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NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters.
It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources.
NWChem has been developed by the High-performance Computational Chemistry group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project.
The suite utilizes parallel-programming tools developed by PNNL staff, and in particular the Global Array toolkit which provide an efficient and portabl shared-memory programming interface for distributed-memory computers.
The functionality of the code, as well as full documentation is provided at the NWChem Home Page
To access the code you will need to have your ID added to the nwchem UNIX group, contact the HPCx helpdesk for this. There is no need to sign a licence agreement for usage on the HPCx system.
NWChem is executed in the usual manner for a LAPI based code, typically using poe. The executable for the NWChem-4.5 version is provided at /usr/local/packages/nwchem/nwchem-4.5/bin/LAPI64/nwchem.
To run the code under Loadleveler you can copy a sample script from the sample directory (/usr/local/packages/nwchem/sample) and adapt as required. You will need to change at least the account field, and the number of nodes requested. The suggested sample script includes the following recommended environment variable settings for running NWChem on HPCx :
export LAPI_USE_SHM=yes export MP_SHARED_MEMORY=yes export MP_EUILIB=us export MP_EUIDEVICE=csss export MP_MSG_API=lapi export MP_CSS_INTERRUPT=yes export AIXTHREAD_SCOPE=S export MP_POLLING_INTERVAL=15000 export RT_GRQ=ONOf these, the polling interval may be adjusted to tune performance. Please see the HPCx documentation for more information on job submission scripts.
You can optionally provide a file, ~/.nwchemrc, containing settings which NWChem will read on start up. A sample .nwchemrc is given below:
ffield amber amber_s /usr/local/packages/nwchem/nwchem-4.5/src/data/amber_s/ amber_x /usr/local/packages/nwchem/nwchem-4.5/src/data/amber_x/ spce /usr/local/packages/nwchem/nwchem-4.5/src/data/solvents/spce.rstIn our experience, you do not need this for QM calculations unless you wish to change the choice of location for files used by the program (e.g. the basis set library file).
There are no distinct pre and post processing phases for NWChem. However, a problem solving environment developed at the EMSL, Ecce, provides a graphical environment for job preparation, launching and results visualisation. Ecce is freely available on signing a licence agreement.
The EMSL Software Agreement (which UoE HPCx Ltd has signed) stipulates that the use of NWChem will be acknowledged in any publications which use results obtained with NWChem. The acknowledgment should be of the form:
NWChem Version 4.5, as developed and distributed by Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington 99352 USA, and funded by the U. S. Department of Energy, was used to obtain some of these results. The words ``A modified version of'' should be added at the beginning, if appropriate. Note: Your EMSL Software Agreement contains the complete specification of the required acknowledgment.
Please use the following citation when publishing results obtained with NWChem:
High Performance Computational Chemistry Group, NWChem, A Computational Chemistry Package for Parallel Computers, Version 4.5 (2003), Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
If you use the DIRDYVTST portion of NWChem, please also use the additional citation:
DIRDYVTST, Yao-Yuan Chuang and Donald G. Truhlar, Department of Chemistry and Super Computer Institute, University of Minnesota; Ricky A. Kendall,Scalable Computing Laboratory, Ames Laboratory and Iowa State University; Bruce C. Garrett and Theresa L. Windus, Environmental Molecular Sciences Laboratory, Pacific Northwest Laboratory.
The developers of NWChem are not provide support to users outside the EMSL, and problems with the code on HPCx should be routed to the HPCx helpdesk.
Please see the NWChem Home Page.
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