To build NAMD, you will need the source for NAMD, along with the
Charm++ software and the FFTW software. The steps for configuring and
building each of these codes, and any known limitations, are described
in the sections below.

NAMD development is supported by the NIH National Center for Research
Resources. The Theoretical and Computational Biophysics Group at the
University of Illinois announced the release of the 2.5 version of
NAMD on Sept. 29, 2003. NAMD is available from the NAMD website.

You will need three different pieces of software to run NAMD.

• The FFTW software (version 2.1.5) from FFTW website.
• The Charm++ software (version 5.8) from the Charm website.
• The NAMD software (version 2.5) from the NAMD website.

First build the FFTW code (version 2.1.5). You will need to use
version 2.1.5 of FFTW, not version 3.0.1. In FFTW 3.0.1 the API
(Application Program Interface) changed. To configure, build, and
install FFTW, do the following:

cd fftw-2.1.5                                        
export CC=pathcc F77=pathf90 CFLAGS=-O3 FFLAGS=-O3   
./configure --enable-float --enable-type-prefix --enable-static \
--prefix=$HOME/fftw   
make                                                
make install                                        

First you have to configure Charm++ to be able to generate an mpi-pathscale target. Copy the files conv-mach.sh and conv-mach.h into a newly created directory in charm-5.8:

cd ../charm-5.8                                                 
mkdir src/arch/mpi-pathscale                                    
cp ~/conv-mach.sh src/arch/mpi-pathscale                        
cp ~/conv-mach.h src/arch/mpi-pathscale                         

Note: In the file conv-mach.sh, you should change
"-L/opt/pathscale/lib/2.4" to the installation directory for
your compiler release.

./build charm++ mpi-pathscale -DCMK_OPTIMIZE=1                  

Now build the NAMD code. Copy the file Linux-amd64-pathcc.arch file into the arch subdirectory and then build NAMD.

Note: Linux-amd64-pathcc.arch assumes that Charm++
was installed in $(HOME)/charm-5.8. If this is not the case,
you need to modify CHARM_LOC in this file. The file Make.charm also needs to point to the directory where Charm++
is installed. There is also an implicit assumption in the file arch/Linux-amd64.fftw that assumes FFTW was built in $(HOME)/fftw. If this is not true, you need to modify that
file as well.

cd ../NAMD_2.5_Source                                         
cp ~/Linux-amd64-pathcc.arch arch                             
./config fftw Linux-amd64-pathcc                              
cd Linux-amd64-pathcc                                         
make                                                          

This process builds and installs NAMD.

There is a bug in pathcc such that if the serial C code in Charm++ is
compiled with -O2 or higher, it will result in a hang during
execution. The workaround is to use -O1 for CMK_SEQ_CC. This
workaround is incorporated in the distributed conv-mach.sh, and seems
to have no performance impact.

We recommend you record what steps you took, along with their output,
in case of problems. You can include this in your email to support.
Here is an example of changing a make command to record the output in a
text file:

make foo 2>&1 | tee make-foo-log.txt

If you have any comments or suggestions about additions to these
pages, please contact support@pathscale.com.