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.


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!!

Thus, it is best to run small jobs on the local resources. For example, allocate an interactive session with 48 CPUs:

[user@biowulf]$ sinteractive --cpus-per-task=48 --mem-per-cpu=2g --time=36:00:00
[user@cn3144 ~]$ module load cisTEM
[user@cn3144 ~]$ cisTEM

Then launch jobs using the simplest run profile:

Simple run profile example

If you are brave and want a challenge, jobs that span multiple nodes can be run. Allocate a basic interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load cisTEM
[user@cn3144 ~]$ cisTEM

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

By default, all cisTEM jobs will run on the interactive node. To submit cisTEM jobs to the cluster, create a run profile under settings with the following:

The Manager Command creates a batch job on the biowulf cluster. This job then launches #ntasks single-threaded jobs on the allocated resources. The number of tasks depends on the job being run. Typical values would be 9, 65, or 257. Then, when you run an action, choose the appropriate Run Profile.

The [ ... etc ... ] should be substituted with appropriate sbatch options, such as:

Here is an example of a run profile that can run 64 commands simultaneously:

Run profile example