56 lines
2.3 KiB
Bash
Executable File
56 lines
2.3 KiB
Bash
Executable File
#!/bin/bash
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# Slurm submission script to start a Jupyterlab instance on the RA cluster for
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# data analysis Cristallina @ SwissFEL.
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# Requirements: user account on RA and access to /sf/cristallina
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# To execute from cristallina console use:
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# ssh your_username@ra.psi.ch "srun /sf/cristallina/applications/conda/jupyter_on_ra.sh"
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# or when using more computing power we start a batch job which takes the options below into account:
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# ssh your_username@ra.psi.ch "sbatch /sf/cristallina/applications/conda/jupyter_on_ra.sh"
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# alternatively we can also run on the SwissFEL computing nodes: sf-cn-1
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#SBATCH --job-name=analysis # Job name
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#SBATCH --partition week # or week, shared, hour, day-rhel8
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#SBATCH --nodes=1 # Run all processes on a single node
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#SBATCH --ntasks=1 # Run a single task
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#SBATCH --cpus-per-task=14 # Number of CPU cores per task
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#SBATCH --mem-per-cpu=16G
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#SBATCH --time=96:00:00 # Time limit hrs:min:sec
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#SBATCH --output=jupyterlab_%j_%N.log # Standard output and error log
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#SBATCH --exclude=ra-c-[085-100] # older AMD Epyc nodes which are problematic with bitshuffle
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echo "Starting Jupyterlab..."
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echo "Date = $(date)"
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echo "Hostname = $(hostname -s)"
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echo "Working Directory = $(pwd)"
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echo ""
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echo "Number of Nodes Allocated = $SLURM_JOB_NUM_NODES"
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echo "Number of Tasks Allocated = $SLURM_NTASKS"
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echo "Number of Cores/Task Allocated = $SLURM_CPUS_PER_TASK"
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# loading our minimal conda environment
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source /sf/cristallina/applications/conda/envs/miniconda/etc/profile.d/conda.sh
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# and activating the actual analysis environment
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# a bit more conservative: conda activate /sf/cristallina/applications/conda/envs/analysis_forge
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conda activate /sf/cristallina/applications/conda/envs/analysis_edge
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# password equivalent
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export JUPYTER_TOKEN=cristallina
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# single user:
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# jupyter lab --no-browser --ip 0.0.0.0 --YDocExtension.disable_rtc=True
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# experimental: use collaboration environment:
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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
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echo "Jupyterlab finished."
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# cleanup
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echo "Cleaning up temporary database files"
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find "/tmp" -type f -name "ystore_[0-9]*.db" -exec rm {} \;
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