[gmx-users] A MPI librabry not recognized by the configure script

[David van der Spoel]

Nicolas Sapay wrote:
> David van der Spoel wrote:
>> Nicolas Sapay wrote:
>>> David van der Spoel wrote:
>>>> Nicolas Sapay wrote:
>>>>> Hi,
>>>>>
>>>>> I'm trying to compile the Gromacs-3.3.3 package with MPI and have 
>>>>> the following issue when I run the configuration script:
>>>>>
>>>>>    ./configure --prefix /home/users/nsapay/local/bin/gromacs-3.3.3
>>>>>    --program-suffix _mpi --enable-mpi --disable-nice MPICC=mpicc 
>>>>> CC=gcc
>>>>>    --without-x
>>>>>    CPPFLAGS=-I/home/users/nsapay/local/bin/fftw-3.1.2/include/
>>>>>    LDFLAGS=-L/home/users/nsapay/local/bin/fftw-3.1.2/lib/
>>>>>     >>> checking size of int... configure: error: cannot compute 
>>>>> sizeof
>>>>>    (int)
>>>>>
>>>>> the config.log file tells me it's because a MPI library is not found:
>>>>>
>>>>>    configure:7621: mpicc -o conftest  -O3 -fomit-frame-pointer
>>>>>    -finline-functions -Wall -Wno-unused -funroll-all-loops
>>>>>    -I/home/users/nsapay/local/bin/fftw-3.1.2/include/
>>>>>    -L/opt/hpmpi/lib/linux_amd64/
>>>>>    -L/home/users/nsapay/local/bin/fftw-3.1.2/lib/  conftest.c  >&5
>>>>>    configure:7624: $? = 0
>>>>>    configure:7630: ./conftest
>>>>>    ./conftest: error while loading shared libraries: libmpio.so.1:
>>>>>    cannot open shared object file: No such file or directory
>>>>>    configure:7633: $? = 127
>>>>>    configure: program exited with status 127

It seems that the crux is up here. Is there a libmpio.so.1 on your 
system? If so, where? Why isn't it found? Could it be that you have to 
source some scripts before compiling and running stuff?



>>>>>
>>>>> I tried to reconfigure the installation by including the directory 
>>>>> where the libmpi is stored:
>>>>>
>>>>>    ./configure --prefix /home/users/nsapay/local/bin/gromacs-3.3.3
>>>>>    --program-suffix _mpi --enable-mpi --disable-nice MPICC=mpicc
>>>>>    CC=gcc  --without-x    
>>>>> CPPFLAGS=-I/home/users/nsapay/local/bin/fftw-3.1.2/include/    
>>>>> LDFLAGS="-L/opt/hpmpi/lib/linux_amd64/
>>>>>    -L/home/users/nsapay/local/bin/fftw-3.1.2/lib/"
>>>>
>>>> You might want to try
>>>> LD=mpicc
>>> Nope, same error...
>> You may need to add fftw library path to ldflags as well.
>>
> I did, but the error is still related to libmpi... Actually, I realize 
> there is this error few lines above:
> 
>    configure:5488: mpicc -E
>    -I/home/users/nsapay/local/bin/fftw-3.1.2/include/ conftest.c
>    conftest.c:18:28: ac_nonexistent.h: No such file or directory
>    configure:5494: $? = 1
> 
> So, there might be something wrong with the conftest compilation 
> itself... But the way, shouldn't conftest be run with "mpirun 
> ./conftest" rather that just "./conftest"? I'm really not a mpicc monk. 
> It's just an intuition
> 
>>
>>>>
>>>>>
>>>>> But it doesn't work. I get exactly the same error message. Why the 
>>>>> libmpio.so.1 library is not recognized by the configuration script? 
>>>>> Note that I have compiled Gromacs without MPI with no particular 
>>>>> issue.  The system is a HP cluster with AMD processors, Red Hat 
>>>>> 4.5, gcc/mpicc 3.4.6.
>>>>>
>>>>> Thanks a lot for your advices
>>>>>
>>>>> -Nicolas
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------ 
>>>>>
>>>>>
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>>>>
>>>>
>>>
>>>
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>>
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se