[gmx-users] gromacs installation with mpi

[Sanku M]

Hi,
 I am using a cluster where user/local/bin has some old mpi executable. But, I 
have installed openmpi-1.3 in my own home directory so that I can use that for 
installing gromacs4.5.4 parallel version. I have also updated the path with the 
openmpi bin directory and library directory in the bash profile.

But, each time, I try to configure gromacs4.5.4 using enable-mpi mode, it 
always looks into the mpi installed in /usr/local/bin directory anad crashes 
saying that the mpicc is not compatible.
I wonder whether there is any particular flag I can use so that I can force 
gromacs to look for openmpi bin and lib folder installed in my home directory.
Thanks
Sanku-- 
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Re: [gmx-users] gromacs installation with mpi

[Justin A. Lemkul]

Sanku M wrote:

Hi,
 I am using a cluster where user/local/bin has some old mpi executable. 
But, I have installed openmpi-1.3 in my own home directory so that I can 
use that for installing gromacs4.5.4 parallel version. I have also 
updated the path with the openmpi bin directory and library directory in 
the bash profile.


But, each time, I try to configure gromacs4.5.4 using enable-mpi mode, 
it always looks into the mpi installed in /usr/local/bin directory anad 
crashes saying that the mpicc is not compatible.
I wonder whether there is any particular flag I can use so that I can 
force gromacs to look for openmpi bin and lib folder installed in my 
home directory.


Are you using cmake or autoconf?  Providing your actual commands here would be 
useful.  The approach is different based on your method of configuration, but 
with cmake you can set -DMPI_COMPILER=/path/to/mpicc or with similarly with 
autoconf, use the MPICC environment variable to point to the mpicc of choice.


-Justin

--


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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Re: [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

--


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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