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PyCoCo
Overview
PyCoCo (“Complementary Coordinates”) is a method for testing and potentially enriching the variety of conformations within an ensemble of molecular structures.
Version 0.3.0 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing this software on the CSF. Please reference the following if using PyCoCo in your work:
Set up procedure
To access the software you must first load the modulefile:
module load apps/binapps/extasy_coco/0.3.0
This will automatically load the Anaconda Python (v2.3.0) modulefile which provides python 2.7.10.
Running the application
Please do not run pyCoCo on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings ## This is a serial jobscript (1 core) so turn off MPI parallelism with --nompi pyCoCo --nompi -i INPUT -t TOPOLOGY -o OUTPUT
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 4 # Single-node multi-core jobs (number of cores can be 2-24) ## $NSLOTS is automatically set to the number of cores given above mpirun -n $NSLOTS pyCoCo -i INPUT -t TOPOLOGY -o OUTPUT
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.