Commit b43a57c6 authored by bliven_s's avatar bliven_s
Browse files

Merge branch 'namd' into 'master'

Add NAMD module

See merge request Pmodules/buildblocks!51
parents f2204e4f 6f9adf7f
NAMD
----
This directory (and /opt/psi/MPI/NAMD) is reserved for a future compiled version of NAMD.
We currently use pre-compiled binaries. These are located in Tools/NAMD.
NAMD
----
NAMD uses a non-commercial license. A disclaimer is printed when the module is loaded.
Installation
============
[Release Notes](https://www.ks.uiuc.edu/Research/namd/cvs/notes.html)
1. A NAMD account is needed to download binaries
2. Create new directory `/opt/psi/MPI/NAMD/$VERSION`
3. Download the latest binary.
- Use `NAMD_$VERSION_Linux-x86_64-verbs-smp-CUDA.tar.gz` for _gpu
- Use `NAMD_$VERSION_Linux-x86_64-verbs-smp.tar.gz` for non-gpu
4. Unpack to the new directory with `tar -xzvf NAMD*.tar.gz --strip-components=1 -C /opt/psi/MPI/NAMD/$VERSION`
5. Clean up:
mkdir bin
find . -maxdepth 1 -executable -type f -exec mv '{}' bin ';'
6. Add new variant to files/variants
7. Run the build-script to install the modulefile and to set the release
#!/usr/bin/env modbuild
# Binary distribution with manual installation. See README.md
pbuild::add_to_group 'Tools'
pbuild::prep() {
:
}
pbuild::configure() {
:
}
pbuild::compile() {
:
}
pbuild::install() {
:
}
NAMD/2.13 unstable
NAMD/2.13_gpu unstable cuda/9.2.148
#%Module1.0
set disclaimer {NAMD is available for Non-Commercial Use only. Before using, please review the
license (http://www.ks.uiuc.edu/Research/namd/license.html). You should also
acknowledge the developers:
"NAMD was developed by the Theoretical and Computational Biophysics Group
in the Beckman Institute for Advanced Science and Technology at the
University of Illinois at Urbana-Champaign."
And cite the reference:
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad
Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant
Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of
Computational Chemistry, 26:1781-1802, 2005. abstract, journal
And link the website: http://www.ks.uiuc.edu/Research/namd/}
module-whatis "Scalable Molecular Dynamics Software"
module-url "http://www.ks.uiuc.edu/Research/namd/"
module-license "NAMD Non-Commercial License (http://www.ks.uiuc.edu/Research/namd/license.html)"
module-maintainer "Spencer Bliven <spencer.bliven@psi.ch"
module-help "NAMD is a parallel molecular dynamics code designed for high-performance
simulation of large biomolecular systems. Based on Charm++ parallel objects,
NAMD scales to hundreds of cores for typical simulations and beyond 500,000
cores for the largest simulations. 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.
${disclaimer}"
puts stderr $disclaimer
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