Re: More NAMD/gm2 problems

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Wed Mar 31 2004 - 02:17:57 CST

Hi, Chris,

 Welcome Charm++ hackers. ;-)
 Building Charm and NAMD with MPI is a little tricky because there are a
few different MPI distributions - MPICH, MPICH-GM, MPI/LAM to name a few.
Some provide mpiCC wrapper, some don't. To make things worse, the mpiCC
wrapper can call gcc or icc as it likes. It is quite difficult for Charm++
to be smart enough to figure things out. :-( For mpi-linux, all the
compiler related config files for Linux are in charm/src/arch/mpi-linux,
also all common config files in charm/src/arch/mpi and charm/src/arch/common.
 Unfortuantely since GM version 2, we found incompatibility problem
running Charm++ programs with the exact error you experienced. The
problem is caused by threadsafe malloc and use of pthread in mpich-gm. We
are still trying to find a solution.
 You may want to try the new "gm2" option I checked in recently. For that,
you need to download charm-5.8 and build charm like:
./build charm++ mpi-linux icc gm2
(I have checked in a fix in cvs for the option "icc", it should work
better now)

Gengbin

On Wed, 31 Mar 2004, Chris Samuel wrote:

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> On Wed, 31 Mar 2004 03:58 pm, David Chalmers wrote:
>
> Hi David, :-)
>
> > Thanks for your reply. We have Charm and NAMD compiled using the
> > intel_cc_80 compiler and mpicc.
>
> I've just joined the list and wanted to give a quick bit of background.
>
> To get Charm++ to compile with the v8 Intel compilers I needed to add an extra
> library search path in, I've done that as a quick hack by adding it into the
> CORE_LIBS definition in the charmc script - see the attached patch.
>
> It's not designed for general use as I patch the script itself, I'd be happier
> if it could be in a config file but as a newcomer to Charm++ it's hard to
> decipher what to set where!
>
> Also I created two files to define an mpicc compiler type to use instead of
> icc. From what I could tell if you try and build an MPI version of Charm++
> at present (./build charm++ mpi-linux) it assumes that the MPICH you're using
> is built with GCC as the build falls back to using gcc in a couple of places
> leading to link failures if MPICH is really using the Intel compilers.
>
> I've attached the two files, cc-mpicc.sh and cc-mpicc.h (attached) in the
> directory charm/src/arch/common which at least let me build Charm++ cleanly
> with the command line:
>
> ./build charm++ mpi-linux mpicc
>
> Perhaps they should have a better name like intel-mpicc ?
>
> Unfortunately, as David says, when I try and run the megatest program it runs
> happily at first before bombing out with those errors. Once it's done that
> the process hangs eating all the CPU it can until its walltime expires and
> Torque terminates it. :-(
>
> cheers!
> Chris
> - --
> Christopher Samuel - (03)9925 4751 - VPAC Systems & Network Admin
> Victorian Partnership for Advanced Computing http://www.vpac.org/
> Bldg 91, 110 Victoria Street, Carlton South, VIC 3053, Australia
>
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