Difference between revisions of "NAMD"
Line 49: | Line 49: | ||
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> | ||
You should have generated TAU performance data. | You should have generated TAU performance data. |
Revision as of 23:50, 15 January 2009
Guide to building and running NAMD 2.6 with TAU
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-amd64 mpicxx ifort -O3 ... %> ./build charm++ mpi-linux-amd64 mpicxx ifort --tau-makefile=$HOME/tau2/x86_64/lib/Makefile-tau-mpi -O3
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:
%> cd mpi-linux-amd64/tests/charm++/simplearrayhello %> make OPTS='-tracemode Tau' %> ./charmrun ./hello +p4
Verify that this program runs without any errors and that you generate profiles files for each processor.
Building NAMD 2.6
Begin in NAMD's home directory:
%> cd NAMD_2.6_Source %> ./config Linux-amd64-g++
Now set NAMD to use TAU, edit arch/Linux-x86_64-MPI-icc.arch to be:
NAMD_ARCH = Linux-x86_64 CHARMOPTS = -memory os -tracemode Tau 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
If everything works properly you should now have a namd2 executable. Test by running:
%> ./charmrun ./namd2 +p4 src/alanin
You should have generated TAU performance data.