Difference between revisions of "MCNPX"

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== Introduction  ==
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[[Category:Software]]
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{|<!--CONFIGURATION: REQUIRED-->
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|{{#vardefine:app|MCNPX}}
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|{{#vardefine:url|http://mcnpx.lanl.gov/}}
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:pbs|1}}            <!--PBS SCRIPTS-->
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|{{#vardefine:policy|}}        <!--POLICY-->
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|{{#vardefine:testing|}}      <!--PROFILING-->
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|{{#vardefine:faq|}}            <!--FAQ-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
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|{{#vardefine:installation|}} <!--INSTALLATION-->
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|}
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<!--BODY-->
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<!--Description-->
 +
{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
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'''MCNPX''' ,  Monte Carlo N-Particle eXtended, is a general-purpose Monte Carlo radiation transport code for modeling the interaction of radiation with everything. It extends the capabilities of MCNP4C3 to nearly all particles, nearly all energies, and to nearly all applications without an additional computational time penalty.
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MCNPX ,  Monte Carlo N-Particle eXtended, is a general-purpose Monte Carlo radiation transport code for modeling the interaction of radiation with everything. It extends the capabilities of MCNP4C3 to nearly all particles, nearly all energies, and to nearly all applications without an additional computational time penalty.
  
 
Please note, MCNPX is installed on HPC Center's RedHat EL6 systems. Please read the section of "Execution Instructions..." below for information on how to access the software.
 
Please note, MCNPX is installed on HPC Center's RedHat EL6 systems. Please read the section of "Execution Instructions..." below for information on how to access the software.
  
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== Version 2.7.0  ==
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<!--Modules-->
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==Required Modules==
 +
===Serial===
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* intel
 +
* mcnpx
  
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The configuration and compilation flags used are:
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==System Variables==
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<pre>
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* AMBERHOME
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configure --with-FC=ifort --with-CC=icc
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<!--Configuration-->
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</pre>
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
 +
|}}
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<!--Run-->
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{{#if: {{#var: exe}}|==Additional Information==
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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|}}
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<!--PBS scripts-->
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{{#if: {{#var: pbs}}|==PBS Script Examples==
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
 +
|}}
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<!--Policy-->
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{{#if: {{#var: policy}}|==Usage Policy==
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WRITE USAGE POLICY HERE (Licensing, usage, access).
 +
|}}
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<!--Performance-->
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{{#if: {{#var: testing}}|==Performance==
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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|}}
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<!--Faq-->
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{{#if: {{#var: faq}}|==FAQ==
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*'''Q:''' **'''A:'''|}}
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<!--Citation-->
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{{#if: {{#var: citation}}|==Citation==
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===Serial Version===
 +
If you publish research that uses {{#var:app}} you have to cite it as follows: <br/>
 +
D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.
  
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Installation location:
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===GPU Version===
 +
If you make use of any of this GPU support in your work please use the following citations: <br/>
  
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<pre>
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Andreas W. Goetz; Mark J. Williamson; Dong Xu; Duncan Poole; Scott Le Grand;  & Ross C. Walker* "Routine microsecond molecular dynamics simulations with AMBER - Part I: Generalized Born", J. Chem. Theory Comput., 2012, 8 (5), pp 1542-1555 , DOI: 10.1021/ct200909j
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/apps/mcnpx/2.7.0
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</pre>
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D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.
  
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==Using Modules==
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|}}
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* What is a Module System:
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<!--Installation-->
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:Module system is a utility to manage application execution environment - compilers, runtime libraries, application executables. Your execution environment can be set by simply loading the appropriate modules. For more information, please refer to [[From_mpi-selector_to_environment_modules]].
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{{#if: {{#var: installation}}|==Installation==
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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*To use MCNPX:
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<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
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module load intel mcnpx
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__NOTOC____NOEDITSECTION__
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==Single-Threaded Execution==
 
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===Required Modules===
 
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<source lang=bash>
 
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module load intel
 
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module load mcnpx
 
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</source>
 
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===Sample Submission Script===
 
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<source lang=bash>
 
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#!/bin/bash
 
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#PBS -N mcnpx
 
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#PBS -r n
 
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#PBS -o mcnpout
 
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#PBS -e mcnperr
 
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#PBS -j oe
 
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#PBS -m abe
 
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#PBS -M <your_email_address>
 
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#PBS -l walltime=99:00:00
 
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#PBS -l nodes=1:ppn=1
 
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#PBS -l pmem=900mb
 
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#PBS -q submit
 
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#
 
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module load intel
 
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module load mcnpx
 
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#
 
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cd $PBS_O_WORKDIR
 
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mcnpx i=m24-0-0B o=m24-0-0Bo
 
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</source>
 
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==Parallel (MPI) Execution==
 
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===Required Modules===
 
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<source lang=bash>
 
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module load intel
 
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module load openmpi
 
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module load mcnpx
 
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</source>
 
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===Sample Submission Script===
 
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<source lang=bash>
 
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#!/bin/bash
 
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#PBS -N mpitest
 
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#PBS -r n
 
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#PBS -o mcnpout
 
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#PBS -e mcnperr
 
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#PBS -j oe
 
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#PBS -m abe
 
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#PBS -M <your_email_address>
 
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#PBS -l walltime=99:00:00
 
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#PBS -l nodes=2:ppn=8:infiniband
 
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#PBS -l pmem=900mb
 
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#PBS -q submit
 
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#
 
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module load intel
 
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module load openmpi
 
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module load mcnpx
 
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#
 
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cd $PBS_O_WORKDIR
 
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mpiexec mcnpx i=m24-0-0B o=m24-0-0Bo
 
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</source>
 
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== Reference  ==
 
−
 
 
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MCNPX website: http://mcnpx.lanl.gov/
 

Revision as of 15:27, 15 January 2013

Description

MCNPX website  

MCNPX , Monte Carlo N-Particle eXtended, is a general-purpose Monte Carlo radiation transport code for modeling the interaction of radiation with everything. It extends the capabilities of MCNP4C3 to nearly all particles, nearly all energies, and to nearly all applications without an additional computational time penalty.

Please note, MCNPX is installed on HPC Center's RedHat EL6 systems. Please read the section of "Execution Instructions..." below for information on how to access the software.

Required Modules

Serial

  • intel
  • mcnpx

System Variables

  • AMBERHOME


PBS Script Examples

See the MCNPX_PBS page for MCNPX PBS script examples.


Citation

Serial Version

If you publish research that uses MCNPX you have to cite it as follows:
D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.

GPU Version

If you make use of any of this GPU support in your work please use the following citations:

Andreas W. Goetz; Mark J. Williamson; Dong Xu; Duncan Poole; Scott Le Grand; & Ross C. Walker* "Routine microsecond molecular dynamics simulations with AMBER - Part I: Generalized Born", J. Chem. Theory Comput., 2012, 8 (5), pp 1542-1555 , DOI: 10.1021/ct200909j

D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.


Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=MCNPX&oldid=10520"