Re: PyNGL/PyNIO and NCL 6.1.x

From: David Brown <dbrown_at_nyahnyahspammersnyahnyah>
Date: Mon May 06 2013 - 16:09:40 MDT

Hi David,
I can't remember for sure, but I think you are building from source. Is that correct? If so, it looks like a problem locating the gfortran library.
Did you set the F2CLIBS and F2CLIBS_PREFIX environment variables, as described in the On my mac 10.8 machine I have these set as follows (bash syntax):

export F2CLIBS=gfortran
export F2CLIBS_PREFIX=/usr/local/lib/

and if I do
    ls /usr/local/lib/*gfortran*
on the command line I get:

$ ls /usr/local/lib/*gfortran*
/usr/local/lib/libgfortran.3.dylib /usr/local/lib/libgfortran.dylib
/usr/local/lib/libgfortran.a /usr/local/lib/

Does this help? If not please let us know.

On May 6, 2013, at 3:16 PM, "David B. Reusch" <> wrote:

> Hi again,
> I'm finally having time to try out PyNIO again. I was successful on this machine (the 10.8 Mac called mawson in my last email) in Dec 2011 (when it was still OS 10.7) but am having trouble now. The build and install *seem* ok but either they aren't or I'm missing something in my environment because I'm getting this error:
>> python
>> Python 2.7.2 (default, Oct 11 2012, 20:14:37)
>> [GCC 4.2.1 Compatible Apple Clang 4.0 (tags/Apple/clang-418.0.60)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import numpy
>> >>> import Nio
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in <module>
>> File "", line 63, in <module>
>> from nio import *
>> ImportError: dlopen(/Library/Python/2.7/site-packages/PyNIO/, 2): Symbol not found: __gfortran_compare_string
>> Referenced from: /Library/Python/2.7/site-packages/PyNIO/
>> Expected in: flat namespace
>> in /Library/Python/2.7/site-packages/PyNIO/
>> >>>
> I've tried a couple things but am not really sure which direction to go to try to fix this (plus all my old notes on installing this and its prereqs are elsewhere). So I was hoping maybe this was something you recognized quickly? I can also share my build and install output if helpful.
> Also, regarding new features, I don't get very fancy and have just been using vanilla aspects of netCDF so far (e.g., no netCDF4 or HDF5 files) so I should be fine if I can just get this install working. Of course, it'll be nice to have all the new stuff someday when the next release comes out, but I have no personal urgency for that right now.
> Thanks,
> Dave
> David Brown said the following on 4/23/13 4:27 PM:
>> Hi Dave,
>> Actually, the PyNIO installation should be independent of NCL nowadays, so the
>> version of NCL should not matter. If you do have NCARG_ROOT defined, it can be used as a backup
>> location for the GRIB2 code tables, but you do not need to have an NCL install to get PyNIO up and
>> running.
>> It is true we have not had a release for awhile, and I am aware that there are new features in our
>> file handling library that would be very nice to get into PyNIO. However, some of the new features we
>> have added to NCL for handling NetCDF4 and HDF5 cannot be automatically incorporated into PyNIO as is.
>> There needs to be some new data structures and code reorganization to get things like groups, variable
>> length arrays and compound data types working. I hope we have a chance to work on this before too long.
>> -dave
>> On Apr 23, 2013, at 3:53 PM, "David B. Reusch" <> wrote:
>>> Hi Mary, Dave B,
>>> I'm actually getting by ok by doing the part I need PyNIO for on
>>> yellowstone. I have to ship some files back and forth but, given my
>>> timeline, it's a lot easier than trying to figure out installs on my
>>> home machines. Turns out I'm only using PyNIO and not PyNGL in this
>>> script, and purely in a read-a-netCDF-file mode, no writing (that email
>>> went out a little too quickly yesterday!).
>>> I went into this thinking I'd have to go back to NCL 6.0 before running
>>> the script, so I did that yesterday on yellowstone: it all worked.
>>> This morning, forgetting to repeat that, it looked like things were
>>> working even with 6.1.1 ( my yellowstone default). But I caught it and
>>> went back to 6.0 to be safe.
>>> Bigger picture, I haven't actually used PyNGL enough to have any
>>> specific feature requests. I converted one plotting script about a year
>>> ago but haven't been back, though it is definitely something I'd like to
>>> use more. Having PyNGL and PyNIO available again would certainly be a
>>> welcome development :-) It's not looking like an urgent/critical need
>>> here at the moment though since I have the yellowstone option out there.
>>> Re: PyNIO and 6.1.1, I'm not even sure I tried reinstalling that back in
>>> January (after my NCL upgrades). Is there any chance the old release
>>> would still work? It'll be a couple weeks before I'll get to it.
>>> For what it's worth, I have a mixed Linux/Mac environment:
>>> Fedora Core 18
>>> Linux 3.8.5-201.fc18.x86_64 #1 SMP Thu Mar 28 21:01:19
>>> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
>>> python 2.7.3
>>> numpy 1.7.0
>>> gcc 4.7.2
>>> OS 10.7
>>> Darwin 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23
>>> 16:26:45 PDT 2012; root:xnu-1699.32.7~1/RELEASE_I386 i386 i386 MacPro2,1
>>> Darwin
>>> python 2.7.1
>>> numpy 1.5.1
>>> gcc 4.2.1
>>> OS 10.8
>>> Darwin mawson 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10
>>> PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 i386 MacBookAir4,2
>>> Darwin
>>> python 2.7.2
>>> numpy 1.6.1
>>> gcc 4.7.2
>>> Thanks,
>>> Dave
>>> Mary Haley said the following on 4/23/13 2:43 PM:
>>>> Hi Dave,
>>>> We keep trying to get to this release, but NCL/ParNCL takes precedence,
>>>> and they have kept us busy lately!
>>>> I have new a PyNGL that works with new transparency capabilities, but the X11 driver needs to be updated.
>>>> Right now it's using the old X11 driver which you have to kill with ctrl-c.
>>>> If you don't care about this issue with the X11 driver, I can try to get you a new PyNGL binary.
>>>> I would need to know the usual:
>>>> uname -a
>>>> what version of Python
>>>> what version of NumPy
>>>> Dave B will have to speak for PyNIO.
>>>> Can you tell us which features you need?
>>>> --Mary
>>>> On Apr 22, 2013, at 4:26 PM, David B. Reusch wrote:
>>>>> Hi,
>>>>> What's the latest status on getting PyNGL/PyNIO to work with the
>>>>> latest-and-greatest version of NCL? I've just discovered a key script
>>>>> that I need for a talk on Monday and am wondering if I'll have to
>>>>> back-level NCL to make it work.
>>>>> Thanks,
>>>>> Dave
>>>>> --
>>>>> Associate Research Professor of Climatology
>>>>> Dept of Earth and Environmental Science
>>>>> MSEC 304; 801 Leroy Place
>>>>> New Mexico Tech
>>>>> Socorro, NM 87801
>>>>> _______________________________________________
>>>>> pyngl-talk mailing list
>>>>> List instructions, subscriber options, unsubscribe:
>>> --
>>> Associate Research Professor of Climatology
>>> Dept of Earth and Environmental Science
>>> MSEC 304; 801 Leroy Place
>>> New Mexico Tech
>>> Socorro, NM 87801
>>> _______________________________________________
>>> pyngl-talk mailing list
>>> List instructions, subscriber options, unsubscribe:
> --
> Associate Research Professor of Climatology
> Dept of Earth and Environmental Science
> MSEC 304; 801 Leroy Place
> New Mexico Tech
> Socorro, NM 87801
Received on Mon May 6 16:09:43 2013

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