singularity now works

activate.sh

@@ -5,7 +5,6 @@ ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
 [[ $0 != $BASH_SOURCE ]] && echo "The activation script must be sourced, otherwise the virtual environment will not work." || ( echo "Vars script must be sourced." && exit 1) ;
 
 source ${ABSOLUTE_PATH}/config.sh
-source ${ABSOLUTE_PATH}/modules.sh
 
 export PYTHONPATH=`echo ${ENV_DIR}/lib/python*/site-packages`:${PYTHONPATH}
 

config.sh

@@ -9,3 +9,5 @@ ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
 export ENV_NAME=`basename $ABSOLUTE_PATH`             # Default Name of the venv is the directory that contains this file
 export ENV_DIR=${ABSOLUTE_PATH}/venv         # Default location of this VENV is "./venv"
 
+export SINGULARITY_IMAGE=/p/project/jb_benchmark/nvidia_singularity_images/nvidia_tensorflow_21.02-tf1-py3.sif
+export SINGULARITY_IMAGE=/p/project/jb_benchmark/nvidia_singularity_images/nvidia_pytorch_bert_20.06-py3-m5.1.sif

create_kernel.sh

 #!/bin/bash
 
-RELATIVE_PATH=`dirname ${BASH_SOURCE}`
-ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
+export RELATIVE_PATH=`dirname ${BASH_SOURCE}`
+export ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
 source ${ABSOLUTE_PATH}/config.sh
 
-KERNELFILE=${ENV_DIR}/kernel.sh
+export KERNELFILE=${ENV_DIR}/kernel.sh
+export KERNELWRAPPER=${ENV_DIR}/kernel_wrapper.sh
 
 echo the name is $ENV_NAME
 
@@ -18,10 +19,22 @@ exec python -m ipykernel $@' > ${KERNELFILE}
 
 chmod a+x ${KERNELFILE}
 
+# Setup wrapper for kernel
+
+echo "singularity run $SINGULARITY_IMAGE ${KERNELFILE}"
+echo "#!/bin/bash
+module purge
+singularity run --overlay ${ABSOLUTE_PATH}/overlay.img $SINGULARITY_IMAGE  bash -c \"
+${KERNELFILE} \\\"\$@\\\"
+\"
+" > ${KERNELWRAPPER}
+
+chmod a+x ${KERNELWRAPPER}
+
 mkdir -p ~/.local/share/jupyter/kernels/${ENV_NAME}
 echo '{
  "argv": [
-  "'"${KERNELFILE}"'", 
+  "'"${KERNELWRAPPER}"'", 
   "-f",
   "{connection_file}"
  ],

modules.sh

-ml GCC/9.3.0  ParaStationMPI/5.4.7-1  Python/3.8.5

requirements.txt

-opencv-python
-ipykernel
+ipykernel==5.1.3

setup.sh

 #!/bin/bash
-RELATIVE_PATH=`dirname ${BASH_SOURCE}`
-ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
+export RELATIVE_PATH=`dirname ${BASH_SOURCE}`
+export ABSOLUTE_PATH=`realpath ${RELATIVE_PATH}`
 
 source ${ABSOLUTE_PATH}/config.sh
-source ${ABSOLUTE_PATH}/modules.sh
+echo path ${ABSOLUTE_PATH}
 
-python -m venv --prompt $ENV_NAME --system-site-packages ${ENV_DIR}
+rm -f overlay.img
+rm -rf overlay
+rm -rf venv
 
-source ${ABSOLUTE_PATH}/activate.sh
+mkdir -p overlay/upper
+mkdir -p overlay/work
+dd if=/dev/zero of=overlay.img bs=1M count=500 && \
+     mkfs.ext3 -d overlay overlay.img
 
-pip install -r ${ABSOLUTE_PATH}/requirements.txt
+singularity run --overlay ${ABSOLUTE_PATH}/overlay.img $SINGULARITY_IMAGE  bash -c '
+python -m venv --prompt $ENV_NAME --system-site-packages ${ENV_DIR};
+
+source ${ABSOLUTE_PATH}/activate.sh;
+
+pip install --cache-dir ${ABSOLUTE_PATH}/cache --upgrade pip
+#conda install -y ipykernel==5.1.3
+conda uninstall -y ipykernel
+
+pip install --cache-dir ${ABSOLUTE_PATH}/cache -r ${ABSOLUTE_PATH}/requirements.txt;
+'