Compute Resources:
-
Have questions or need help with compute, including activation or issues? Follow this link.
Docker Usage:
-
The information contained on this page assumes that you have a knowledge base of using Docker to create images and push them to a repository for use. If you need to review that information, please see the links below.
-
Docker Basics: Building, Tagging, & Pushing A Custom Docker Image
Software Included
-
cisTem (https://cistem.org/software)
Development Notes
-
The official cisTEM documentation can be found here.
Dockerfile
-
The cisTEM image is hosted at the following location.
gcr.io/ris-registry-shared/cistem
Requirements for Usage in RIS
-
The following LSF variables are necessary for the image to run.
export LSF_DOCKER_PORTS='8080:8080' export PASSWORD=PASSWORD
-
Please see our documentation for more information on selecting a port.
The password cannot be left blank.
-
Once your LSF variables are set you can start up the docker image with the following command.
bsub -Is -G group-name -R 'rusage[mem=64000] select[port8080=1]' -q general-interactive -a 'docker(gcr.io/ris-registry-shared/cistem)' supervisord -c /app/supervisord.conf
If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with -G group_name or by setting the LSB_SUB_USER_GROUP variable.
-
Once the job is running it will output the node that the job started on.
<<Starting on compute1-exec-N.ris.wustl.edu>>
-
This then will be needed as part of the web address required to access the GUI.
https://compute1-exec-N.compute.ris.wustl.edu:8080/vnc.html
-
The password it asks for will be the one you set with the variable above.
-
To open the cisTEM application, type the following into the terminal inside the GUI and hit enter.
cisTEM
If you want to change the GUI display size in the browser, you can do so by using the following variables before running the job. The default width is 1024 and the default height is 768.
export DISPLAY_WIDTH=width export DISPLAY_HEIGHT=height