From 9beff10fe693d11cd176253998dce36e1738abb7 Mon Sep 17 00:00:00 2001
From: Jakub Vonka <jakub.vonka@psi.ch>
Date: Tue, 3 Feb 2026 11:19:14 +0100
Subject: [PATCH] Removing cluster tools (now with own repo at
 /sf/cristallina/applications/it/cluster_tools)

---
 cluster_tools/jupyter_on_ra.sh          |  55 ------------
 cluster_tools/jupyter_on_sf.sh          |  51 -----------
 cluster_tools/ra_cluster_cristallina.sh | 113 ------------------------
 cluster_tools/start_jupyter.sh          |  60 -------------
 small_useful_scripts/tunnel2jupytera.sh |  58 ------------
 5 files changed, 337 deletions(-)
 delete mode 100755 cluster_tools/jupyter_on_ra.sh
 delete mode 100755 cluster_tools/jupyter_on_sf.sh
 delete mode 100644 cluster_tools/ra_cluster_cristallina.sh
 delete mode 100755 cluster_tools/start_jupyter.sh
 delete mode 100644 small_useful_scripts/tunnel2jupytera.sh

diff --git a/cluster_tools/jupyter_on_ra.sh b/cluster_tools/jupyter_on_ra.sh
deleted file mode 100755
index 78114b9..0000000
--- a/cluster_tools/jupyter_on_ra.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/bash
-# Slurm submission script to start a Jupyterlab instance on the RA cluster for 
-# data analysis Cristallina @ SwissFEL. 
-
-# Requirements: user account on RA and access to /sf/cristallina
-
-# To execute from cristallina console use:
-# ssh your_username@ra.psi.ch "srun /sf/cristallina/applications/conda/jupyter_on_ra.sh" 
-# or when using more computing power we start a batch job which takes the options below into account:
-# ssh your_username@ra.psi.ch "sbatch /sf/cristallina/applications/conda/jupyter_on_ra.sh"
-
-# alternatively we can also run on the SwissFEL computing nodes: sf-cn-1
-
-#SBATCH --job-name=analysis             # Job name
-#SBATCH --partition week                # or week, shared, hour, day-rhel8
-#SBATCH --nodes=1                       # Run all processes on a single node
-#SBATCH --ntasks=1                      # Run a single task
-#SBATCH --cpus-per-task=14              # Number of CPU cores per task
-#SBATCH --mem-per-cpu=16G
-#SBATCH --time=96:00:00                 # Time limit hrs:min:sec
-#SBATCH --output=jupyterlab_%j_%N.log   # Standard output and error log
-#SBATCH --exclude=ra-c-[085-100]        # older AMD Epyc nodes which are problematic with bitshuffle
-
-echo "Starting Jupyterlab..."
-
-echo "Date              = $(date)"
-echo "Hostname          = $(hostname -s)"
-echo "Working Directory = $(pwd)"
-echo ""
-echo "Number of Nodes Allocated      = $SLURM_JOB_NUM_NODES"
-echo "Number of Tasks Allocated      = $SLURM_NTASKS"
-echo "Number of Cores/Task Allocated = $SLURM_CPUS_PER_TASK"
-
-# loading our minimal conda environment
-source /sf/cristallina/applications/conda/envs/miniconda/etc/profile.d/conda.sh
-
-# and activating the actual analysis environment
-# a bit more conservative: conda activate /sf/cristallina/applications/conda/envs/analysis_forge
-conda activate /sf/cristallina/applications/conda/envs/analysis_edge
-
-# password equivalent
-export JUPYTER_TOKEN=cristallina
-
-# single user: 
-# jupyter lab --no-browser --ip 0.0.0.0 --YDocExtension.disable_rtc=True
-
-# experimental: use collaboration environment:
-jupyter lab --no-browser --ip 0.0.0.0 --YDocExtension.ystore_class=cristallina.jupyter_helper.MySQLiteYStore --YDocExtension.document_save_delay=10 --MySQLiteYStore.document_ttl=1800
-
-echo "Jupyterlab finished."
-
-# cleanup
-echo "Cleaning up temporary database files"
-find "/tmp" -type f -name "ystore_[0-9]*.db" -exec rm {} \;
-
diff --git a/cluster_tools/jupyter_on_sf.sh b/cluster_tools/jupyter_on_sf.sh
deleted file mode 100755
index b6bbe74..0000000
--- a/cluster_tools/jupyter_on_sf.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/bash
-# Slurm submission script to start a Jupyterlab instance on the SF cluster for 
-# data analysis Cristallina @ SwissFEL. 
-
-# Requirements: user account on SF and access to /sf/cristallina
-
-# To execute from cristallina console use:
-# ssh your_username@ra.psi.ch "srun /sf/cristallina/applications/conda/jupyter_on_ra.sh" 
-# or when using more computing power we start a batch job which takes the options below into account:
-# ssh your_username@ra.psi.ch "sbatch /sf/cristallina/applications/conda/jupyter_on_ra.sh"
-
-# alternatively we can also run on the SwissFEL computing nodes: sf-cn-1
-
-#SBATCH --job-name=analysis             # Job name
-#SBATCH --partition prod-aramis         # or week, shared, hour, day-rhel8
-#SBATCH --nodes=1                       # Run all processes on a single node
-#SBATCH --ntasks=1                      # Run a single task
-
-
-
-#SBATCH --output=jupyterlab_%j_%N.log   # Standard output and error log
-
-
-echo "Starting Jupyterlab..."
-
-echo "Date              = $(date)"
-echo "Hostname          = $(hostname -s)"
-echo "Working Directory = $(pwd)"
-echo ""
-echo "Number of Nodes Allocated      = $SLURM_JOB_NUM_NODES"
-echo "Number of Tasks Allocated      = $SLURM_NTASKS"
-echo "Number of Cores/Task Allocated = $SLURM_CPUS_PER_TASK"
-
-# loading our minimal conda environment
-source /sf/cristallina/applications/conda/envs/miniconda/etc/profile.d/conda.sh
-
-# and activating the actual analysis environment
-# a bit more conservative: conda activate /sf/cristallina/applications/conda/envs/analysis_forge
-conda activate /sf/cristallina/applications/conda/envs/analysis_edge
-
-# password equivalent
-export JUPYTER_TOKEN=cristallina
-
-# single user: jupyter lab --no-browser --ip 0.0.0.0
-# experimental: use collaboration environment
-
-jupyter lab --no-browser --ip 0.0.0.0 --YDocExtension.ystore_class=cristallina.jupyter_helper.MySQLiteYStore
-
-echo "Jupyterlab finished."
-
-
diff --git a/cluster_tools/ra_cluster_cristallina.sh b/cluster_tools/ra_cluster_cristallina.sh
deleted file mode 100644
index 8a60dbc..0000000
--- a/cluster_tools/ra_cluster_cristallina.sh
+++ /dev/null
@@ -1,113 +0,0 @@
-#!/bin/bash
-
-
-function find_my_pgroups(){
-  echo "You seem to have access to these pgroups:"
-  for d in /sf/*/data/p*/raw; do
-    ls $d >/dev/null 2>/dev/null && echo $d
-  done | cut -d\/ -f5
-}
-
-
-if [ "$#" -ne 2 ]; then
-  echo "Usage:   $0 <pgroup> <human comment>"
-  echo "Example: $0 p17123 commisioning_spectrometer"
-  echo
-  find_my_pgroups
-  exit 1
-fi
-
-# Change privileges of a newly created files such the whole group (e.g. users in pgroup for an experiment) can write to them 
-# Add a line to ~/.bashrc if it doesn't exist already and source the file again
-grep -qxF 'umask 0002' ~/.bashrc || echo 'umask 0002' >> ~/.bashrc 
-source ~/.bashrc
-
-
-pgroup=$1
-comment=$2
-shortcut_folder_path="./pgroup_shortcuts"
-#ppath=${pgroup::3}
-timestamp=$(date "+%Y%m%d-%H%M%S")
-
-source=/sf/cristallina/data/$pgroup
-target=$shortcut_folder_path/$pgroup-$comment
-
-# If folder pgroup_shortcuts does not exist, crate it
-mkdir -p $shortcut_folder_path
-
-if [ -d $target ]; then
-  echo "pgroup symlink (\"$target\") exists already."
-  echo "Won't create symlink."
-elif [ ! -d $source ]; then
-  echo "pgroup folder (\"$source\") does not exist."
-  echo "Won't create symlink."
-  find_my_pgroups
-else
-  echo "Creating symlink to pgroup $pgroup at $target..."
-  ln -s $source $target
-fi
-
-
-#echo
-#pgroup_conda=$source/anaconda
-#if [ -d $pgroup_conda ]; then
-#  echo "conda folder in pgroup $pgroup exists already."
-#else
-#  echo "No conda installation in pgroup $pgroup yet."
-#  echo "Conda install may take some time..."
-#  set -e
-
-#  source /opt/psi/Programming/anaconda/2019.07/conda/etc/profile.d/conda.sh
-#  conda activate alvra-analysis
-#  conda env export --prefix /sf/alvra/anaconda/alvra-analysis --file packages-$timestamp.yaml
-#  time conda env create --prefix $pgroup_conda/alvra-analysis-$pgroup --file packages-$timestamp.yaml
-#  rm packages-$timestamp.yaml
-#  conda activate $pgroup_conda/alvra-analysis-$pgroup
-#  conda install --yes --channel paulscherrerinstitute alvra_tools
-#  conda env export --prefix $pgroup_conda/alvra-analysis-$pgroup --file $pgroup_conda/packages-$timestamp.yaml
-#  conda deactivate
-
-#  set +e
-#fi
-
-condarc=~/.condarc
-condarc_bak=$condarc-$timestamp
-
-if [ -f $condarc ]; then
-  cp $condarc $condarc_bak
-fi
-
-
-echo
-echo "Updating .condarc:"
-# later added means higher priority
-#source /opt/psi/Programming/anaconda/2019.07/conda/etc/profile.d/conda.sh
-#conda config --add envs_dirs /sf/alvra/anaconda
-#conda config --add envs_dirs $pgroup_conda
-#conda config --add channels conda-forge
-#conda config --add channels paulscherrerinstitute
-miniconda=/sf/cristallina/applications/conda/envs/miniconda
-source ${miniconda}/etc/profile.d/conda.sh
-conda config --add envs_dirs /sf/cristallina/applications/conda/envs
-conda activate analysis_edge
-
-
-# delete backup if identical to updated original
-if [ -f $condarc_bak ]; then
-  cmp --silent $condarc $condarc_bak
-  if [ $? -eq 0 ]; then
-    echo
-    echo ".condarc unchanged."
-    rm $condarc_bak
-  else
-    echo
-    echo "Created backup: $condarc_bak"
-    echo
-    echo "Your old .condarc:"
-    echo "=================="
-    cat $condarc_bak
-  fi
-fi
-
-
-
diff --git a/cluster_tools/start_jupyter.sh b/cluster_tools/start_jupyter.sh
deleted file mode 100755
index 52e8a63..0000000
--- a/cluster_tools/start_jupyter.sh
+++ /dev/null
@@ -1,60 +0,0 @@
-#!/bin/bash
-
-# cleanup old log files
-mv jupyterlab*.log ~/old_logs 2>/dev/null
-
-
-# shortname, used in slurm queue
-SHORT=$(echo $USER | cut -c1-7)
-
-# Jupyter (Lab) does not like to run with several instances 
-# as the same user on a NFS system as this causes broken databases.
-# So we abort here in this case.
-if [ "$(squeue | grep $SHORT | awk '{print $3}')" == "analysis" ]; then
-  echo "Jupyter instance already running. Aborting."
-  exit 1
-fi
-
-# submits the batch job to the RA cluster
-sbatch jupyter_on_ra.sh
-
-# prepare spinner
-i=1
-sp="/-\|"
-printf 'Waiting for Jupyterlab to start.  '
-
-
-# wait until the Jupyterlab instance shows up
-while [  "$(squeue | grep $SHORT | wc -w )" -lt 2 ]
-do 
-    sleep 0.25
-    printf "\b${sp:i++%${#sp}:1}"
-done
-
-
-printf '\nWaiting for Jupyterlab logfile.  '
-
-# and wait till there is a logfile (parsing ls, I know...)
-while [  "$(ls jupyterlab*.log 2>/dev/null | xargs cat | wc -w )" -lt 50 ]
-do
-    sleep 0.25
-    printf "\b${sp:i++%${#sp}:1}"
-done
-
-# wait a bit till the startup of the jupyterlab server is complete
-sleep 2
-printf '\nScanning for corresponding node in logfile.  '
-
-LOGFILE=$(find . -maxdepth 1 -name "jupyterlab*" -printf "%T@ %Tc %p\n" | sort -n | awk '{print $NF}') 
-
-
-until grep -q -E "Jupyter Server.*is running at" $LOGFILE
-do
-    sleep 0.25
-    printf "\b${sp:i++%${#sp}:1}"
-done
-
-# and output the corresponding entry
-OUTPUT=$(grep -o "http://r.*" $LOGFILE )
-printf  "\nJupyter instances running at: \n${OUTPUT/token=.../token=cristallina}\n"
-
diff --git a/small_useful_scripts/tunnel2jupytera.sh b/small_useful_scripts/tunnel2jupytera.sh
deleted file mode 100644
index cc4b6e9..0000000
--- a/small_useful_scripts/tunnel2jupytera.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-
-### Small script to create an SSH tunnel from outside of PSI network to access RA.
-### Change to your PSI account username and run. Once running, going to https://localhost:5000 leads to jupyera.psi.ch without needing VPN.
-
-def_user=$USER
-def_addr="jupytera"
-def_port="5000"
-def_debug=false
-def_node=false
-
-function show_usage {
-    echo "usage: $0 [-u USER] [-p PORT] [-s]"
-    echo "    -u, --user USER    set user (default: ${def_user})"
-    echo "    -p, --port PORT    set local port (default: ${def_port})"
-    echo "    -s, --staging      tunnel to jupytera staging (default: jupytera production)"
-    echo "    -n, --node         node at which jupyter is running"
-    echo "    -d, --debug        turn on debug mode (default: off)"
-    echo "    -h, --help, -?     show this help"
-}
-
-user=${def_user}
-addr=${def_addr}
-port=${def_port}
-debug=${def_debug}
-node=${def_node}
-
-while [[ "$#" -gt 0 ]]; do
-    case $1 in
-        -u|--user) user="$2" ; shift ;;
-        -p|--port) port="$2" ; shift ;;
-        -n|--node) node="$2" ; shift ;;
-        -s|--staging) addr="jupytera-staging" ;;
-        -d|--debug) debug=true ;;
-        -h|--help|-\?) show_usage ; exit ;;
-        *) echo "unknown argument: $1" ; show_usage ; exit 1 ;;
-    esac
-    shift
-done
-
-
-echo "Creating tunnel to ${addr}.psi.ch on https://localhost:${port}/ ..."
-echo
-echo "Username: ${user}"
-
-# If node not given, link to a generic jupyter from spawner. If node given and a notebook already started there, link there.
-if [ "${node}" = false ]; then
-    cmd="ssh -J ${user}@hop.psi.ch ${user}@ra.psi.ch -L ${port}:${addr}.psi.ch:443"
-else
-    echo "Establishing tunnel to ${node}"
-    cmd="ssh -J ${user}@hop.psi.ch ${user}@ra.psi.ch -L ${port}:${node}.psi.ch:8888"
-fi
-
-if ${debug} ; then
-  echo "DEBUG:" $cmd
-else
-  $cmd
-fi