[gmx-users] gromacs installation with mpi

[Justin A. Lemkul]

Sanku M wrote:
> Hi,
>   I intially tried the following command line for config log:
> ./configure --prefix=/home/berne/jm3745/UTIL/GROMACS_4.5.4_MPI/ 
> --program-suffix=_4mpi --disable-shared -enable-mpi
> 
> and in the bash_profile I had set the path for my desired mpi executable:
> PATH=$PATH:/home/berne/jm3745/UTIL/OPENMPI/bin:$HOME/bin:/home/berne/jm3745/UTIL/fftw/bin:
> export CPPFLAGS=-I/home/berne/jm3745/UTIL/fftw/include
> export 
> LDFLAGS=-L/home/berne/jm3745/UTIL/fftw/lib:/home/berne/jm3745/UTIL/OPENMPI/lib
> 
> But, the program crashes saying that 'can not compile or link using mpicc'.
> Looking inside config.log file, I found the following details:
> configure:5396: checking for mpicc
> configure:5412: found /usr/local/bin/mpicc
> configure:5423: result: mpicc
> configure:5438: checking whether the MPI cc command works
> configure:5452: mpicc -o conftest -g -O2 
> -I/home/berne/jm3745/UTIL/fftw/include 
> -L/home/berne/jm3745/UTIL/fftw/lib:/home/berne/jm3745/UTIL/OPENMPI/lib 
> conftest.c  >&5
> /usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
> searching for -lmpich
> /usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
> searching for -lmpich
> /usr/bin/ld: cannot find -lmpich
> collect2: ld returned 1 exit status
> configure:5452: $? = 1
> 
> So, apparently, the program is searching for mpicc in /usr/local/bin 
> directory for mpicc in stead of ~/UTIL/openmpi/bin directory which I 
> hoped for.
> 
> So, then I tried another options for configuring using following command 
> ( by putting CC to be  ~/UTIL/openmpi/bin/mpicc)
> ./configure --prefix=/home/berne/jm3745/UTIL/GROMACS_4.5.4_MPI/ 
> --program-suffix=_4mpi --disable-shared -enable-mpi 
> CC= ~/UTIL/openmpi/bin/mpicc
> 
> But, here again, I got the same error: ''can not compile or link using 
> mpicc'.
> Now, looking inside the config.log, I find the exactly same problem as 
> earlier: it still recognizes mpicc from /usr/local/bin:
> and config.log says:
> configure:5396: checking for mpicc
> configure:5412: found /usr/local/bin/mpicc
> configure:5423: result: mpicc
> configure:5438: checking whether the MPI cc command works
> configure:5452: mpicc -o conftest -g -O2 
> -I/home/berne/jm3745/UTIL/fftw/include 
> -L/home/berne/jm3745/UTIL/fftw/lib:/home/berne/jm3745/UTIL/OPENMPI/lib 
> conftest.c  >&5
> /usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
> searching for -lmpich
> /usr/bin/ld: skipping incompatible /usr/local/lib/libmpich.a when 
> searching for -lmpich
> /usr/bin/ld: cannot find -lmpich
> collect2: ld returned 1 exit status
> 
> So, no matter what I do, it just does not recognize anything else other 
> than /usr/local/bin.
> Any help will be highly appreciated.

You're using the wrong environment variable.  Use MPICC, not CC.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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