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Subject: Re: [OMPI users] gfortran bindings apparently not built on mac os leopard
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2008-06-18 08:52:45


FWIW, I added this issue to the FAQ under the "OS X" section to make
it a little easier to find.

On Jun 17, 2008, at 5:17 PM, Jeff Squyres wrote:

> Sorry for not replying earlier -- glad you figured it out.
>
> Yes, if you didn't also reset the LIBRARY_PATH, the "wrong" libmpi
> (and friends) will get picked up, and it will therefore use the hard-
> coded directory path in those "wrong" libraries to find the wrapper
> data text files (the ones without Fortran support).
>
>
> On Jun 17, 2008, at 4:15 PM, Weirs, V Gregory wrote:
>
>>
>> Alright, I’m an idiot. I didn’t adjust my DYLD_LIBRARY_PATH.
>> Sorry about that-
>> Greg
>>
>> On 6/17/08 7:08 AM, "Jeff Squyres" <jsquyres_at_[hidden]> wrote:
>>
>> This is pretty odd.
>>
>> What files do you see in $prefix/share/openmpi/mpi*txt?
>>
>> What do you see from:
>>
>> grep required_file $prefix/share/openmpi/mpi*txt
>>
>>
>>
>> On Jun 16, 2008, at 2:12 PM, Weirs, V Gregory wrote:
>>
>> >
>> > Dave Gunter:
>> >
>> > According to ./configure —help, by default —enable-mpi-f77 and —
>> > enable-mpi-f90 are set. Also, ompi_info (see output in run_output
>> in
>> > the tarball) seems to indicate they are there. I rebuilt with them
>> > just to be sure, and got the same results.
>> >
>> >
>> > Doug Reeder:
>> > In my run_output file, you can see results of ‘which mpif77’ that
>> > shows I am using the version I built. (current is a symlink to
>> 1.2.6-
>> > gcc4.0). In any case, I get the same results with the absolute
>> path /
>> > usr/local/openmpi/1.2.6-4.0/bin/mpif77.
>> >
>> >
>> > Thanks,
>> > Greg
>> >
>> >
>> > On 6/16/08 11:04 AM, "users-request_at_[hidden]" <users-request_at_[hidden]
>> > > wrote:
>> >
>> > Send users mailing list submissions to
>> > users_at_[hidden]
>> >
>> > To subscribe or unsubscribe via the World Wide Web, visit
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> > or, via email, send a message with subject or body 'help' to
>> > users-request_at_[hidden]
>> >
>> > You can reach the person managing the list at
>> > users-owner_at_[hidden]
>> >
>> > When replying, please edit your Subject line so it is more specific
>> > than "Re: Contents of users digest..."
>> >
>> >
>> > Today's Topics:
>> >
>> > 1. Re: gfortran bindings apparently not built on mac os
>> > leopard
>> > (David Gunter)
>> > 2. Re: gfortran bindings apparently not built on mac os
>> > leopard
>> > (Doug Reeder)
>> > 3. Re: gfortran bindings apparently not built on mac os
>> > leopard
>> > (Doug Reeder)
>> > 4. help me please, about Open MPI (Tony Smith)
>> > 5. Re: help me please, about Open MPI (Andreas Sch?fer)
>> >
>> >
>> >
>> ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Mon, 16 Jun 2008 10:37:22 -0600
>> > From: David Gunter <dog_at_[hidden]>
>> > Subject: Re: [OMPI users] gfortran bindings apparently not built on
>> > mac os leopard
>> > To: Open MPI Users <users_at_[hidden]>
>> > Message-ID: <4683C284-4FEF-45CA-A2BC-8BE91A439485_at_[hidden]>
>> > Content-Type: text/plain; charset="windows-1252"; Format="flowed";
>> > DelSp="yes"
>> >
>> > I believe you still must add "--enable-f77" and "--enable-f90" to
>> the
>> > OMPI configure line in addition to setting the FC and F77 env
>> > variables.
>> >
>> > -david
>> > --
>> > David Gunter
>> > HPC-3: Parallel Tools Team
>> > Los Alamos National Laboratory
>> >
>> > On Jun 16, 2008, at 10:25 AM, Weirs, V Gregory wrote:
>> >
>> > >
>> > >
>> > > I am having trouble building mpif77/mpif90 with gfortran on Mac
>> OS
>> > > 10.5. Or maybe just running. The configure, make all, and make
>> > > install seemed to go just fine, finding my gfortran and
>> apparently
>> > > using it, but the scripts mpif77 and mpif90 give the error that
>> my
>> > > openmpi was not built with fortran bindings. Mpicc and mpicxx
>> don?t
>> > > give this error. Ompi_info says the f77 and f90 bindings were
>> > built.
>> > >
>> > > I know that OS X 10.5 comes with openmpi mpicc and mpicxx
>> installed,
>> > > but not fortran bindings, and I was careful to put the openmpi I
>> > > built first in the path.
>> > >
>> > > Some run output (mpif77 ?version, ompi_info), config.log,
>> > > configure.log, make.out, make-install.out are in the attached
>> > tarball.
>> > >
>> > > Any clues?
>> > >
>> > > Thanks,
>> > > Greg
>> > >
>> > >
>> > > --
>> > > V. Gregory Weirs
>> > > Sandia National Laboratories vgweirs_at_[hidden]
>> > > P.O.Box 5800, MS 0378 phone: 505 845 2032
>> > > Albuquerque, NM 87185-0378 fax: 505 284 0154
>> > > <dig.tar.gz>_______________________________________________
>> > > users mailing list
>> > > users_at_[hidden]
>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>> > -------------- next part --------------
>> > HTML attachment scrubbed and removed
>> >
>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Mon, 16 Jun 2008 09:32:21 -0700
>> > From: Doug Reeder <dlr_at_[hidden]>
>> > Subject: Re: [OMPI users] gfortran bindings apparently not built on
>> > mac os leopard
>> > To: Open MPI Users <users_at_[hidden]>
>> > Message-ID: <5047581C-F2E2-473B-8576-3E11F0D54DEA_at_[hidden]>
>> > Content-Type: text/plain; charset="windows-1252"; Format="flowed";
>> > DelSp="yes"
>> >
>> > Greg,
>> >
>> > If you use the absolute path names to run your mpif77 and mpif90
>> what
>> > output do you get. In spite of the results from which mpif77, the
>> > outputs from mpif77 and mpif90 look suspiciously like the outputs
>> > from the apple supplied versions in /usr/bin.
>> >
>> > Doug Reeder
>> > On Jun 16, 2008, at 9:25 AM, Weirs, V Gregory wrote:
>> >
>> > >
>> > >
>> > > I am having trouble building mpif77/mpif90 with gfortran on Mac
>> OS
>> > > 10.5. Or maybe just running. The configure, make all, and make
>> > > install seemed to go just fine, finding my gfortran and
>> apparently
>> > > using it, but the scripts mpif77 and mpif90 give the error that
>> my
>> > > openmpi was not built with fortran bindings. Mpicc and mpicxx
>> don?t
>> > > give this error. Ompi_info says the f77 and f90 bindings were
>> > built.
>> > >
>> > > I know that OS X 10.5 comes with openmpi mpicc and mpicxx
>> > > installed, but not fortran bindings, and I was careful to put the
>> > > openmpi I built first in the path.
>> > >
>> > > Some run output (mpif77 ?version, ompi_info), config.log,
>> > > configure.log, make.out, make-install.out are in the attached
>> > tarball.
>> > >
>> > > Any clues?
>> > >
>> > > Thanks,
>> > > Greg
>> > >
>> > >
>> > > --
>> > > V. Gregory Weirs
>> > > Sandia National Laboratories vgweirs_at_[hidden]
>> > > P.O.Box 5800, MS 0378 phone: 505 845 2032
>> > > Albuquerque, NM 87185-0378 fax: 505 284 0154
>> > > <dig.tar.gz>
>> > > _______________________________________________
>> > > users mailing list
>> > > users_at_[hidden]
>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>> > -------------- next part --------------
>> > HTML attachment scrubbed and removed
>> >
>> > ------------------------------
>> >
>> > Message: 3
>> > Date: Mon, 16 Jun 2008 09:42:55 -0700
>> > From: Doug Reeder <dlr_at_[hidden]>
>> > Subject: Re: [OMPI users] gfortran bindings apparently not built on
>> > mac os leopard
>> > To: Open MPI Users <users_at_[hidden]>
>> > Message-ID: <08B5C06D-8B64-4189-ADAE-E9FBE6BE567F_at_[hidden]>
>> > Content-Type: text/plain; charset="windows-1252"; Format="flowed";
>> > DelSp="yes"
>> >
>> > Greg,
>> >
>> > In your run_output file you don't appear to be using the openmpi
>> > versions that you built. From your make-install.out file it looks
>> > like your versions are in /usr/local/openmpi/1.2.6-gcc4.0/bin. You
>> > need to use that absolute path or prepend that path to your PATH
>> > environment variable.
>> >
>> > Doug Reeder
>> > On Jun 16, 2008, at 9:25 AM, Weirs, V Gregory wrote:
>> >
>> > >
>> > >
>> > > I am having trouble building mpif77/mpif90 with gfortran on Mac
>> OS
>> > > 10.5. Or maybe just running. The configure, make all, and make
>> > > install seemed to go just fine, finding my gfortran and
>> apparently
>> > > using it, but the scripts mpif77 and mpif90 give the error that
>> my
>> > > openmpi was not built with fortran bindings. Mpicc and mpicxx
>> don?t
>> > > give this error. Ompi_info says the f77 and f90 bindings were
>> > built.
>> > >
>> > > I know that OS X 10.5 comes with openmpi mpicc and mpicxx
>> > > installed, but not fortran bindings, and I was careful to put the
>> > > openmpi I built first in the path.
>> > >
>> > > Some run output (mpif77 ?version, ompi_info), config.log,
>> > > configure.log, make.out, make-install.out are in the attached
>> > tarball.
>> > >
>> > > Any clues?
>> > >
>> > > Thanks,
>> > > Greg
>> > >
>> > >
>> > > --
>> > > V. Gregory Weirs
>> > > Sandia National Laboratories vgweirs_at_[hidden]
>> > > P.O.Box 5800, MS 0378 phone: 505 845 2032
>> > > Albuquerque, NM 87185-0378 fax: 505 284 0154
>> > > <dig.tar.gz>
>> > > _______________________________________________
>> > > users mailing list
>> > > users_at_[hidden]
>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>> > -------------- next part --------------
>> > HTML attachment scrubbed and removed
>> >
>> > ------------------------------
>> >
>> > Message: 4
>> > Date: Mon, 16 Jun 2008 12:51:31 -0400
>> > From: Tony Smith <dtustudy8_at_[hidden]>
>> > Subject: [OMPI users] help me please, about Open MPI
>> > To: <users_at_[hidden]>
>> > Message-ID: <BAY104-W32BC5D00DA99730856FD48FDA90_at_phx.gbl>
>> > Content-Type: text/plain; charset="windows-1252"
>> >
>> >
>> >
>> >
>> >
>> > Dear Sir:
>> >
>> >
>> >
>> > I am trying to install Open MPI on a cluster that has been
>> installed
>> > with mpich-
>> >
>> > gm MPI.
>> >
>> >
>> >
>> > I have followed the steps on your website.
>> >
>> > I can compile and run the Hello_c application correctly.
>> >
>> >
>> >
>> > But, how can I make sure that the application is run by Open MPI
>> not
>> > by mpich-
>> >
>> > gm MPI ?
>> >
>> >
>> >
>> > I have changed PATH and LD_LIBRARY_PATH:
>> >
>> >
>> >
>> > I deleted /opt/mpich-gm/bin from PATH and added
>> >
>> > /ptmp/myname/openmpi123/ompi123_install/bin/ into PATH.
>> >
>> >
>> >
>> > LD_LIBRARY_PATH=/ptmp/myname/openmpi123/ompi123_install/lib
>> >
>> >
>> >
>> > And then, I got
>> >
>> >
>> >
>> > -bash-3.00$ which mpirun
>> > /ptmp/myname/openmpi123/ompi123_install/bin/mpirun
>> >
>> >
>> >
>> > In my job script , I used
>> >
>> >
>> >
>> > "time mpirun -np 16 /ptmp/jxding/openmpi123/openmpi-1.2.3/
>> examples/
>> > hello_c"
>> >
>> > Then I added "which mpirun" in my job script, and then submited my
>> > job to the
>> > cluster , I got :
>> > ====================================
>> >
>> > /opt/mpich-gm/bin/mpirun
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > Hello, world, I am 0 of 1
>> > 0.117u 0.165s 0:09.54 2.8% 0+0k 0+0io 0pf+0w
>> >
>> > ====================================
>> >
>> > So , it means that the application is still using MPICH-GM not Open
>> > MPI.
>> >
>> > Would you please help me with that ?
>> >
>> >
>> > thanks,
>> >
>> >
>> >
>> > Tony
>> >
>> >
>> >
>> > June 16 2008
>> > _________________________________________________________________
>> > Now you can invite friends from Facebook and other groups to join
>> > you on Windows Live? Messenger. Add now.
>> > https://www.invite2messenger.net/im/?source=TXT_EML_WLH_AddNow_Now
>> > -------------- next part --------------
>> > HTML attachment scrubbed and removed
>> >
>> > ------------------------------
>> >
>> > Message: 5
>> > Date: Mon, 16 Jun 2008 19:05:06 +0200
>> > From: Andreas Sch?fer <gentryx_at_[hidden]>
>> > Subject: Re: [OMPI users] help me please, about Open MPI
>> > To: Open MPI Users <users_at_[hidden]>
>> > Message-ID: <20080616170506.GB7069_at_[hidden]>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > Dear Mister Smith,
>> >
>> > Thank you for installing Open MPI.
>> >
>> > On 12:51 Mon 16 Jun , Tony Smith wrote:
>> > > I have changed PATH and LD_LIBRARY_PATH:
>> >
>> > Please be aware that you have to make those changes within your job
>> > script. Otherwise they will only affect your local shell.
>> >
>> > > But, how can I make sure that the application is run by Open MPI
>> > not by mpich-
>> >
>> > You could enforce a certain mpirun by using its absolute path, e.g
>> > "/ptmp/myname/openmpi123/ompi123_install/bin/mpirun foo" instead of
>> > just "mpirun foo".
>> >
>> > > I deleted /opt/mpich-gm/bin from PATH and added
>> >
>> > You should not need to delete, just add in front of MPICH.
>> >
>> > > Would you please help me with that ?
>> >
>> > I utterly hope I just did.
>> >
>> > Most sincerely yours ;-)
>> > -Andreas
>> >
>> >
>> > --
>> > ============================================
>> > Andreas Sch?fer
>> > Cluster and Metacomputing Working Group
>> > Friedrich-Schiller-Universit?t Jena, Germany
>> > PGP/GPG key via keyserver
>> > I'm a bright... http://www.the-brights.net
>> > ============================================
>> >
>> > (\___/)
>> > (+'.'+)
>> > (")_(")
>> > This is Bunny. Copy and paste Bunny into your
>> > signature to help him gain world domination!
>> > -------------- next part --------------
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>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>> > End of users Digest, Vol 923, Issue 4
>> > *************************************
>> >
>> >
>> >
>> >
>> > --
>> > V. Gregory Weirs
>> > Sandia National Laboratories vgweirs_at_[hidden]
>> > P.O.Box 5800, MS 0378 phone: 505 845 2032
>> > Albuquerque, NM 87185-0378 fax: 505 284 0154
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> --
>> Jeff Squyres
>> Cisco Systems
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>>
>>
>> --
>> V. Gregory Weirs
>> Sandia National Laboratories vgweirs_at_[hidden]
>> P.O.Box 5800, MS 0378 phone: 505 845 2032
>> Albuquerque, NM 87185-0378 fax: 505 284 0154
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> Cisco Systems
>
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users

-- 
Jeff Squyres
Cisco Systems