Re: Building NAMD for Opteron Cluster with ICC

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Mar 06 2009 - 23:18:12 CST

You'll actually want to build with mpicxx as the compiler (or whatever
the appropriate mpi wrapper for your compiler is), not icc. Also, don't
select SMP unless (as noted in the charm++ docs and by the build script)
you want to run on a *single, SMP node*.
Best,
Peter

Chris Share wrote:
> Hi,
>
> I'd like to build NAMD on an AMD Opteron Cluster using Infiniband and running 64-bit CentOS 5. I've managed to successfully build NAMD on my local machine (not the cluster) using several different configurations (GCC, PGI, CUDA). However, I'm unclear as to how to proceed in the case of the cluster build. I'd like to use the Intel compilers as these give the best performance. I'd also like to use MPI.
>
> Firstly, how should I build Charm++?
>
> Am I right in thinking that the Charm++ build configuration should be:
>
> ./build charm++ mpi-linux-amd64 icc smp
>
> When I run this I get the following error:
>
> Selected Compiler: icc
> Selected Options: smp
> Copying src/scripts/Makefile to mpi-linux-amd64-smp-icc/tmp
> Soft-linking over bin
> Soft-linking over lib
> Soft-linking over lib_so
> Soft-linking over include
> Soft-linking over tmp
> Generating mpi-linux-amd64-smp-icc/tmp/conv-mach-pre.sh
> Performing '/usr/bin/gmake charm++ OPTS=' in mpi-linux-amd64-smp-icc/tmp
> /usr/bin/gmake headerlinks
> gmake[1]: Entering directory `/nfs/user2/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-smp-icc/tmp'
> ./configure
> checking machine name... mpi-linux-amd64-smp-icc
> checking "C++ compiler as"... "icpc -fpic -cxxlib-icc -D_REENTRANT "
> checking "whether C++ compiler works"... "no"
> Cannot compile C++ programs with icpc -fpic -cxxlib-icc -D_REENTRANT
> (check your charm++ version)
> gmake[1]: *** [conv-autoconfig.h] Error 1
> gmake[1]: Leaving directory `/nfs/user2/cpsmusic/NAMD_INTEL/namd2/charm-6.0/mpi-linux-amd64-smp-icc/tmp'
> gmake: *** [headers] Error 2
> -------------------------------------------------
> Charm++ NOT BUILT. Either cd into mpi-linux-amd64-smp-icc/tmp and try
> to resolve the problems yourself, visit
> http://charm.cs.uiuc.edu/
> for more information. Otherwise, email the developers at ppl_at_cs.uiuc.edu
>
> Am I on the right track here?
>
> Any help would be appreciated.
>
> Cheers,
>
> Chris
>
>
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