A domain specific language FreeFem++(3.61-1) for numerical simulation by finite element methods is available on OCTOPUS.
Prerequisites
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There are two commands of FreeFem++, FreeFem++-nw for OpenMP parallelism inside of one node, and FreeFem++-mpi for MPI parallelism that can run on multiple nodes. Please set PATH environmental variable by bash export command.
$ export PATH=/octfs/apl/FreeFem/3.61-1/bin:$PATH
$ FreeFem++-nw file.edp
Usage with job script
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Please run FreeFem++ by batch processing
The following script aims to run FreeFem++-mpi for OpenMP parallelism inside of one node, where edp file is given as file.edp. There are two FreeFem++ scripts, test-PARDISO.edp and test-MUMPseq.edp in /octfs/apl/FreeFem/example/EDP .
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#!/bin/bash #PBS -q OCTOPUS #PBS -l cpunum_job=24,elapstim_req=1:00:00 #PBS -v OMP_NUM_THREADS=24 #PBS -v MKL_NUM_THREADS=24 cd $PBS_O_WORKDIR export PATH=/octfs/apl/FreeFem/3.61-1/bin:$PATH FreeFem++-nw ./file.edp |
The following script aims to run FreeFem++-mpi for MPI parallelism, where edp file is given as file.edp. There are three FreeFem++ scripts, test-MUMPS.edp, test-hpddm.edp, and test-hypre.edp in /octfs/apl/FreeFem/example/EDP .
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#!/bin/bash #PBS -q OCTOPUS #PBS -l elapstim_req=1:00:00 #PBS -T intmpi #PBS -b 1 #PBS -v OMP_NUM_THREADS=1 #PBS -v MKL_NUM_THREADS=1 cd $PBS_O_WORKDIR export PATH=/octfs/apl/FreeFem/3.61-1/bin:$PATH mpirun ${NQSII_MPIOPTS} -np 24 FreeFem++-mpi ./file.edp |
Details of job scripts will be found here.
qsub command
