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--- calcoloscientifico:cluster:softwareapplicativo:conda_user [18/09/2025 16:46] – fabio.spataro
+++ calcoloscientifico:cluster:softwareapplicativo:conda_user [25/02/2026 15:08] (versione attuale) – fabio.spataro
@@ Linea 123: / Linea 123: @@
 It is also possible to install python packages using the "pip" command.
+==== Example with conda and pip ====
+General template that can be used to create personal or group environments:
+<code bash hpc-make-condaenv-networkx>
+#!/bin/bash
+set -e
+PYTHON_VERSION='3.12'
+CONDAENV_NAME='networkx'
+CONDAENV_RELEASE='py3.12'
+CONDAENV_DEFAULT='yes'
+NETWORKX_VERSION='3.6.1'
+help() {
+    cat <<EOF
+Synopsis:
+  $(basename $0) [--dry-run]
+  $(basename $0) [--pip-dry-run]
+  $(basename $0) --help
+Usage:
+  $(basename $0)
+  $(basename $0) --dry-run
+  $(basename $0) --pip-dry-run
+Example:
+  $(basename $0)
+  $(basename $0) --dry-run
+  $(basename $0) --pip-dry-run
+Options:
+  -d, --dry-run                 Only display what would have been done by conda
+      --pip-dry-run             Only display what would have been done by pip
+  -h, --help                    Display a help message and quit
+EOF
+}
+die() {
+    if [ $# -ge 1 ]; then
+        echo "$(basename "$0"): $@" >&2
+    fi
+    exit 1
+}
+# Command line options
+opt=$(getopt \
+    --options hd \
+    --longoptions help,pip-dry-run,dry-run \
+    --name $(basename $0) \
+    -- \
+    "$@")
+retval=$?
+if [ $retval -ne 0 ]; then
+    exit $retval
+fi
+eval set -- "$opt"
+while true; do
+    case "$1" in
+        -h|--help)
+            shift
+            help
+            exit;;
+        -d|--dry-run)
+            shift
+            opt_dry_run=true;;
+        --pip-dry-run)
+            shift
+            opt_pip_dry_run=true;;
+        --)
+            shift
+            break;;
+        *)
+            die 'options parsing error'
+            exit 1;;
+    esac
+done
+# CONDA dry run
+if [ -n "$opt_dry_run" ]; then
+    unset PYTHON_VERSION
+fi
+# PIP dry run
+if [ -n "$opt_pip_dry_run" ]; then
+    unset NETWORKX_VERSION
+fi
+# CONDA environment name
+if [ -n "$NETWORKX_VERSION" ]; then
+    CONDAENV_VERSION="$NETWORKX_VERSION"
+else
+    if [ -n "$PYTHON_VERSION" ]; then
+        PY=${PYTHON_VERSION:+$(echo $PYTHON_VERSION | sed -re 's/([0-9]+)\.([0-9]+).*/py\1.\2/')}
+    fi
+    CONDAENV_VERSION=${PY:+${PY}-}$(date '+%Y.%m.%d')
+fi
+if [ -n "$CONDAENV_RELEASE" ]; then
+    CONDAENV_VERSION="${CONDAENV_VERSION}-${CONDAENV_RELEASE}"
+fi
+CONDAENV="${CONDAENV_NAME}-${CONDAENV_VERSION}"
+module load miniconda3
+source "$CONDA_PREFIX/etc/profile.d/conda.sh"
+if [ $UID = 0 ]; then
+    CONDAENV_PREFIX="/hpc/share/tools/miniconda3/envs/$CONDAENV"
+    CONDAENV_SYMLNK="/hpc/share/tools/miniconda3/envs/$CONDAENV_NAME"
+else
+    if [ -z "$CONDA_ENVS_PATH" ]; then
+        echo 'Error: the CONDA_ENVS_PATH envarionment variable is not set' 1>&2
+        exit 1
+    fi
+    if [ -z "$CONDA_PKGS_DIRS" ]; then
+        echo 'Error: the CONDA_PKGS_DIRS envarionment variable is not set' 1>&2
+        exit 1
+    fi
+    echo "CONDA_ENVS_PATH: $CONDA_ENVS_PATH"
+    echo "CONDA_PKGS_DIRS: $CONDA_PKGS_DIRS"
+    CONDAENV_PREFIX="$CONDA_ENVS_PATH/$CONDAENV"
+    CONDAENV_SYMLNK="$CONDA_ENVS_PATH/$CONDAENV_NAME"
+fi
+echo "CONDAENV_PREFIX: $CONDAENV_PREFIX"
+if echo "$CONDAENV_DEFAULT" | egrep -q '^[yY][Ee][Ss]$'; then
+    echo "CONDAENV_SYMLNK: $CONDAENV_SYMLNK"
+fi
+echo
+if [ -z "$opt_dry_run" ]; then
+    if [ -d "$CONDAENV_PREFIX" ]; then
+        echo -n "Should we remove the already existing condaenv '$CONDAENV_NAME' (yes/no)? "
+        read ans
+        case "$ans" in
+            [yY]|[yY][Ee][Ss])
+                conda env remove --name "$CONDAENV"
+                ;;
+            [nN]|[nN][oO])
+                ;;
+            *)
+                echo
+                exec "$0"
+                exit
+                ;;
+        esac
+    fi
+    if [ -d "$CONDAENV_PREFIX" ]; then
+        echo -n "Should we proceed with the modification of the condaenv '$CONDAENV_NAME' (yes/no)? "
+    else
+        echo -n "Should we proceed with the creation of the condaenv '$CONDAENV_NAME' (yes/no)? "
+    fi
+    read ans
+    case "$ans" in
+        [yY]|[yY][Ee][Ss])
+            ;;
+        [nN]|[nN][oO])
+            exit 1
+            ;;
+        *)
+            echo
+            exec "$0"
+            exit
+            ;;
+    esac
+fi
+conda info
+if [ ! -d "$CONDAENV_PREFIX" ]; then
+    # CONDA create
+    conda create \
+        --yes \
+        ${opt_dry_run:+--dry-run} \
+        --prefix "$CONDAENV_PREFIX" \
+        --override-channels \
+        --channel conda-forge \
+        python${PYTHON_VERSION:+=$PYTHON_VERSION} \
+        pip \
+        matplotlib
+fi
+if [ -n "$opt_dry_run" ]; then
+    conda deactivate
+    exit
+fi
+CONDADEF_PIP="$(which pip)"
+conda activate "$CONDAENV"
+CONDAENV_PIP="$(which pip)"
+# PIP check
+if [ "$CONDADEF_PIP" = "$CONDAENV_PIP" ]; then
+    echo "Error: condaenv pip is conda default pip: '$CONDAENV_PIP'" 1>&2
+    exit 1
+fi
+# PIP install or upgrade pip
+pip install --upgrade ${opt_pip_dry_run:+--dry-run} pip
+# PIP install or upgrade
+pip install --upgrade ${opt_pip_dry_run:+--dry-run} \
+    networkx${NETWORKX_VERSION:+==$NETWORKX_VERSION}
+conda list || true
+conda deactivate
+# PIP dry run
+if [ -n "$opt_pip_dry_run" ]; then
+    exit
+fi
+# CONDA environment symbolic link
+if echo "$CONDAENV_DEFAULT" | egrep -q '^[yY][Ee][Ss]$'; then
+    rm -f "$CONDAENV_SYMLNK"
+    ln -s "$CONDAENV_PREFIX" "$CONDAENV_SYMLNK"
+    symlinks -cs $(dirname "$CONDAENV_PREFIX")
+    ls -lard "$CONDAENV_SYMLNK"*
+fi
+</code>
+This script is located in
+<code>
+/hpc/share/tools/conda/bin/hpc-make-condaenv-networkx
+</code>
 ==== Creating a user environment ====
@@ Linea 191: / Linea 434: @@
 <code>
 [<USER>@ui01 ~]$ srun --nodes=1 --ntasks-per-node=2 --partition=gpu --qos=gpu --gres=gpu:p100:1 --mem=8G --pty bash
+[<USER>@wn41 ~]$ module load miniconda3
 [...]
+[<USER>@wn41 ~]$ exit
+[<USER>@ui01 ~]$
 </code>