Re: PyNGL/PyNIO binary for MacOS 10.9?

From: Mary Haley <haley_at_nyahnyahspammersnyahnyah>
Date: Wed Dec 04 2013 - 12:33:37 MST

Hi Charlie,

Sorry for the delay in response. I was mostly off email the last 1.5 weeks.

I don't think there should be an issue with the different versions of numpy. As numpy progresses through versions, I've noticed that they've gotten more backwards compatible.

If you were using numpy 1.6 and trying to use a binary compiled with numpy 1.7, then I might worry.

Also, if there were an issue, I think you would see some immediate error messages.

--Mary

On Nov 22, 2013, at 12:36 PM, Charlie Koven <ckoven@gmail.com> wrote:

> Hi Mary,
>
> Great, thanks for that. It works for me now after loading the HPC library into my /usr/local directory Ngl and Nio load and Ngl is able to generate graphics. I used the 1.5.0-alpha Ngl version. One thing is that I am using the macports numpy 1.7.1 for this do you know of any issues in using the libraries compiled for numpy 1.6.2 with 1.7.1?
>
> Charlie
>
>
>
> On Nov 22, 2013, at 8:27 AM, Mary Haley <haley@ucar.edu> wrote:
>
>> It looks like there's a mismatch between the version of gcc/gfortran that you have, and the gcc/gfortran I used to compile PyNGL and PyNIO.
>>
>> I was hoping that by compiling libgfortran.a statically, this would cover this issue, but here, it looks like the gcc system library is the culprit.
>>
>> I'm using gcc/gfortran version 4.7.1. You might be able to install these yourself using macports:
>>
>> port install gcc47
>>
>> or HPC, which is what I used:
>>
>> http://hpc.sourceforge.net
>>
>> I believe I downloaded the "gcc-4.7-bin.tar.gz" file, and it assumes that you are untarring it under the top root "/" directory, because it wants to put things in "usr/local".
>>
>> -Mary
>>
>> On Nov 21, 2013, at 4:45 PM, Charles Koven <cdkoven@lbl.gov> wrote:
>>
>>> Hi Mary,
>>>
>>> I tried installing those files but am getting the following error when I load them.
>>>
>>> Also, I realized I gave bad info in my first email; the numpy version was for the system python, not the macports version. the macports version of bumpy is 1.7.1. Anyway I tried loading the PyNGL/PyNIO libraries in both places:
>>>
>>> ( /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ for the macports python)
>>> ( /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/ for the default python)
>>>
>>> and I get the same error (except for the paths) no matter which version I use. Anything obvious I am doing wrong?
>>>
>>> Thanks,
>>> Charlie
>>>
>>>
>>>
>>> Python 2.7.5 (default, Aug 25 2013, 00:04:04)
>>> [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
>>> Type "help", "copyright", "credits" or "license" for more information.
>>>
>>>
>>>>>> import Nio
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in <module>
>>> File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNIO/Nio.py", line 63, in <module>
>>> from nio import *
>>> ImportError: dlopen(/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNIO/nio.so, 2): Symbol not found: ___addtf3
>>> Referenced from: /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNIO/nio.so
>>> Expected in: /usr/lib/libSystem.B.dylib
>>> in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNIO/nio.so
>>>
>>>
>>>>>> import Ngl
>>> Traceback (most recent call last):
>>> File "<stdin>", line 1, in <module>
>>> File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNGL/Ngl.py", line 39, in <module>
>>> import fplib
>>> ImportError: dlopen(/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNGL/fplib.so, 2): Symbol not found: ___addtf3
>>> Referenced from: /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNGL/fplib.so
>>> Expected in: /usr/lib/libSystem.B.dylib
>>> in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyNGL/fplib.so
>>>>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Nov 21, 2013, at 2:58 PM, Mary Haley <haley@ucar.edu> wrote:
>>>
>>>>
>>>> On Nov 21, 2013, at 3:34 PM, Louis Wicker <Louis.Wicker@noaa.gov> wrote:
>>>>
>>>>> Mary - I just tried installing this on my system, I just upgraded to Mavricks.
>>>>>
>>>>> Nio went okay, but import Ngl error exits as
>>>>>
>>>>> ImportError: dlopen(/Volumes/Master/Users/wicker/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/PyNGL/fplib.so, 2): Library not loaded: /opt/X11/lib/libfontconfig.1.dylib
>>>>> Referenced from: /Volumes/Master/Users/wicker/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/PyNGL/fplib.so
>>>>> Reason: Incompatible library version: fplib.so requires version 10.0.0 or later, but libfontconfig.1.dylib provides version 8.0.0
>>>>>
>>>>> Is this hard to fix at your or my end?
>>>>
>>>> Hi Lou,
>>>>
>>>> I can try to fix this by building in fontconfig statically or perhaps first you can try installing this package via MacPorts:
>>>>
>>>> port install fontconfig
>>>>
>>>> or
>>>>
>>>> sudo port install fontconfig
>>>>
>>>> You might also have to do:
>>>>
>>>> port install freetype
>>>>
>>>>
>>>> This software will be installed to /opt.
>>>>
>>>> MacPorts is available from
>>>>
>>>> http://www.macports.org/
>>>>
>>>> If none of this works, let me know and I'll see if I can build things statically.
>>>>
>>>> I've uploaded a PyNGL 1.5.0-alpha version and will send an email shortly about it. This still has the fontconfig dependency.
>>>>
>>>> --Mary
>>>>
>>>>>
>>>>> Lou
>>>>>
>>>>>
>>>>>
>>>>> On 11/21/13, 4:25 PM, Mary Haley wrote:
>>>>>> Hi Charlie,
>>>>>>
>>>>>> I don't have a MacOS 10.9 system handy, but 10.8 binaries should work fine (at least this is the case with other executables I've tried).
>>>>>>
>>>>>> I put PyNGL 1.4.0 and PyNIO 1.4.1, compiled with Python 275 and Numpy 162 on ftp:
>>>>>>
>>>>>> ftp
>>>>>> ftp.ucar.edu
>>>>>>
>>>>>> <log in as "anonymous">
>>>>>> <Use email address as password>
>>>>>> cd /pub/scd/haley
>>>>>> get PyNIO-1.4.1.macos-10.8-x86_64-py275-numpy162.tar.gz
>>>>>> get PyNGL-1.4.0.macos-10.8-x86_64-py275-numpy162.tar.gz
>>>>>> quit
>>>>>>
>>>>>> You'll want to "tar -zxvf" this file in the root directory of where your python is installed. I'm using a python that I built myself (and not the macports version), so my python installation is pretty basic:
>>>>>>
>>>>>> lib/python2.7/site-packages
>>>>>> bin/python2.7*
>>>>>> bin/python
>>>>>>
>>>>>> If your installation doesn't look like this, for example, if you have "lib64" instead of "lib", then you may need to untar the file somewhere temporary, and change the directories as necessary.
>>>>>>
>>>>>> --Mary
>>>>>>
>>>>>> On Nov 21, 2013, at 2:09 PM, Mary Haley
>>>>>> <haley@ucar.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>> Hi Charlie,
>>>>>>>
>>>>>>> I can try to compile you a new version of both.
>>>>>>>
>>>>>>> Thanks for the numpy and python versions. I'll see what I can do.
>>>>>>>
>>>>>>> --Mary
>>>>>>>
>>>>>>> On Nov 20, 2013, at 12:45 PM, Charlie Koven
>>>>>>> <ckoven@gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>> Hi Mary, Dave,
>>>>>>>>
>>>>>>>> I updated my laptop to the latest MacOS, version 10.9, up from version 10.6 where it had been before. Naturally this broke the PyNGL and PyNIO versions that had been on it. Any chance that there are binaries that would work on the new system? The basic info of my machine is below; I am using the python and numpy that is installed by macports.
>>>>>>>>
>>>>>>>> uname -a
>>>>>>>> Darwin xxxxxxx.dhcp.lbl.gov 13.0.0 Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013; root:xnu-2422.1.72~6/RELEASE_X86_64 x86_64
>>>>>>>>
>>>>>>>> python
>>>>>>>> Python 2.7.5 (default, Aug 25 2013, 00:04:04)
>>>>>>>> [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
>>>>>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>>>
>>>>>>>>>>> import numpy
>>>>>>>>>>>
>>>>>>>> numpy.__version__
>>>>>>>>
>>>>>>>>>>> numpy.__version__
>>>>>>>>>>>
>>>>>>>> '1.6.2'
>>>>>>>>
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Charlie Koven
>>>>>>>> Lawrence Berkeley Lab
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>>>>>
>>>>> --
>>>>>
>>>>> ----------------------------------------------------------------------------
>>>>> | Dr. Louis J. Wicker
>>>>> | NSSL/FRDD Rm 3366
>>>>> | National Weather Center
>>>>> | 120 David L. Boren Boulevard, Norman, OK 73072
>>>>> |
>>>>> | E-mail:
>>>>> Louis.Wicker@noaa.gov
>>>>>
>>>>> | HTTP:
>>>>> www.nssl.noaa.gov/~lwicker
>>>>>
>>>>> | Phone: (405) 325-6340
>>>>> | Fax: (405) 325-6780
>>>>> |
>>>>> |
>>>>> I "In fact the hardest part of research is always to find
>>>>> | a question that's big enough thats worth answering
>>>>> | but little enough that you can actually answer it"
>>>>> |
>>>>> | Edward Witten
>>>>> ----------------------------------------------------------------------------
>>>>> |
>>>>> | "The contents of this message are mine personally and
>>>>> | do not reflect any position of the Government or NOAA."
>>>>> |
>>>>> ----------------------------------------------------------------------------
>>>>>
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>>>>
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>>>
>>>
>>> Charlie Koven
>>>
>>> Lawrence Berkeley National Laboratory
>>> 1 Cyclotron Rd., MS 50-4037
>>> Berkeley, CA 94720
>>>
>>> 510.486.6724
>>> cdkoven@lbl.gov
>>>
>>>
>>>
>>>
>>
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Received on Wed Dec 4 12:33:44 2013

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