Re: installing NAMD on opteron cluster with MPI

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Fri Mar 04 2005 - 01:00:59 CST

Hi,

Is this a cluster installed Scyld or Clustermatic? Could it be some
missing shared library on compute nodes?

Also try if it can run on just one processor (the localhost).

Gengbin

Lina M Nilsson wrote:

> Hi. We are trying to install NAMD on a Beowulf opteron 64-bit cluster
> with MPI but have not gotten NAMD install correctly / generate any of
> the normal output files. Instead, we get the “broken pipe” error
> message below. Does anyone have any idea what we could try? (Our
> install procedure, which worked fine on another cluster that uses
> opteron 64 processors, is listed below).
> Thanks, Lina Nilsson
>
> Output message:
>
> # LSBATCH: User input ./script2_gi
> ------------------------------------------------------------
>
> Successfully completed.
>
> Resource usage summary:
>
> CPU time : 3.41 sec. Max Memory : 2 MB Max Swap : 11 MB
>
> Max Processes : 1 Max Threads : 1
>
> The output (if any) follows:
>
> nodes: 4 proc: 8 cp: omitting directory
> `/hreidar/home/werk/pechmann/talin/job' cp: omitting directory
> `/hreidar/home/werk/pechmann/talin/NAMD' starting from n417 companion
> nodes: n356 n351 n349 /usr/local/apli/mpich/bin/mpirun: line 1: 14291
> Broken pipe
> /hreidar/home/werk/pechmann/NAMD/NAMD_2.5_Source/Linux-amd64-g++//namd2
> "min.template.inp" -p4pg /scratch/werk/pechmann/PI14081 -p4wd
> /scratch/werk/pechmann
>
>
> COMPLILING PROTOCOL
>
>
> I) Build fftw: --------------
>
> ./configure --enable-type-prefix --enable-float
> --prefix=/asgard/home/phys/gianluca/NAMD/fftw-2.1.5/gcc
>
> make
>
> make install
>
>
> II) Build charm++ -----------------
>
> Go to NAMD_2.5_Source and untar there the newest version of charm++
> (e.g. charm-5.8, delete the charm.tar delivered with the NAMD-tarball!)
>
> tar xvfz charm-5.8.tar.gz
>
> ln -s charm-5.8 charm
>
> cd charm
>
> setenv PATH /usr/local/apli/mpich/bin:{$PATH}
>
> ./build charm++ mpi-linux --incdir=/usr/local/apli/mpich/include
> --libdir=/usr/local/apli/mpich/lib --no-shared -O -DCMK_OPTIMIZE=1
>
> cd ../../../../
>
> vi Make.charm: CHARMBASE =
> /asgard/home/phys/gianluca/NAMD/NAMD_2.5_Source/charm
>
> vi arch/Linux-amd64.fftw: FFTDIR=/asgard/home/phys/gianluca/NAMD/fftw/gcc
>
> vi arch/Linux-amd64-g++.arch: CHARMARCH = mpi-linux CXXOPTS = -O3
> -march=k8 -m64 -fexpensive-optimizations -ffast-math COPTS = -O3
> -march=k8 -m64 -fexpensive-optimizations -ffast-math
>
>
> ./config fftw Linux-amd64-g++
>
> cd Linux-amd64-g++ make
>
>
> ----------------------------------- didnt work, then:
>
> in NAMD_2.5_Source/arch/Linux-amd64-g++.arch
>
> instead: CXXOPTS = -O3 -march=k8 -m64 -fexpensive-optimizations
> -ffast-math
>
> CXXOPTS = -O0 -march=k8 -m64 -fexpensive-optimizations -ffast-math
>
> instead: COPTS = -O3 -march=k8 -m64 -fexpensive-optimizations -ffast-math
>
> COPTS = -O0 -march=k8 -m64 -fexpensive-optimizations -ffast-math
>
> "-march=athlon" instead of "-march=k8". dropp
> "-fexpensive-optimizations -ffast-math"
>
> ------------------------------------ tried:
>
> COPTS = -O0 -march=k8 -m64
>
>
> Lina Nilsson
>
>
> Research Assistant
> Department of Bioengineering
> University of Washington, Seattle
> p:(206) 685-4432
> f:(206) 685-4434
>
>

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