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Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2
From: Gunter, David O (dog_at_[hidden])
Date: 2012-12-06 17:27:01


My gcc 4.7.2 build appears to be ignoring the one in /usr/lib64 and using the one in its own install tree:
/usr/projects/hpcsoft/moonlight/gcc/4.7.2/lib64/libgfortran.so.3

-david

--
David Gunter
HPC-3: Infrastructure Team
Los Alamos National Laboratory
On Dec 6, 2012, at 2:50 PM, Paul Hatton wrote:
> Ahh, it's looking in /usr/lib64 and finding libgfortran.so.3 which is older than the one expected by gcc 4.7 (system gcc is 4.4.6). Looking at my gcc installation I don't have any shared libraries in there, just static ones.
> 
> David - if you don't mind a slight diversion, where is your libgfortran.so.3? Does your system have one in /usr/lib64 (assuming you're on a 64-bit system) or in /usr/projects/hpcsoft/moonlight/gcc/4.7.2/somewhere?
> 
> I'll have a play with my setup as well. Should have spotted this myself.
> 
> Thanks for your help
> 
> -- 
> Paul Hatton
> High Performance Computing and Visualisation Specialist
> IT Services, The University of Birmingham
> Ph: 0121-414-3994  Mob: 07785-977340  Skype: P.S.Hatton
> [Service Manager, Birmingham Environment for Academic Research]
> [Also Technical Director, IBM Visual and Spatial Technology Centre]
> 
> 
>> -----Original Message-----
>> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On
>> Behalf Of Jeff Squyres
>> Sent: 06 December 2012 21:30
>> To: Open MPI Users
>> Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc
>> 4.7.2
>> 
>> It looks like your gfortran compiler is broken...?
>> 
>> configure:53489: checking Fortran 90 kind of MPI_INTEGER_KIND
>> (selected_int_kind(9))
>> configure:53507: gfortran   -o conftest conftestf.f90
>> configure:53514: $? = 0
>> configure:53554: ./conftest
>> ./conftest: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not
>> found (required by ./conftest)
>> configure:53561: $? = 1
>> 
>> 
>> 
>> On Dec 6, 2012, at 1:22 PM, Paul Hatton wrote:
>> 
>>> failed one attached.
>>> 
>>> --
>>> Paul Hatton
>>> High Performance Computing and Visualisation Specialist
>>> IT Services, The University of Birmingham
>>> Ph: 0121-414-3994  Mob: 07785-977340  Skype: P.S.Hatton
>>> [Service Manager, Birmingham Environment for Academic Research]
>>> [Also Technical Director, IBM Visual and Spatial Technology Centre]
>>> 
>>> 
>>>> -----Original Message-----
>>>> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]]
>> On
>>>> Behalf Of Jeff Squyres
>>>> Sent: 06 December 2012 21:17
>>>> To: Open MPI Users
>>>> Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc
>>>> 4.7.2
>>>> 
>>>> This does not appear to be the right config.log -- the test in
>> question
>>>> passed:
>>>> 
>>>> configure:53489: checking Fortran 90 kind of MPI_INTEGER_KIND
>>>> (selected_int_kind(9))
>>>> configure:53507: gfortran   -o conftest conftestf.f90
>>>> configure:53514: $? = 0
>>>> 
>>>> 
>>>> 
>>>> On Dec 6, 2012, at 1:11 PM, Paul Hatton wrote:
>>>> 
>>>>> Thanks. zip-ed config.log attached
>>>>> 
>>>>> --
>>>>> Paul Hatton
>>>>> High Performance Computing and Visualisation Specialist
>>>>> IT Services, The University of Birmingham
>>>>> Ph: 0121-414-3994  Mob: 07785-977340  Skype: P.S.Hatton
>>>>> [Service Manager, Birmingham Environment for Academic Research]
>>>>> [Also Technical Director, IBM Visual and Spatial Technology Centre]
>>>>> 
>>>>> 
>>>>>> -----Original Message-----
>>>>>> From: users-bounces_at_[hidden] [mailto:users-bounces_at_open-
>> mpi.org]
>>>> On
>>>>>> Behalf Of Jeff Squyres
>>>>>> Sent: 06 December 2012 20:54
>>>>>> To: Open MPI Users
>>>>>> Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc
>>>>>> 4.7.2
>>>>>> 
>>>>>> I have not tested with gfortran 4.7.2.
>>>>>> 
>>>>>> Can you send the config.log file? (please compress)
>>>>>> 
>>>>>> 
>>>>>> On Dec 6, 2012, at 12:42 PM, Paul Hatton wrote:
>>>>>> 
>>>>>>> I've searched the FAQ but not come up with anything about this
>> ...
>>>>>> with OpenMPI 1.6.3 and gcc 4.7.2, when I
>>>>>>> 
>>>>>>> ./configure  --prefix=/gpfs/apps/openmpi/1.6.3/gcc_4.7.2-tm-ib \
>>>>>>> F77=gfortran FC=gfortran CC=gcc CXX=c++ \
>>>>>>> --with-tm=/gpfs/sysapps/torque/4.1.2 \
>>>>>>> --with-openib \
>>>>>>> 2>&1|tee ../logs/configure-`date +%y_%m_%d_%Hh%Mm`.log
>>>>>>> 
>>>>>>> configure fails with
>>>>>>> 
>>>>>>> checking Fortran 90 kind of MPI_INTEGER_KIND
>>>>>> (selected_int_kind(9))...
>>>>>>> configure: error: Could not determine kind of
>>>>>> selected_int_kind(MPI_INTEGER_KIND)
>>>>>>> 
>>>>>>> Has anyone built 1.6.3 with gcc 4.7.2? It build fine with Intel
>>>>>> 2013.0.079 and also the system (Scientific Linux 6.3) gcc which is
>>>>>> 4.4.6
>>>>>>> 
>>>>>>> I've attached the output from the configure command.
>>>>>>> 
>>>>>>> Thanks
>>>>>>> 
>>>>>>> --
>>>>>>> Paul Hatton
>>>>>>> High Performance Computing and Visualisation Specialist
>>>>>>> IT Services, The University of Birmingham
>>>>>>> Ph: 0121-414-3994  Mob: 07785-977340  Skype: P.S.Hatton
>>>>>>> [Service Manager, Birmingham Environment for Academic Research]
>>>>>>> [Also Technical Director, IBM Visual and Spatial Technology
>> Centre]
>>>>>>> 
>>>>>>> <configure-
>>>>>> 
>> 12_12_06_19h48m.log>_______________________________________________
>>>>>>> users mailing list
>>>>>>> users_at_[hidden]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> Jeff Squyres
>>>>>> jsquyres_at_[hidden]
>>>>>> For corporate legal information go to:
>>>>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> users mailing list
>>>>>> users_at_[hidden]
>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>> 
>>>>> 
>>>>> 
>>>> 
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>>>>> 
>>>>> <config.zip>_______________________________________________
>>>>> users mailing list
>>>>> users_at_[hidden]
>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>> 
>>>> 
>>>> --
>>>> Jeff Squyres
>>>> jsquyres_at_[hidden]
>>>> For corporate legal information go to:
>>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>> 
>>>> 
>>>> _______________________________________________
>>>> users mailing list
>>>> users_at_[hidden]
>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>> 
>>> 
>>> 
>> ***********************************************************************
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>>> **
>> **
>>> ** WARNING:  This email contains an attachment of a very suspicious
>> type.  **
>>> ** You are urged NOT to open this attachment unless you are
>> absolutely     **
>>> ** sure it is legitimate.  Opening this attachment may cause
>> irreparable   **
>>> ** damage to your computer and your files.  If you have any questions
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>>> 
>>> 
>>> <config.zip>_______________________________________________
>>> users mailing list
>>> users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> 
>> 
>> --
>> Jeff Squyres
>> jsquyres_at_[hidden]
>> For corporate legal information go to:
>> http://www.cisco.com/web/about/doing_business/legal/cri/
>> 
>> 
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
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