Scalability problem with NAMD2.6 on Intel Xeon EM64T processors

From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Fri Jan 12 2007 - 10:56:07 CST

To NAMD Developers and Users,

I have a problem getting NAMD2.6 working in parallel. The efficiency is getting worse when I use  more than 4 cpus per node.

Can any one check the way I installed the NAMD on my system?
And if it is OK, I appreciate any suggestions to solve this problem.


My System:
Dell 1955 Linux cluster. Each node is equipped with two Quad-core Intel Xeon EM64T processors (2.6GHz) and 8 GB of memory. All nodes are connected with Gigabit Ethernet. The cluster's EM64T processors run a 64-bit Linux kernel.


Installation Instructions:

fftw-2.1.5 Installation:
-------------------------

./configure --prefix=/ibrix/home/mfm42/opt/fftw --enable-mpi --enable-float --enable-type-prefix --enable-debug --enable-dependency-tracking --enable-static

make

make install

###################################################################################

tcl-8.4.13 Installation:
------------------------

./configure --prefix=/ibrix/home/mfm42/opt/tcl --enable-64bit --disable-shared

make

make install

###################################################################################

charm++ Installation:
---------------------

Edit the file charm/src/arch/mpi-linux-amd64/conv-mach.sh:
1)change mpiCC to mpicxx
2)use /opt/mpich/gnu/bin as the path to mpicc and mpicxx.

./build charm++ mpi-linux-amd64 --basedir=/opt/mpich/gnu --no-build-shared -O -verbose -DCMK_OPTIMIZE=1 > build.log

###################################################################################

namd Installation:
------------------

Edit namd/Make.charm
(set CHARMBASE to the full path to charm-??)

Edit various configuration files:
1) namd/arch/Linux-amd64.fftw    (fix path to files,
                                  delete -I$(HOME)/fftw/include and -L$(HOME)/fftw/lib)
2) namd/arch/Linux-amd64.tcl     (fix path to files
                                  delete -I$(HOME)/tcl/include and -L$(HOME)/tcl/lib
                                  use -ltcl8.4 instead of -ltcl8.3
                                  add -DUSE_NON_CONST to TCLFLAGS)
3) namd/arch/Linux-amd64-MPI.arch use /opt/mpich/gnu/bin as a path to
                                  mpicxx and mpicc instead of g++/gcc

Set up build directory and compile:
  ./config tcl fftw Linux-amd64-MPI
  cd Linux-amd64-MPI
  make > make.log



Submission command:
/opt/mpiexec/bin/mpiexec /ibrix/home/mfm42/opt/namd-GE/Linux-amd64-MPI/namd2 gamma_150_sys.namd "+strategy USE_GRID" > gamma_150_sys.log


Thanks

Morad Alawneh
Department of Chemistry and Biochemistry, BYU
Provo, UT

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