NAMD

Guide to building and running NAMD 2.6 with TAU

Current this guide is for build NAMD and charm++ from source on x86 64-bit architecture. One would follow similar step on other machines but we have experienced additional difficulties.

Building Charm++

After downloading NAMD_2.6_Source.tar.gz do the following:

%> tar xzf NAMD_2.6_Source.tar.gz
%> cd NAMD_2.6_Source
%> tar xf charm-5.9.tar
%> cd charm-5.9
%> ./build charm++ net-linux-amd64

Wait for charm to finish building then test the configuration by:

%> cd net-linux-amd64/tests/charm++/simplearrayhello
%> make
%> ./hello
%> ./charmrun ++local ./hello

Verify that this program running with any error before continuing.

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.

Building NAMD 2.6

There are several patches that need to be applied before can run NAMD with TAU instrumentation but we will put those aside for now to concentrate on building NAMD with TAU auto-instrumentation.

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:

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. Finally 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

Begin in NAMD's home directory:

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