Merge pull request #34 from mathiasbockwoldt/jobscripts

Jobscripts and partitions

applications/chemistry/ADF/advanced.rst

@@ -36,7 +36,7 @@ This is a brief introduction to how to create fragments necessary for among othe
 **Running with fragments:**
 
 * Download and modify script for fragment create run, e.g. this template: Create.TZP.sh  (modify ACCOUNT, add desired atoms and change to desired basis and desired functional)
-* Run the create job in the same folder as the one where you want to run your main job(s) (qsub Create.TZP.sh).
+* Run the create job in the same folder as the one where you want to run your main job(s) (sbatch Create.TZP.sh).
 * Put the line cp $init/t21.* .  in your ADF run script (in your $HOME/bin directory)
 * In job.inp, specify correct file name in FRAGMENT section, e.g. “H   t21.H_tzp”. * Submit job.inp as usual.
 

applications/chemistry/files/job_adf.sh

@@ -5,15 +5,15 @@
 #-------------------------------------
 # This script asks for a given set of cores nodes and cores. Stallo has got 16 or 20 cores/node,
 # asking for something that adds up to both is our general recommodation (80, 160 etc), you would
-# then need to use --ntasks instead of -N and --ntasks-per-node. (replace both).
+# then need to use --ntasks instead of --nodes and --ntasks-per-node. (replace both).
 # Runtime for this job is 59 minutes; syntax is hh:mm:ss.
 # Memory is set to the maximum advised for a full node, 1500MB/core - giving a total
 # of 30000MB/node and leaving some for the system to use. Memory
 # can be specified pr core, virtual or total pr job (be carefull).
 #-------------------------------------
 # SLURM-section
 #SBATCH --job-name=adf_runex
-#SBATCH -N 2
+#SBATCH --nodes=2
 #SBATCH --ntasks-per-node=20
 #SBATCH --time=00:59:00
 #SBATCH --mem-per-cpu=1500MB # Be ware of memory needs, might be a lot higher if you are running Zora basis, for example.
@@ -43,11 +43,9 @@ mkdir -p $SCM_TMPDIR
 # Preparing and moving inputfiles to tmp:
 
 submitdir=$SLURM_SUBMIT_DIR
-tempdir=$SCM_TMPDIR
 
-cd $submitdir
-cp ${input}.${ext} $tempdir
-cd $tempdir
+cp ${input}.${ext} $SCM_TMPDIR
+cd $SCM_TMPDIR
 
 # In case necessary, set SCM_IOBUFFERSIZE
 #export SCM_IOBUFFERSIZE=1024 # Or higher if necessary.
@@ -57,7 +55,7 @@ cd $tempdir
 
 # Running the program:
 
-time adf  -n $cores < ${input}.${ext} > adf_$input.out
+time adf -n $cores < ${input}.${ext} > adf_$input.out
 
 # Cleaning up and moving files back to home/submitdir:
 # Make sure to move all essential files specific for the given job/software.
@@ -75,8 +73,7 @@ echo $(ls -ltr)
 
 # ALWAYS clean up after yourself. Please do uncomment the following line
 #cd $submitdir
-#rm  $tempdir/*
-#rmdir $tempdir
+#rm -r $tempdir/*
 
 echo "Job finished at"
 date

applications/chemistry/files/job_band.sh

@@ -5,15 +5,15 @@
 #-------------------------------------
 # This script asks for a given set of cores nodes and cores. Stallo has got 16 or 20 cores/node,
 # asking for something that adds up to both is our general recommodation (80, 160 etc), you would
-# then need to use --ntasks instead of -N and --ntasks-per-node. (replace both).
+# then need to use --ntasks instead of --nodes and --ntasks-per-node. (replace both).
 # Runtime for this job is 59 minutes; syntax is hh:mm:ss.
 # Memory is set to the maximum advised for a full node,
 # of 30000MB/node and leaving some for the system to use. Memory
 # can be specified pr core, virtual or total pr job (be carefull).
 #-------------------------------------
 # SLURM-section
 #SBATCH --job-name=band_runex
-#SBATCH -N 2
+#SBATCH --nodes=2
 #SBATCH --ntasks-per-node=20
 #SBATCH --time=00:59:00
 #SBATCH --mem-per-cpu=1500MB # Be ware of memory needs!

applications/chemistry/files/job_g09.sh

@@ -12,7 +12,7 @@
 #-------------------------------------
 # SLURM-section
 #SBATCH --job-name=g09_runex
-#SBATCH -N 2
+#SBATCH --nodes=2
 #SBATCH --ntasks-per-node=20
 #SBATCH --time=00:59:00
 #SBATCH --mem-per-cpu=1500MB

applications/chemistry/files/job_molcas.sh

@@ -5,15 +5,15 @@
 #-------------------------------------
 # This script asks for a given set of cores nodes and cores. Stallo has got 16 or 20 cores/node,
 # asking for something that adds up to both is our general recommodation (80, 160 etc), you would
-# then need to use --ntasks instead of -N and --ntasks-per-node. (replace both).
+# then need to use --ntasks instead of --nodes and --ntasks-per-node. (replace both).
 # Runtime for this job is 59 minutes; syntax is hh:mm:ss.
 # Memory is set to the maximum advised for a full node, 1500MB/core - giving a total
 # of 30000MB/node and leaving some for the system to use. Memory
 # can be specified pr core, virtual or total pr job (be carefull).
 #-------------------------------------
 # SLURM-section
 #SBATCH --job-name=molcas_runex
-#SBATCH -N 1
+#SBATCH --nodes=1
 #SBATCH --ntasks-per-node=20
 ##SBATCH --ntasks=20
 #SBATCH --time=00:59:00

applications/chemistry/files/job_vasp.sh

@@ -12,7 +12,7 @@
 #-------------------------------------
 # SLURM-section
 #SBATCH --job-name=vasp_runex
-#SBATCH -N 2
+#SBATCH --nodes=2
 #SBATCH --ntasks-per-node=20
 #SBATCH --time=02:00:00
 ##SBATCH --mem-per-cpu=1500MB
@@ -25,29 +25,27 @@
 # Section for defining job variables and settings:
 
 proj=CeO2job # Name of job folder
-input=${proj}/{INCAR,KPOINTS,POTCAR,POSCAR} # Input files from job folder
+input=$(ls ${proj}/{INCAR,KPOINTS,POTCAR,POSCAR}) # Input files from job folder
 
 # We load all the default program system settings with module load:
 
 module purge
-module load VASP/5.4.1.plain
+module load VASP/5.4.1.plain-intel-2016a
 # You may check other available versions with "module avail VASP"
 
 # Now we create working directory and temporary scratch for the job(s):
 # Necessary variables are defined in the notur and the software modules.
 
 export VASP_WORKDIR=/global/work/$USER/$SLURM_JOB_ID
 
-mkdir -p /global/work/$USER/$SLURM_JOB_ID
+mkdir -p $VASP_WORKDIR
 
 # Preparing and moving inputfiles to tmp:
 
 submitdir=$SLURM_SUBMIT_DIR
-tempdir=$VASP_WORKDIR
 
-cd $submitdir
-cp $input $tempdir
-cd $tempdir
+cp $input $VASP_WORKDIR
+cd $VASP_WORKDIR
 
 ######################################
 # Section for running the program and cleaning up:
@@ -59,11 +57,11 @@ time mpirun vasp_std
 # Cleaning up and moving files back to home/submitdir:
 # Make sure to move all essential files specific for the given job/software.
 
-cp OUTCAR $submitdir/${input}.OUTCAR
+cp OUTCAR $submitdir/${proj}.OUTCAR
 
 # To zip some of the output might be a good idea!
-#gzip $resultszip
-#mv $resultzip.gz $submitdir/
+#gzip results.gz OUTCAR
+#mv $results.gz $submitdir/
 
 # Investigate potentially other files to keep:
 echo $(pwd)
@@ -72,8 +70,7 @@ echo $(ls -ltr)
 # ALWAYS clean up after yourself. Please do uncomment the following line
 # If we have to, we get really grumpy!
 #cd $submitdir
-#rm  $tempdir/*
-#rmdir $tempdir
+#rm -r $VASP_WORKDIR/*
 
 echo "Job finished at"
 date

jobs/partitions.rst

@@ -24,9 +24,12 @@ multinode:
     Request this partition if you ask for more resources than you will find on
     one node and request walltime longer than 48 hrs.
 
+highmem:
+    Use this partition to use the high memory nodes with 128 GB. You will have to apply for access to this partition by sending us an email explaining why you need these high memory nodes.
+
 To figure out the walltime limits for the various partitions, type::
 
-  $ sinfo --format="%P %l"
+  $ sinfo --format="%P %l"  # small L
 
 As a service to users that needs to submit short jobs for testing and debugging, we have a service called devel.
 These jobs have higher priority, with a maximum of 4 hrs of walltime and no option for prolonging runtime.