Slurm Tips for vg: Difference between revisions
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7. Build vg as a Slurm job. This will send the build out to the cluster as a 64-core, 80G memory job, and keep the output logs in your terminal. | 7. Build vg as a Slurm job. This will send the build out to the cluster as a 64-core, 80G memory job, and keep the output logs in your terminal. | ||
srun -c 64 --mem=80G make -j64 | srun -c 64 --mem=80G --time=00:30:00 make -j64 | ||
This will leave your vg binary at '''~/workspace/vg/bin/vg'''. | This will leave your vg binary at '''~/workspace/vg/bin/vg'''. | ||
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* If you want an interactive session with appreciable resources, you can schedule one with '''srun'''. For example, to get 16 cores and 120G memory all for you, run: | * If you want an interactive session with appreciable resources, you can schedule one with '''srun'''. For example, to get 16 cores and 120G memory all for you, run: | ||
srun -c 16 --mem 120G --pty bash -i | srun -c 16 --mem 120G --time=08:00:00 --partition=medium --pty bash -i | ||
* To send out a job without making a script file for it, use '''sbatch --wrap "your command here"'''. | * To send out a job without making a script file for it, use '''sbatch --wrap "your command here"'''. | ||
Revision as of 15:11, 5 January 2024
This page explains how to set up a development environment for vg on the Phoenix cluster.
Setting Up
1. After connecting to the VPN, connect to the cluster head node:
ssh phoenix.prism
This node is relatively small, so you shouldn't run real work on it, but it is the place you need to be to submit Slurm jobs.
2. Make yourself a user directory under /private/groups, which is where large data must be stored. For example, if you are in the Paten lab:
mkdir /private/groups/patenlab/$USER
3. (Optional) Link it over to your home directory, so it is easy to use storage there to store your repos. The /private/groups storage may be faster than the home directory storage.
mkdir -p /private/groups/patenlab/$USER/workspace ln -s /private/groups/patenlab/$USER/workspace ~/workspace
4. Make sure you have SSH keys created and add them to Github.
cat ~/.ssh/id_ed25519.pub || (ssh-keygen -t dsa && cat ~/.ssh/id_ed25519.pub) # Paste into https://github.com/settings/ssh/new
5. Make a place to put your clone, and clone vg:
mkdir -p ~/workspace cd ~/workspace git clone --recursive git@github.com:vgteam/vg.git cd vg
6. vg's dependencies should already be installed on the cluster nodes. If any of them seem to be missing, tell cluster-admin@soe.ucsc.edu to install them.
7. Build vg as a Slurm job. This will send the build out to the cluster as a 64-core, 80G memory job, and keep the output logs in your terminal.
srun -c 64 --mem=80G --time=00:30:00 make -j64
This will leave your vg binary at ~/workspace/vg/bin/vg.
Misc Tips
- If you want an interactive session with appreciable resources, you can schedule one with srun. For example, to get 16 cores and 120G memory all for you, run:
srun -c 16 --mem 120G --time=08:00:00 --partition=medium --pty bash -i
- To send out a job without making a script file for it, use sbatch --wrap "your command here".
- You can use arguments from SBATCH lines on the command line!
- You can use Slurm Commander to watch the state of the cluster with the scom command.
