Devloped ML images for Alma9; Added a few keras related packages in t…

…he images ml-tensorflow-*

alma9/Dir-Mamba

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+/home/yesw/Mamba

alma9/_activate_current_env.sh

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+# This script should never be called directly, only sourced:
+
+#     source _activate_current_env.sh
+
+# shellcheck shell=bash
+
+# Initialize Micromamba for the current shell
+
+# if [[ "X$X_MAMBA" == "X" ]]; then
+   eval "$("${MAMBA_EXE}" shell hook --shell=bash)"
+   micromamba activate "${ENV_NAME:-base}"
+#   export X_MAMBA=$CONDA_DEFAULT_ENV
+   # export CONDA_PROMPT_MODIFIER="(${ENV_NAME:-base})"
+# fi

alma9/check-gpu-in-tensorflow.py

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+import tensorflow as tf
+print(tf.__version__)
+
+gpus = tf.config.list_physical_devices('GPU')
+if gpus:
+  print("gpus=",gpus)
+  # Restrict TensorFlow to only use the first GPU
+  try:
+    tf.config.set_visible_devices(gpus[0], 'GPU')
+    logical_gpus = tf.config.list_logical_devices('GPU')
+    tf.test.gpu_device_name()
+    print(len(gpus), "Physical GPUs,", len(logical_gpus), "Logical GPU")
+  except RuntimeError as e:
+    # Visible devices must be set before GPUs have been initialized
+    print(e)

alma9/create-newEnv-on-base.sh

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+PROGNAME=$BASH_SOURCE
+myName="${BASH_SOURCE:-$0}"
+myDir=$(dirname $myName)
+myDir=$(readlink -f $myDir)
+
+usage()
+{
+  cat << EO
+        Create a new env on top of the existing base env
+
+        Usage: source $PROGNAME -h|--help
+               source $PROGNAME -p|--prefix prefixDir
+EO
+}
+
+if [ "$BASH_SOURCE" = "$0" ]; then
+   echo "DO NOT run this script, please _source_  $PROGNAME instead"
+   usage
+   return 1
+fi
+
+while [ $# -gt 0 ]
+do
+  case "$1" in
+    -h|--help)
+      usage
+      return 0
+      ;;
+    -p|--prefix)
+      if [ -n "$2" ] && [ ${2:0:1} != "-" ]; then
+        prefixDir=$2
+        shift 2
+      else
+        echo "Error: Argument for $1 is missing" >&2
+        return 1
+      fi
+      ;;
+    *) # unsupported flags
+      echo "Error: Unsupported flag or arg $1" >&2
+      return 1
+      ;;
+  esac
+done
+
+
+CondaRoot=$MAMBA_ROOT_PREFIX
+[ "X$CondaRoot" = "X" ] && CondaRoot=$CONDA_PREFIX
+if [ "X$CondaRoot" = "X" ]; then
+   echo "Neither envvar MAMBA_ROOT_PREFIX nor CONDA_PREFIX is found, exit now"
+   return 1
+fi
+
+if [ "$prefixDir" = "" ]; then
+   echo "missing prefixDir"
+   usage
+   return 1
+fi
+
+if [[ "$prefixDir" != */* ]]; then
+   prefixDir="./$prefixDir"
+fi
+
+
+shellName=$(readlink /proc/$$/exe | awk -F "[/-]" '{print $NF}')
+typeset -f micromamba >/dev/null || eval "$($MAMBA_EXE shell hook --shell=$shellName)"
+
+envDir=$prefixDir
+micromamba env create -p $prefixDir
+if [ $? -ne 0 ]; then
+   echo "Failure in creating a new env under $envDir/"
+fi
+envDir=$(readlink -f $envDir)
+
+
+curDir=$PWD
+cd $envDir
+ln -s $CONDA_PREFIX baseEnv_dir
+gtar xfz $CondaRoot/newEnv-base.tgz
+
+
+cat > pyvenv.cfg <<EOF
+home = $CONDA_PREFIX/bin
+include-system-site-packages = true
+version = $(python3 --version | cut -d' ' -f2)
+EOF
+
+prepare_UserEnv_setup()
+{
+   if [ "$myDir" = "/" ]; then
+      cp -p /setup-UserEnv-in-container.sh .
+      BindPaths='$myDir'
+      if [ "X$SINGULARITY_BIND" != "X" ]; then
+         BindPaths="$SINGULARITY_BIND"',$myDir'
+      fi
+      Image=$SINGULARITY_CONTAINER
+      sed -i -e "s#BindPaths=.*#BindPaths=$BindPaths#" -e "s#Image=.*#Image=$Image#" setup-UserEnv-in-container.sh
+   else
+      cp -p $myDir/setupMe-on-host.sh .
+      # add the default channel: conda-forge
+      micromamba config get channels 2>&1 | grep conda-forge >/dev/null || micromamba config append channels conda-forge
+   fi
+}
+
+prepare_UserEnv_setup
+
+cd $curDir
+
+# activate the new new
+micromamba activate $envDir
+echo "Next time, you can just run the following to activate your extended env"
+if [ "$myDir" = "/" ]; then
+   echo -e "\tsource $envDir/setup-UserEnv-in-container.sh"
+else
+   echo -e "\tsource $envDir/setupMe-on-host.sh"
+fi

alma9/create-py_newEnv-on-base.sh

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+CondaRoot=/opt/conda
+
+redCol="\e[1;31;47m"
+PROGNAME=$BASH_SOURCE
+usage()
+{
+  cat << EO
+        Create a new python env on top of the existing base env
+
+        Usage: source $PROGNAME -h|--help
+               source $PROGNAME [-w|--workdir workDir]
+
+	If no workDir is specified, the current directory will be used.
+EO
+}
+
+if [ $BASH_SOURCE == $0 ]; then
+   echo -e "DO NOT run this script, please ${redCol} source $PROGNAME \e[0m instead\n"
+   usage
+   exit 1
+fi
+
+workDir=""
+while (( "$#" )); do
+  case "$1" in
+    -h|--help)
+      usage
+      return 0
+      ;;
+    -w|--workdir)
+      if [ -n "$2" ] && [ ${2:0:1} != "-" ]; then
+        workDir=$2
+        shift 2
+      else
+        echo "Error: Argument for $1 is missing" >&2
+        return 1
+      fi
+      ;;
+    *) # unsupported flags
+      echo "Error: Unsupported flag or arg $1" >&2
+      return 1
+      ;;
+  esac
+done
+
+isPWD=no
+if [ "$workDir" == "" ]; then
+   workDir=$PWD
+   isPWD=yes
+fi
+
+if [ "$isPWD" == "no" -a ! -d $workDir ]; then
+   mkdir -p $workDir
+   if [ $? -ne 0 ]; then
+      echo "$workDir does not exist, cannot create it either; exit now"
+      return 1
+   fi
+fi
+
+export PIPENV_VENV_IN_PROJECT=1
+
+# [[ $(type -t micromamba) != "function" ]] && source /usr/local/bin/_activate_current_env.sh
+
+if [ "$isPWD" == "no" ]; then
+   cd $workDir
+fi
+
+pipenv --site-packages install
+sed -i  '/^VIRTUAL_ENV=/s#=.*#=$(realpath ${BASH_SOURCE%/*/*})#' .venv/bin/activate
+
+ln -s $CONDA_PREFIX/lib/*.so* .venv/lib/
+
+echo ""
+echo -e "To add a package, run ${redCol}pipenv install\e[0m"
+echo -e "To activate this project's virtualenv, run ${redCol}pipenv shell\e[0m"
+echo -e "Alternatively, run a command inside the virtualenv with ${redCol}pipenv run\e[0m"

alma9/entrypoint.sh

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+#!/bin/bash
+
+# export LD_LIBRARY_PATH=/usr/lib64:/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda-11.1/lib64:/usr/local/cuda-11.2/lib64
+
+## Do whatever you need with env vars here ...
+# source /usr/local/bin/_activate_current_env.sh
+source /printme.sh
+
+# Hand off to the CMD
+if [[ "X$1" =~ X.*bash ]]; then
+   CMD="$@ -rcfile /usr/local/bin/_activate_current_env.sh"
+   eval "set $CMD"
+fi
+exec "$@"

alma9/gtar-newEnv-on-base.sh

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+#!/bin/sh
+
+CondaRoot=/opt/conda
+listFilename=./list-of-dirs-$$.txt
+name_newEnv=newEnv
+root_newEnv=/tmp/conda
+prefix_envEnv=$root_newEnv/envs/$name_newEnv
+
+mkdir -p $root_newEnv
+micromamba env create -n $name_newEnv -r $root_newEnv
+cd $prefix_envEnv
+ln -s $CondaRoot baseEnv_dir
+
+echo -e "conda-meta\nbin\nsbin" > $listFilename
+find $CondaRoot/etc -type d | sed "s#$CondaRoot/##" >> $listFilename
+find $CondaRoot/ssl -type d | sed "s#$CondaRoot/##" >> $listFilename
+find $CondaRoot/share/jupyter -type d | sed "s#$CondaRoot/##" >> $listFilename
+find $CondaRoot/x86_64-conda-linux-gnu | sed "s#$CondaRoot/##" >> $listFilename
+find $CondaRoot/lib -type d | grep -v "site-packages" | sed "s#$CondaRoot/##" >> $listFilename
+
+mkdir -p `cat $listFilename`
+while read subdir; do
+  cd $subdir
+  parentDots=$(echo $subdir | sed 's%[^/]*%..%g')
+  ln -s $parentDots/baseEnv_dir/$subdir/* ./ 2>/dev/null
+  cd $prefix_envEnv
+done <$listFilename
+rm -f $listFilename
+
+# special activate and deactivate scrpt to handle envvar PYTHONPATH
+cat > etc/conda/activate.d/activate-python.sh <<EOF
+# save the original PYTHONPATH if set
+if ! [ -z "\${PYTHONPATH+_}" ] ; then
+    CONDA_BACKUP_PYTHONPATH="\$PYTHONPATH"
+    PYTHONPATH=\$CONDA_PREFIX/lib:\$CONDA_PREFIX/lib/python$(python3 --version | cut -d' ' -f2 | cut -d'.' -f1-2)/site-packages:\${PYTHONPATH}
+else
+    export PYTHONPATH=\$CONDA_PREFIX/lib:\$CONDA_PREFIX/lib/python$(python3 --version | cut -d' ' -f2 | cut -d'.' -f1-2)/site-packages
+fi
+EOF
+
+cat > etc/conda/deactivate.d/deactivate-python.sh <<EOF
+# restore the original PYTHONPATH if available
+if ! [ -z "\${CONDA_BACKUP_PYTHONPATH+_}" ] ; then
+    export PYTHONPATH=\$CONDA_BACKUP_PYTHONPATH
+    unset CONDA_BACKUP_PYTHONPATH
+else
+    unset PYTHONPATH
+fi
+EOF
+
+# special file and subdir
+rm -f conda-meta/history
+rm -f baseEnv_dir
+rm -f lib/python*/site-packages
+
+gtar cfz $CondaRoot/newEnv-base.tgz *
+rm -rf $root_newEnv