Re: NAMD on Linux cluster with Myrinet

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Sat Oct 09 2004 - 21:59:57 CDT

One suggestion is to compile both charm and namd with the -no-gcc flag.

I found this while searching for help with elan switches...different
monster but it seems that icc8.0 will pick gcc headers instead of the
mpi specific headers...

Just my 2cents

Brian

On Sat, 9 Oct 2004, 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 http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> 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 paranoid'.
> 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
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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