So i figured it out. My $TMPDIR was set to something funky like: /var/folders/jd/qh5zn6jn5kz_byz9gxz5kl2m0000gn/T but if I manually set it to export TMPDIR=/tmp the messages go away. Not sure why it was originally set to something weird like that. Thanks anyway, Justin On Wed, Sep 21, 2016 at 3:55 AM, Justin Chang <jychang48@gmail.com> wrote:
Yeah I saw that google mailing list, and I tried deleted the openmpi-sessions-* directory under $TMPDIR but the message is not going away and said directory keeps reappearing. Perhaps maybe I should clear the pip cache?
On Wed, Sep 21, 2016 at 3:29 AM, David Ham <David.Ham@imperial.ac.uk> wrote:
Hmm. FWIW I can't reproduce this. I've updated everything from homebrew and in particular have open-mpi 2.0.1 and mpi4py 2.0.0 installed as above. If I run:
python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank"
then I just get the expected output of "0"
Regards,
David
On Wed, 21 Sep 2016 at 04:37 Justin Chang <jychang48@gmail.com> wrote:
It has come back. I tried the steps Lawrence suggested but the messages won't go away:
(firedrake)➜ ~ python -c "from firedrake import *"
[Justins-MacBook-Pro-2.local:00492] [[25811,0],0] bind() failed on error Address already in use (48)
[Justins-MacBook-Pro-2.local:00492] [[25811,0],0] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228
(firedrake)➜ ~ python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank"
[Justins-MacBook-Pro-2.local:00563] [[26380,0],0] bind() failed on error Address already in use (48)
[Justins-MacBook-Pro-2.local:00563] [[26380,0],0] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228
0
(firedrake)➜ ~ pip uninstall mpi4py
Uninstalling mpi4py-2.0.0:
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py-2.0.0-py2.7.egg-info
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/MPI.pxd
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/MPI.so
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__init__.py
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__init__.pyc
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__main__.py
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/__main__.pyc
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/dl.so
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/MPI.pxd
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/__init__.pxd
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/__init__.pyx
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/libmpi.pxd
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi.pxi
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI.h
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.MPI_api.h
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.h
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/include/mpi4py/mpi4py.i
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libmpe.dylib
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt-hyb.dylib
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt-mpi.dylib
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/lib-pmpi/libvt.dylib
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/libmpi.pxd
/Users/justin/Software/firedrake/lib/python2.7/site-packages/mpi4py/mpi.cfg
Proceed (y/n)? y
Successfully uninstalled mpi4py-2.0.0
(firedrake)➜ ~ pip install --no-binary :all: mpi4py
Collecting mpi4py
Using cached mpi4py-2.0.0.tar.gz
Skipping bdist_wheel for mpi4py, due to binaries being disabled for it.
Installing collected packages: mpi4py
Running setup.py install for mpi4py ... done
Successfully installed mpi4py-2.0.0
(firedrake)➜ ~ python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank"
[Justins-MacBook-Pro-2.local:00849] [[26222,0],0] bind() failed on error Address already in use (48)
[Justins-MacBook-Pro-2.local:00849] [[26222,0],0] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228
0
Any ideas here?
Thanks, Justin
On Tue, Sep 20, 2016 at 4:47 AM, Justin Chang <jychang48@gmail.com> wrote:
Wait, sorry, my MPI error/warning messages disappeared without a trace. I am not sure how I "fixed" it.
I'll holler again if I see something else.
On Tue, Sep 20, 2016 at 4:39 AM, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> wrote:
On 20/09/16 09:30, Justin Chang wrote:
Hi all,
I upgraded homebrew on my macbook and had to remove firedrake because the compiled libraries were pointing to old/nonexistent brew packages. So when I tried to install a fresh copy of firedrake, i get this message:
$ python firedrake-install --developer --disable_ssh --log
Installing command line tools...
Installing required packages via homebrew. You can safely ignore warnings that packages are already installed
Creating firedrake virtualenv in 'firedrake'.
/Users/justin/Software/firedrake/bin/pip install -vvv -U pip
Traceback (most recent call last):
File "firedrake-install", line 1016, in <module>
framework = fix_osx_virtualenv_python()
File "firedrake-install", line 973, in fix_osx_virtualenv_python
shutil.copytree(appsrc, appdest)
File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 208, in copytree
raise Error, errors
shutil.Error:
[('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Info.plist', '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Info.plist'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python', '/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python', "[Errno 1] Operation not permitted:
'/Users/justin/Software/firedrake/Python.app/Contents/MacOS/Python'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS', '/Users/justin/Software/firedrake/Python.app/Contents/MacOS', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/MacOS'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/PkgInfo', '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/PkgInfo'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonApplet.icns',
'/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns', "[Errno 1] Operation not permitted:
'/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonApplet.icns'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonInterpreter.icns',
'/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', "[Errno 1] Operation not permitted:
'/Users/justin/Software/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources', '/Users/justin/Software/firedrake/Python.app/Contents/Resources', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents/Resources'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/version.plist', '/Users/justin/Software/firedrake/Python.app/Contents/version.plist', "[Errno 1] Operation not permitted:
'/Users/justin/Software/firedrake/Python.app/Contents/version.plist'"), ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', '/Users/justin/Software/firedrake/Python.app/Contents', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app/Contents'"),
('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', '/Users/justin/Software/firedrake/Python.app', "[Errno 1] Operation not permitted: '/Users/justin/Software/firedrake/Python.app'")]
And when I run the script again, it installs correctly. I guess this meant the virtualenv was "successfully" installed the first time.
However, I get this strange MPI warning/error that I have never before seen:
$ python -c "from firedrake import *"
[Justins-MacBook-Pro-2.local:88453] [[15547,0],0] bind() failed on error Address already in use (48)
[Justins-MacBook-Pro-2.local:88453] [[15547,0],0] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228
My firedrake programs appear to run without any error, but these messages still seem very suspicious. Any ideas what this could be? My homebrew upgrade/update has now given me Open MPI 2.0.1, and I am wondering if anyone else is having this issue.
Can you run an mpi4py program?
In the virtualenv:
$ python -c "from mpi4py import MPI; print MPI.COMM_WORLD.rank"
If that fails, try uninstalling mpi4py
$ pip uninstall mpi4py
And then reinstalling, but crucially without using the pip cache:
$ pip install --no-binary :all: mpi4py
Cheers,
Lawrence
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