CSD-System
Overview
CSD-System is a suite of tools for structural chemists. It includes the CSD Python API and GoldSuite.
Versions 2021 and 2020 are installed on the CSF.
Gold is part of this software suite.
Restrictions on use
This is not free or open source software. To gain access
- you must be an employee or student of the University of Manchester. Visitors/Collaborators are not allowed access.
The software may be used for
- any and all scientific research purposes, for publishable or proprietary work, and in any collaboration which does not involve payment of fees between the partners.
To gain access to this software: Please email its-ri-team@manchester.ac.uk and confirm that you will comply with the above conditions.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/binapps/csd/2021.3 module load apps/binapps/csd/2021.2 module load apps/binapps/csd/2021 module load apps/binapps/csd/2020
Running the application
Please do not run CSD on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example, this one runs a code which uses the CSD Python API:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript module load apps/binapps/csd/2020 # We need to set a variable to cope with the lack of display on the compute nodes export CCDC_PYTHON_API_NO_QAPPLICATION=0 python mypythoncode.py > myresults.txt
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Using gold
It is not possible to run GOLD on the login nodes (it is not registered/licensed there), instead use qrsh. For example:
qrsh -l short module load apps/binapps/csd/2020 gold &
Please note that you may see some messages and warnings when launching gold, as long as the GUI opens all should be well. Please note that the CSF is not an ideal platform for such applications and therefore the GUI may be slow to open and to run. You might be able to improve this by accessing he CSF via the virtual desktop service.