Merge pull request #5 from dmricciuto/cades-slurm

Changes for Slurm system on cades
dmricciuto · Mar 24, 2020 · 8e507a7 · 8e507a7
2 parents 1742dca + 8aa5273
commit 8e507a7
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Showing 4 changed files with 13 additions and 15 deletions.
diff --git a/scripts/ccsm_utils/Machines/config_machines.xml b/scripts/ccsm_utils/Machines/config_machines.xml
@@ -390,7 +390,7 @@
    <!-- customize these fields as appropriate for your system (max tasks) and
                                       desired layout (change '${group}/${USER}' to your
         prefered location). -->
-      <DESC> OR-CONDO, CADES-CCSI, os is Linux, 32 pes/nodes, batch system is PBS</DESC>
+      <DESC> OR-CONDO, CADES-CCSI, os is Linux, 32 pes/nodes, batch system is SLURM</DESC>
       <OS>LINUX</OS>
       <COMPILERS>gnu,intel</COMPILERS>
       <MPILIBS>openmpi,mpi-serial</MPILIBS>
@@ -402,7 +402,7 @@
       <DOUT_L_MSROOT>csm/$CASE</DOUT_L_MSROOT>
       <CCSM_BASELINE>/lustre/or-hydra/cades-ccsi/proj-shared/project_acme/baselines</CCSM_BASELINE>
       <BATCHQUERY>qstat -f </BATCHQUERY>
-      <BATCHSUBMIT>qsub </BATCHSUBMIT>
+      <BATCHSUBMIT>sbatch </BATCHSUBMIT>
       <SUPPORTED_BY>Fengming Yuan</SUPPORTED_BY>
       <GMAKE_J>4</GMAKE_J>
       <MAX_TASKS_PER_NODE>32</MAX_TASKS_PER_NODE>

diff --git a/scripts/ccsm_utils/Machines/env_mach_specific.cades b/scripts/ccsm_utils/Machines/env_mach_specific.cades
@@ -65,12 +65,12 @@ setenv BLAS_LIBDIR /software/tools/spack/opt/spack/linux-x86_64/gcc-5.3.0/netlib
 
 # CMake is required for building PIO
 #module load linux-x86_64/[email protected]%[email protected]+ncurses-sr4jjqc
-module load cmake/3.6.1
+module load cmake/3.12.0
 
 # for PFLOTRAN
 setenv PETSC_DIR $USER_SOFTWARES/petsc4pf/openmpi-1.10.2-gcc-5.3
 setenv PETSC_ARCH arch-orcondo-openmpi-gcc53-debug
-
+#setenv PERL5LIB /software/user_tools/current/cades-ccsi/perl5/lib/perl5/
 setenv PETSC_LIB ${PETSC_DIR}/lib
 
 #-------------------------------------------------------------------------------

diff --git a/scripts/ccsm_utils/Machines/mkbatch.cades b/scripts/ccsm_utils/Machines/mkbatch.cades
@@ -33,15 +33,13 @@ endif
 
 cat >! $file << EOF1
 #!/bin/csh -f
-#PBS -N ${jobname}
-#PBS -q batch
-#PBS -l nodes=${mppnodes}:ppn=$ppn
-#PBS -l walltime=${walltime}
-#PBS -j oe
-#PBS -S /bin/csh -V
-#PBS -W group_list=cades-ccsi
-#PBS -A ccsi
-#PBS -l qos=std
+#SBATCH -J ${jobname}
+#SBATCH -p burst
+#SBATCH -N ${mppnodes}
+#SBATCH --ntasks-per-node=$ppn
+#SBATCH -t ${walltime}
+#SBATCH --mem=128G
+#SBATCH -A ccsi
 EOF1
 
 #################################################################################

diff --git a/scripts/site_fullrun.py b/scripts/site_fullrun.py
@@ -265,7 +265,7 @@
         output = open('./site_fullrun.pbs','w')
         input = open(ad_case+'/'+ad_case+'.run')
         for s in input:
-            if ("#!" in s or '#PBS' in s):
+            if ("#!" in s or '#SBATCH' in s):
                 output.write(s)
         input.close()
         output.write("\n")
@@ -283,5 +283,5 @@
             os.system('chmod u+x site_fullrun.pbs')
 	    os.system('./site_fullrun.pbs')
         else:
-	    os.system('qsub site_fullrun.pbs')
+	    os.system('sbatch site_fullrun.pbs')