update gromacs version with cuda version

.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

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