Re: [OMPI users] CentOS 6.3 & OpenMPI 1.6.3

[Yevgeny Kliteynik]

Joseph, 

Indeed, there was a problem in the MXM rpm.
The fixed MXM has been published at the same location: 
  http://mellanox.com/downloads/hpc/mxm/v1.1/mxm-latest.tar

-- YK

On 12/4/2012 9:20 AM, Joseph Farran wrote:
> Hi Mike.
> 
> Removed the old mxm, downloaded and installed:
> 
> /tmp/mxm/v1.1/per-ofed/1.5.4.1/mxm-1.1.3a5e745-1.x86_64-rhel6u3.rpm
> 
> I am suing OFED 1.5.4.1 and it still fails at the same spot:
> 
> make[2]: Entering directory 
> `/data/apps/sources/openmpi-1.6.3/ompi/mca/mtl/mxm'
> CC mtl_mxm.lo
> CC mtl_mxm_cancel.lo
> CC mtl_mxm_component.lo
> CC mtl_mxm_endpoint.lo
> CC mtl_mxm_probe.lo
> CC mtl_mxm_recv.lo
> CC mtl_mxm_send.lo
> CCLD mca_mtl_mxm.la
> /bin/grep: /usr/local/mofed-inst/1.5.4.1/lib/librdmacm.la: No such file or 
> directory
> /bin/sed: can't read /usr/local/mofed-inst/1.5.4.1/lib/librdmacm.la: No such 
> file or directory
> libtool: link: `/usr/local/mofed-inst/1.5.4.1/lib/librdmacm.la' is not a 
> valid libtool archive
> make[2]: *** [mca_mtl_mxm.la] Error 1
> make[2]: Leaving directory `/data/apps/sources/openmpi-1.6.3/ompi/mca/mtl/mxm'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/data/apps/sources/openmpi-1.6.3/ompi'
> make: *** [all-recursive] Error 1
> 
> 
> On 12/2/2012 10:18 PM, Mike Dubman wrote:
>> ohh.. you have MOFED 1.5.4.1, thought it was 1.5.3-3.1.0
>> will provide you a link to mxm package compiled with this MOFED version 
>> (thanks to no ABI in OFED).
>>
>> On Sun, Dec 2, 2012 at 10:04 PM, Joseph Farran > > wrote:
>>
>> 1.5.4.1
>>
>>
> 
> 

[OMPI users] MPI_WAIT is a non-local operation

[赵印]

What does it means ??? 

Re: [OMPI users] Windows support for OpenMPI

[Damien]

So far, I count three people interested in OpenMPI on Windows. That's 
not a case for ongoing support.


Damien

On 04/12/2012 11:32 AM, Durga Choudhury wrote:

All

Since I did not see any Microsoft/other 'official' folks pick up the 
ball, let me step up. I have been lurking in this list for quite a 
while and I am a generic scientific programmer (i.e. I use many 
frameworks such as OpenCL/OpenMP etc, not just MPI)
Although I am primarily a Linux user, I do own multiple versions of 
Visual Studio licenses and have a small cluster that dual boots to 
Windows/Linux (and more nodes can be added on demand). I cannot do any 
large scale testing on this, but I can build and run regression tests etc.


If the community needs the Windows support to continue, I can take up 
that responsibility, until a more capable person/group is found at least.


Thanks
Durga


On Mon, Dec 3, 2012 at 12:32 PM, Damien > wrote:


All,

I completely missed the message about Shiqing departing as the
OpenMPI Windows maintainer.  I'll try and keep Windows builds
going for 1.6 at least, I have 2011 and 2013 Intel licenses and
VS2008 and 2012, but not 2010.  I see that the 1.6.3 code base
already doesn't build on Windows in VS2012  :-(.

While I can try and keep builds going, I don't have access to a
Windows cluster right now, and I'm flat out on two other projects.
I can test on my workstation, but that will only go so far.
Longer-term, there needs to be a decision made on whether Windows
gets to be a first-class citizen in OpenMPI or not.  Jeff's
already told me that 1.7 is lagging behind on Windows.  It would
be a shame to have all the work Shiqing put in gradually decay
because it can't be supported enough.  If there's any
Microsoft/HPC/Azure folks observing this list, or any other
vendors who run on Windows with OpenMPI, maybe we can see what can
be done if you're interested.

Damien
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[OMPI users] error configuring OpenMPI 1.6.3 with gcc 4.7.2

[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

[Jeff Squyres]

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]
> 
> ___
> 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/

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

[Gunter, David O]

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]
> 
> ___
> 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

[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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** **
** This warning was added by the IU Computer Science Dept. mail scanner.   **
*


<>

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

[Jeff Squyres]

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/

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

[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

[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

[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.   **
> >
> ***
> **
> >
> >
> > ___
> > 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 

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

[Jeff Squyres]

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-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/
>> 
>> 
>> ___

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

[Gunter, David O]

Mine was with a non-default-location gcc-4.7.2 as well.

$which gfortran
/usr/projects/hpcsoft/moonlight/gcc/4.7.2/bin/gfortran
$ gfortran --version
GNU Fortran (GCC) 4.7.2
Copyright (C) 2012 Free Software Foundation, Inc.

GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
You may redistribute copies of GNU Fortran
under the terms of the GNU General Public License.
For more information about these matters, see the file named COPYING



-david

--
David Gunter
HPC-3: Infrastructure Team
Los Alamos National Laboratory




On Dec 6, 2012, at 2:18 PM, Paul Hatton wrote:

> 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
> 
> ___
> 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

[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 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 

Re: [OMPI users] Romio and OpenMPI builds

[Brock Palen]

Eric,

You are correct, our builds do not show lustre support:

 MCA io: information "io_romio_user_configure_params" (value: , data 
source: default value)

So to enable this, when I build OpenMPI I should pass:

--with-io-romio-flags='--with-file-system=testfs+ufs+nfs+lustre'

We have Lustre, local filesystems (ufs), and NFSv3 and NFSv4 clients. So that 
list should be good for our site.

Would this be a good recommendation for us to include in all our MPI builds?

Brock Palen
www.umich.edu/~brockp
CAEN Advanced Computing
bro...@umich.edu
(734)936-1985



On Dec 3, 2012, at 7:12 PM, Eric Chamberland wrote:

> Le 12/03/2012 05:37 PM, Brock Palen a écrit :
>> I was trying to use hints with ROMIO and lustre prompted by another post on 
>> this list.
>> 
>> I have a simple MPI-IO code and I cannot using the notes I find set the 
>> lustre striping using the config file and setting ROMIO_HINTS.
>> 
>> Question:
>> 
>> How can I check which ADIO drivers ROMIO in OPenMPI was built with when I 
>> built it?
>> Can I make ROMIO go into 'verbose' mode and have it print what it is setting 
>> all its values to?
> Try "ompi_info -a" and check for lustre in the output:
> 
> ompi_info -a | grep -i romio
> ...
>  MCA io: information "io_romio_user_configure_params" (value: 
> <--with-file-system=testfs+ufs+nfs+lustre>, data source: default value)
>  User-specified command line parameters passed to 
> ROMIO's configure script
>  MCA io: information "io_romio_complete_configure_params" 
> (value: <--with-file-system=testfs+ufs+nfs+lustre  CFLAGS='-DNDEBUG -O3 
> -xHOST -Wall -finline-functions -fno-strict-aliasing -restrict -pthread' 
> CPPFLAGS='  
> -I/clumeq/src/Open-MPI/1.6.3/intel/openmpi-1.6.3/opal/mca/hwloc/hwloc132/hwloc/include
>  
> -I/clumeq/src/Open-MPI/1.6.3/intel/Build/opal/mca/hwloc/hwloc132/hwloc/include
>-I/usr/include/infiniband -I/usr/include/infiniband' FFLAGS='' LDFLAGS=' ' 
> --enable-shared --enable-static --with-file-system=testfs+ufs+nfs+lustre  
> --prefix=/software/MPI/openmpi/1.6.3_intel --with-mpi=open_mpi 
> --disable-aio>, data source: default value)
>  Complete set of command line parameters passed to 
> ROMIO's configure script
> 
> Eric
> 
> ___
> 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

[Gunter, David O]

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-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 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

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

[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
> >
> > --
> > 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
> >