Merge pull request #31 from brianhlin/sw2260_pbs_mem

Fix mem requests (SOFTWARE-2260)

config/blah.config.template

@@ -96,6 +96,9 @@ pbs_nologaccess=yes
 #locally from the logs if BLParser is not present
 pbs_fallback=no
 
+#Set to 'yes' to request pvmem when submitting jobs
+pbs_set_pvmem=no
+
 
 ##LSF common variables
 

src/scripts/pbs_submit.sh

@@ -117,7 +117,7 @@ fi
 #local batch system-specific file output must be added to the submit file
 bls_local_submit_attributes_file=${blah_libexec_directory}/pbs_local_submit_attributes.sh
 
-${pbs_binpath}/qstat --version | grep PBSPro
+${pbs_binpath}/qstat --version 2>&1 | grep PBSPro > /dev/null 2>&1
 is_pbs_pro=$?
 # Begin building the select statement: select=x where x is the number of 'chunks'
 # to request. Chunk requests should precede any resource requests (resource
@@ -126,15 +126,20 @@ is_pbs_pro=$?
 # Only one chunk is required for OSG needs at this time.
 pbs_select="#PBS -l select=1"
 
-if [ "x$bls_opt_req_mem" != "x" ]
-then
-  # Different schedulers require different memory checks
-  echo "#PBS -l pmem=${bls_opt_req_mem}mb" >> $bls_tmp_file
-  echo "#PBS -l pvmem=${bls_opt_req_mem}mb" >> $bls_tmp_file
-  pbs_select="$pbs_select:mem=${bls_opt_req_mem}mb"
-  if [ "$is_pbs_pro" -neq "0" ]; then
-      echo "#PBS -l mem=${bls_opt_req_mem}mb" >> $bls_tmp_file
-  fi
+if [ "x$bls_opt_req_mem" != "x" ]; then
+    # Max amount of virtual memory allocated to a single process
+    if [[ "x$pbs_set_pvmem" == "xyes" ]]; then
+        echo "#PBS -l pvmem=${bls_opt_req_mem}mb" >> $bls_tmp_file
+    fi
+    # Max amount of physical memory allocated to a single process
+    if [[ "$bls_opt_smpgranularity" == 1 ]]; then
+        echo "#PBS -l pmem=${bls_opt_req_mem}mb" >> $bls_tmp_file
+    fi
+    # Total amount of memory allocated to the job
+    pbs_select="$pbs_select:mem=${bls_opt_req_mem}mb"
+    if [ "$is_pbs_pro" != 0 ]; then
+        echo "#PBS -l mem=${bls_opt_req_mem}mb" >> $bls_tmp_file
+    fi
 fi
 
 bls_set_up_local_and_extra_args
@@ -144,7 +149,7 @@ bls_set_up_local_and_extra_args
 [ -z "$bls_opt_queue" ] || grep -q "^#PBS -q" $bls_tmp_file || echo "#PBS -q $bls_opt_queue" >> $bls_tmp_file
 
 # Extended support for MPI attributes
-if [ "$is_pbs_pro" -eq "0" ]; then
+if [ "$is_pbs_pro" == 0 ]; then
     pbs_select="$pbs_select:ncpus=1"
 else
     if [ "x$bls_opt_wholenodes" == "xyes" ]; then
@@ -204,7 +209,7 @@ else
   [ -z "$bls_fl_subst_and_accumulate_result" ] || echo "#PBS -W stageout=\\'$bls_fl_subst_and_accumulate_result\\'" >> $bls_tmp_file
 fi
 
-if [ "$is_pbs_pro" -eq "0" ]; then
+if [ "$is_pbs_pro" == 0 ]; then
     echo $pbs_select >> $bls_tmp_file
 fi