[gmx-users] Help, cannot compile with mpi

Florian Dommert dommert at fias.uni-frankfurt.de
Sat Apr 12 22:57:42 CEST 2008


 it seems fabracht is using Ubuntu and not very familiar with the MPI
and compiling. So I suggest to install the LAM-MPI from the repositories
of Ubuntu. They are not the latest version, but I do not think, its a
good idea to compile a very important library and install it in the root
directories, if I am not sure, that it is faultless.

My proposal is to use the LAM-MPI of Ubuntu and install GROMACS as well
as the FFTW3 libraries in a directory like $HOME/local. It allows an
easy uninstall process, by deleting the install directories. This is
provided as you need no superuser rights during the installation and
thats why no system dependencies are changed. In case you want to give
all user access to the installation, GROMACS and the FFTW3 can also be
installed in the /usr/local directory. But I suggest a further prefix
like /usr/local/fftw3, to enable the easy uninstallation process.

At the end a little example for the compiling of GROMACS with a FFTW3 in
the directory $FFTW3=$HOME/local/fftw3


./configure --prefix=$FFTW3 --enable-float
make && make install
make distclean
./configure --prefix=$FFTW3 --enable-type-prefix
make && make install

Now you have installed the FFTW3 libraries in $FFTW3 and no superuser
rights were required.

LDFLAGS=-L$FFTW3/lib CPPFLAGS=-I$FFTW3/include ./configure
--prefix=$HOME/local/gmx --enable-mpi
make install

then put your $HOME/local/gmx/bin your path of the .bashrc, source
(source ~/.bashrc) it and GROMACS should work with Ubuntu on a multicore

Run the gmxtests after booting LAM and you will recognized if your
compilation works.

Hopefully I have not confused you and you can have fun with GROMACS

Best Regards


Diego Enry wrote:
> ./configure can't find "mpicc". If it was really intalled, so the
> location of the binaries is not in the variable $PATH.
> find where you installed LAM binaries and put it on $PATH
> example for bash, type on terminal:
> export PATH=$PATH:/usr/local/lam/bin/
> You should put this export line on /etc/bash.bashrc so all users won't
> need to use the export command (or type the fill path) everytime they
> want to use it..
> On Sat, Apr 12, 2008 at 2:19 PM, fabracht sdf <fabracht at gmail.com> wrote:
>> I've tried to recompile gromacs, this time i tried to enable mpi so tha t i
>> can run in parallel. I did what you advised in my last post. I've checked on
>> the gromacs homepage, and tried to find instructions for that. Eventually
>> what i did was.
>>  In the gromacs directory i typed:
>> make distclean
>> and then i wrote the command line described below.
>> i says it can't compile and link mpi code with cc.
>> lam-mpi is already installed, i would really appreciate some help with this
>> problem.
>>  Thank you
>> root at ubuntu-desktop:~/Desktop/gromacs-3.3.3#./configure --enable-mpi
>> checking build system type... i686-pc-linux-gnu
>> checking host system type... i686-pc-linux-gnu
>> checking for a BSD-compatible install... /usr/bin/install -c
>>  checking whether build environment is sane... yes
>> checking for a thread-safe mkdir -p... /bin/mkdir -p
>> checking for gawk... no
>> checking for mawk... mawk
>> checking whether make sets $(MAKE)... yes
>> checking how to create a ustar tar archive... gnutar
>>  checking for cc... cc
>> checking for C compiler default output file name... a.out
>> checking whether the C compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables...
>>  checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether cc accepts -g... yes
>> checking for cc option to accept ISO C89... none needed
>> checking for style of include used by make... GNU
>>  checking dependency style of cc... gcc3
>> checking dependency style of cc... gcc3
>> checking for mpxlc... no
>> checking for mpicc... no
>> checking for mpcc... no
>> checking for hcc... no
>> checking whether the MPI cc command works... configure: error: Cannot
>> compile and link MPI code with cc
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Florian Dommert

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert

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