diff --git a/EM/dynamo/1.1.538/config b/EM/dynamo/1.1.538/config new file mode 100644 index 0000000..ba8d2f5 --- /dev/null +++ b/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 + diff --git a/EM/dynamo/README.md b/EM/dynamo/README.md index cef3056..a8fb8c3 100644 --- a/EM/dynamo/README.md +++ b/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 `$V/config`. 3. Run `build ` 4. module load dynamo/$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 $DYNAMO_ROOT/cuda make clean diff --git a/EM/dynamo/build b/EM/dynamo/build index f4e547a..cf1303c 100755 --- a/EM/dynamo/build +++ b/EM/dynamo/build @@ -51,6 +51,8 @@ pbuild::prep() { download_dynamo "$DYNAMO_ID" "$TAR_FILE" mkdir -p "$PREFIX" unpack "$TAR_FILE" "$PREFIX/bin" + + cp -n "$BUILDBLOCK_DIR/dynamo_activate_MCR.sh" "$PREFIX/bin/" } pbuild::configure() { diff --git a/EM/dynamo/dynamo_activate_MCR.sh b/EM/dynamo/dynamo_activate_MCR.sh new file mode 100644 index 0000000..2a45d91 --- /dev/null +++ b/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 diff --git a/EM/dynamo/files/variants b/EM/dynamo/files/variants index d7b2939..21537f4 100644 --- a/EM/dynamo/files/variants +++ b/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