Biowulf High Performance Computing at the NIH
cisTEM on Biowulf

cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

References:

Documentation
Important Notes

cisTEM is a beta release. The program may crash for unknown reasons. Please submit issues to the cisTEM Forum.

Interactive use of cisTEM requires a graphical X11 connection.NX and XQuartz work reasonably well.

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

There are a few very big problems with running cisTEM on the Biowulf cluster!!

The NIH staff has made available a special QOS for allocating an interactive session for longer than normal. From within an NX or XQuartz session, allocate a minimal allocation for 5 days:

[user@biowulf]$ sinteractive --qos=cistem --time=5-00:00:00
...
[user@cn3144 ~]$

Access to the cistem QOS is only by request. Please contact staff@hpc.nih.gov to be granted access.

Start a cisTEM job on the batch system with appropriate allocations:

[user@cn3144 ~]$ sbatch \
  --partition=multinode \
  --constraint=ibfdr \
  --time=1-00:00:00 \
  --ntasks=128 \
  --ntasks-per-node=8 \
  --mem-per-cpu=2g \
  --wrap="ml cisTEM; generate_run_profile > ${SLURM_JOB_ID}_run_profile.txt; cisTEM; rm ${SLURM_JOB_ID}_run_profile.txt"
15465689

Once the batch job begins running, the CisTEM GUI should pop up:

cisTEM splash page

Click on 'Create a new project', fill in the boxes, then click 'Settings', then 'Import'. There should be a file whose name matches the jobid:

[user@cn3144 ~]$ ls *.txt
15465689_run_profile.txt
cisTEM run_profile import

Click 'Open'. Now you have a custom run profile specifically for the current batch job:

cisTEM run_profile import

Any tasks run within CisTEM using this run profile will launch commands across the cpus allocated in the batch job.