Difference between revisions of "NAMD"

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= Guide to building and running NAMD 2.6 with TAU =
+
[[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.
  
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<pre>
 
<pre>
 
%> cd charm
 
%> cd charm
%> ./build charm++ net-linux-amd64 -O3
+
%> ./build charm++ mpi-linux-x86_64 mpicxx ifort -O3
 
...
 
...
%> ./build charm++ mpi-linux-amd64 --tau-makefile=$HOME/tau2/x86_64/lib/Makefile-tau-mpi -O3
+
%> ./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 to use. Wait for charm to finish building then test the configuration by:
+
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-amd64/tests/charm++/simplearrayhello
+
%> 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 generate profiles files for each processor.
+
Verify that this program runs without any errors and that you get a profile file for each processor.
 +
 
 +
==Building NAMD==
  
==Building TAU==
+
Begin in NAMD's home directory:
Make sure to have the latest version of TAU installed on your system. To configure TAU to work with charm++ do the following:
 
 
<pre>
 
<pre>
%> cd tau2
+
%> cd NAMD_2.6_Source
%> ./configure -pdt=<path to pdt> -charm=<path to the NAMD_2.6_Source/charm-5.9>
+
%> ./config Linux-x86_64-icc --charm-base $CHARMROOT --with-cuda --cuda-prefix $CUDAROOT --with-fftw --with-fftw3 --fftw-prefix $FFTW
...
 
%> make clean install
 
 
</pre>
 
</pre>
To confirm TAU is working properly with charm++ try running this example program:
+
 
 +
Now set NAMD to use TAU, edit '''arch/Linux-x86_64-icc.arch''' adding this line:
 
<pre>
 
<pre>
%> cd examples/charm
+
CHARMOPTS = -tracemode Tau
%> export PATH=<path to NAMD/charm-5.9/bin>
 
%> make
 
%> ./charmrun ++local ./pgm
 
 
</pre>
 
</pre>
Verify that profile files have been generated in this directory.
 
uilding NAMD 2.6==
 
  
Begin in NAMD's home directory:
+
Then build NAMD
 
<pre>
 
<pre>
%> cd NAMD_2.6_Source
+
%> cd Linux-x86_64-icc
%> ./config Linux-amd64-g++
+
%> make
%> cd Linux-amd64-g++
 
 
</pre>
 
</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 ++local ./namd2 src/alanin
+
%> ./charmrun ./namd2 +p4 src/alanin
 
</pre>
 
</pre>
You should have generated TAU performance data.
+
 
 +
== 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


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:

NAMD-mean-profile.png

Histogram of the enqueueWorkA routine across 32 processors:

NAMD-work-profile.png

A comparison of Timestep per second between two different MPI implementations on Ranger:

NAMD-mpi-comparison.png

File:Namd-apoa1.ppk