Running NWChem

First Run

For first time users, you need to setup your NWChem environment. Make a copy of the file /usr/local/share/NWChem-6.3/data/default.nwchemrc to your home directory.
For example: cp /usr/local/share/NWChem-6.3/data/default.nwchemrc ~/.nwchemrc

Important Note for SCF, DFT, MP2, CCSD Modules

These modules by default write a lot of their calculations to disk. In the past, this was because systems were tight on memory or compute cabability and writing their calculations to disk would save on time when it needed to use these calulations later on. Today this is no longer the case and in fact can slow down the entire cluster due to the increased IO traffic over the network. Please use these settings to disable the caching of this data to disk:

semidirect memsize 200000000 filesize 0 # this uses 1.6 GB of memory and no disk for caching integrals

direct # all integrals are computed on the fly

scratchdisk 1024 # use 1 GB of disk per process for intermediates

nodisk # most integrals are computed on-the-fly

See an example job script below:

NWChem code


Using Local Disk on Node

It may be desirable to have your job run on the local disk on a node instead of writing to the network disk. The grid engine automaticly creates a directory for each job and this location can be used for this purpose. First stage your files to $TMPDIR, then change directory using cd, run NWChem within that directory. $TMPDIR will be destroyed after the job completes. In the following example, all output from NWChem is captured to the job output log file.

NWChem code