Difference between revisions of "NAMD"
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| − | = | + | [[Category:Applications]] |
| + | [[Category:Showcase]] | ||
| + | |||
| + | = Background = | ||
| + | |||
| + | {| | ||
| + | !Link | ||
| + | !Code | ||
| + | !Version | ||
| + | !Date | ||
| + | |- | ||
| + | |[http://www.ks.uiuc.edu/Research/namd/ NAMD homepage] | ||
| + | |[http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD Download Page] | ||
| + | |2.6 | ||
| + | |February 2009 | ||
| + | |} | ||
| + | |||
| + | == Background == | ||
| + | |||
Currently this guide is for building NAMD and charm++ from source on x86 64-bit architecture. One would follow similar step on other machines but some of the file names would be changed. | Currently this guide is for building NAMD and charm++ from source on x86 64-bit architecture. One would follow similar step on other machines but some of the file names would be changed. | ||
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Verify that this program runs without any errors and that you get a profile file for each processor. | Verify that this program runs without any errors and that you get a profile file for each processor. | ||
| − | ==Building NAMD | + | ==Building NAMD== |
Begin in NAMD's home directory: | Begin in NAMD's home directory: | ||
| Line 48: | Line 66: | ||
%> make | %> make | ||
</pre> | </pre> | ||
| + | |||
| + | == Running NAMD == | ||
If everything works properly you should now have a '''namd2''' executable. Test by running: | If everything works properly you should now have a '''namd2''' executable. Test by running: | ||
| Line 53: | Line 73: | ||
%> ./charmrun ./namd2 +p4 src/alanin | %> ./charmrun ./namd2 +p4 src/alanin | ||
</pre> | </pre> | ||
| − | + | ||
| + | == Performance Data == | ||
| + | |||
| + | [[Image:NAMD-mean-profile.png|750px]] | ||
| + | [[Image:NAMD-work-profile.png|750px]] | ||
| + | [[Image:NAMD-mpi-comparison.png|750px]] | ||
Revision as of 01:27, 28 February 2012
Contents
Background
| Link | Code | Version | Date |
|---|---|---|---|
| NAMD homepage | Download Page | 2.6 | February 2009 |
Background
Currently this guide is for building NAMD and charm++ from source on x86 64-bit architecture. One would follow similar step on other machines but some of the file names would be changed.
Building Charm++
Automatic instrumentation of charm applications using TAU is available in the unreleased version of Charm++ which you can download here: http://charm.cs.uiuc.edu/download/ (click on the nightly CVS source archive). To compile Charm++:
%> cd charm %> ./build charm++ mpi-linux-x86_64 mpicxx ifort -O3 ... %> ./build Tau mpi-linux-x86_64 mpicxx ifort --tau-makefile=<tau_dir>/x86_64/lib/Makefile.tau-mpi -O3
As always the TAU Makefile you specify determines what profiling/tracing options are set. Wait for charm to finish building then test the configuration by:
%> cd mpi-linux-x86_64-ifort-mpicx/tests/charm++/simplearrayhello %> make OPTS='-tracemode Tau -no-trace-mpi' %> ./charmrun ./hello +p4
Verify that this program runs without any errors and that you get a profile file for each processor.
Building NAMD
Begin in NAMD's home directory:
%> cd NAMD_2.6_Source %> ./config Linux-x86_64-MPI-icc
Now set NAMD to use TAU, edit arch/Linux-x86_64-MPI-icc.arch to be:
NAMD_ARCH = Linux-x86_64 CHARMARCH = mpi-linux-x86_64-ifort-mpicxx CHARMOPTS = -memory os -tracemode Tau -no-trace-mpi FLOATOPTS = -ip -fno-rtti -xW CXX = $(CHARMC) -DMEMUSAGE_USE_SBRK CXXLINK = -i-static -O3 $(FLOATOPTS) CXXNOALIASOPTS = -O3 -fno-alias $(FLOATOPTS) CC = $(CHARMC)
Then build NAMD
%> cd Linux-x86_64-MPI-icc %> make
Running NAMD
If everything works properly you should now have a namd2 executable. Test by running:
%> ./charmrun ./namd2 +p4 src/alanin
Performance Data
