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Subject: Re: [OMPI users] gfortran bindings apparently not built on mac os leopard
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2008-06-17 17:17:38


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
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> >
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> >
> > 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