large case done

Gromacs/testcase_ion_channel_large/prepare.sh

 #!/bin/bash
-compile_gromacs_dir_name=$1
 
-if [ -z "$compile_gromacs_dir_name" ]
-then
-echo "compile_gromacs_dir_name missing"
-echo "example : ./prepare.sh compile_01-13-20-16-20-05"
-exit 1
+if [ -z "$1" ]
+  then
+    echo "Please provide the targeted machine from:"
+    ls ../machines/
+    echo ""
+    echo "Example: ./prepare.sh occigen-bdw"
+    exit 1
 fi
+machine_dir="../machines/$1"
 
-run_date=`date +"%m-%d-%y-%H-%M-%S"`
-run_dir=run_${run_date}_${compile_gromacs_dir_name}
-mkdir $run_dir
-cd $run_dir
-cp ../ion_channel.tpr .
-cp ../../machines/${GROMACS_MACHINE}/batch_large_ion_channel.slurm batch_large_ion_channel.slurm.tmp.tmp
-awk '$1=$1' FS="GROMACS_HOME" OFS="../../${compile_gromacs_dir_name}/gromacs/2019.4" batch_large_ion_channel.slurm.tmp.tmp > batch_large_ion_channel.slurm.tmp
-awk '$1=$1' FS="GROMACS_HOME" OFS="../../${compile_gromacs_dir_name}/gromacs/2019.4"  batch_large_ion_channel.slurm.tmp >  batch_large_ion_channel.slurm
+cp ${machine_dir}/batch_large_ion_channel.slurm batch_large_ion_channel.slurm.tmp.tmp
+awk '$1=$1' FS="GROMACS_HOME" OFS="../gromacs/2019.4" batch_large_ion_channel.slurm.tmp.tmp > batch_large_ion_channel.slurm.tmp
+awk '$1=$1' FS="GROMACS_HOME" OFS="..//gromacs/2019.4"  batch_large_ion_channel.slurm.tmp >  batch_large_ion_channel.slurm
 rm -f  batch_large_ion_channel.slurm.tmp.tmp batch_large_ion_channel.slurm.tmp

Gromacs/testcase_ion_channel_large/run.sh

 #!/bin/bash
-run_gromacs_dir_name=$1
-
-if [ -z "$run_gromacs_dir_name" ]
-then
-echo "run_gromacs_dir_name missing"
-echo "example : ./run.sh run_01-13-20-17-10-24_compile_01-13-20-16-20-05"
-exit 1
-fi
-
-cd $run_gromacs_dir_name
-${GROMACS_LAUNCH_SCRIPT_COMMAND} batch_large_ion_channel.slurm
+sbatch batch_large_ion_channel.slurm

Gromacs/testcase_ion_channel_large/validate.sh

 #!/bin/bash
-run_gromacs_dir_name=$1
-
-if [ -z "$run_gromacs_dir_name" ]
-then
-echo "run_gromacs_dir_name missing"
-echo "example : ./validate.sh run_01-13-20-17-10-24_compile_01-13-20-16-20-05"
-exit 1
-fi
-
-cd $run_gromacs_dir_name
 perf=`grep Performance results | awk '{ print $2 }'`
 end_sim=`grep "Statistics over 1000001 steps using 100001 frames" large_ion_channel.log`