diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 19ad3a2..07bae14 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -1,4 +1,4 @@ -FROM kyanagis/exprorer_msmd:2023.09.19 +FROM kyanagis/exprorer_msmd:2024.02.13 # ====== settings for git / ssh ======= RUN echo "mkdir -p /root/.ssh" >> /etc/bash.bashrc diff --git a/script/template/mdrun.sh b/script/template/mdrun.sh index 49ad177..d6b4bfb 100644 --- a/script/template/mdrun.sh +++ b/script/template/mdrun.sh @@ -1,5 +1,6 @@ #!/bin/sh +hostname ncpus=$1 ## initialize @@ -9,9 +10,6 @@ if [ A$GMX = "A" ];then GMX=gmx fi -## for OpenMP parallelization -export OMP_NUM_THREADS=$ncpus -## for thread-MPI parallelization finished_info=finished_step_list touch $finished_info @@ -26,19 +24,20 @@ do fi rm -f ${now}.out.mdp ${now}.tpr ${now}.log ${now}.gro ${now}.trr ${now}.edr ${now}.cpt - echo $GMX grompp -f ${now}.mdp -o ${now}.tpr \ + echo $GMX grompp -maxwarn 1 -f ${now}.mdp -o ${now}.tpr \ -c ${prev}.gro -p ${top} \ -r ${prev}.gro -n index.ndx - echo $GMX mdrun -reprod -v -s ${now}.tpr \ - -cpo ${now}.cpt -x ${now}.xtc -c ${now}.gro -e ${now}.edr -g ${now}.log \ - && echo $now >> $finished_info + echo $GMX mdrun -nt $ncpus -v -s ${now}.tpr \ + -cpo ${now}.cpt -x ${now}.xtc -c ${now}.gro -e ${now}.edr -g ${now}.log - $GMX grompp -f ${now}.mdp -o ${now}.tpr \ + $GMX grompp -maxwarn 1 -f ${now}.mdp -o ${now}.tpr \ -c ${prev}.gro -p ${top} \ -r ${prev}.gro -n index.ndx - $GMX mdrun -reprod -v -s ${now}.tpr \ + $GMX mdrun -nt $ncpus -v -s ${now}.tpr \ -cpo ${now}.cpt -x ${now}.xtc -c ${now}.gro -e ${now}.edr -g ${now}.log \ - && echo $now >> $finished_info + || exit + + echo $now >> $finished_info done