[gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny

[Mark Abraham]

----- Original Message -----
From: Christian Mücksch <muecksch at 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 at 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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