Usage on K computer at RIKEN R-CCS
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