Merge branch 'dynamo' into 'master'

Built dynamo/1.1.538

See merge request Pmodules/buildblocks!420

EM/dynamo/1.1.538/config

@@ -0,0 +1,3 @@
+# Google drive file hash, from https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Downloads
+DYNAMO_ID=11_HqORqfwX21odS4zTuQKLbzHDSYgeog
+

EM/dynamo/README.md

@@ -10,9 +10,21 @@ Installation should be done on merlin with an -adm account
 2. Add google drive download link to `$V/config`.
 3. Run `build <version>`
 4. module load dynamo/$V
-5. Compile stand-alone: `dynamo_setup_linux.sh`
-6. Compile MPI: `source dynamo_setup_cluster.sh mpic++ dynamo_activate_linux_shipped_MCR.sh`
-7. Compile Cuda:
+5. `cd $DYNAMO_HOME/bin`. Further steps are taken from `README_dynamo_installation.txt`
+6. [Compile stand-alone](https://www.dynamo-em.org/w/index.php?title=Installation)
+
+    dynamo_setup_linux.sh
+
+7. [Compile MPI](https://www.dynamo-em.org/w/index.php?title=MPI_Cluster):
+  - With the shipped MCRLinux directory:
+
+    source dynamo_setup_cluster.sh mpic++ dynamo_activate_linux_shipped_MCR.sh
+
+  - With MCR from pmodules:
+
+    source dynamo_setup_cluster.sh mpic++ dynamo_activate_MCR.sh
+
+8. Compile Cuda:
 
     cd $DYNAMO_ROOT/cuda
     make clean

EM/dynamo/build

@@ -51,6 +51,8 @@ pbuild::prep() {
     download_dynamo "$DYNAMO_ID" "$TAR_FILE"
     mkdir -p "$PREFIX"
     unpack "$TAR_FILE" "$PREFIX/bin"
+
+    cp -n "$BUILDBLOCK_DIR/dynamo_activate_MCR.sh" "$PREFIX/bin/"
 }
 
 pbuild::configure() {

EM/dynamo/dynamo_activate_MCR.sh

@@ -0,0 +1,18 @@
+# Activates MCR from pmodules
+
+DYNAMO_FOLDER=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+MCR_ROOT=${MATLAB_DIR:?No matlab module loaded}
+
+
+# Checks  availability of the MCR folder
+if ! [ -d $MCR_ROOT ]; then
+  echo "ATTENTION:  the Matlab module is not loaded."
+  return
+fi
+
+echo "MCR for linux has been found in location:" $MCR_ROOT
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MCR_ROOT/runtime/glnxa64:$MCR_ROOT/bin/glnxa64:$MCR_ROOT/sys/os/glnxa64:$MCR_ROOT/sys/opengl/lib/glnxa64
+
+echo Activating Dynamo as standalone
+
+source $DYNAMO_FOLDER/dynamo_activate_linux.sh

EM/dynamo/files/variants

@@ -1 +1,2 @@
 dynamo/1.1.514	unstable	b:psi-python36/5.0.1 gcc/9.3.0 openmpi/4.0.4_slurm cuda/11.1.0 matlab/2019a
+dynamo/1.1.538	unstable	b:psi-python36/5.0.1 gcc/11.2.0 cuda/11.5.1 openmpi/4.1.4_slurm matlab/2023a