add gromacs mpi

docs/udocker/udocker-04.md

@@ -56,7 +56,7 @@ Access the INCD advanced computing facility at Lisbon using ssh:
 
 ```bash
 ssh -l <username> cirrus8.a.incd.pt
-module load python/3.10.13
+module load python
 ```
 
 * The end user can download and execute udocker without system administrator intervention.
@@ -69,6 +69,7 @@ export PATH=$HOME/udocker-1.3.10/udocker:$PATH
 ```
 
 ---
+
 ## In the beginning - I
 
 Make a directory for the tutorial and set en variable of udocker to that dir:
@@ -166,7 +167,7 @@ udocker run -v $TUT_DIR/udocker-files/tensorflow:/home/user -w /home/user tf_gpu
 
 ---
 
-## Job output
+## Job output of tensoflow run
 
 And, if all goes well you should see in the keras-xxx.out something like this:
 
@@ -194,9 +195,9 @@ Epoch 5/5
 
 * I have a tarball that I built with docker from a Dockerfile in part 3 of this tutorial: `gromacs.tar`.
 * It was saved with:
-    * `docker save -o gromacs.tar gromacs`
+  * `docker save -o gromacs.tar gromacs`
 * Now we will load the tarball with udocker:
-    * `udocker load -i gromacs.tar gromacs`
+  * `udocker load -i gromacs.tar gromacs`
 
 ---
 
@@ -248,7 +249,7 @@ sbatch run-gromacs.sh
 
 ---
 
-## Job output
+## Job output of Gromacs run
 
 The Gromacs output files can be found in `$HOME/udocker-tutorial/gromacs/output`, and the slurm job output in `$HOME/udocker-tutorial/udocker-files/gromacs-*.out/err`
 

udocker-files/prep-gromacs-mpi.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+#SBATCH --job-name=prep_gromacs
+#SBATCH --ntasks=1
+#SBATCH --partition=hpc
+#SBATCH --output=gromacs-prep-%j.out
+#SBATCH --error=gromacs-prep-%j.err
+
+export TUT_DIR=$HOME/udocker-tutorial
+export PATH=$HOME/udocker-1.3.10/udocker:$PATH
+cd $TUT_DIR
+export UDOCKER_DIR=$TUT_DIR/.udocker
+module load python
+
+echo "###############################"
+hostname
+echo ">> udocker command"
+which udocker
+echo
+echo ">> List images"
+udocker images
+echo
+echo ">> Create container"
+udocker create --name=grom_mpi gromacs-mpi
+echo
+echo ">> Set execmode to F3"
+udocker setup --execmode=F3 grom_mpi
+echo
+echo ">> List containers"
+udocker ps -m -p

udocker-files/prep-gromacs.sh

@@ -9,7 +9,7 @@ export TUT_DIR=$HOME/udocker-tutorial
 export PATH=$HOME/udocker-1.3.10/udocker:$PATH
 cd $TUT_DIR
 export UDOCKER_DIR=$TUT_DIR/.udocker
-module load python/3.10.13
+module load python
 
 echo "###############################"
 hostname

udocker-files/prep-keras.sh

@@ -9,7 +9,7 @@ export TUT_DIR=$HOME/udocker-tutorial
 export PATH=$HOME/udocker-1.3.10/udocker:$PATH
 cd $TUT_DIR
 export UDOCKER_DIR=$TUT_DIR/.udocker
-module load python/3.10.13
+module load python
 
 echo "###############################"
 hostname

udocker-files/run-gromacs-mpi.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH --job-name=run_gromacs_mpi
+#SBATCH --ntasks=16
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-core=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --partition=hpc
+#SBATCH --output=gromacs-mpi-%j.out
+#SBATCH --error=gromacs-mpi-%j.err
+
+export TUT_DIR=$HOME/udocker-tutorial
+export PATH=$HOME/udocker-1.3.10/udocker:$PATH
+export UDOCKER_DIR=$TUT_DIR/.udocker
+export OUT_NAME=output/ud-tutorial
+export TRR=${OUT_NAME}.trr
+export XTC=${OUT_NAME}.xtc
+export EDR=${OUT_NAME}.edr
+export LOG=${OUT_NAME}.log
+module load python/3.10.13
+module load gcc11/openmpi/4.1.4
+cd $TUT_DIR
+module list
+
+echo "###############################"
+srun --mpi=pmi2 udocker run -v=$TUT_DIR/gromacs:/home/user -w=/home/user grom_mpi \
+    gmx mdrun -s /home/user/input/md.tpr -e $EDR -x $XTC -o $TRR -g $LOG \
+    -maxh 0.50 -resethway -noconfout -nsteps 10000

udocker-files/run-gromacs.sh

@@ -13,7 +13,7 @@ export TRR=${OUT_NAME}.trr
 export XTC=${OUT_NAME}.xtc
 export EDR=${OUT_NAME}.edr
 export LOG=${OUT_NAME}.log
-module load python/3.10.13
+module load python
 cd $TUT_DIR
 
 echo "###############################"

udocker-files/run-keras.sh

@@ -10,7 +10,7 @@
 export TUT_DIR=$HOME/udocker-tutorial
 export PATH=$HOME/udocker-1.3.10/udocker:$PATH
 export UDOCKER_DIR=$TUT_DIR/.udocker
-module load python/3.10.13
+module load python
 cd $TUT_DIR
 
 echo "###############################"