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We can also get more granular in talking about where to store your files, specifically what directories a cluster user can write to on O2. Every cluster user has a /home directory with a 100GiB quota. When you login to the cluster, you will be placed in your home directory. This directory is named like /home/user, where "user" is replaced with your eCommons HMS ID in lowercase. Additionally, each cluster user can use /n/scratch3 for storage of temporary or intermediary files. The per-user scratch3 quota is 10TiB or 1 million files/directories. Any file on scratch3 that is not accessed for 30 days will be deleted, and there are no backups of scratch3 data. A cluster user must create their scratch3 directory using a provided script. Finally, there are lab or group directories. These are located under /n/groups, /n/data1, or /n/data2. The quota for group directories is shared for all group members, and there is not a standard quota that all groups have. Any of these directory options (/home, /n/scratch3, group directory) can be used to store data that will be computed against on O2. When you submit a job to the SLURM scheduler on O2, you will need to mention in which directory your data (that you want to compute on) is stored and where you want the output data to be stored.
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Note: Any time <userid> is mentioned in this document, it should be replaced with your HMS account, ID (formerly called an eCommons ID () and omit the <>). Likewise, <jobid> should be replaced with an actual job ID, such as 12345. The name of a batch job submission script should be inserted wherever <jobscript> is mentioned.
SLURM command | Sample command syntax | Meaning |
|---|---|---|
sbatch |
| Submit a batch (non-interactive) job. |
srun |
| Start an interactive session for five minutes in the interactive queue with default 1 CPU core and 4GB of memory |
squeue |
| View status of your jobs in the queue. Only non-completed jobs will be shown. We have an easier-to-use alternative command called O2squeue. |
scontrol |
| Look at a running job in detail. For more information about the job, add the |
scancel |
| Cancel a job. |
scontrol |
| Pause a job |
scontrol |
| Release a held job (allow it to run) |
sacct |
| Check job accounting data. Running We have an easier-to-use alternative command called O2sacct. |
sinfo |
| See node and partition information. Use the |
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You will need to connect to O2 with the -XY flags in your SSH command. Substitute <username> for your eCommonsHMS ID:
| Code Block |
|---|
$ ssh -XY <username>@o2.hms.harvard.edu |
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