The followings are recommended installation scheme, an example of the batch script file (run.sh) for hybrid MPI/OpenMP computation with 64 MPI processes and 4 OpenMP threads (256 CPU cores in total), and a command to submit a job. Please see also the user guide of the computer system.

Installation

$ cd /home/user/genesis
$ ./configure --host=k
$ make
$ make install

Note that in K computer and other FX10/FX100 machines, prst_setup (Parallel I/O tool) is not installed, because Fujitsu compilers are not suitable for compiling the program.

Batch script

#!/bin/bash -x
#PJM --rsc-list "elapse=24:00:00"
#PJM --rsc-list "node=32"
#PJM --mpi "proc=64"
#PJM --stg-transfiles all
#PJM --stgin  "./spdyn ./"
#PJM --stgin  "./input.pdb ./"
#PJM --stgin  "./input.psf ./"
#PJM --stgin  "./par_all36_prot_lipid.prm ./"
#PJM --stgin  "./top_all36_prot_lipid.rtf ./"
#PJM --stgin  "./INP2 ./"
#PJM --stgin  "./md1.rst ./ confirm=no"
#PJM --stgout "./md2.dcd /data/hp??????/MD/results/dcd/" # "hp??????" is your project id"
#PJM --stgout "./md2.rst ./"
#PJM -s

. /work/system/Env_base
export OMP_NUM_THREADS=4
mpiexec ./spdyn INP2

Usage

# Execute run1.sh to run3.sh sequentially
$ pjsub --step run1.sh
$ pjsub --step --sparam "jid=XXXXXXX" run2.sh
$ pjsub --step --sparam "jid=XXXXXXX" run3.sh

# Check running jobs
$ pjsub -E

# Delete a job
$ pjdel JOB_ID

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