[pyngl-talk] release of Pyngl version compatible with Ncl 6.1 or Ncl 6.2.1
Mary Haley
haley at ucar.edu
Thu Jun 25 15:14:16 MDT 2015
Charlie,
I don't know yet about getting PyNGL to work, but PyNIO was built with GNU
V4.9.2, and not V4.8. This *might* be the issue, but I would be surprised
if it is.
How did you link the libgomp.1.dylib file?
Maybe the better way to have done this is via the DYLD_LIBRARY_PATH
environment variable.
For example:
export DYLD_LIBRARY_PATH=/opt/local/lib/gcc48
or, if you already have that variable set to something:
export DYLD_LIBRARY_PATH=/opt/local/lib/gcc48:$DYLD_LIBRARY_PATH
--Mary
On Thu, Jun 25, 2015 at 10:25 AM, Charlie Koven <ckoven at gmail.com> wrote:
> Mary,
>
> Thanks! I tried to use both of these (the 10.10 PyNio and the 10.9 PyNGL)
> but still no luck. Initially when I tried to load the Nio and Ngl modules,
> I was getting libgomp errors like this:
>
> ImportError:
> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so,
> 2): Library not loaded: /usr/local/lib/libgomp.1.dylib
> Referenced from:
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so
> Reason: image not found
>
> So I made sure I had gcc48 installed via macports (as suggested here:
> http://www.ncl.ucar.edu/Download/macosx.shtml ) and put a link in
> /usr/local/lib to /opt/local/lib/gcc48/libgomp.1.dylib, but after that, I
> still got the following errors, and I’m not sure if these require Nio and
> Ngl to be compiled differently.
>
> Thanks,
> Charlie
>
>
>
> In [*1*]: import Ngl
> ---------------------------------------------------------------------------
> ImportError Traceback (most recent call
> last)
> <ipython-input-1-ec4bb7966c2f> in <module>()
> ----> 1 import Ngl
>
>
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/Ngl.py
> in <module>()
> * 42*
> * 43* # PyNGL analysis functions
> ---> 44 import fplib
> * 45*
> * 46* import sys
>
> ImportError:
> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/fplib.so,
> 2): Symbol not found: ___addtf3
> Referenced from:
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/fplib.so
> Expected in: /usr/lib/libSystem.B.dylib
> in
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/fplib.so
>
> In [*2*]: import Nio
> ---------------------------------------------------------------------------
> ImportError Traceback (most recent call
> last)
> <ipython-input-2-d77b80fd2dfc> in <module>()
> ----> 1 import Nio
>
>
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/Nio.py
> in <module>()
> * 81* '''
> * 82*
> ---> 83 from nio import *
> * 84* from nio import _C_API
> * 85*
>
> ImportError:
> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so,
> 2): Symbol not found: __ZNSt8__detail15_List_node_base7_M_hookEPS0_
> Referenced from:
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so
> Expected in: /usr/lib/libstdc++.6.dylib
> in
> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so
>
>
>
>
>
>
> On Jun 25, 2015, at 4:49 PM, Mary Haley <haley at ucar.edu> wrote:
>
> Hi Charlie,
>
> I built a PyNIO binary for Yosemite, but I didn't have time to do the
> PyNGL binary. I recently upgraded to Yosemite, and I'm still getting all
> my builds sorted out.
>
> Please try the
> "PyNIO-1.5.0-beta.macos-10.10-x86_64-py279-numpy192-gnu492.tar.gz" binary
> that I've put at:
>
> http://www.pyngl.ucar.edu/Training/SEA2015/binaries.shtml#Python279NumPy192
>
> --Mary
>
> On Wed, Jun 24, 2015 at 1:27 PM, Mary Haley <haley at ucar.edu> wrote:
>
>> Charlie,
>>
>> We have some additional beta binaries at:
>>
>> http://www.pyngl.ucar.edu/Training/SEA2015/binaries.shtml
>>
>> but these are only for MacOS 10.8 and 10.9.
>>
>> I might be able to provide a yosemite version, as I think my home machine
>> is running this. I'll leave a note for myself to check.
>>
>> --Mary
>>
>>
>> On Sat, Jun 20, 2015 at 10:13 AM, Charlie Koven <ckoven at gmail.com> wrote:
>>
>>> Hi All,
>>>
>>> Just tried to install binaries onto a new computer (macos yosemite) and
>>> getting errors. Any chance of making a binary for this OS version?
>>>
>>> Thanks,
>>> Charlie
>>>
>>>
>>>
>>> the binaries I tried to install but didn’t work were:
>>> PyNGL-1.5.0-beta.macos-10.9-x86_64-py278-numpy191.tar.gz
>>> PyNIO-1.4.1.macos-10.8-x86_64-py275-numpy162.tar.gz
>>>
>>> The versions on my computer are:
>>> Python 2.7.10
>>> numpy 1.9.2
>>>
>>> uname -a
>>> Darwin admins-MBP 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23
>>> 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_6
>>>
>>> gcc --version
>>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
>>> --with-gxx-include-dir=/usr/include/c++/4.2.1
>>> Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)
>>> Target: x86_64-apple-darwin14.3.0
>>> Thread model: posix
>>>
>>>
>>>
>>>
>>>
>>> In [*2*]: import Nio
>>>
>>> ---------------------------------------------------------------------------
>>> ImportError Traceback (most recent call
>>> last)
>>> <ipython-input-2-d77b80fd2dfc> in <module>()
>>> ----> 1 import Nio
>>>
>>>
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/Nio.py
>>> in <module>()
>>> * 61* '''
>>> * 62*
>>> ---> 63 from nio import *
>>> * 64* from nio import _C_API
>>> * 65*
>>>
>>> ImportError:
>>> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so,
>>> 2): Symbol not found: ___addtf3
>>> Referenced from:
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so
>>> Expected in: /usr/lib/libSystem.B.dylib
>>> in
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNIO/nio.so
>>>
>>> In [*3*]: import Ngl
>>>
>>> ---------------------------------------------------------------------------
>>> ImportError Traceback (most recent call
>>> last)
>>> <ipython-input-3-ec4bb7966c2f> in <module>()
>>> ----> 1 import Ngl
>>>
>>>
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/Ngl.py
>>> in <module>()
>>> * 39*
>>> * 40* # PyNGL analysis functions
>>> ---> 41 import fplib
>>> * 42*
>>> * 43* import sys
>>>
>>> ImportError:
>>> dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/fplib.so,
>>> 2): Symbol not found: ___addtf3
>>> Referenced from:
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/fplib.so
>>> Expected in: /usr/lib/libSystem.B.dylib
>>> in
>>> /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PyNGL/fplib.so
>>>
>>> In [*4*]:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Dec 10, 2014, at 11:22 PM, Mary Haley <haley at ucar.edu> wrote:
>>>
>>> I have some binaries ready for you guys to try, and will keep uploading
>>> a few more (I'm doing some Python 2.7.6/numpy 1.9.1 combinations too).
>>>
>>> *https://www.pyngl.ucar.edu/Download/files/
>>> <https://www.pyngl.ucar.edu/Download/files/>*
>>>
>>> The install and test instructions are the same as they were for 1.4.1:
>>>
>>> *http://www.pyngl.ucar.edu/Download/install_from_binary.shtml
>>> <http://www.pyngl.ucar.edu/Download/install_from_binary.shtml>*
>>>
>>> The file names should be pretty self-explanatory:
>>>
>>> PyNGL-1.5.0-beta.Linux-Debian-6.0-i686-py278-numpy191-gcc445.tar.gz
>>> <http://www.pyngl.ucar.edu/Download/files/PyNGL-1.5.0-beta.Linux-Debian-6.0-i686-py278-numpy191-gcc445.tar.gz>
>>>
>>> The above is a 32-bit binary compiled on a Debian Linux system with
>>> Python 2.7.8, NumPy 1.9.1, and gcc 4.1.2.
>>>
>>> I only have Debian and RedHat binaries (one of the binaries has an SL
>>> name which is Scientific Linux and RedHat based).
>>>
>>> If you have Ubuntu, then I recommend going with a Debian binary.
>>> If you have CentOS, then try a RedHat binary.
>>>
>>> Once you have the software installed, you can try the attached
>>> pyngltest.py script, or run one of the examples available with "pynglex":
>>>
>>> pynglex -l --> to get list of examples
>>> pynlgex xy1 ---> to run example "xy1.py"
>>>
>>>
>>> Many of these call Nio.open_file, so you will need to have PyNIO
>>> installed.
>>>
>>> If you have problems with a particular PyNGL-1.5-0-beta binary, then
>>> email me with
>>>
>>> - The name of the PyNGL binary you downloaded
>>> - A description of your system:
>>>
>>> uname -a
>>>
>>> gcc --version
>>>
>>>
>>> - The output from running the attached pyngltest.py script
>>> - The "map1.ps" file, if it exists.
>>> - Any other information, like error messages, flavor of linux, etc.
>>>
>>>
>>> I haven't looked into incorporating these into anaconda or some other
>>> packaged set of Python software yet. I first just want to get them into the
>>> hands of some testers.
>>>
>>> Thanks again for your patience. I will appreciate hearing from folks
>>> whether this new version is or isn't working for them.
>>>
>>> --Mary
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Dec 10, 2014 at 8:38 AM, Mary Haley <haley at ucar.edu> wrote:
>>>
>>>> Hi All,
>>>>
>>>> I'm sorry I haven't been responsive on this. I've been trying to find a
>>>> block of time to dedicate to doing some minor updates of PyNGL and create
>>>> some binaries.
>>>>
>>>> I got most of the updates done, so I'll create some binaries for you to
>>>> try this week.
>>>>
>>>> I will use Python 2.7.8 and numpy 1.9.1 since these are the latest
>>>> versions. Once I have the binaries ready and if these two versions don't
>>>> work for you, let me know.
>>>>
>>>> --Mary
>>>>
>>>>
>>>> On Fri, Oct 24, 2014 at 10:59 AM, Mary Haley <haley at ucar.edu> wrote:
>>>>
>>>>> Hi Thomas,
>>>>>
>>>>> I can provide you with a beta version of PyNGl that works with NCL V
>>>>> 6.1 (and V6.2). Just let me know what version of numpy and python you have,
>>>>> and what type of system (Linux, 32 or 64-bit system, version of gcc).
>>>>>
>>>>> Our release schedule has slipped because we are still tying up lose
>>>>> ends with NCL.
>>>>>
>>>>> --Mary
>>>>>
>>>>>
>>>>> On Fri, Oct 24, 2014 at 2:15 AM, Thomas Arsouze <
>>>>> thomas.arsouze at ensta-paristech.fr> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> do you have any estimation when a new version of Pyngl will be
>>>>>> available ?
>>>>>> I would like to use Pyngl but only got Ncl 6.1 and later installed on
>>>>>> the computers at my lab.
>>>>>>
>>>>>> Thanks in advance.
>>>>>>
>>>>>> Sincerly,
>>>>>> Thomas.
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>>
>>>>
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>>
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