README.md

@@ -44,7 +44,7 @@ The preparation steps only need to be executed once. You need to carry out those
 * Start and interactive job with
 
 ```
-bsub -Is -W 0:10 -n 1 -R "rusage[mem=2048]" bash
+srun --ntasks=1 --time=00:10:00 --mem-per-cpu=2048 --pty bash
 ```
 
 When using Euler, switch to the new software stack (in case you haven't set it as default yet), either using
@@ -111,6 +111,7 @@ Options:
         -n | --numcores       NUM_CPU          Number of CPU cores to be used on the cluster
         -W | --runtime        RUN_TIME         Run time limit for the code-server in hours and minutes HH:MM
         -m | --memory         MEM_PER_CORE     Memory limit in MB per core
+        -b | --batchsys       BATCH_SYS        Batch system to use (LSF or SLURM)
 
 Optional arguments:
 
@@ -120,12 +121,14 @@ Optional arguments:
         -i | --interval       INTERVAL         Time interval for checking if the job on the cluster already started
         -k | --key            SSH_KEY_PATH     Path to SSH key with non-standard name
         -v | --version                         Display version of the script and exit
+        -j | --jobargs        JOB_ARGS         Additional job arguments
+
 
 Examples:
 
-        ./start_vscode.sh -u sfux -n 4 -W 04:00 -m 2048
+        ./start_vscode.sh -u sfux -b SLURM -n 4 -W 04:00 -m 2048
 
-        ./start_vscode.sh --username sfux --numcores 2 --runtime 01:30 --memory 2048
+        ./start_vscode.sh --username sfux --batchsys SLURM --numcores 2 --runtime 01:30 --memory 2048
 
         ./start_vscode.sh -c /c/Users/sfux/.vsc_config
 
@@ -138,6 +141,8 @@ VSC_RUN_TIME="01:00"        # Run time limit for the code-server in hours and mi
 VSC_MEM_PER_CPU_CORE=1024   # Memory limit in MB per core
 VSC_WAITING_INTERVAL=60     # Time interval to check if the job on the cluster already started
 VSC_SSH_KEY_PATH=""         # Path to SSH key with non-standard name
+VSC_BATCH_SYSTEM="SLURM"    # Batch system to use (SLURM or LSF)
+VSC_JOB_ARGS=""             # Additional job arguments
 ```
 
 ### Reconnect to a code-server session
@@ -159,3 +164,5 @@ This example is from a Linux computer. If you are using git bash on Windows, the
 
 ## Contributions
 * Andreas Lugmayr
+* Mike Boss
+* Nadia Marounina

cleanup.sh

+#!/bin/bash
+
+if [[ $# -lt 1 ]]
+then
+    echo -e "Error: No ETH username is specified, terminating script\n"
+    exit 1
+fi
+
+VSC_USERNAME=$1
+
+VSC_TUNNEL=$(cat reconnect_info | grep -o -E '[0-9]+:([0-9]+\.[0-9]+\.[0-9]+\.[0-9]+):[0-9]+')
+TUNNEL_JOBS=$(ps -u | grep $VSC_TUNNEL | grep ssh | awk '{ print $2 }')
+
+for TUNNEL_JOB in $TUNNEL_JOBS; do echo $TUNNEL_JOB; kill $TUNNEL_JOB; done
+
+ssh -T $VSC_USERNAME@euler.ethz.ch bkill $(cat reconnect_info  | grep BJOB | awk '{print $NF}') 

start_vscode.sh

@@ -2,16 +2,19 @@
 
 ###############################################################################
 #                                                                             #
-#  Script to run on a local computer to start a code-server on Euler and      #
-#  connect it with a local browser to it                                      #
+#  Script for local computer to start a code-server on Euler and use a SSH-   #
+#  tunnel to connect it with a local browser                                  #
 #                                                                             #
 #  Main author    : Samuel Fux                                                #
-#  Contributions  : Andreas Lugmayr                                           #
-#  Date           : October 2021                                              #
+#  Contributions  : Andreas Lugmayr, Mike Boss, Nadia Marounina,              #
+#                   Haoyang Zhou, Loïc Hausammann                             #
+#  Date           : Oct 2021-2023                                             #
 #  Location       : ETH Zurich                                                #
-#  Version        : 0.1                                                       #
 #  Change history :                                                           #
 #                                                                             #
+#  05.05.2023    Added variable for standard port                             #
+#  24.10.2022    Added Slurm support                                          #
+#  19.05.2022    JOBID is now saved to reconnect_info file                    #
 #  28.10.2021    Initial version of the script based on Jupyter script        #
 #                                                                             #
 ###############################################################################
@@ -21,7 +24,7 @@
 ###############################################################################
 
 # Version
-VSC_VERSION="0.1"
+VSC_VERSION="0.5"
 
 # Script directory
 VSC_SCRIPTDIR=$(pwd)
@@ -34,30 +37,39 @@ VSC_HOSTNAME="euler.ethz.ch"
 # 2. Command line options overwrite defaults
 # 3. Config file options  overwrite command line options
 
-# Configuration file default    : $HOME/.vsc_config
+# Configuration file default        : $HOME/.vsc_config
 VSC_CONFIG_FILE="$HOME/.vsc_config"
 
-# Username default              : no default
+# Username default                  : no default
 VSC_USERNAME=""
 
-# Number of CPU cores default   : 1 CPU core
+# Number of CPU cores default       : 1 CPU core
 VSC_NUM_CPU=1
 
-# Runtime limit default         : 1:00 hour
+# Runtime limit default             : 1:00 hour
 VSC_RUN_TIME="01:00"
 
-# Memory default                : 1024 MB per core
+# Memory default                    : 1024 MB per core
 VSC_MEM_PER_CPU_CORE=1024
 
-# Number of GPUs default        : 0 GPUs
+# Number of GPUs default            : 0 GPUs
 VSC_NUM_GPU=0
 
-# Waiting interval default      : 60 seconds
+# Waiting interval default          : 60 seconds
 VSC_WAITING_INTERVAL=60
 
-# SSH key location default      : no default
+# SSH key location default          : no default
 VSC_SSH_KEY_PATH=""
 
+# Batch system                      : Slurm
+VSC_BATCH_SYSTEM="SLURM"
+
+# Additional job arguments default  : no default
+VSC_JOB_ARGS=""
+
+# Standard port for code-server     : 8899
+VSC_REMOTE_PORT=8899
+
 ###############################################################################
 # Usage instructions                                                          #
 ###############################################################################
@@ -68,12 +80,13 @@ $0: Script to start a VSCode on Euler from a local computer
 
 Usage: start_vscode.sh [options]
 
-Options:
+Required options:
 
-        -u | --username       USERNAME         ETH username for SSH connection to Euler
+        -b | --batchsys       BATCH_SYS        Batch system to use (LSF or SLURM)
+        -m | --memory         MEM_PER_CORE     Memory limit in MB per core
         -n | --numcores       NUM_CPU          Number of CPU cores to be used on the cluster
+        -u | --username       USERNAME         ETH username for SSH connection to Euler
         -W | --runtime        RUN_TIME         Run time limit for the code-server in hours and minutes HH:MM
-        -m | --memory         MEM_PER_CORE     Memory limit in MB per core
 
 Optional arguments:
 
@@ -81,14 +94,17 @@ Optional arguments:
         -g | --numgpu         NUM_GPU          Number of GPUs to be used on the cluster
         -h | --help                            Display help for this script and quit
         -i | --interval       INTERVAL         Time interval for checking if the job on the cluster already started
+        -j | --jobargs        JOB_ARGS         Additional job arguments
         -k | --key            SSH_KEY_PATH     Path to SSH key with non-standard name
+        -p | --port           CS_PORT          Port number to be used by code-server
         -v | --version                         Display version of the script and exit
 
+
 Examples:
 
-        ./start_vscode.sh -u sfux -n 4 -W 04:00 -m 2048
+        ./start_vscode.sh -u sfux -b SLURM -n 4 -W 04:00 -m 2048
 
-        ./start_vscode.sh --username sfux --numcores 2 --runtime 01:30 --memory 2048
+        ./start_vscode.sh --username sfux --batchsys SLURM --numcores 2 --runtime 01:30 --memory 2048
 
         ./start_vscode.sh -c $HOME/.vsc_config
 
@@ -101,6 +117,9 @@ VSC_RUN_TIME="01:00"        # Run time limit for the code-server in hours and mi
 VSC_MEM_PER_CPU_CORE=1024   # Memory limit in MB per core
 VSC_WAITING_INTERVAL=60     # Time interval to check if the job on the cluster already started
 VSC_SSH_KEY_PATH=""         # Path to SSH key with non-standard name
+VSC_BATCH_SYSTEM="SLURM"    # Batch system to use (SLURM or LSF)
+VSC_JOB_ARGS=""             # Additional job arguments
+VSC_REMOTE_PORT=8899        # Port to be used with the code-server
 
 EOF
 exit 1
@@ -160,6 +179,19 @@ do
                 shift
                 shift
                 ;;
+                -b|--batchsys)
+                VSC_BATCH_SYSTEM=$2
+                shift
+                shift
+                ;;
+                -j|--jobargs)
+                VSC_JOB_ARGS=$2
+                shift
+                shift
+                ;;
+                -p|--port)
+                VSC_REMOTE_PORT=$2
+                ;;
                 *)
                 echo -e "Warning: ignoring unknown option $1 \n"
                 shift
@@ -267,6 +299,28 @@ else
         echo -e "Using SSH key $VSC_SSH_KEY_PATH"
 fi
 
+
+# check if VSC_BATCH_SYSTEM is set to SLURM or LSF
+case $VSC_BATCH_SYSTEM in
+        LSF)
+        echo -e "Using LSF batch system"
+        ;;
+        SLURM)
+        echo -e "Using Slurm batch system"
+        ;;
+        *)
+        echo -e "Error: Unknown batch system $VSC_BATCH_SYSTEM. Please either specify LSF or SLURM as batch system"
+        ;;
+esac
+
+# check if VSC_REMOTE_PORT an integer
+if ! [[ "$VSC_REMOTE_PORT" =~ ^[0-9]+$ ]]; then
+        echo -e "Error: $VSC_REMOTE_PORT -> Incorrect format. Please specify the port number as an integer and try again\n"
+        display_help
+fi
+
+echo -e "Using port number $VSC_REMOTE_PORT for the code-server"
+
 # put together string for SSH options
 VSC_SSH_OPT="$VSC_SKPATH $VSC_USERNAME@$VSC_HOSTNAME"
 
@@ -296,18 +350,42 @@ ENDSSH
 ###############################################################################
 
 # run the code-server job on Euler and save the ip of the compute node in the file vscip in the home directory of the user on Euler
-echo -e "Connecting to $VSC_HOSTNAME to start the code-server in a batch job"
+echo -e "Connecting to $VSC_HOSTNAME to start the code-server in a $BATCH_SYS batch job"
+case $VSC_BATCH_SYSTEM in
+        "LSF")
+        VSC_BJOB_OUT=$(ssh $VSC_SSH_OPT bsub -n $VSC_NUM_CPU -W $VSC_RUN_TIME -R "rusage[mem=$VSC_MEM_PER_CPU_CORE]" $VSC_SNUM_GPU $VSC_JOB_ARGS<<ENDBSUB
+        module load $VSC_MODULE_COMMAND
+        export XDG_RUNTIME_DIR="\$HOME/vsc_runtime"
+        VSC_IP_REMOTE="\$(hostname -i)"
+        echo "Remote IP:\$VSC_IP_REMOTE" >> /cluster/home/$VSC_USERNAME/vscip
+        code-server --bind-addr=\${VSC_IP_REMOTE}:\${VSC_REMOTE_PORT}
+ENDBSUB
+)       ;;
+        "SLURM")
 
-ssh $VSC_SSH_OPT bsub -n $VSC_NUM_CPU -W $VSC_RUN_TIME -R "rusage[mem=$VSC_MEM_PER_CPU_CORE]" $VSC_SNUM_GPU > BJOB_ID_FILE<<ENDBSUB
+        VSC_RUN_TIME="${VSC_RUN_TIME}":00" "
+
+        if [ "$VSC_NUM_GPU" -gt "0" ]; then
+        
+                VSC_SNUM_GPU="-G $VSC_NUM_GPU"
+        
+        fi
+
+        VSC_BJOB_OUT=$(ssh $VSC_SSH_OPT sbatch --ntasks=1 --cpus-per-task=$VSC_NUM_CPU  "--time=$VSC_RUN_TIME" "--mem-per-cpu=$VSC_MEM_PER_CPU_CORE" -e "error.dat" $VSC_SNUM_GPU $VSC_JOB_ARGS<<ENDBSUB
+#!/bin/bash
 module load $VSC_MODULE_COMMAND
 export XDG_RUNTIME_DIR="\$HOME/vsc_runtime"
 VSC_IP_REMOTE="\$(hostname -i)"
 echo "Remote IP:\$VSC_IP_REMOTE" >> /cluster/home/$VSC_USERNAME/vscip
-code-server --bind-addr=\${VSC_IP_REMOTE}:8899
+code-server --bind-addr=\${VSC_IP_REMOTE}:\${VSC_REMOTE_PORT}
 ENDBSUB
+)
+                ;;
+esac
 
-BJOB_ID=$(cat BJOB_ID_FILE | awk '{print $2}'| sed 's/[><]//g')
-rm BJOB_ID_FILE
+# TODO: get jobid for both cases (LSF/Slurm)
+# store jobid in a variable
+# VSC_BJOB_ID=$(echo $VSC_BJOB_OUT | awk '/is submitted/{print substr($2, 2, length($2)-2);}')
 
 # wait until batch job has started, poll every $VSC_WAITING_INTERVAL seconds to check if /cluster/home/$VSC_USERNAME/vscip exists
 # once the file exists and is not empty the batch job has started
@@ -321,10 +399,9 @@ ENDSSH
 # give the code-server a few seconds to start
 sleep 7
 
-# get remote ip, port and token from files stored on Euler
+# get remote ip and token from files stored on Euler
 echo -e "Receiving ip, port and token from the code-server"
 VSC_REMOTE_IP=$(ssh $VSC_SSH_OPT "cat /cluster/home/$VSC_USERNAME/vscip | grep -m1 'Remote IP' | cut -d ':' -f 2")
-VSC_REMOTE_PORT=8899
 
 # check if the IP, the port and the token are defined
 if  [[ "$VSC_REMOTE_IP" == "" ]]; then
@@ -350,6 +427,10 @@ VSC_LOCAL_PORT=$((3 * 2**14 + RANDOM % 2**14))
 echo -e "Using local port: $VSC_LOCAL_PORT"
 
 # write reconnect_info file
+#
+# FIXME: add jobid
+# BJOB ID           : $VSC_BJOB_ID
+
 cat <<EOF > $VSC_SCRIPTDIR/reconnect_info
 Restart file
 Remote IP address : $VSC_REMOTE_IP
@@ -357,7 +438,6 @@ Remote port       : $VSC_REMOTE_PORT
 Local port        : $VSC_LOCAL_PORT
 SSH tunnel        : ssh $VSC_SSH_OPT -L $VSC_LOCAL_PORT:$VSC_REMOTE_IP:$VSC_REMOTE_PORT -N &
 URL               : http://localhost:$VSC_LOCAL_PORT
-BJOB ID           : $BJOB_ID
 EOF
 
 # setup SSH tunnel from local computer to compute node via login node
@@ -372,7 +452,7 @@ sleep 5
 # save url in variable
 VSC_URL=http://localhost:$VSC_LOCAL_PORT
 echo -e "Starting browser and connecting it to the code-server"
-echo -e "Connecting to url $VSc_URL"
+echo -e "Connecting to url $VSC_URL"
 
 # start local browser if possible
 if [[ "$OSTYPE" == "linux-gnu" ]]; then
@@ -384,4 +464,4 @@ elif [[ "$OSTYPE" == "msys" ]]; then # Git Bash on Windows 10
 else
         echo -e "Your operating system does not allow to start the browser automatically."
         echo -e "Please open $VSC_URL in your browser."
-fi
+fi
\ No newline at end of file

vsconfig.example

@@ -5,3 +5,4 @@ VSC_RUN_TIME="01:00"        # Run time limit for the code-server in hours and mi
 VSC_MEM_PER_CPU_CORE=1024   # Memory limit in MB per core
 VSC_WAITING_INTERVAL=60     # Time interval to check if the job on the cluster already started
 VSC_SSH_KEY_PATH=""         # Path to SSH key with non-standard name
+VSC_JOB_ARGS=""             # Additional arguments when submitting the job