETRS(sunrealtype** a, sunindextype n, sunindextype* p, sunrealtype* b) -{ - SUNDlsMat_denseGETRS(a, n, p, b); -} - void SUNDlsMat_denseGETRS(sunrealtype** a, sunindextype n, sunindextype* p, sunrealtype* b) { @@ -246,11 +189,6 @@ void SUNDlsMat_denseGETRS(sunrealtype** a, sunindextype n, sunindextype* p, * the lower triangle of C. */ -sunindextype densePOTRF(sunrealtype** a, sunindextype m) -{ - return (SUNDlsMat_densePOTRF(a, m)); -} - sunindextype SUNDlsMat_densePOTRF(sunrealtype** a, sunindextype m) { sunrealtype *a_col_j, *a_col_k; @@ -289,11 +227,6 @@ sunindextype SUNDlsMat_densePOTRF(sunrealtype** a, sunindextype m) * */ -void densePOTRS(sunrealtype** a, sunindextype m, sunrealtype* b) -{ - SUNDlsMat_densePOTRS(a, m, b); -} - void SUNDlsMat_densePOTRS(sunrealtype** a, sunindextype m, sunrealtype* b) { sunrealtype *col_j, *col_i; @@ -334,12 +267,6 @@ void SUNDlsMat_densePOTRS(sunrealtype** a, sunindextype m, sunrealtype* b) * */ -int denseGEQRF(sunrealtype** a, sunindextype m, sunindextype n, - sunrealtype* beta, sunrealtype* v) -{ - return (SUNDlsMat_denseGEQRF(a, m, n, beta, v)); -} - int SUNDlsMat_denseGEQRF(sunrealtype** a, sunindextype m, sunindextype n, sunrealtype* beta, sunrealtype* v) { @@ -404,12 +331,6 @@ int SUNDlsMat_denseGEQRF(sunrealtype** a, sunindextype m, sunindextype n, * v (of length m) must be provided as workspace. */ -int denseORMQR(sunrealtype** a, sunindextype m, sunindextype n, sunrealtype* beta, - sunrealtype* vn, sunrealtype* vm, sunrealtype* v) -{ - return (SUNDlsMat_denseORMQR(a, m, n, beta, vn, vm, v)); -} - int SUNDlsMat_denseORMQR(sunrealtype** a, sunindextype m, sunindextype n, sunrealtype* beta, sunrealtype* vn, sunrealtype* vm, sunrealtype* v) @@ -441,11 +362,6 @@ int SUNDlsMat_denseORMQR(sunrealtype** a, sunindextype m, sunindextype n, return (0); } -void denseCopy(sunrealtype** a, sunrealtype** b, sunindextype m, sunindextype n) -{ - SUNDlsMat_denseCopy(a, b, m, n); -} - void SUNDlsMat_denseCopy(sunrealtype** a, sunrealtype** b, sunindextype m, sunindextype n) { @@ -460,11 +376,6 @@ void SUNDlsMat_denseCopy(sunrealtype** a, sunrealtype** b, sunindextype m, } } -void denseScale(sunrealtype c, sunrealtype** a, sunindextype m, sunindextype n) -{ - SUNDlsMat_denseScale(c, a, m, n); -} - void SUNDlsMat_denseScale(sunrealtype c, sunrealtype** a, sunindextype m, sunindextype n) { @@ -478,11 +389,6 @@ void SUNDlsMat_denseScale(sunrealtype c, sunrealtype** a, sunindextype m, } } -void denseAddIdentity(sunrealtype** a, sunindextype n) -{ - SUNDlsMat_denseAddIdentity(a, n); -} - void SUNDlsMat_denseAddIdentity(sunrealtype** a, sunindextype n) { sunindextype i; @@ -490,19 +396,13 @@ void SUNDlsMat_denseAddIdentity(sunrealtype** a, sunindextype n) for (i = 0; i < n; i++) { a[i][i] += ONE; } } -void denseMatvec(sunrealtype** a, sunrealtype* x, sunrealtype* y, - sunindextype m, sunindextype n) -{ - SUNDlsMat_denseMatvec(a, x, y, m, n); -} - void SUNDlsMat_denseMatvec(sunrealtype** a, sunrealtype* x, sunrealtype* y, sunindextype m, sunindextype n) { sunindextype i, j; sunrealtype* col_j; - for (i = 0; i < m; i++) { y[i] = 0.0; } + for (i = 0; i < m; i++) { y[i] = ZERO; } for (j = 0; j < n; j++) { diff --git a/src/sundials/sundials/sundials_direct.c b/src/sundials/sundials/sundials_direct.c index 2bf135b..02ff31d 100644 --- a/src/sundials/sundials/sundials_direct.c +++ b/src/sundials/sundials/sundials_direct.c @@ -23,11 +23,6 @@ #define ZERO SUN_RCONST(0.0) #define ONE SUN_RCONST(1.0) -SUNDlsMat NewDenseMat(sunindextype M, sunindextype N) -{ - return (SUNDlsMat_NewDenseMat(M, N)); -} - SUNDlsMat SUNDlsMat_NewDenseMat(sunindextype M, sunindextype N) { SUNDlsMat A; @@ -68,11 +63,6 @@ SUNDlsMat SUNDlsMat_NewDenseMat(sunindextype M, sunindextype N) return (A); } -sunrealtype** newDenseMat(sunindextype m, sunindextype n) -{ - return (SUNDlsMat_newDenseMat(m, n)); -} - sunrealtype** SUNDlsMat_newDenseMat(sunindextype m, sunindextype n) { sunindextype j; @@ -98,12 +88,6 @@ sunrealtype** SUNDlsMat_newDenseMat(sunindextype m, sunindextype n) return (a); } -SUNDlsMat NewBandMat(sunindextype N, sunindextype mu, sunindextype ml, - sunindextype smu) -{ - return (SUNDlsMat_NewBandMat(N, mu, ml, smu)); -} - SUNDlsMat SUNDlsMat_NewBandMat(sunindextype N, sunindextype mu, sunindextype ml, sunindextype smu) { @@ -151,11 +135,6 @@ SUNDlsMat SUNDlsMat_NewBandMat(sunindextype N, sunindextype mu, sunindextype ml, return (A); } -sunrealtype** newBandMat(sunindextype n, sunindextype smu, sunindextype ml) -{ - return (SUNDlsMat_newBandMat(n, smu, ml)); -} - sunrealtype** SUNDlsMat_newBandMat(sunindextype n, sunindextype smu, sunindextype ml) { @@ -183,8 +162,6 @@ sunrealtype** SUNDlsMat_newBandMat(sunindextype n, sunindextype smu, return (a); } -void DestroyMat(SUNDlsMat A) { SUNDlsMat_DestroyMat(A); } - void SUNDlsMat_DestroyMat(SUNDlsMat A) { free(A->data); @@ -194,8 +171,6 @@ void SUNDlsMat_DestroyMat(SUNDlsMat A) A = NULL; } -void destroyMat(sunrealtype** a) { SUNDlsMat_destroyMat(a); } - void SUNDlsMat_destroyMat(sunrealtype** a) { free(a[0]); @@ -204,8 +179,6 @@ void SUNDlsMat_destroyMat(sunrealtype** a) a = NULL; } -int* NewIntArray(int N) { return (SUNDlsMat_NewIntArray(N)); } - int* SUNDlsMat_NewIntArray(int N) { int* vec; @@ -218,8 +191,6 @@ int* SUNDlsMat_NewIntArray(int N) return (vec); } -int* newIntArray(int N) { return (SUNDlsMat_newIntArray(N)); } - int* SUNDlsMat_newIntArray(int n) { int* v; @@ -232,11 +203,6 @@ int* SUNDlsMat_newIntArray(int n) return (v); } -sunindextype* NewIndexArray(sunindextype N) -{ - return (SUNDlsMat_NewIndexArray(N)); -} - sunindextype* SUNDlsMat_NewIndexArray(sunindextype N) { sunindextype* vec; @@ -249,11 +215,6 @@ sunindextype* SUNDlsMat_NewIndexArray(sunindextype N) return (vec); } -sunindextype* newIndexArray(sunindextype n) -{ - return (SUNDlsMat_newIndexArray(n)); -} - sunindextype* SUNDlsMat_newIndexArray(sunindextype n) { sunindextype* v; @@ -266,11 +227,6 @@ sunindextype* SUNDlsMat_newIndexArray(sunindextype n) return (v); } -sunrealtype* NewRealArray(sunindextype N) -{ - return (SUNDlsMat_NewRealArray(N)); -} - sunrealtype* SUNDlsMat_NewRealArray(sunindextype N) { sunrealtype* vec; @@ -283,11 +239,6 @@ sunrealtype* SUNDlsMat_NewRealArray(sunindextype N) return (vec); } -sunrealtype* newRealArray(sunindextype N) -{ - return (SUNDlsMat_newRealArray(N)); -} - sunrealtype* SUNDlsMat_newRealArray(sunindextype m) { sunrealtype* v; @@ -300,24 +251,18 @@ sunrealtype* SUNDlsMat_newRealArray(sunindextype m) return (v); } -void DestroyArray(void* p) { SUNDlsMat_DestroyArray(p); } - void SUNDlsMat_DestroyArray(void* V) { free(V); V = NULL; } -void destroyArray(void* p) { SUNDlsMat_destroyArray(p); } - void SUNDlsMat_destroyArray(void* v) { free(v); v = NULL; } -void AddIdentity(SUNDlsMat A) { SUNDlsMat_AddIdentity(A); } - void SUNDlsMat_AddIdentity(SUNDlsMat A) { sunindextype i; @@ -334,8 +279,6 @@ void SUNDlsMat_AddIdentity(SUNDlsMat A) } } -void SetToZero(SUNDlsMat A) { SUNDlsMat_SetToZero(A); } - void SUNDlsMat_SetToZero(SUNDlsMat A) { sunindextype i, j, colSize; @@ -366,8 +309,6 @@ void SUNDlsMat_SetToZero(SUNDlsMat A) } } -void PrintMat(SUNDlsMat A, FILE* outfile) { SUNDlsMat_PrintMat(A, outfile); } - void SUNDlsMat_PrintMat(SUNDlsMat A, FILE* outfile) { sunindextype i, j, start, finish; diff --git a/src/sundials/sundials/sundials_errors.c b/src/sundials/sundials/sundials_errors.c index 667a3a4..acc3a0e 100644 --- a/src/sundials/sundials/sundials_errors.c +++ b/src/sundials/sundials/sundials_errors.c @@ -10,17 +10,18 @@ * SUNDIALS Copyright End * -----------------------------------------------------------------*/ -#include "sundials/sundials_errors.h" - #include #include #include + #include #include +#include +#include +#include -#include "sundials/sundials_logger.h" -#include "sundials/sundials_types.h" #include "sundials_logger_impl.h" +#include "sundials_macros.h" #include "sundials_utils.h" SUNErrCode SUNErrHandler_Create(SUNErrHandlerFn eh_fn, void* eh_data, @@ -62,7 +63,8 @@ const char* SUNGetErrMsg(SUNErrCode code) void SUNLogErrHandlerFn(int line, const char* func, const char* file, const char* msg, SUNErrCode err_code, - void* err_user_data, SUNContext sunctx) + SUNDIALS_MAYBE_UNUSED void* err_user_data, + SUNContext sunctx) { char* file_and_line = sunCombineFileAndLine(line, file); if (msg == NULL) { msg = SUNGetErrMsg(err_code); } @@ -72,8 +74,10 @@ void SUNLogErrHandlerFn(int line, const char* func, const char* file, } void SUNAbortErrHandlerFn(int line, const char* func, const char* file, - const char* msg, SUNErrCode err_code, - void* err_user_data, SUNContext sunctx) + SUNDIALS_MAYBE_UNUSED const char* msg, + SUNDIALS_MAYBE_UNUSED SUNErrCode err_code, + SUNDIALS_MAYBE_UNUSED void* err_user_data, + SUNContext sunctx) { char* file_and_line = sunCombineFileAndLine(line, file); SUNLogger_QueueMsg(sunctx->logger, SUN_LOGLEVEL_ERROR, file_and_line, func, diff --git a/src/sundials/sundials/sundials_futils.c b/src/sundials/sundials/sundials_futils.c index e494fe7..3a0d0f2 100644 --- a/src/sundials/sundials/sundials_futils.c +++ b/src/sundials/sundials/sundials_futils.c @@ -17,6 +17,7 @@ #include #include #include +#include /* Create a file pointer with the given file name and mode. */ SUNErrCode SUNDIALSFileOpen(const char* filename, const char* mode, FILE** fp_out) diff --git a/src/sundials/sundials/sundials_hashmap.c b/src/sundials/sundials/sundials_hashmap.c new file mode 100644 index 0000000..acf1c12 --- /dev/null +++ b/src/sundials/sundials/sundials_hashmap.c @@ -0,0 +1,342 @@ +/* ----------------------------------------------------------------- + * Programmer: Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * A simple hashmap implementation for char* keys and + * void* values. Uses linear probing to resolve collisions. + * The values can be anything, but will be freed by + * the hash map upon its destruction. + * -----------------------------------------------------------------*/ + +#include +#include +#include + +#include +#include + +#include "sundials_hashmap_impl.h" +#include "sundials_macros.h" + +static const uint64_t HASH_PRIME = 14695981039346656037U; +static const uint64_t HASH_OFFSET_BASIS = 1099511628211U; + +/* + For a nice discussion on popular hashing algorithms see: + https://softwareengineering.stackexchange.com/questions/49550/which-hashing-algorithm-is-best-for-uniqueness-and-speed/145633#145633 + + This is a 64-bit implementation of the 'a' modification of the + Fowler-Noll-Vo hash (i.e., FNV1-a). + */ +static uint64_t fnv1a_hash(const char* str) +{ + uint64_t hash = HASH_OFFSET_BASIS; + char c; + while ((c = *str++)) { hash = (hash ^ c) * HASH_PRIME; } + return hash; +} + +/* + This function creates a new SUNHashMap object allocated to hold + up to 'max_size' entries. + + **Arguments:** + * ``max_size`` -- the max number of entries in the hashmap + * ``map`` -- on input, a SUNHasMap pointer, on output the SUNHashMap will be + allocated + + **Returns:** + * A SUNErrCode indicating success or a failure + */ +SUNErrCode SUNHashMap_New(int max_size, SUNHashMap* map) +{ + int i; + + if (max_size <= 0) { return SUN_ERR_ARG_OUTOFRANGE; } + + *map = NULL; + *map = (SUNHashMap)malloc(sizeof(**map)); + + if (!map) { return SUN_ERR_MALLOC_FAIL; } + + (*map)->size = 0; + (*map)->max_size = max_size; + + (*map)->buckets = NULL; + (*map)->buckets = + (SUNHashMapKeyValue*)malloc(max_size * sizeof(*((*map)->buckets))); + + if (!(*map)->buckets) + { + free(*map); + return SUN_ERR_MALLOC_FAIL; + } + + /* Initialize all buckets to NULL */ + for (i = 0; i < max_size; i++) { (*map)->buckets[i] = NULL; } + + return SUN_SUCCESS; +} + +/* + This function frees the SUNHashMap object. + + **Arguments:** + * ``map`` -- on input, a SUNHasMap pointer, on output the SUNHashMap will be + deallocated and set to ``NULL`` + * ``freevalue`` -- callback function that should free the value object + + **Returns:** + * A SUNErrCode indicating success or a failure + */ +SUNErrCode SUNHashMap_Destroy(SUNHashMap* map, void (*freevalue)(void* ptr)) +{ + int i; + + if (map == NULL || freevalue == NULL) { return SUN_SUCCESS; } + + for (i = 0; i < (*map)->max_size; i++) + { + if ((*map)->buckets[i] && (*map)->buckets[i]->value) + { + freevalue((*map)->buckets[i]->value); + } + + if ((*map)->buckets[i]) { free((*map)->buckets[i]); } + } + if ((*map)->buckets) { free((*map)->buckets); } + if (*map) { free(*map); } + *map = NULL; + + return SUN_SUCCESS; +} + +/* + This function iterates the map over the range [start, N]. N is either the + index at which ``yieldfn`` indicates the iteration should stop, or the max + entries in the map. + + **Arguments:** + * ``map`` -- the ``SUNHashMap`` object to operate on + * ``start`` -- the start of the iteration range + * ``yieldfn`` -- the callback function to call every iteration + this should return -1 to continue the iteration, or >= 0 to + stop; the first argument is the current index, the second + argument is the current key-value pair, and the final + argument is the same pointer ``ctx`` as the final argument + to SUNHashMapIterate. + * ``ctx`` -- a pointer to pass on to ``yieldfn`` + + **Returns:** + * ``max_size`` -- iterated the whole map + * ``>=0`` -- the index at which the iteration stopped + * ``<-1`` -- an error occurred + */ +int SUNHashMap_Iterate(SUNHashMap map, int start, + int (*yieldfn)(int, SUNHashMapKeyValue, const void*), + const void* ctx) +{ + int i; + + if (map == NULL || yieldfn == NULL) { return (-2); } + + for (i = start; i < map->max_size; i++) + { + int retval = yieldfn(i, map->buckets[i], ctx); + if (retval >= 0) + { + return (retval); /* yieldfn indicates the loop should break */ + } + if (retval < -1) { return (retval); /* error occurred */ } + } + + return (map->max_size); +} + +static int sunHashMapLinearProbeInsert(int idx, SUNHashMapKeyValue kv, + SUNDIALS_MAYBE_UNUSED const void* ctx) +{ + /* find the next open spot */ + if (kv == NULL) { return (idx); /* open spot found at idx */ } + return (-1); /* keep looking */ +} + +/* + This function creates a key-value pair and attempts to insert it into the map. + Will use linear probing if there is a collision. + + **Arguments:** + * ``map`` -- the ``SUNHashMap`` object to operate on + * ``key`` -- the key to store + * ``value`` -- the value associated with the key + + **Returns:** + * ``0`` -- success + * ``-1`` -- an error occurred + * ``-2`` -- the map is full + */ +int SUNHashMap_Insert(SUNHashMap map, const char* key, void* value) +{ + int idx; + int retval; + SUNHashMapKeyValue kvp; + + if (map == NULL || key == NULL || value == NULL) { return (-1); } + + /* We want the index to be in (0, map->max_size) */ + idx = (int)(fnv1a_hash(key) % map->max_size); + + /* Check if the bucket is already filled */ + if (map->buckets[idx] != NULL) + { + /* Find the next open spot */ + retval = SUNHashMap_Iterate(map, idx, sunHashMapLinearProbeInsert, NULL); + if (retval < 0) { return (-1); /* error occurred */ } + if (retval == map->max_size) { return (-2); /* no open entry */ } + + idx = retval; + } + + /* Create the key-value pair */ + kvp = (SUNHashMapKeyValue)malloc(sizeof(*kvp)); + if (kvp == NULL) { return (-1); } + + kvp->key = key; + kvp->value = value; + + /* Insert the key-value pair */ + map->buckets[idx] = kvp; + map->size++; + + return (0); +} + +static int sunHashMapLinearProbeGet(int idx, SUNHashMapKeyValue kv, + const void* key) +{ + /* target key cannot be NULL */ + if (key == NULL) { return (-2); } + + /* find the matching entry */ + if (kv == NULL) { return (-1); /* keep looking since this bucket is empty */ } + if (!strcmp(kv->key, (const char*)key)) + { + return (idx); /* found it at idx */ + } + return (-1); /* keep looking */ +} + +/* + This function gets the value for the given key. + + **Arguments:** + * ``map`` -- the ``SUNHashMap`` object to operate on + * ``key`` -- the key to look up + * ``value`` -- the value associated with the key + + **Returns:** + * ``0`` -- success + * ``-1`` -- an error occurred + * ``-2`` -- key not found + */ +int SUNHashMap_GetValue(SUNHashMap map, const char* key, void** value) +{ + int idx; + int retval; + + if (map == NULL || key == NULL || value == NULL) { return (-1); } + + /* We want the index to be in (0, map->max_size) */ + idx = (int)(fnv1a_hash(key) % map->max_size); + + /* Check if the key exists */ + if (map->buckets[idx] == NULL) { return (-2); } + + /* Check to see if this is a collision */ + if (strcmp(map->buckets[idx]->key, key)) + { + /* Keys did not match, so we have a collision and need to probe */ + retval = SUNHashMap_Iterate(map, idx + 1, sunHashMapLinearProbeGet, key); + if (retval < 0) { return (-1); /* error occurred */ } + if (retval == map->max_size) { return (-2); /* not found */ } + } + + /* Return a reference to the value only */ + *value = map->buckets[idx]->value; + + return (0); +} + +/* + This function allocates a new array the same max_size as the map, + then it sorts map into a new array of key-value pairs leaving + the map unchanged. + + **Arguments:** + * ``map`` -- the ``SUNHashMap`` object to operate on + * ``sorted`` -- pointer to the sorted array of key-value pairs, this + function will allocate the array + * ``compar`` -- comparator function that is passed to the C standard qsort + function + + **Returns:** + * A SUNErrCode indicating success or a failure + */ +SUNErrCode SUNHashMap_Sort(SUNHashMap map, SUNHashMapKeyValue** sorted, + int (*compar)(const void*, const void*)) +{ + int i; + + if (!map || !compar) { return SUN_ERR_ARG_CORRUPT; } + + *sorted = (SUNHashMapKeyValue*)malloc(map->max_size * sizeof(**sorted)); + if (!(*sorted)) { return SUN_ERR_MALLOC_FAIL; } + + /* Copy the buckets into a new array */ + for (i = 0; i < map->max_size; i++) { (*sorted)[i] = map->buckets[i]; } + + qsort(*sorted, map->max_size, sizeof(SUNHashMapKeyValue), compar); + + return SUN_SUCCESS; +} + +/* + This function allocates a new array with just they values of the map. + + **Arguments:** + * ``map`` -- the ``SUNHashMap`` object to operate on + * ``values`` -- pointer to the array of keys + * ``value_size`` -- the size of the values in bytes + + **Returns:** + * A SUNErrCode indicating success or a failure + */ +#if SUNDIALS_MPI_ENABLED +SUNErrCode SUNHashMap_Values(SUNHashMap map, void*** values, size_t value_size) +{ + int i; + int count = 0; + + if (!map) { return SUN_ERR_ARG_CORRUPT; } + + *values = (void**)malloc(map->size * value_size); + if (!values) { return SUN_ERR_MALLOC_FAIL; } + + /* Copy the values into a new array */ + for (i = 0; i < map->max_size; i++) + { + if (map->buckets[i]) { (*values)[count++] = map->buckets[i]->value; } + } + + return SUN_SUCCESS; +} +#endif diff --git a/src/sundials/sundials/sundials_hashmap_impl.h b/src/sundials/sundials/sundials_hashmap_impl.h new file mode 100644 index 0000000..235947e --- /dev/null +++ b/src/sundials/sundials/sundials_hashmap_impl.h @@ -0,0 +1,57 @@ +/* ----------------------------------------------------------------- + * Programmer: Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------- + * A simple hashmap implementation for char* keys and + * void* values. Uses linear probing to resolve collisions. + * The values can be anything, but will be freed by + * the hash map upon its destruction. + * -----------------------------------------------------------------*/ + +#ifndef _SUNDIALS_HASHMAP_IMPL_H +#define _SUNDIALS_HASHMAP_IMPL_H + +#include +#include + +typedef struct SUNHashMapKeyValue_* SUNHashMapKeyValue; + +struct SUNHashMapKeyValue_ +{ + const char* key; + void* value; +}; + +typedef struct SUNHashMap_* SUNHashMap; + +struct SUNHashMap_ +{ + int size; /* current number of entries */ + int max_size; /* max number of entries */ + SUNHashMapKeyValue* buckets; +}; + +SUNErrCode SUNHashMap_New(int max_size, SUNHashMap* map); +SUNErrCode SUNHashMap_Destroy(SUNHashMap* map, void (*freevalue)(void* ptr)); +int SUNHashMap_Iterate(SUNHashMap map, int start, + int (*yieldfn)(int, SUNHashMapKeyValue, const void*), + const void* ctx); +int SUNHashMap_Insert(SUNHashMap map, const char* key, void* value); +int SUNHashMap_GetValue(SUNHashMap map, const char* key, void** value); +SUNErrCode SUNHashMap_Sort(SUNHashMap map, SUNHashMapKeyValue** sorted, + int (*compar)(const void*, const void*)); + +#if SUNDIALS_MPI_ENABLED +SUNErrCode SUNHashMap_Values(SUNHashMap map, void*** values, size_t value_size); +#endif + +#endif diff --git a/src/sundials/sundials/sundials_iterative_impl.h b/src/sundials/sundials/sundials_iterative_impl.h index 5ebf796..ea6c17c 100644 --- a/src/sundials/sundials/sundials_iterative_impl.h +++ b/src/sundials/sundials/sundials_iterative_impl.h @@ -15,6 +15,9 @@ * different iterative solvers. * ---------------------------------------------------------------------------*/ +#ifndef _SUNDIALS_ITERATIVE_IMPL_H +#define _SUNDIALS_ITERATIVE_IMPL_H + #include /* ----------------------------------------------------------------------------- @@ -33,3 +36,5 @@ struct _SUNQRData N_Vector vtemp2; sunrealtype* temp_array; }; + +#endif diff --git a/src/sundials/sundials/sundials_lapack_defs.h.in b/src/sundials/sundials/sundials_lapack_defs.h.in new file mode 100644 index 0000000..1e6a0c0 --- /dev/null +++ b/src/sundials/sundials/sundials_lapack_defs.h.in @@ -0,0 +1,117 @@ +/* ----------------------------------------------------------------- + * Programmer: Cody J. Balos @ LLNL + * ----------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * -----------------------------------------------------------------*/ + +#ifndef _SUNDIALS_LAPACK_H +#define _SUNDIALS_LAPACK_H + +#include + +#ifdef __cplusplus /* wrapper to enable C++ usage */ +extern "C" { +#endif + +/* Define LAPACK name-mangling macros. Depending on the inferred scheme, one of + * the following six macros will be defined: + * + * #define SUNDIALS_LAPACK_FUNC(name,NAME) name + * #define SUNDIALS_LAPACK_FUNC(name,NAME) name ## _ + * #define SUNDIALS_LAPACK_FUNC(name,NAME) name ## __ + * #define SUNDIALS_LAPACK_FUNC(name,NAME) NAME + * #define SUNDIALS_LAPACK_FUNC(name,NAME) NAME ## _ + * #define SUNDIALS_LAPACK_FUNC(name,NAME) NAME ## __ + */ +@LAPACK_MANGLE_MACRO1@ + +/* Define LAPACK name-mangling macro for C identifiers + * which contain underscores. + */ +@LAPACK_MANGLE_MACRO2@ + +/* + * ================================================================== + * Blas and Lapack functions + * ================================================================== + */ + +#if defined(SUNDIALS_LAPACK_FUNC) + +#define dgbtrf_f77 SUNDIALS_LAPACK_FUNC(dgbtrf, DGBTRF) +#define dgbtrs_f77 SUNDIALS_LAPACK_FUNC(dgbtrs, DGBTRS) +#define dgetrf_f77 SUNDIALS_LAPACK_FUNC(dgetrf, DGETRF) +#define dgetrs_f77 SUNDIALS_LAPACK_FUNC(dgetrs, DGETRS) + +#define sgbtrf_f77 SUNDIALS_LAPACK_FUNC(sgbtrf, SGBTRF) +#define sgbtrs_f77 SUNDIALS_LAPACK_FUNC(sgbtrs, SGBTRS) +#define sgetrf_f77 SUNDIALS_LAPACK_FUNC(sgetrf, SGETRF) +#define sgetrs_f77 SUNDIALS_LAPACK_FUNC(sgetrs, SGETRS) + +#else + +#define dgbtrf_f77 dgbtrf_ +#define dgbtrs_f77 dgbtrs_ +#define dgetrf_f77 dgetrf_ +#define dgetrs_f77 dgetrs_ + +#define sgbtrf_f77 sgbtrf_ +#define sgbtrs_f77 sgbtrs_ +#define sgetrf_f77 sgetrf_ +#define sgetrs_f77 sgetrs_ + +#endif + +/* LAPACK */ + +extern void dgbtrf_f77(const sunindextype* m, const sunindextype* n, + const sunindextype* kl, const sunindextype* ku, + double* ab, sunindextype* ldab, sunindextype* ipiv, + sunindextype* info); + +extern void dgbtrs_f77(const char* trans, const sunindextype* n, + const sunindextype* kl, const sunindextype* ku, + const sunindextype* nrhs, double* ab, + const sunindextype* ldab, sunindextype* ipiv, double* b, + const sunindextype* ldb, sunindextype* info); + +extern void dgetrf_f77(const sunindextype* m, const sunindextype* n, double* a, + sunindextype* lda, sunindextype* ipiv, sunindextype* info); + +extern void dgetrs_f77(const char* trans, const sunindextype* n, + const sunindextype* nrhs, double* a, + const sunindextype* lda, sunindextype* ipiv, double* b, + const sunindextype* ldb, sunindextype* info); + +extern void sgbtrf_f77(const sunindextype* m, const sunindextype* n, + const sunindextype* kl, const sunindextype* ku, + float* ab, sunindextype* ldab, sunindextype* ipiv, + sunindextype* info); + +extern void sgbtrs_f77(const char* trans, const sunindextype* n, + const sunindextype* kl, const sunindextype* ku, + const sunindextype* nrhs, float* ab, + const sunindextype* ldab, sunindextype* ipiv, float* b, + const sunindextype* ldb, sunindextype* info); + +extern void sgetrf_f77(const sunindextype* m, const sunindextype* n, float* a, + sunindextype* lda, sunindextype* ipiv, sunindextype* info); + +extern void sgetrs_f77(const char* trans, const sunindextype* n, + const sunindextype* nrhs, float* a, + const sunindextype* lda, sunindextype* ipiv, float* b, + const sunindextype* ldb, sunindextype* info); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/src/sundials/sundials/sundials_logger.c b/src/sundials/sundials/sundials_logger.c index 2b109f6..bc4d686 100644 --- a/src/sundials/sundials/sundials_logger.c +++ b/src/sundials/sundials/sundials_logger.c @@ -16,18 +16,19 @@ #include #include #include + #include #include +#include #include - -#include "sundials/sundials_errors.h" -#include "sundials/sundials_types.h" +#include #if SUNDIALS_MPI_ENABLED #include #endif #include "sundials_logger_impl.h" +#include "sundials_macros.h" #include "sundials_utils.h" /* max number of files that can be opened */ @@ -65,6 +66,7 @@ void sunCreateLogMessage(SUNLogLevel lvl, int rank, const char* scope, free(formatted_txt); } +#if SUNDIALS_LOGGING_LEVEL > 0 static FILE* sunOpenLogFile(const char* fname, const char* mode) { FILE* fp = NULL; @@ -78,13 +80,15 @@ static FILE* sunOpenLogFile(const char* fname, const char* mode) return fp; } +#endif static void sunCloseLogFile(void* fp) { if (fp && fp != stdout && fp != stderr) { fclose((FILE*)fp); } } -static sunbooleantype sunLoggerIsOutputRank(SUNLogger logger, int* rank_ref) +static sunbooleantype sunLoggerIsOutputRank(SUNDIALS_MAYBE_UNUSED SUNLogger logger, + int* rank_ref) { sunbooleantype retval; @@ -371,6 +375,13 @@ SUNErrCode SUNLogger_QueueMsg(SUNLogger logger, SUNLogLevel lvl, va_end(args); } +#else + /* silence warnings when all logging is disabled */ + ((void)logger); + ((void)lvl); + ((void)scope); + ((void)label); + ((void)msg_txt); #endif return retval; @@ -417,6 +428,9 @@ SUNErrCode SUNLogger_Flush(SUNLogger logger, SUNLogLevel lvl) } } } +#else + /* silence warnings when all logging is disabled */ + ((void)lvl); #endif return retval; diff --git a/src/sundials/sundials/sundials_logger_impl.h b/src/sundials/sundials/sundials_logger_impl.h index 7cecc00..6fbb7ca 100644 --- a/src/sundials/sundials/sundials_logger_impl.h +++ b/src/sundials/sundials/sundials_logger_impl.h @@ -21,7 +21,7 @@ #include #include -#include "sundials_hashmap.h" +#include "sundials_hashmap_impl.h" #include "sundials_utils.h" #define SUNDIALS_LOGGING_ERROR 1 diff --git a/src/sundials/sundials/sundials_macros.h b/src/sundials/sundials/sundials_macros.h new file mode 100644 index 0000000..4bf007e --- /dev/null +++ b/src/sundials/sundials/sundials_macros.h @@ -0,0 +1,39 @@ +/* ----------------------------------------------------------------------------- + * Programmer(s): David J. Gardner @ LLNL + * ----------------------------------------------------------------------------- + * SUNDIALS Copyright Start + * Copyright (c) 2002-2024, Lawrence Livermore National Security + * and Southern Methodist University. + * All rights reserved. + * + * See the top-level LICENSE and NOTICE files for details. + * + * SPDX-License-Identifier: BSD-3-Clause + * SUNDIALS Copyright End + * ----------------------------------------------------------------------------- + * SUNDIALS macros + * ---------------------------------------------------------------------------*/ + +#ifndef _SUNDIALS_MACROS_H +#define _SUNDIALS_MACROS_H + +#include "sundials/sundials_config.h" + +/* ----------------------------------------------------------------------------- + * SUNDIALS_MAYBE_UNUSED + * + * This maps to an attribute that can be used to silence warnings about unused + * classes, typedefs, variables, functions, or methods when the entity cannot be + * removed. For example, functions or variables that are only used when error + * checks or profiling is enabled. + * ---------------------------------------------------------------------------*/ + +#if __cplusplus >= 201703L || __STDC_VERSION__ > 201710L +#define SUNDIALS_MAYBE_UNUSED [[maybe_unused]] +#elif defined(SUNDIALS_C_COMPILER_HAS_ATTRIBUTE_UNUSED) +#define SUNDIALS_MAYBE_UNUSED __attribute__((unused)) +#else +#define SUNDIALS_MAYBE_UNUSED +#endif + +#endif /* _SUNDIALS_MACROS_H */ diff --git a/src/sundials/sundials/sundials_nvector.c b/src/sundials/sundials/sundials_nvector.c index a6549d8..9b15332 100644 --- a/src/sundials/sundials/sundials_nvector.c +++ b/src/sundials/sundials/sundials_nvector.c @@ -284,8 +284,8 @@ N_Vector N_VClone(N_Vector w) { N_Vector result = NULL; SUNDIALS_MARK_FUNCTION_BEGIN(getSUNProfiler(w)); - result = w->ops->nvclone(w); - result->sunctx = w->sunctx; + result = w->ops->nvclone(w); + if (result) { result->sunctx = w->sunctx; } SUNDIALS_MARK_FUNCTION_END(getSUNProfiler(w)); return result; } @@ -294,8 +294,8 @@ N_Vector N_VCloneEmpty(N_Vector w) { N_Vector result; SUNDIALS_MARK_FUNCTION_BEGIN(getSUNProfiler(w)); - result = w->ops->nvcloneempty(w); - result->sunctx = w->sunctx; + result = w->ops->nvcloneempty(w); + if (result) { result->sunctx = w->sunctx; } SUNDIALS_MARK_FUNCTION_END(getSUNProfiler(w)); return result; } @@ -335,7 +335,11 @@ void N_VSpace(N_Vector v, sunindextype* lrw, sunindextype* liw) sunrealtype* N_VGetArrayPointer(N_Vector v) { - return ((sunrealtype*)v->ops->nvgetarraypointer(v)); + if (v->ops->nvgetarraypointer) + { + return (sunrealtype*)v->ops->nvgetarraypointer(v); + } + else { return NULL; } } sunrealtype* N_VGetDeviceArrayPointer(N_Vector v) @@ -349,7 +353,7 @@ sunrealtype* N_VGetDeviceArrayPointer(N_Vector v) void N_VSetArrayPointer(sunrealtype* v_data, N_Vector v) { - v->ops->nvsetarraypointer(v_data, v); + if (v->ops->nvsetarraypointer) { v->ops->nvsetarraypointer(v_data, v); } return; } diff --git a/src/sundials/sundials/sundials_profiler.c b/src/sundials/sundials/sundials_profiler.c index bfc7196..c852448 100644 --- a/src/sundials/sundials/sundials_profiler.c +++ b/src/sundials/sundials/sundials_profiler.c @@ -12,11 +12,16 @@ * SUNDIALS Copyright End * -----------------------------------------------------------------*/ +#include +#include +#include + #include #include - -#include "sundials/sundials_errors.h" -#include "sundials/sundials_types.h" +#include +#include +#include +#include #if SUNDIALS_MPI_ENABLED #include @@ -32,14 +37,9 @@ #error SUNProfiler needs POSIX or Windows timers #endif -#include -#include -#include -#include -#include - #include "sundials_debug.h" -#include "sundials_hashmap.h" +#include "sundials_hashmap_impl.h" +#include "sundials_macros.h" #define SUNDIALS_ROOT_TIMER ((const char*)"From profiler epoch") @@ -57,7 +57,7 @@ typedef struct _sunTimespec #if SUNDIALS_MPI_ENABLED static SUNErrCode sunCollectTimers(SUNProfiler p); #endif -static void sunPrintTimers(int idx, SUNHashMapKeyValue kv, FILE* fp, void* pvoid); +static void sunPrintTimer(SUNHashMapKeyValue kv, FILE* fp, void* pvoid); static int sunCompareTimes(const void* l, const void* r); static int sunclock_gettime_monotonic(sunTimespec* tp); @@ -419,7 +419,7 @@ SUNErrCode SUNProfiler_Print(SUNProfiler p, FILE* fp) /* Print all the other timers out */ for (i = 0; i < p->map->size; i++) { - if (sorted[i]) { sunPrintTimers(i, sorted[i], fp, (void*)p); } + if (sorted[i]) { sunPrintTimer(sorted[i], fp, (void*)p); } } free(sorted); } @@ -442,7 +442,7 @@ SUNErrCode SUNProfiler_Print(SUNProfiler p, FILE* fp) #if SUNDIALS_MPI_ENABLED static void sunTimerStructReduceMaxAndSum(void* a, void* b, int* len, - MPI_Datatype* dType) + SUNDIALS_MAYBE_UNUSED MPI_Datatype* dType) { sunTimerStruct* a_ts = (sunTimerStruct*)a; sunTimerStruct* b_ts = (sunTimerStruct*)b; @@ -522,7 +522,7 @@ SUNErrCode sunCollectTimers(SUNProfiler p) /* Print out the: timer name, percentage of exec time (based on the max), max across ranks, average across ranks, and the timer counter. */ -void sunPrintTimers(int idx, SUNHashMapKeyValue kv, FILE* fp, void* pvoid) +void sunPrintTimer(SUNHashMapKeyValue kv, FILE* fp, void* pvoid) { SUNProfiler p = (SUNProfiler)pvoid; sunTimerStruct* ts = (sunTimerStruct*)kv->value; @@ -542,8 +542,8 @@ int sunCompareTimes(const void* l, const void* r) double left_max; double right_max; - const SUNHashMapKeyValue left = *((SUNHashMapKeyValue*)l); - const SUNHashMapKeyValue right = *((SUNHashMapKeyValue*)r); + const SUNHashMapKeyValue left = *((const SUNHashMapKeyValue*)l); + const SUNHashMapKeyValue right = *((const SUNHashMapKeyValue*)r); if (left == NULL && right == NULL) { return 0; } if (left == NULL) { return 1; } diff --git a/src/sundials/sundials/sundials_utils.h b/src/sundials/sundials/sundials_utils.h index 6866ffa..44ce2a7 100644 --- a/src/sundials/sundials/sundials_utils.h +++ b/src/sundials/sundials/sundials_utils.h @@ -71,7 +71,7 @@ static inline int sunvasnprintf(char** str, const char* fmt, va_list args) *str = (char*)malloc(size + 1); if (NULL == *str) { return -1; } - size = vsprintf(*str, fmt, args); + size = vsnprintf(*str, size + 1, fmt, args); return size; } diff --git a/src/sundials/sunlinsol/band/sunlinsol_band.c b/src/sundials/sunlinsol/band/sunlinsol_band.c index 775466b..d72e37a 100644 --- a/src/sundials/sunlinsol/band/sunlinsol_band.c +++ b/src/sundials/sunlinsol/band/sunlinsol_band.c @@ -17,11 +17,14 @@ #include #include + #include #include #include #include +#include "sundials_macros.h" + #define ZERO SUN_RCONST(0.0) #define ONE SUN_RCONST(1.0) #define ROW(i, j, smu) (i - j + smu) @@ -46,7 +49,8 @@ * Function to create a new band linear solver */ -SUNLinearSolver SUNLinSol_Band(N_Vector y, SUNMatrix A, SUNContext sunctx) +SUNLinearSolver SUNLinSol_Band(SUNDIALS_MAYBE_UNUSED N_Vector y, SUNMatrix A, + SUNContext sunctx) { SUNFunctionBegin(sunctx); SUNLinearSolver S; @@ -107,12 +111,12 @@ SUNLinearSolver SUNLinSol_Band(N_Vector y, SUNMatrix A, SUNContext sunctx) * ----------------------------------------------------------------- */ -SUNLinearSolver_Type SUNLinSolGetType_Band(SUNLinearSolver S) +SUNLinearSolver_Type SUNLinSolGetType_Band(SUNDIALS_MAYBE_UNUSED SUNLinearSolver S) { return (SUNLINEARSOLVER_DIRECT); } -SUNLinearSolver_ID SUNLinSolGetID_Band(SUNLinearSolver S) +SUNLinearSolver_ID SUNLinSolGetID_Band(SUNDIALS_MAYBE_UNUSED SUNLinearSolver S) { return (SUNLINEARSOLVER_BAND); } @@ -156,7 +160,7 @@ int SUNLinSolSetup_Band(SUNLinearSolver S, SUNMatrix A) } int SUNLinSolSolve_Band(SUNLinearSolver S, SUNMatrix A, N_Vector x, N_Vector b, - sunrealtype tol) + SUNDIALS_MAYBE_UNUSED sunrealtype tol) { SUNFunctionBegin(S->sunctx); sunrealtype **A_cols, *xdata; diff --git a/src/sundials/sunlinsol/dense/sunlinsol_dense.c b/src/sundials/sunlinsol/dense/sunlinsol_dense.c index 13a1fa9..41e6a1b 100644 --- a/src/sundials/sunlinsol/dense/sunlinsol_dense.c +++ b/src/sundials/sunlinsol/dense/sunlinsol_dense.c @@ -17,12 +17,14 @@ #include #include + #include +#include #include #include -#include "sundials/sundials_errors.h" #include "sundials_logger_impl.h" +#include "sundials_macros.h" #define ONE SUN_RCONST(1.0) @@ -46,7 +48,8 @@ * Function to create a new dense linear solver */ -SUNLinearSolver SUNLinSol_Dense(N_Vector y, SUNMatrix A, SUNContext sunctx) +SUNLinearSolver SUNLinSol_Dense(SUNDIALS_MAYBE_UNUSED N_Vector y, SUNMatrix A, + SUNContext sunctx) { SUNFunctionBegin(sunctx); SUNLinearSolver S; @@ -102,12 +105,12 @@ SUNLinearSolver SUNLinSol_Dense(N_Vector y, SUNMatrix A, SUNContext sunctx) * ----------------------------------------------------------------- */ -SUNLinearSolver_Type SUNLinSolGetType_Dense(SUNLinearSolver S) +SUNLinearSolver_Type SUNLinSolGetType_Dense(SUNDIALS_MAYBE_UNUSED SUNLinearSolver S) { return (SUNLINEARSOLVER_DIRECT); } -SUNLinearSolver_ID SUNLinSolGetID_Dense(SUNLinearSolver S) +SUNLinearSolver_ID SUNLinSolGetID_Dense(SUNDIALS_MAYBE_UNUSED SUNLinearSolver S) { return (SUNLINEARSOLVER_DENSE); } @@ -146,7 +149,7 @@ int SUNLinSolSetup_Dense(SUNLinearSolver S, SUNMatrix A) } int SUNLinSolSolve_Dense(SUNLinearSolver S, SUNMatrix A, N_Vector x, N_Vector b, - sunrealtype tol) + SUNDIALS_MAYBE_UNUSED sunrealtype tol) { SUNFunctionBegin(S->sunctx); sunrealtype **A_cols, *xdata; diff --git a/src/sundials/sunmatrix/band/sunmatrix_band.c b/src/sundials/sunmatrix/band/sunmatrix_band.c index 2384504..f3d06c7 100644 --- a/src/sundials/sunmatrix/band/sunmatrix_band.c +++ b/src/sundials/sunmatrix/band/sunmatrix_band.c @@ -22,11 +22,13 @@ #include #include + #include +#include #include #include -#include "sundials/sundials_errors.h" +#include "sundials_macros.h" #define ZERO SUN_RCONST(0.0) #define ONE SUN_RCONST(1.0) @@ -230,7 +232,10 @@ sunrealtype* SUNBandMatrix_Column(SUNMatrix A, sunindextype j) * ----------------------------------------------------------------- */ -SUNMatrix_ID SUNMatGetID_Band(SUNMatrix A) { return SUNMATRIX_BAND; } +SUNMatrix_ID SUNMatGetID_Band(SUNDIALS_MAYBE_UNUSED SUNMatrix A) +{ + return SUNMATRIX_BAND; +} SUNMatrix SUNMatClone_Band(SUNMatrix A) { @@ -428,6 +433,7 @@ SUNErrCode SUNMatSpace_Band(SUNMatrix A, long int* lenrw, long int* leniw) * ----------------------------------------------------------------- */ +SUNDIALS_MAYBE_UNUSED static sunbooleantype compatibleMatrices(SUNMatrix A, SUNMatrix B) { /* both matrices must have the same number of columns @@ -437,6 +443,7 @@ static sunbooleantype compatibleMatrices(SUNMatrix A, SUNMatrix B) return SUNTRUE; } +SUNDIALS_MAYBE_UNUSED static sunbooleantype compatibleMatrixAndVectors(SUNMatrix A, N_Vector x, N_Vector y) { diff --git a/src/sundials/sunmatrix/dense/sunmatrix_dense.c b/src/sundials/sunmatrix/dense/sunmatrix_dense.c index 5067379..c1250a9 100644 --- a/src/sundials/sunmatrix/dense/sunmatrix_dense.c +++ b/src/sundials/sunmatrix/dense/sunmatrix_dense.c @@ -20,10 +20,12 @@ #include #include + #include +#include #include -#include "sundials/sundials_errors.h" +#include "sundials_macros.h" #define ZERO SUN_RCONST(0.0) #define ONE SUN_RCONST(1.0) @@ -178,7 +180,10 @@ sunrealtype* SUNDenseMatrix_Column(SUNMatrix A, sunindextype j) * ----------------------------------------------------------------- */ -SUNMatrix_ID SUNMatGetID_Dense(SUNMatrix A) { return SUNMATRIX_DENSE; } +SUNMatrix_ID SUNMatGetID_Dense(SUNDIALS_MAYBE_UNUSED SUNMatrix A) +{ + return SUNMATRIX_DENSE; +} SUNMatrix SUNMatClone_Dense(SUNMatrix A) { @@ -346,6 +351,7 @@ SUNErrCode SUNMatSpace_Dense(SUNMatrix A, long int* lenrw, long int* leniw) * ----------------------------------------------------------------- */ +SUNDIALS_MAYBE_UNUSED static sunbooleantype compatibleMatrices(SUNMatrix A, SUNMatrix B) { /* both matrices must have the same shape */ @@ -357,6 +363,7 @@ static sunbooleantype compatibleMatrices(SUNMatrix A, SUNMatrix B) return SUNTRUE; } +SUNDIALS_MAYBE_UNUSED static sunbooleantype compatibleMatrixAndVectors(SUNMatrix A, N_Vector x, N_Vector y) { diff --git a/src/sundials/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c b/src/sundials/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c index 1ec2289..ff1d45a 100644 --- a/src/sundials/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c +++ b/src/sundials/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.c @@ -18,11 +18,13 @@ #include #include #include + #include #include #include #include "sundials_logger_impl.h" +#include "sundials_macros.h" /* Internal utility routines */ static SUNErrCode AndersonAccelerate(SUNNonlinearSolver NLS, N_Vector gval, @@ -129,7 +131,8 @@ SUNNonlinearSolver SUNNonlinSol_FixedPointSens(int count, N_Vector y, int m, GetType, Initialize, Setup, Solve, and Free operations ============================================================================*/ -SUNNonlinearSolver_Type SUNNonlinSolGetType_FixedPoint(SUNNonlinearSolver NLS) +SUNNonlinearSolver_Type SUNNonlinSolGetType_FixedPoint( + SUNDIALS_MAYBE_UNUSED SUNNonlinearSolver NLS) { return (SUNNONLINEARSOLVER_FIXEDPOINT); } @@ -165,9 +168,11 @@ SUNErrCode SUNNonlinSolInitialize_FixedPoint(SUNNonlinearSolver NLS) by the Sys function provided to the nonlinear solver. ---------------------------------------------------------------------------*/ -int SUNNonlinSolSolve_FixedPoint(SUNNonlinearSolver NLS, N_Vector y0, +int SUNNonlinSolSolve_FixedPoint(SUNNonlinearSolver NLS, + SUNDIALS_MAYBE_UNUSED N_Vector y0, N_Vector ycor, N_Vector w, sunrealtype tol, - sunbooleantype callSetup, void* mem) + SUNDIALS_MAYBE_UNUSED sunbooleantype callSetup, + void* mem) { SUNFunctionBegin(NLS->sunctx); /* local variables */ diff --git a/src/sundials/sunnonlinsol/newton/sunnonlinsol_newton.c b/src/sundials/sunnonlinsol/newton/sunnonlinsol_newton.c index c796171..c4c0af9 100644 --- a/src/sundials/sunnonlinsol/newton/sunnonlinsol_newton.c +++ b/src/sundials/sunnonlinsol/newton/sunnonlinsol_newton.c @@ -18,12 +18,14 @@ #include #include #include + #include #include #include #include #include "sundials_logger_impl.h" +#include "sundials_macros.h" /* Content structure accessibility macros */ #define NEWTON_CONTENT(S) ((SUNNonlinearSolverContent_Newton)(S->content)) @@ -126,7 +128,8 @@ SUNNonlinearSolver SUNNonlinSol_NewtonSens(int count, N_Vector y, GetType, Initialize, Setup, Solve, and Free operations ============================================================================*/ -SUNNonlinearSolver_Type SUNNonlinSolGetType_Newton(SUNNonlinearSolver NLS) +SUNNonlinearSolver_Type SUNNonlinSolGetType_Newton( + SUNDIALS_MAYBE_UNUSED SUNNonlinearSolver NLS) { return (SUNNONLINEARSOLVER_ROOTFIND); } @@ -170,7 +173,8 @@ SUNErrCode SUNNonlinSolInitialize_Newton(SUNNonlinearSolver NLS) Note return values beginning with * are package specific values returned by the Sys, LSetup, and LSolve functions provided to the nonlinear solver. ----------------------------------------------------------------------------*/ -int SUNNonlinSolSolve_Newton(SUNNonlinearSolver NLS, N_Vector y0, N_Vector ycor, +int SUNNonlinSolSolve_Newton(SUNNonlinearSolver NLS, + SUNDIALS_MAYBE_UNUSED N_Vector y0, N_Vector ycor, N_Vector w, sunrealtype tol, sunbooleantype callLSetup, void* mem) { @@ -203,6 +207,20 @@ int SUNNonlinSolSolve_Newton(SUNNonlinearSolver NLS, N_Vector y0, N_Vector ycor, Preform Newton iteraion */ for (;;) { + /* initialize current iteration counter for this solve attempt */ + NEWTON_CONTENT(NLS)->curiter = 0; + +#if SUNDIALS_LOGGING_LEVEL >= SUNDIALS_LOGGING_INFO + SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, __func__, + "begin-attempt", "iter = %ld, nni = %ld", + (long int)NEWTON_CONTENT(NLS)->curiter, + NEWTON_CONTENT(NLS)->niters); + SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, __func__, + "start-iterate", "iter = %ld, nni = %ld", + (long int)NEWTON_CONTENT(NLS)->curiter, + NEWTON_CONTENT(NLS)->niters); +#endif + /* compute the nonlinear residual, store in delta */ retval = NEWTON_CONTENT(NLS)->Sys(ycor, delta, mem); if (retval != SUN_SUCCESS) { break; } @@ -215,16 +233,6 @@ int SUNNonlinSolSolve_Newton(SUNNonlinearSolver NLS, N_Vector y0, N_Vector ycor, if (retval != SUN_SUCCESS) { break; } } - /* initialize current iteration counter for this solve attempt */ - NEWTON_CONTENT(NLS)->curiter = 0; - -#if SUNDIALS_LOGGING_LEVEL >= SUNDIALS_LOGGING_INFO - SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, - "SUNNonlinSolSolve_Newton", "begin-iteration", - "iter = %ld, nni = %ld", (long int)0, - NEWTON_CONTENT(NLS)->niters); -#endif - /* looping point for Newton iteration. Break out on any error. */ for (;;) { @@ -248,16 +256,24 @@ int SUNNonlinSolSolve_Newton(SUNNonlinearSolver NLS, N_Vector y0, N_Vector ycor, NEWTON_CONTENT(NLS)->ctest_data); #if SUNDIALS_LOGGING_LEVEL >= SUNDIALS_LOGGING_INFO - SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, - "SUNNonlinSolSolve_Newton", "end-of-iterate", - "iter = %ld, nni = %ld, wrmsnorm = %.16g", + SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, __func__, + "end-iterate", "iter = %ld, nni = %ld, wrmsnorm = %.16g", NEWTON_CONTENT(NLS)->curiter, - NEWTON_CONTENT(NLS)->niters, N_VWrmsNorm(delta, w)); + NEWTON_CONTENT(NLS)->niters - 1, N_VWrmsNorm(delta, w)); #endif + /* Update here so begin/end logging iterations match */ + NEWTON_CONTENT(NLS)->curiter++; + /* if successful update Jacobian status and return */ if (retval == SUN_SUCCESS) { +#if SUNDIALS_LOGGING_LEVEL >= SUNDIALS_LOGGING_INFO + SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, __func__, + "end-attempt", "success, iter = %ld, nni = %ld", + (long int)NEWTON_CONTENT(NLS)->curiter, + NEWTON_CONTENT(NLS)->niters); +#endif NEWTON_CONTENT(NLS)->jcur = SUNFALSE; return SUN_SUCCESS; } @@ -265,14 +281,20 @@ int SUNNonlinSolSolve_Newton(SUNNonlinearSolver NLS, N_Vector y0, N_Vector ycor, /* check if the iteration should continue; otherwise exit Newton loop */ if (retval != SUN_NLS_CONTINUE) { break; } - /* not yet converged. Increment curiter and test for max allowed. */ - NEWTON_CONTENT(NLS)->curiter++; + /* not yet converged, test for max allowed iterations. */ if (NEWTON_CONTENT(NLS)->curiter >= NEWTON_CONTENT(NLS)->maxiters) { retval = SUN_NLS_CONV_RECVR; break; } +#if SUNDIALS_LOGGING_LEVEL >= SUNDIALS_LOGGING_INFO + SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, __func__, + "start-iterate", "iter = %ld, nni = %ld", + (long int)NEWTON_CONTENT(NLS)->curiter, + NEWTON_CONTENT(NLS)->niters); +#endif + /* compute the nonlinear residual, store in delta */ retval = NEWTON_CONTENT(NLS)->Sys(ycor, delta, mem); if (retval != SUN_SUCCESS) { break; } @@ -281,6 +303,13 @@ int SUNNonlinSolSolve_Newton(SUNNonlinearSolver NLS, N_Vector y0, N_Vector ycor, /* all errors go here */ +#if SUNDIALS_LOGGING_LEVEL >= SUNDIALS_LOGGING_INFO + SUNLogger_QueueMsg(NLS->sunctx->logger, SUN_LOGLEVEL_INFO, __func__, + "end-attempt", "failure, iter = %ld, nni = %ld", + (long int)NEWTON_CONTENT(NLS)->curiter, + NEWTON_CONTENT(NLS)->niters); +#endif + /* If there is a recoverable convergence failure and the Jacobian-related data appears not to be current, increment the convergence failure count, reset the initial correction to zero, and loop again with a call to