From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Sat Jan 13 2007 - 10:18:46 CST
Hello Morad,
How big is the system your are studying? Perhaps it does not have enough atoms to justify more that 4 cpus.
The switch/cables may be defective.
I am not sure that adding debugging symbols and dependency tracking to the fftw libraries is a good idea for production simulations.
The compile wiki at http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile
Doesn't have these flags for ffttw compilation.
Can you post some timing information to so how bad it really is?
Regards
Brian Bennion
At 08:56 AM 1/12/2007, you wrote:
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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