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Gromacs

Created Wednesday 24 August 2016

Overview

Classic Molecular Dynamics code using force fields, Gromacs is able to similate 10^8 partciles

http://www.gromacs.org/

Source

git clone git://git.gromacs.org/gromacs.git gromacs.git

Some patches are required (unless marked 'RESOLVED'):

• Patch1 (fixes [http://redmine.gromacs.org/issues/1280 Issue 1280]) 'RESOLVED'
• Patch2 (fixes [http://redmine.gromacs.org/issues/1281 Issue 1281]) 'RESOLVED'
• Patch3 (fixes [http://redmine.gromacs.org/issues/1282 Issue 1282]) 'RESOLVED'
• Patch4 (fixes [http://redmine.gromacs.org/issues/1283 Issue 1283]) 'RESOLVED'
• Patch5 (fixes [http://redmine.gromacs.org/issues/1284 Issue 1284]) 'RESOLVED'

Building in Blue Gene/Q

This is how to build Gromacs on Blue Gene/Q:

mkdir build && \
cd build && \
cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-CXX \
-DCMAKE_PREFIX_PATH=/soft/libraries/alcf/current/xl/FFTW3

NOTE: You must ./build in an empty build directory.

QPX

It would be nice to add QPX kernels to Gromacs.

• http://bugzilla.gromacs.org/issues/1064 has details.
• http://www.gromacs.org/Developer_Zone/Programming_Guide/Verlet_SIMD_kernels Implementing support for a new SIMD instruction set
• Need to ask for pointers on the nonbonded vector code, which appears to be auto-generated.

Update: QPX support has recently been introduced in Gromacs. Peruse the Gromacs developer list for more information.

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