我让PBS指挥这样的事情
#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
它得到了类似这样的错误,由PBS错误日志抛出。
/var/spool/torque/mom_priv/jobs/6265.node01.SC: line 28: gnuplot: command not found
我已经确保GNUPlot的路径已经添加到path环境变量中。
然而,奇怪的是,如果我交换命令序列,比如先交换gnuplot,然后交换mpirun,就不会有任何错误。我怀疑mpirun之后的一些命令需要一些特殊的配置,但我不知道如何做到这一点
已遵循此解决方案,但无效。
sleep command not found in torque pbs but works in shell
编辑:
似乎前后mpirun仍有错误。这就是结果:
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)
这很奇怪,因为当我试图找到gnuplot时,/usr/local/bin中有一个
ls -l /usr/local/bin/gnuplot
-rwxr-xr-x 1 root root 3262113 Sep 18 2017 /usr/local/bin/gnuplot
此外,如果我在没有PBS的情况下运行这些命令,它似乎会像我预期的那样执行:
/scratch4/marcell/CellMLSimulator/bin/CellMLSimulator -ionmodel grandi2010 -solverType CVode -irepeat 4 -dt 0.01
gnuplot -p plotting.gnu
