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Change hh5 to xp65 conda #44

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Change hh5 to xp65 conda #44

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9676944
Change hh5 to xp65 conda
adele-morrison Apr 16, 2025
9142a68
remove path to jupyter
adele-morrison Apr 17, 2025
f7db6d6
add hh5 to storage, so qmonitor works
adele-morrison Apr 17, 2025
558096f
Update gadi_jupyter
navidcy Apr 17, 2025
b62d530
Update gadi_jupyter
navidcy Apr 17, 2025
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23 changes: 15 additions & 8 deletions gadi_jupyter
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Original file line number Diff line number Diff line change
Expand Up @@ -177,9 +177,16 @@ set -eu
WORKDIR="$WORKDIR"
mkdir -p "\$WORKDIR"

# Check if a hh5 member
if [ ! -d /g/data/hh5 ]; then
echo "ERROR: \$USER is not a member of hh5. Join at https://my.nci.org.au/mancini/project/hh5/join" >&2
# Check if an xp65 member
if [ ! -d /g/data/xp65 ]; then
echo "ERROR: \$USER is not a member of xp65. Join at https://my.nci.org.au/mancini/project/xp65/join" >&2
echo "x x x x ERROR"
exit
fi

# Check if an ik11 member
if [ ! -d /g/data/ik11 ]; then
echo "ERROR: \$USER is not a member of ik11. Join at https://my.nci.org.au/mancini/project/ik11/join" >&2
echo "x x x x ERROR"
exit
fi
Expand All @@ -200,8 +207,8 @@ cat > "\$WORKDIR/runjp.sh" <<EOQ

module purge

eval "\\\$(/g/data/hh5/public/apps/miniconda3/bin/conda shell.bash hook)"
conda activate "${CONDA_ENV}"
module use /g/data/xp65/public/modules
module load conda/analysis3

set -eu

Expand All @@ -228,8 +235,8 @@ export DASK_TEMPORARY_DIRECTORY="\\\$TMPDIR"
$STRACE jupyter lab --NotebookApp.token="\\\$TOKEN" --no-browser --ip="\\\$HOSTNAME" --port "\\\$PORT" --port-retries=0
EOQ

# Required for conda
storage="gdata/hh5"
# Required for conda + nci_scripts
storage="gdata/xp65+gdata/ik11"

if [ -n "$STORAGE" ]; then
storage="$STORAGE+\$storage"
Expand Down Expand Up @@ -334,7 +341,7 @@ fi
set -e
echo

$SSH "$LOGINNODE" /g/data/hh5/public/apps/nci_scripts/qmonitor $jobid
$SSH "$LOGINNODE" /g/data/ik11/nci_scripts/qmonitor $jobid

# Move the cursor past the progress bars
echo
Expand Down