Skip to content

Latest commit

 

History

History
77 lines (69 loc) · 2.92 KB

README.K-Computer.md

File metadata and controls

77 lines (69 loc) · 2.92 KB

Build PnetCDF on The K computer

This file contains information of building PnetCDF on the K computer at the RIKEN Advanced Institute for Computational Science in Kobe, Japan. http://www.aics.riken.jp/en/k-computer/about/

The MPI compilers on the K computer are wrappers of Fujitsu compilers:
    Language    MPI compiler    Sequential compiler
  -----------  --------------  --------------------
    Fortran     mpifrtpx        (frtpx)
    C           mpifccpx        (fccpx)
    C++         mpiFCCpx        (FCCpx)

The K computer is a cross-compile system. Be sure to run configure with the --build and --host flags to put it in "cross compile mode". This will make configure use compile-only tests, instead of the usual compile-and-run tests (running tests on the K computer login node will not work.) Below shows a configure command that was used to build PnetCDF successfully on K.

./configure --prefix=/path/to/install \
            --host=sparc64-unknown-linux-gnu \
            --build=x86_64-redhat-linux \
            MPICC=mpifccpx \
            MPICXX=mpiFCCpx \
            MPIF77=mpifrtpx \
            MPIF90=mpifrtpx \
            CFLAGS="-Kfast" \
            CXXFLAGS="-Kfast" \
            FFLAGS="-Kfast" \
            FCFLAGS="-Kfast" \
            MANIFEST_TOOL=: \
            TESTMPIRUN="mpiexec -n NP" \
            TESTSEQRUN="mpiexec -n 1"

For users who would customize the source codes and edit configure.ac, it is necessary to run command "autoreconf" to generate an updated "configure" file. However, there is a bug in autoconf 2.69 that causes building the PnetCDF Fortran interfaces to fail. Please read file README.Fujitsu for the bug patch to autoconf 2.69. If this bug fix is not applied to (or unable to due to permission issue) the autoconf utility, please add LDFLAGS="-L." to the configure command line. Adding LDFLAGS="-L." is necessary as the Fujitsu Fortran compiler requires no "-L" for its internal library files. Without this, configure command may fail.

To build shared library, add configure command-line option "--enable-shared" and set the MPICC, MPICXX, and LDFLAGS environment variables to the followings.

            MPICC="mpifccpx -Xg" \
            MPICXX="mpiFCCpx -Xg" \
            LDFLAGS="-Wl,-shared"

Testing PnetCDF:

  • One way to run "make check" or "make ptest" on K's compute nodes is through an interactive job. An example command to submit an interactive job requesting 4 nodes for 20 minutes is shown below. 
      pjsub --interact --rsc-list "node=4" --rsc-list "elapse=00:20:00" \
        --sparam "wait-time=3600"
  • Once in the interactive mode, run command 
      source /work/system/Env_base
  make -s check
  make -s ptest
  • To exit the interactive mode, run command 
     exit

Copyright (C) 2017, Northwestern University and Argonne National Laboratory. See COPYRIGHT notice in top-level directory.