Namd

De acordo com a página do Namd, “NAMD, recipient of a 2002 Gordon Bell Award, a 2012 Sidney Fernbach Award, and a 2020 Gordon Bell Prize, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code.”.

Versões Disponíveis

namd/2.12 (multicore)
namd/2.12-tcp (multinode)
namd/2.13-smp (multicore)
namd/2.13-tcp (multinode)

Submissão de Jobs em Paralelo

Crie um arquivo chamado, por exemplo, submit_paral_jobs.sh.

#!/bin/bash
#SBATCH -t 24:00:00 -n 16

export INPUT="namd-mpi.namd"
export OUTPUT="*"

module load namd/2.12-tcp
job-nanny namd_mpi.sh namd-mpi.namd

Para submeter o processo, basta usar o comando:

sbatch submit_paral_jobs.sh

Submissão de Jobs Seriais

Crie um arquivo chamado, por exemplo, submit_serial_jobs.sh.

#!/bin/bash
#SBATCH -t 24:00:00 -c 8

export INPUT="namd-smp.namd"
export OUTPUT="*"

module load namd/2.12
job-nanny namd2 +p 4 namd-smp.namd

Para submeter o processo, basta usar o comando:

sbatch submit_serial_jobs.sh

Referências

Para informações adicionais sobre o software, consulte a página do Namd.