NAMD

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++ net-linux-amd64 -O3
...
%> ./build charm++ mpi-linux-amd64 --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 TAU

Make sure to have the latest version of TAU installed on your system. To configure TAU to work with charm++ do the following:

%> cd tau2
%> ./configure -pdt=<path to pdt> -charm=<path to the NAMD_2.6_Source/charm-5.9>
...
%> make clean install

To confirm TAU is working properly with charm++ try running this example program:

%> cd examples/charm
%> export PATH=<path to NAMD/charm-5.9/bin>
%> make
%> ./charmrun ++local ./pgm

Verify that profile files have been generated in this directory.

Preparing NAMD 2.6

1. First edit Make.charm in NAMD's home so that CHARMBASE is set to the directory where charm-5.9 resides. 2. Next create a selective instrumentation file with these commands:

%> cat select.tau
BEGIN_EXCLUDE_LIST
void Sequencer::thread#
void Controller::thread#
int NAMD_read_int#
void PDBDATA::scan#
Real PDBAtom::zcoor#
Real PDBAtom::ycoor#
Real PDBAtom::xcoor#
Bool Molocule::is_hydrogen#
END_EXCLUDE_LIST

BEGIN_FILE_EXCLUDE_LIST
*mainfunc.C
*memusage.C
*BackEnd.C
END_FILE_EXCLUDE_LIST

And save this file in the NAMD home directory.

3. lastly edit arch/Linux-amd64-g++.arch so that it resembles:

include /share/home/00968/tg802155/tau2/include/Makefile
NAMD_ARCH = Linux-amd64
CHARMARCH = net-linux-amd64

TAU_SELECT_FILE=/share/home/00968/tg802155/NAMD_2.6_Source/select.tau

CXX = $(TAU_COMPILER) -optTauSelectFile=$(TAU_SELECT_FILE) g++
CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math
CC = $(TAU_COMPILER) -optTauSelectFile=$(TAU_SELECT_FILE) gcc
COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math

Building NAMD 2.6

Begin in NAMD's home directory:

%> cd NAMD_2.6_Source
%> ./config Linux-amd64-g++
%> cd Linux-amd64-g++

Make one final modification to the Makefile in Linux-amd64-g++ directory, find this line:

namd2:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
  $(MAKEBUILDINFO)
  $(CHARMC) -verbose -ld++-option \
  "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
  -module NeighborLB -module commlib -language charm++ \

change the file to be:

namd2:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
  $(MAKEBUILDINFO)
  $(CHARMC) -L$(TAU_LIB_DIR) -ltau$(TAU_CONFIG) -verbose -ld++-option \
  "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
  -module NeighborLB -module commlib -language charm++ \

Now run:

%> make

If everything works properly you should now have a namd2 executable. Test by running:

%> ./charmrun ++local ./namd2 src/alanin

You should have generated a performance data file, profile.0.0.0.