From f0215f250ff56751a58d4f6331ebf926cc77f746 Mon Sep 17 00:00:00 2001
From: Tim Aidan Graulich <63345846+tgraulich@users.noreply.github.com>
Date: Thu, 19 Dec 2024 15:04:55 +0100
Subject: [PATCH 1/4] Update documentation to make sure the correct cplex
 option file is used on the HPC.

---
 .../gh-pages/running_on_hpc/submitting_a_job.md            | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md b/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md
index c2fa54ed..4840d247 100644
--- a/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md
+++ b/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md
@@ -10,7 +10,10 @@ Remember to study the log report after your job finishes, so you can be more acc
 
 After having transferred our Balmorel model through WinSCP (see [previous page](access.md)), we need to submit a job. This means creating a job script that asks for the right amount of memory usage and time before completion. This is done through a job script, illustrated in the code snippet below. We refer to [this general guide](https://www.hpc.dtu.dk/?page_id=1416) by DTU Computing Center for the exact explanations of the different elements. Note that the paths in the `export` commands are specific to our setup at DTU's clusters. 
 
-The bottom commands assumes that the job script is submitted from inside your Balmorel folder, and that your Balmorel project contains a "scenario1" scenario - see [how to create new scenarios](../get_started/scenario_setup.md). The `--threads=$LSB_DJOB_NUMPROC` command makes sure that Balmorel does not use more cores than defined  in your job script (four in this case, due to `#BSUB -n 4`)
+The bottom commands assumes that the job script is submitted from inside your Balmorel folder, and that your Balmorel project contains a "scenario1" scenario - see [how to create new scenarios](../get_started/scenario_setup.md). The `threads=$LSB_DJOB_NUMPROC` command makes sure that Balmorel does not use more cores than defined  in your job script (four in this case, due to `#BSUB -n 4`)
+:::{warning}
+Please make sure to switch to the solver options file `cplex.op2`, by going into the `balgams.opt` file and setting `$Setglobal USEOPTIONFILE 2`. Otherwise CPLEX will overwrite the number of chosen threads and will ue more resources than requested.
+:::
 ```bash
 #!/bin/sh 
 ### General options 
@@ -48,7 +51,7 @@ export LD_LIBRARY_PATH=/appl/gams/47.6.0:$LD_LIBRARY_PATH
 # Go to model folder of your scenario - this assumes that the job script is at the same level of the Balmorel folder
 cd scenario1/model 
 # Run Balmorel
-gams Balmorel --threads=$LSB_DJOB_NUMPROC
+gams Balmorel threads=$LSB_DJOB_NUMPROC
 ```
 
 ## Submitting the Job from PuTTY

From ebfe36072b7062e40c773f0a9a2f1a5ca812394b Mon Sep 17 00:00:00 2001
From: Tim Aidan Graulich <63345846+tgraulich@users.noreply.github.com>
Date: Thu, 19 Dec 2024 15:05:15 +0100
Subject: [PATCH 2/4] Update submitting_a_job.md

---
 base/documentation/gh-pages/running_on_hpc/submitting_a_job.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md b/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md
index 4840d247..71f219ea 100644
--- a/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md
+++ b/base/documentation/gh-pages/running_on_hpc/submitting_a_job.md
@@ -11,9 +11,11 @@ Remember to study the log report after your job finishes, so you can be more acc
 After having transferred our Balmorel model through WinSCP (see [previous page](access.md)), we need to submit a job. This means creating a job script that asks for the right amount of memory usage and time before completion. This is done through a job script, illustrated in the code snippet below. We refer to [this general guide](https://www.hpc.dtu.dk/?page_id=1416) by DTU Computing Center for the exact explanations of the different elements. Note that the paths in the `export` commands are specific to our setup at DTU's clusters. 
 
 The bottom commands assumes that the job script is submitted from inside your Balmorel folder, and that your Balmorel project contains a "scenario1" scenario - see [how to create new scenarios](../get_started/scenario_setup.md). The `threads=$LSB_DJOB_NUMPROC` command makes sure that Balmorel does not use more cores than defined  in your job script (four in this case, due to `#BSUB -n 4`)
+
 :::{warning}
 Please make sure to switch to the solver options file `cplex.op2`, by going into the `balgams.opt` file and setting `$Setglobal USEOPTIONFILE 2`. Otherwise CPLEX will overwrite the number of chosen threads and will ue more resources than requested.
 :::
+
 ```bash
 #!/bin/sh 
 ### General options 

From 47176f74fb2cc7c16e9945cb93863ad873597186 Mon Sep 17 00:00:00 2001
From: Tim Aidan Graulich <63345846+tgraulich@users.noreply.github.com>
Date: Thu, 19 Dec 2024 15:06:15 +0100
Subject: [PATCH 3/4] Adding new cplex options file for runs on the HPC

---
 base/model/cplex.op2 | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 base/model/cplex.op2

diff --git a/base/model/cplex.op2 b/base/model/cplex.op2
new file mode 100644
index 00000000..c5d2ff6d
--- /dev/null
+++ b/base/model/cplex.op2
@@ -0,0 +1,11 @@
+* Option file 2 for CPLEX solver for HPC runs. For possible options, see the GAMS Solver Manual.
+* To use with CPLEX,  set  '$Setglobal USEOPTIONFILE 2' in balgams.opt.
+* Do not change this file, it is predefined.
+* To use other options with CPLEX, make and/or use some other file, see USEOPTIONFILE in balgams.opt.
+* "LPmethod  4": Barrier method
+* If memory tight, set the Threads parameter to 1.
+* advind is set to 0 by default since for large problems a better performance has been experienced. If 0, the optimization will not use the previous solution to try to find the next run faster.
+
+LPmethod  4
+advind 0
+predual -1

From c89cf7864103aba09ab926ec9337c05841782eec Mon Sep 17 00:00:00 2001
From: Tim Aidan Graulich <63345846+tgraulich@users.noreply.github.com>
Date: Thu, 19 Dec 2024 15:07:17 +0100
Subject: [PATCH 4/4] Adding option for new cplex option file in balgams.opt

---
 base/model/balgams.opt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/base/model/balgams.opt b/base/model/balgams.opt
index 9158cab3..1553e485 100644
--- a/base/model/balgams.opt
+++ b/base/model/balgams.opt
@@ -152,6 +152,7 @@ option intVarUp = 0
 $Setglobal USEOPTIONFILE 4
 *!option 0   No option file is used. Note that not setting anything will generate an error.
 *!option 1   Use option file SolverName.opt.
+*!option 2   Predefined, don't change. Used with CPLEX it opens cplex.op2 and sets 'LPmethod 4' to run barrior method. Also does not set any Threads option to allow running on HPC.
 *!option 4   Predefined, don't change. Used with CPLEX it opens cplex.op4 and sets 'LPmethod 4' to run barrior method.
 *!option 6   Predefined, don't change. Used with CPLEX it opens cplex.op6 and sets 'LPmethod 6' to run multiple methods in parallel.