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

[Nicolas Sapay]

David van der Spoel wrote:
> 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?
The library is in the directory "/opt/hpmpi/lib/linux_amd64/". Is is 
appears in command line for the compilation of conftest, but this 
directory do not seem to be correctly included in my environment. I'll 
ask the system administrator of the cluster. I may need to export a 
variable or load a module...

>
>
>
>>>>>>
>>>>>> 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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>>
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>
>

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