Re: installing NAMD on opteron cluster with MPI

From: John Saeger (list_at_whimsey.com)
Date: Wed Mar 09 2005 - 15:12:08 CST

Did you compile the version of NAMD that you are using yourself? Where
did you get the source code? What version of linux is your cluster
running? What is the version of the kernel?

John

Lina Nilsson wrote:
> Hey-
> The cluster supposedly uses neither Scyld or Clustermatic, but I have
> never been able to get a more precise answer about the 'home-made'
> solution used. but I also don't really know what I should ask about as
> far as checking compatibility with NAMD.
> NAMD (AMD-64 version) doesn't run on local host either, but gives a
> segmentation fault.
> Any thoughts?
> Lina
>
> Gengbin Zheng wrote:
>
>>
>> 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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