I have PBS command something like this
#PBS -N marcell_single_cell
#PBS -l nodes=1:ppn=1
#PBS -l walltime=20000:00:00
#PBS -e stderr.log
#PBS -o stdout.log
# Specific the shell types
#PBS -S /bin/bash
# Specific the queue type
#PBS -q dque
#uncomment this if you want to debug the process
#set -vx
cd $PBS_O_WORKDIR
ulimit -s unlimited
NPROCS=`wc -l < $PBS_NODEFILE`
#export PATH=$PBS_O_PATH
echo This job has allocated $NPROCS nodes
echo Cleaning old files...
rm -rf *.png *.plt *.log
echo Cleaning success
/opt/Lib/openmpi-2.1.3/bin/mpirun -np $NPROCS /scratch4/marcell/CellMLSimulator/bin/CellMLSimulator -ionmodel grandi2010 -solverType CVode -irepeat 4 -dt 0.01
gnuplot -p plotting.gnu
It got error something like this, thrown by the PBS error log.
/var/spool/torque/mom_priv/jobs/6265.node01.SC: line 28: gnuplot: command not found
I've already make sure that the path of GNUPlot is already been added to the PATH environment variable.
However, the strange part is, if I interchange the sequence of command, like gnuplot first and then mpirun, there isn't any error. I suspect that some commands after mpirun need some special configs, but I dunno how to do that
Already following this solution, but no avail.
sleep command not found in torque pbs but works in shell
EDITED:
it seems that the before and after mpirun still got error. and this is the which result:
which: no gnuplot in (/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/pgi/linux86-64/9.0-4/bin:/opt/openmpi/bin:/usr/kerberos/bin:/prog/tools/grace/grace/bin:/home/prog/ansys_inc/v121/fluent/bin:/bin:/usr/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64:/scratch7/feber/jdk1.8.0_101:/scratch7/feber/code/apache-maven/bin:/usr/local/bin:/scratch7/cml/bin)
It's strange, since when I try to find the gnuplot, there is one in the /usr/local/bin
ls -l /usr/local/bin/gnuplot
-rwxr-xr-x 1 root root 3262113 Sep 18 2017 /usr/local/bin/gnuplot
moreover, if I run those commands without PBS, it seems executed as I expected:
/scratch4/marcell/CellMLSimulator/bin/CellMLSimulator -ionmodel grandi2010 -solverType CVode -irepeat 4 -dt 0.01
gnuplot -p plotting.gnu
It's very likely that your system has different "login/head nodes" and "compute nodes". This is a commonly used practice in many supercomputing clusters. While you build and launch your application from the head node, it gets executed on one or more compute nodes.
The compute nodes can have different hardware and software compared to the head nodes. In your case, gnuplot is installed only on the head node, as you can see from the different outputs of which gnuplot. To solve this, you have three approaches:
Request the system administrators to install gnuplot on the compute nodes.
Build and install your own version of gnuplot in a file-system accessible from the compute nodes. It could be your home directory or somewhere else depending on your cluster. In general, the filesystem where your application is will be available. In your case, anywhere under /scratch4/marcell/ would probably work.
Run gnuplot on the head node after the MPI jobs finish as a post-processing step. PBS/Torque does not provide a direct way to do this. You'll need to write a separate bash (not PBS) script to do this.