Difference between revisions of "NAMD"
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| − | = | + | [[Category:Applications]] |
| + | [[Category:Showcase]] | ||
| + | |||
| + | = Background = | ||
| + | |||
| + | {| | ||
| + | !Link | ||
| + | !Code | ||
| + | !Version | ||
| + | !Machine | ||
| + | !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 | ||
| + | |Linux x86_64 | ||
| + | |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. | ||
| Line 6: | Line 26: | ||
<pre> | <pre> | ||
%> cd charm | %> cd charm | ||
| − | %> ./build charm++ mpi-linux- | + | %> ./build charm++ mpi-linux-x86_64 mpicxx ifort -O3 |
... | ... | ||
| − | %> ./build | + | %> ./build Tau mpi-linux-x86_64 mpicxx ifort --tau-makefile=<tau_dir>/x86_64/lib/Makefile.tau-icpc-mpi --no-build-shared -O3 |
</pre> | </pre> | ||
| − | As always the TAU Makefile you specify determines what profiling/tracing options | + | 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: |
<pre> | <pre> | ||
| − | %> cd mpi-linux- | + | %> cd mpi-linux-x86_64-ifort-mpicx/tests/charm++/simplearrayhello |
| − | %> make OPTS='-tracemode Tau' | + | %> make OPTS='-tracemode Tau -no-trace-mpi' |
%> ./charmrun ./hello +p4 | %> ./charmrun ./hello +p4 | ||
</pre> | </pre> | ||
| − | Verify that this program runs without any errors and that you | + | 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: | ||
<pre> | <pre> | ||
%> cd NAMD_2.6_Source | %> cd NAMD_2.6_Source | ||
| − | %> ./config Linux- | + | %> ./config Linux-x86_64-icc --charm-base $CHARMROOT --with-cuda --cuda-prefix $CUDAROOT --with-fftw --with-fftw3 --fftw-prefix $FFTW |
</pre> | </pre> | ||
| − | Now set NAMD to use TAU, edit 'arch/Linux-x86_64 | + | Now set NAMD to use TAU, edit '''arch/Linux-x86_64-icc.arch''' adding this line: |
<pre> | <pre> | ||
| − | + | CHARMOPTS = -tracemode Tau | |
| + | </pre> | ||
| − | < | + | Then build NAMD |
| + | <pre> | ||
| + | %> cd Linux-x86_64-icc | ||
| + | %> make | ||
| + | </pre> | ||
| − | + | == NAMD with CUDA == | |
| − | + | To profile NAMD's CUDA kernel I few modifications need to be made to the build steps: | |
| − | |||
| − | |||
| − | + | in charm, do: | |
| − | + | ||
| + | %> ./build Tau mpi-linux-x86_64 mpicxx ifort --tau-makefile=<tau_dir>/x86_64/lib/Makefile.tau-icpc-mpi-cupti --no-build-shared -O3 | ||
| + | (change TAU makefile) | ||
| + | |||
| + | rebuild NAMD. | ||
| + | |||
| + | and run NAMD by doing: | ||
| + | |||
| + | mpirun -np 3 tau_exec -T icpc,mpi,cupti -cupti ./namd2 src/apoa1/apoa1.namd | ||
| + | |||
| + | (have the '-T' options match the TAU makefile) | ||
| + | == 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: | ||
<pre> | <pre> | ||
| − | %> ./charmrun | + | %> ./charmrun ./namd2 +p4 src/alanin |
</pre> | </pre> | ||
| − | + | ||
| + | == Performance Data == | ||
| + | |||
| + | Mean profile of a run with the performance benchmark ALANIN: | ||
| + | |||
| + | [[Image:NAMD-mean-profile.png|750px]] | ||
| + | |||
| + | Histogram of the enqueueWorkA routine across 32 processors: | ||
| + | |||
| + | [[Image:NAMD-work-profile.png|750px]] | ||
| + | |||
| + | A comparison of Timestep per second between two different MPI implementations on Ranger: | ||
| + | |||
| + | [[Image:NAMD-mpi-comparison.png|750px]] | ||
| + | |||
| + | [[Image:namd-apoa1.ppk]] | ||
Latest revision as of 19:20, 10 May 2012
Contents
Background
| Link | Code | Version | Machine | Date |
|---|---|---|---|---|
| NAMD homepage | Download Page | 2.6 | Linux x86_64 | 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-icpc-mpi --no-build-shared -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-icc --charm-base $CHARMROOT --with-cuda --cuda-prefix $CUDAROOT --with-fftw --with-fftw3 --fftw-prefix $FFTW
Now set NAMD to use TAU, edit arch/Linux-x86_64-icc.arch adding this line:
CHARMOPTS = -tracemode Tau
Then build NAMD
%> cd Linux-x86_64-icc %> make
NAMD with CUDA
To profile NAMD's CUDA kernel I few modifications need to be made to the build steps:
in charm, do:
%> ./build Tau mpi-linux-x86_64 mpicxx ifort --tau-makefile=<tau_dir>/x86_64/lib/Makefile.tau-icpc-mpi-cupti --no-build-shared -O3
(change TAU makefile)
rebuild NAMD.
and run NAMD by doing:
mpirun -np 3 tau_exec -T icpc,mpi,cupti -cupti ./namd2 src/apoa1/apoa1.namd
(have the '-T' options match the TAU makefile)
Running NAMD
If everything works properly you should now have a namd2 executable. Test by running:
%> ./charmrun ./namd2 +p4 src/alanin
Performance Data
Mean profile of a run with the performance benchmark ALANIN:
Histogram of the enqueueWorkA routine across 32 processors:
A comparison of Timestep per second between two different MPI implementations on Ranger:
