----- 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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