- Original Message -
From: Christian Mücksch mueck...@rhrk.uni-kl.de
Date: Friday, June 25, 2010 0:21
Subject: [gmx-users] Problems with installing mpi-version of Gromacs on Cluster
with Debian-Lenny
To: MAILINGLIST GROMACS gmx-users@gromacs.org
Dear All,
I've been trying to compile and get Gromacs (version 4.0.7)
working on a cluster that runs with Debian Lenny.
I set the following variables:
export SOFT=$HOME/GROMACS
export PATH=$PATH:$SOFT/bin
export LDFLAGS=-L$SOFT/lib
export CPPFLAGS=-I$SOFT/include
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SOFT/lib
export MPICC=$SOFT/bin/mpicc
and then did
./configure --prefix=$SOFT --disable-float --program-
suffix=_mpi_d --enable-mpi
after I installed the Gromacs-version without mpi. Before
configuring Gromacs I compiled the latest version of OPEN-MPI
with gcc-4.3.
I did exactly the same on another cluster that runs with Debian
Etch and everything worked fine and was pretty straightforward.
Here I get the following error during configuring:
checking whether your compiler can handle assembly files
(*.s)... no
configure: error: Upgrade your compiler (or disable assembly loops)
The exact error from the config.log looks like this:
configure:32822: checking whether your compiler can handle
assembly files (*.s)
configure:32841: /usr/bin/mpicc -O3 -fomit-frame-pointer -
finline-functions -Wall -Wno-unused -funroll-all-loops -c
conftestasm.sconftestasm.s: Assembler messages:
conftestasm.s:2: Error: bad register name `%rsp'
configure:32844: $? = 1
configure:32857: result: no
configure:32859: error: Upgrade your compiler (or disable
assembly loops).
When I compiled Gromacs with the --disable-x86-64-sse option,
then my submitted jobs run extremely slow compared to the other
cluster.Although MPI is running and the CPU-loads are all 100%
the speed is nearly as slow as running on a single CPU.
I also tried compiling with MVAPICH with is already installed on
the cluster but I get the same error.
Unfortunately I could not compile OPEN-MPI with the follwing flags:
export CC=gcc-4.3 -m64
export CXX=g++-4.3 -m64
export F77=gfortran-4.3 -m64
Do you have any idea what could be the cause of the problem so
that I can tell the Cluster-Admin what specific package to install?
Any help would be deeply appreciated since I'm new to this whole
MPI topic and I could not find a way around this problem.
Your version of gcc isn't able to deal with the assembly code used by GROMACS
to get its speed. Three solutions come to mind:
1) Upgrade gcc - it is a compiler collection, and the gcc module on Debian
looks to me like it has only the C compiler in it. The GNU assembler is in the
binutils package, so installing that looks like the first place to start/check.
2) Compile for this architecture on some machine that has a better set of tools
for compiling for scientific applications.
3) Cross-compile for this architecture on some such machine.
Mark
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