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Info
titleAccess to SDF files

If you were working on SDF, note that S3DF is completely separate (aside from the account name). Even though path names might look similar, they are on different file systems. You can still access all your SDF files by prepending "/fs/ddn/" to the paths you were used to.

Info
titleSoftware and Containers

Fermitools and other analysis software (e.g., 3ML) are available via shared Conda installation, so you don't need to install Conda yourself.

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See Fermitools/Conda Shared Installation at SLAC.  If you do want your own Conda, you shouldn't install it in your home directory due to quota limits; put it in your Fermi-supplied user space. Follow

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the S3DF documentation

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 instructions to install Conda and set a prefix path for the Conda installation that will put it and any environments you create in your group-provided space. However, you should use a prefix to your personal space, e.g., /sdf/group/fermi/u/$USER/miniconda3, instead of the path in their example.

You can also run a RHEL6 Singularity container (for apps that are not portable to RHEL/Centos7).

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See Using RHEL6 Singularity Container.

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titleSlurm Batch Usage

For generic advice on running in batch,

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see Running on SLAC Central Linux.  Note that the actual batch system has changed and we have not updated the doc to reflect that. This is advice on copying data to local scratch, etc.

  • LSB_JOBID -> SLURM_JOB_ID
  • scratch space during job execution:
    • at job start, a directory is automatically created on the scratch of the worker: ${LSCRATCH} = /lscratch/${USER}/slurm_job_id_${SLURM_JOB_ID}
    • once all of a user's jobs on a node are completed/exited, their corresponding LSCRATCH directory on that host is deleted.



Info
titleUsing cron

You can run cronjobs in S3DF. Users don't have to worry about token expiration like on AFS. Select one of the iana interactive nodes (and remember which one!) to run on.

Note: crontab does NOT inherit your environment. You'll need to set that up yourself.

Since crontab is per host (no trscrontab), if the node is reinstalled or removed, the crontab will be lost. It's probably best to save your crontab as a file in your home directory so that you can re-add your cronjobs if this happens:

crontab -l > ~/crontab.backup

Then to re-add the jobs back in:

crontab ~/crontab.backup

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