Public install at GA (DIII-D)¶
The supported servers for executing OMFIT at GA are the iris and saturn clusters, which use UNIX modules to administer software.
To load the stable or unstable versions users can do:
> module purge # purge existing modules (some OMFIT environments conflict with default Python environment)
# do one of the following
> module load omfit # to load the OMFIT stable version - recommended (if not developing or instructed otherwise)
> module load omfit/unstable # to load the OMFIT unstable version - leading edge
> omfit # start OMFIT (notice that the stable/unstable version depends on the loaded module)
Tip
New users might want to take a look at the Run section.
Scratch areas on iris¶
It is very important that you understand the policies for the scratch areas of iris, as given under the heading “Scratch areas” of https://diii-d.gat.com/diii-d/Iris. In particular, when OMFIT imports a module, it makes a copy of the files of the module in a subdirectory of the environmental variable OMFIT_TMPDIR, which on iris is /local-scratch. These files will be deleted after 32 days, even if the OMFIT session is active, and their absence causes OMFIT to not be able to save the current session to a project. If you know that you will have a session open for a very long time, then you could try setting OMFIT_TMPDIR to something else, but it is likely to cause other problems, and so it is just better to be aware of this time limit, and be sure to save your sessions at least daily. Also, there is a limited amount of space on the /local-scratch drives, which is sufficient for most workflows, but not SOLPS and GATO workflows, where really setting OMFIT_TMPDIR to /cluster-scratch is more appropriate for its larger disk space.
Loading older projects and further explanation of available modules¶
If you have problems loading an old project, especially OMFITprofiles results, there are several omfit modules set up on iris that you should try, each one having its own version of python and OMFIT:
omfit/v0.24 # good for very old projects on iris
omfit/v0.25 # was omfit (omfit/master) prior to 4 Dec 2018
omfit/v0.26 # was omfit/unstable prior to 4 Dec 2018
omfit/v1.0 # has newest python environment
Recall the -p command line option for omfit to easily open a project from the command line:
module load omfit
omfit -p /fusion/projects/omfit-results/<user>/projects/<project_name>
Memory or CPU intensive jobs¶
The iris cluster has two types of nodes: login nodes and worker nodes. When you ssh iris, there is an algorithm to put you on the least loaded iris login node, which will be irisa, irisb, irisc, or irisd. It is possible that your OMFIT job can be killed on one of these nodes if the node is running out of memory, and you have the largest job. Instead of running on a login node, it is possible to start OMFIT on a worker node (iris01 to iris26) by the following methodology requiring two separate simultaneous terminal sessions:
# TERMINAL 1:
srun -p interactive,medium --ntasks-per-node=1 --pty /bin/bash
echo $SLURM_NODELIST
# TERMINAL 2 on an iris login node:
ssh -X HOST_FROM_TERMINAL_1
module load omfit
omfit
Note that the interactive partition reserves for a 3 hour time limit, after which your session will be killed.
Other partitions are short (30 mins), medium (1 day), long (7 days).
More details about running on iris can be found at https://diii-d.gat.com/diii-d/Iris
Remote connection to GA workstations¶
If you are outside of the GA network you will need to go through the cybele firewall which accepts incoming connections on the port 2039.
The firewall also accepts NoMachine connections (make sure to use the SSH login, otherwise it will not work). This is the best way to run OMFIT on the GA workstations.
From Windows you can also use mobaxterm (X11 server + ssh client) to run graphical applications on a Unix server. This will however perform significanlty worse than NoMachine.
Connection to D3DRDB SQL database¶
Connection to the D3DRDB relational database requires the file D3DRDB.sybase_login to be present in the $HOME directory of the user on the workstation where OMFIT is running. You should be able to copy this file from the $HOME folder on the GA iris cluster. If this file is not available to you contact the GA computer group: iris-support [at] fusion.gat.com
Guest wifi at GA blocks access to GitHub¶
This issue can be circumvented by accessing git using ssh over the https port. Edit ~/.ssh/config and add:
Host github.com
Hostname ssh.github.com
Port 443
tensorflow¶
Due to the age of the operating system on iris, the latest versions of tensorflow that are compatible with the latest versions of numpy are not compatible with iris. To get a tensorflow version of OMFIT, use:
module purge
module load omfit/tensorflow
Contacts¶
In case of problems please contact Orso Meneghini, or Sterling Smith.