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Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2
From: Paul Hatton (p.s.hatton_at_[hidden])
Date: 2012-12-06 16:50:39


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
> >>>
> >>>
> >>>
> >>
> ***********************************************************************
> >> ******
> >>> **
> >> **
> >>> ** 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
> >> **
> >>> ** about the validity of this message, PLEASE SEEK HELP BEFORE
> >> OPENING IT. **
> >>> **
> >> **
> >>> ** This warning was added by the IU Computer Science Dept. mail
> >> scanner.   **
> >>>
> >>
> ***********************************************************************
> >> ******
> >>>
> >>>
> >>> <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
> >
> >
> >
> ***********************************************************************
> ******
> > **
> **
> > ** 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
> **
> > ** about the validity of this message, PLEASE SEEK HELP BEFORE
> OPENING IT. **
> > **
> **
> > ** This warning was added by the IU Computer Science Dept. mail
> scanner.   **
> >
> ***********************************************************************
> ******
> >
> >
> > <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/
> 
> 
> _______________________________________________
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