Dear all,I am a beginner using PLUMED and recently I've been trying to realize some codes for running metadynamics using PLUMED. I submitted the job using the command sbatch run_cpu.sh, which has the content as follows:
#!/bin/sh
#SBATCH --job-name NaCl-m
#SBATCH --qos normal
#SBATCH --nodes=8
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task 24
#SBATCH --time 24:00:00
#SBATCH --partition shas
module load gromacs/2018.3
export OMP_NUM_THREADS=24
mpirun -np 8 gmx_mpi mdrun -deffnm NaCl -g NaCl_log.log -ntomp 24 -plumed plumed.dat
What I don't quite understand is the reason for using "export OMP_NUM_THREADS=24" instead of using "export PLUMED_NUM_THREADS=24". For the last command-line, I don't know why there was no command for the file input, for example, some .tpr file produced by grompp. Also, I'm not sure about what the command of "-plumed plumed.dat" was doing (for example, what was it used for, what were the input files and output files). (Did it input the file "plumed.dat"? After some examination, I found it seemed that it not only input this file.) And my last question is, as I enter "plumed --help", it turned out that the command "plumed" was not found. However, I have actually run one metadynamics simulation successfully using PLUMED. Is this error normal? I'm sorry that these questions seem quite dumb. I've tried to find answers, but it was in vain. Thank you all in advance! Wei-Tse
1) OMP_NUM_THREADS is a signal to a library, which takes care of parallelization. In this case it affects how the Gromacs is run. You do not have to specify it again for Plumed.
2) The -deffnm NaCl in the mpirun command defines the default file name (without extension) for input and output files. If you do not use the -deffnm option, the default settings will be used (e.g. the Gromacs will search for the topol.tpr file)
3) -plumed plumed.dat specifies the file with the commands to be executed by Plumed
4) The Gromacs was compiled (and patched) in such a way that Gromacs knows the location of the Plumed package. Your terminal probably does not know that. You have to search for the location of the Plumed binary and run the command plumed -help with the full path or you may add the path to plumed binary to your PATH variable in the terminal
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