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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 10:15:40


Thanks Brian -- I've updated the FAQ.

On Jun 18, 2008, at 9:56 AM, Brian W. Barrett wrote:

> Thanks for adding the section, but the information contained within
> is wrong (as was the information in this e-mail thread). OS X
> essentially *always* adds a -rpath to both executables depending on
> libraries and libraries depending on other libraries. There is no
> need to set LD_LIBRARY_PATH, which on OS X is only used by the
> linker at link time and by dlopen, but not the linker at run time.
> Setting DYLD_LIBRARY_PATH is not only unnecessary, but considered
> harmful. There are very few situations where one would need to set
> DYLD_LIBRARY_PATH, and they should never be part of a production
> environment.
>
> If you built Open MPI as a set of static libraries, there is a
> library search order problem (which neither of the two LIBRARY_PATH
> variables will solve) in that OS X searches the entire library path
> for a shared library of the specified name, then searches the entire
> library path again for a static library of the specified name.
> Since /usr/lib/libmpi.dylib would then always be found before <my
> install/lib/libmpi.a, you'd have a problem. An easy workaround is
> to add -Wl,-search_paths_first to the link line when linking MPI
> applications. I'd accomplish this by adding the following to OMPI's
> configure:
>
> --with-wrapper-ldflags="-Wl,-search_paths_first"
>
> Getting back to the original problem, unless the user already has
> set DYLD_LIBRARY_PATH (which they shouldn't do), there is no need to
> modify DYLD_LIBRARY_PATH for OMPI to work properly (even with the
> system installed version in /usr/lib). We should not mention
> DYLD_LIBRARY_PATH in the FAQ. If we do mention it, it should only
> be to say that it should not be set.
>
> Brian
>
>
> On Wed, 18 Jun 2008, Jeff Squyres wrote:
>
>> 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!
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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
>>
>>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users

-- 
Jeff Squyres
Cisco Systems