Open MPI logo

Open MPI User's Mailing List Archives

  |   Home   |   Support   |   FAQ   |  

This web mail archive is frozen.

This page is part of a frozen web archive of this mailing list.

You can still navigate around this archive, but know that no new mails have been added to it since July of 2016.

Click here to be taken to the new web archives of this list; it includes all the mails that are in this frozen archive plus all new mails that have been sent to the list since it was migrated to the new archives.

Subject: Re: [OMPI users] gfortran bindings apparently not built on mac os leopard
From: Brian W. Barrett (brbarret_at_[hidden])
Date: 2008-06-18 09:56:23


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!
>>>> -------------- next part --------------
>>>> A non-text attachment was scrubbed...
>>>> Name: not available
>>>> Type: application/pgp-signature
>>>> Size: 197 bytes
>>>> Desc: not available
>>>> URL:
>>>> <http://www.open-mpi.org/MailArchives/users/attachments/20080616/ab34ce85/attachment.bin
>>>> >
>>>>
>>>> ------------------------------
>>>>
>>>> _______________________________________________
>>>> 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
>
>
>