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The following best practices document is provided as courtesy of the HPC Advisory Council.
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References
Overview
NAMD, is a parallel molecular dynamics code designed for high-performance simulation of large bio-molecular systems. Based on Charm++ parallel objects. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. For more information about NAMD, refer to
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This post show the installation, configuration and slurm script execution for hpcx and intel MPI layers.
Versions and Setup Details
- This example uses NAMD version 2.12 sources. Download
- Setup used: Heimdall
- OS RHEL 6.6
- Intel Compiler
- HPC-X installed
Prerequisites
- Download NAMD_2.12_Source.tar.gz from here.
- You may need to compile tcl and fttw packages, if not available on your server, refer NAMD homepage for more info.
Compile NAMD
1. Extract the NAMD tar file and charm tar
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$ cd Linux-x86_64-icc $ make -j 10 ... $ ls -al namd2 -rwxrwxr-x 1 namd namd 27015710 Sep 27 16:44 namd2 |
Run the Benchmark
Download the input file from http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz or use other file.
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$ mpirun -np <number of procs> <MPI FLAGS> namd2 apoa1.namd |
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