[OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

2012-12-06 Thread Paul Hatton
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
Description: configure-12_12_06_19h48m.log


Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

2012-12-06 Thread Paul Hatton
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-boun...@open-mpi.org [mailto:users-boun...@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]
> >
> >  12_12_06_19h48m.log>___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> --
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users


*
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** sure it is legitimate.  Opening this attachment may cause irreparable   **
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** about the validity of this message, PLEASE SEEK HELP BEFORE OPENING IT. **
** **
** This warning was added by the IU Computer Science Dept. mail scanner.   **
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<>


Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

2012-12-06 Thread Paul Hatton
Thanks. Is this with gcc in the default location (/usr/bin/gcc) or elsewhere? 
It may not be relevant, but I built v4.7.2 and installed it outside of the 
system area:

[appmaint@bb2login04 openmpi-1.6.3]$ which gcc
/gpfs/apps/gcc/v4.7.2/bin/gcc
[appmaint@bb2login04 openmpi-1.6.3]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/gpfs/apps/gcc/v4.7.2/libexec/gcc/x86_64-unknown-linux-gnu/4.7.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --prefix=/gpfs/apps/gcc/v4.7.2 --disable-multilib
Thread model: posix
gcc version 4.7.2 (GCC)
[appmaint@bb2login04 openmpi-1.6.3]$ module unload apps/gcc
[appmaint@bb2login04 openmpi-1.6.3]$ which gcc
/usr/bin/gcc

clutching at straws a bit here ... but I have built it with Intel 2013.0.079 
which is also installed in the applications area and loaded with a module.

-- 
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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On
> Behalf Of Gunter, David O
> Sent: 06 December 2012 21:06
> To: Open MPI Users
> Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc
> 4.7.2
> 
> I just tried with the following:
> 
> $ gcc --version
> gcc (GCC) 4.7.2
> Copyright (C) 2012 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is
> NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
> 
> $ ./configure  --prefix=/tmp/dog/openmpi/1.6.3-gcc-4.7.2 F77=gfortran
> FC=gfortran CC=gcc CXX=c++ --with-
> platform=contrib/platform/lanl/tlcc2/optimized-panasas 2>&1 | tee
> test.log
> 
> configure completed without error as did the subsequent make.
> 
> Here's the relevant part of the configure output:
> 
> ...
> checking Fortran 90 kind of MPI_INTEGER_KIND (selected_int_kind(9))...
> 4
> checking Fortran 90 kind of MPI_ADDRESS_KIND (selected_int_kind(18))...
> 8
> checking Fortran 90 kind of MPI_OFFSET_KIND (selected_int_kind(18))...
> (cached) 8
> ...
> 
> --
> David Gunter
> HPC-3: Infrastructure Team
> Los Alamos National Laboratory
> 
> 
> 
> 
> On Dec 6, 2012, at 1:42 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]
> >
> >  12_12_06_19h48m.log>___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users



Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

2012-12-06 Thread Paul Hatton
Oh, sorry - I tried a build with the system gcc and it worked. I'll repeat the 
failed one and get it to you. Sorry about that.

-- 
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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] 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-boun...@open-mpi.org [mailto:users-boun...@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]
> >>>
> >>>  >> 12_12_06_19h48m.log>___
> >>> users mailing list
> >>> us...@open-mpi.org
> >>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >>
> >>
> >> --
> >> Jeff Squyres
> >> jsquy...@cisco.com
> >> For corporate legal information go to:
> >> http://www.cisco.com/web/about/doing_business/legal/cri/
> >>
> >>
> >> ___
> >> users mailing list
> >> us...@open-mpi.org
> >> 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.   **
> >
> ***
> **
> >
> >
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> --
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users



Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

2012-12-06 Thread Paul Hatton
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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] 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-boun...@open-mpi.org [mailto:users-boun...@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]
> >>>
> >>>  >> 12_12_06_19h48m.log>___
> >>> users mailing list
> >>> us...@open-mpi.org
> >>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> >>
> >>
> >> --
> >> Jeff Squyres
> >> jsquy...@cisco.com
> >> For corporate legal information go to:
> >> http://www.cisco.com/web/about/doing_business/legal/cri/
> >>
> >>
> >> ___
> >> users mailing list
> >> us...@open-mpi.org
> >> 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.   **
> >
&g

Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

2012-12-06 Thread Paul Hatton
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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] 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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org]
> 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-boun...@open-mpi.org [mailto:users-bounces@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 determi

Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

2012-12-06 Thread Paul Hatton
Thanks. This is obviously (now) a problem with my gcc build which isn't 
appropriate for this list. I'll re-visit this and post a solution once I've 
(hopefully) got this working. I don't have any shared libraries (*.so.*) in my 
gcc tree so something went badly wrong ...

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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On
> Behalf Of Gunter, David O
> Sent: 06 December 2012 22:27
> To: Open MPI Users
> Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with gcc
> 4.7.2
> 
> 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-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org]
> 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-boun...@open-mpi.org [mailto:users-bounces@open-
> mpi.org]
> >> 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
> >>>>>
> >>>>> --
> &

[OMPI users] FW: error configuring OpenMPI 1.6.3 with gcc 4.7.2

2013-02-04 Thread Paul Hatton
For completeness to the list and archive in case it helps anyone else now or in 
the future 

The problem was due to me not adding the lib64 directory for my gcc build to 
LD_RUN_PATH, which is needed when gcc is linking other applications, as well as 
LD_LIBRARY_PATH which is used at run time. Just needed (Bourne shell) to

export LD_RUN_PATH=/gpfs/apps/gcc/v4.7.2/lib64:$LD_RUN_PATH

before configure-ing OpenMPI with the new gcc on the PATH. Thanks to all who 
responded to this and pointed me in the right direction.

-- 
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: Paul Hatton [mailto:p.s.hat...@bham.ac.uk]
> Sent: 06 December 2012 22:37
> To: 'Open MPI Users'
> Subject: RE: [OMPI users] error configuring OpenMPI 1.6.3 with gcc
> 4.7.2
> 
> Thanks. This is obviously (now) a problem with my gcc build which
> isn't appropriate for this list. I'll re-visit this and post a
> solution once I've (hopefully) got this working. I don't have any
> shared libraries (*.so.*) in my gcc tree so something went badly
> wrong ...
> 
> 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-boun...@open-mpi.org [mailto:users-bounces@open-
> mpi.org] On
> > Behalf Of Gunter, David O
> > Sent: 06 December 2012 22:27
> > To: Open MPI Users
> > Subject: Re: [OMPI users] error configuring OpenMPI 1.6.3 with
> gcc
> > 4.7.2
> >
> > 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-boun...@open-mpi.org [mailto:users-bounces@open-
> mpi.org]
> > 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.
> > >&