Re: NAMD on Linux cluster with Myrinet

From: Florian Barth (
Date: Mon Oct 11 2004 - 19:49:48 CDT

Hash: SHA1

Hello Alberto,

i recently (two days ago) compiled NAMD 2.5 on my linux cluster with
myrinet. in order for charm to work with myrinet i compiled it with

./build charm++ mpi-linux gm2 -O3 -I$MPICH/include -L$MPICH/lib
- -L$GM/lib -lmpich -lgm -DCMK_OPTIMIZE=1

note the gm2 flag for gm version 2.xx. as i have athlon cpus i didn't
use icc but gcc3.3 instead. you must have mpich-gm >1.2.5..12 installed
in oder for everything to work (at least with the mpi-linux version).
mpich-gm should be compiled with the same compiler used for building charm.


        Florian Barth

- --
Florian Barth
Institute of Technical Biochemistry
University of Stuttgart
Allmandring 31
70569 Stuttgart

Alberto Santana wrote:
| Hi folks,
| We are using version 8.0 of Intel's compiler and GM-2.0.11_Linux. I
| downloaded charm-5.8 and built it with ./build charm++ net-linux icc
| gm --basedir=/usr/opt/gm -O -DCMK_OPTIMIZE=1. This step went very smooth.
| NAMD compiled without a problem. A test run gave the following output:
| Charm++: scheduler running in netpoll mode.
| Info: NAMD 2.5 for Linux-i686-GM
| Info:
| Info: Please visit
| Info: and send feedback or bug reports to
| Info:
| Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
| Info: in all publications reporting results obtained with NAMD.
| Info:
| Info: Based on Charm++/Converse 0143160 for net-linux-gm-icc
| Info: Built Sat Oct 9 20:13:10 EDT 2004 by santana on master
| Info: Sending usage information to NAMD developers via UDP. Sent data is:
| Info: 1 NAMD 2.5 Linux-i686-GM 4 node3 santana
| Info: Running on 4 processors.
| Info: 9733 kB of memory in use.
| Measuring processor speeds...------------- Processor 1 Exiting: Caught
| Signal ------------
| Signal: segmentation violation
| Suggestion: Try running with '++debug', or linking with '-memory
| Fatal error on PE 1> segmentation violation
| The question is: What is the secret behind making NAMD run on Myrinet?
| Has anyone managed to get this thing right?
| Alberto

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