made run.sh use physical cores

polyamorphism_optimization/run.sh

@@ -4,17 +4,18 @@
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=8
 #SBATCH --gres=gpu:1
-#SBATCH --exclude=linux-05,linux-08,linux-02,linux-03,linux-04,linux-07
+##SBATCH --exclude=linux-05,linux-06,linux-07,linux-08
 
-#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2025.2* ] ; then
-#    echo "Version loaded is not 2025.2! Exiting!"
+#if [ "$(gmx --version | grep "GROMACS version")" != GROMACS*2023.3* ] ; then
+#    echo "Version loaded is not 2023.3! Exiting!"
 #    exit 1
 #fi
 
+PHYS_CORES=$(lscpu | awk -F: '/Core\(s\) per socket/ {print $2+0}')
 if [ -n "$SLURM_CPUS_PER_TASK" ]; then
     NT="-nt $SLURM_CPUS_PER_TASK"
-elif [ $(nproc) -lt 9 ] ; then
-    NT="-nt $(nproc)"
+elif [ "$PHYS_CORES" -lt 9 ] ; then
+    NT="-nt $PHYS_CORES"
 else
     NT="-nt 8"
 fi
@@ -29,7 +30,7 @@ mkdir -p "$WORKDIR/out"
 export GMX_MAXCONSTRWARN=-1;
 gmx -nobackup grompp \
     -f $WORKDIR/mdp_parameters.mdp \
-    -o $WORKDIR/tpr_run.tpr \
+    -o $WORKDIR/out/tpr_run.tpr \
     -c $WORKDIR/gro_start.gro \
     -r $WORKDIR/gro_start.gro \
     -p $WORKDIR/topology.top \
@@ -42,7 +43,7 @@ if [ $? != 0 ] ; then
 fi
 
 gmx mdrun \
-    -s $WORKDIR/tpr_run.tpr \
+    -s $WORKDIR/out/tpr_run.tpr \
     -o $WORKDIR/out/trr_traj.trr \
     -c $WORKDIR/out/out.gro \
     -x $WORKDIR/out/xtc_traj.xtc \