Re: clustermatic 4 and 5 Namd/charm

From: Rene Salmon (rsalmon_at_tulane.edu)
Date: Sat Jan 01 2005 - 14:56:56 CST

Hi,

The problem with charm was indeed the missing libs on the slave nodes.
After I added the missing libs the charm tests worked fine.

Next I moved to compile NAMD. I just followed your instructions and
copied the "Linux-i686-Clustermatic.arch" to
"Linux-amd64-Clustermatic.arch" here is what the file looks like:

NAMD_2.5_Source/arch# cat Linux-amd64-Clustermatic.arch
include .rootdir/arch/Linux-amd64-g++.arch

CHARMARCH = net-linux-amd64-clustermatic

--------
here is what Linux-amd64-g++.arch looks like:

NAMD_2.5_Source/arch# cat Linux-amd64-g++.arch
NAMD_ARCH = Linux-amd64
CHARMARCH = net-linux-amd64-clustermatic

CXX = g++ -DSOCKLEN_T=socklen_t -DNO_STRSTREAM_H
CXXOPTS = -O3 -fexpensive-optimizations -ffast-math
CC = gcc
COPTS = -O3 -fexpensive-optimizations -ffast-math

-----------------------

Next I tried to configure and compile:

NAMD_2.5_Source/arch# ./config Linux-amd64-Clustermatic

this worked and generated the NAMD executables with out any errors.
I ran this test on NAMD:

  ./charmrun ++skipmaster ++verbose ++startpe 0 +p2 ./namd2 /tmp/alanin

WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 9
WRITING COORDINATES TO OUTPUT FILE AT STEP 9
WRITING VELOCITIES TO OUTPUT FILE AT STEP 9
==========================================
WallClock: 1.611247 CPUTime: 1.201816 Memory: 8895 kB
Charmrun> Graceful exit.

It seems to be working fine. Thank you very much for getting me this far.

----------------------
I would like to have the fftw libs with NAMD so I tried this:

NAMD_2.5_Source/arch# ./config tcl fftw Linux-amd64-Clustermatic

If I add the fftw or tcl or both I get error messages and I do not get a
NAMD binary.

I installed fftw-3.0.1 from the fftw website with out any problems and
just pointed the Linux-amd64.fftw to the fftw install.

I also have tcl-8.4 installed on the system and I edited the
Linux-amd64.tcl file to reflect the location of the libs and include files
for tcl.

Is there anything special I need to do to get NAMD to compile with fftw
support? I checked the NAMD www site for precompiled libraries for both
tcl and fftw for amd64 but found nothing. Anyone have these libs
precompiled to work with NAMD?

Thank you very much for all the help

Rene

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