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20 changes: 12 additions & 8 deletions sphinx_docs/source/nersc-workflow.rst
Original file line number Diff line number Diff line change
Expand Up @@ -78,13 +78,18 @@ each OpenMP thread per physical core, so it is best to set ``OMP_NUM_THREADS`` t
.. literalinclude:: ../../job_scripts/perlmutter-cpu/perlmutter_cpu.slurm
:language: sh


Submitting and checking status
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. note::

Jobs should be run in your ``$SCRATCH`` directory. By default,
SLURM will change directory into the submission directory.
Jobs should be run in your ``$SCRATCH`` directory and not
your home directory.

By default, SLURM will change directory into the submission
directory.

Alternately, you can run in the common file system, ``$CFS/m3018``,
which everyone in the project has access to.

Jobs are submitted as:

Expand All @@ -110,7 +115,8 @@ to cancel a job, you would use ``scancel``.
Filesystems
^^^^^^^^^^^

We can run on the common filesystem, CFS, to share files with everyone
In addition to ``$SCRATCH``, there is a project-wide directory
on the common filesystem, CFS. This allows us to share files with everyone
in the project. For instance, for project ``m3018``, we would do:

.. prompt:: bash
Expand Down Expand Up @@ -153,9 +159,7 @@ You can view the job dependency using:

squeue -l -j job-id

where ``job-id`` is the number of the job. A job can be canceled
using ``scancel``, and the status can be checked using ``squeue -u
username`` or ``squeue --me``.
where ``job-id`` is the number of the job.



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