Discussion:
[OMPI users] OS X + Xcode 8 : dyld: Symbol not found: _clock_gettime
Christophe Peyret
2016-10-03 14:09:43 UTC
Permalink
Hello,

since Xcode8 update, I have problem problem with mpirun function : _clock_gettime is not found


dyld: Symbol not found: _clock_gettime
Referenced from: /opt/openmpi-1.10.4/lib//libopen-pal.13.dylib
Expected in: flat namespace

Trace/BPT trap: 5

Any idea ?

Christophe
George Bosilca
2016-10-03 16:42:25 UTC
Permalink
This function is not available on OS X, and the corresponding OMPI module
shouldn't have been compiled. How did you configure you OMPI install ?

George.


On Mon, Oct 3, 2016 at 10:09 AM, Christophe Peyret <
Post by Christophe Peyret
Hello,
_clock_gettime is not found
dyld: Symbol not found: _clock_gettime
Referenced from: /opt/openmpi-1.10.4/lib//libopen-pal.13.dylib
Expected in: flat namespace
Trace/BPT trap: 5
Any idea ?
Christophe
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Nathan Hjelm
2016-10-03 16:58:55 UTC
Permalink
I didn't think we even used clock_gettime() on Linux in 1.10.x. A quick check of the git branch confirms that.

ompi-release git:(v1.10) ✗ find . -name '*.[ch]' | xargs grep clock_gettime
ompi-release git:(v1.10) ✗

-Nathan

On Oct 03, 2016, at 10:50 AM, George Bosilca <***@icl.utk.edu> wrote:

This function is not available on OS X, and the corresponding OMPI module shouldn't have been compiled. How did you configure you OMPI install ?

  George.


On Mon, Oct 3, 2016 at 10:09 AM, Christophe Peyret <***@onera.fr> wrote:
Hello,

since Xcode8 update, I have problem problem with mpirun function : _clock_gettime is not found


dyld: Symbol not found: _clock_gettime
  Referenced from: /opt/openmpi-1.10.4/lib//libopen-pal.13.dylib
  Expected in: flat namespace

Trace/BPT trap: 5

Any idea ?

Christophe
George Bosilca
2016-10-03 17:56:33 UTC
Permalink
I have plenty of references to clock_gettime, both on the 1.10 git branch
and on the tarball on the website.

George.
Post by Nathan Hjelm
I didn't think we even used clock_gettime() on Linux in 1.10.x. A quick
check of the git branch confirms that.
ompi-release git:(v1.10) ✗ find . -name '*.[ch]' | xargs grep clock_gettime
ompi-release git:(v1.10) ✗
-Nathan
This function is not available on OS X, and the corresponding OMPI module
shouldn't have been compiled. How did you configure you OMPI install ?
George.
On Mon, Oct 3, 2016 at 10:09 AM, Christophe Peyret <
Post by Christophe Peyret
Hello,
_clock_gettime is not found
dyld: Symbol not found: _clock_gettime
Referenced from: /opt/openmpi-1.10.4/lib//libopen-pal.13.dylib
Expected in: flat namespace
Trace/BPT trap: 5
Any idea ?
Christophe
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
Gilles Gouaillardet
2016-10-04 11:20:45 UTC
Permalink
Christophe,

If i read between the lines, you had Open MPI running just fine, then you upgraded xcode and that broke OpenMPI. Am i right so far ?

Did you build Open MPI by yourself, or did you get binaries from somewhere (such as brew) ?
In the first case, you need to rebuild Open MPI.
(You have to run configure && make install, so Open MPI is aware clock_gettime is not available)

I will check how brew binaries were built, and ensure they do not use clock_gettime.

Cheers,

Gilles
Post by Christophe Peyret
Hello,
since Xcode8 update, I have problem problem with mpirun function : _clock_gettime is not found
dyld: Symbol not found: _clock_gettime
  Referenced from: /opt/openmpi-1.10.4/lib//libopen-pal.13.dylib
  Expected in: flat namespace
Trace/BPT trap: 5
Any idea ?
Christophe
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