[ncl-install] NCL/PyNGL Anaconda test - Some result

[Shi-Pei Hsu]

Hi Mary,

Sorry I forgot to provide the environment variable of NCL in conda:

(ncl_test)[hsushipei at master ncl_testing_code]$ ncl -V

r16433

(ncl_test)[hsushipei at master ncl_testing_code]$ which ncl

~/miniconda2/envs/ncl_test/bin/ncl

(ncl_test)[hsushipei at master ncl_testing_code]$ env | grep NCARG

OLD_NCARG_ROOT=/data5/hsushipei/software/ncl-6.2.0

NCARG_ROOT=/home/hsushipei/miniconda2/envs/ncl_test


Best,


Shi-Pei

On Tue, Mar 15, 2016 at 1:24 PM, Shi-Pei Hsu <hsushipei1 at gmail.com> wrote:

> Hi Mary,
>
> For NCL tests:
>
> After some more example-testing and comparison, I found that the error
> message, "Segmentation fault (Core dumped)", would emerge if "png" was
> specified in function "gsn_open_wks" while "x11", PostScript, PDF and SVG
> outputs work fine(but for NCL-6.2.0, they all work successfully.). As a
> result, I compared the version of cairo, libpng, freetype and pixman of
> "ncl_test" with "Build NCL from source
> <http://www.ncl.ucar.edu/Download/build_from_src.shtml#pkgconfig>".I
> noticed that libpng in conda environment seems too new, with 1.6.7 instead
> of 1.2.52 that NCL-building documentation mentioned and maybe this is why
> "Segmentation fault" came out. I tried to install those packages with
> correct version
>
> $ conda create --name ncl_test_cairo_pkg --channel dbrown --channel
> khallock ncl=dev cairo=1.12.18 libpng=1.2.50 freetype=2.5.5 pixman=0.32.6
>
> but failed due to dependency conflict:
>
> The following specifications were found to be in conflict:
>
>   - cairo 1.12.18* -> freetype 2.4*|2.5*|2.5.*
>
>   - cairo 1.12.18* -> libpng 1.5.13|1.6.*|1.6.17
>
>   - cairo 1.12.18* -> pixman 0.26.2
>
>   - freetype 2.5.5* -> libpng 1.6.*
>
>   - libpng 1.2.50*
>
>   - ncl dev* -> libpng
>
> Use "conda info <package>" to see the dependencies for each package.
>
> I guess maybe this is because the cairo was previously built with
> libpng-1.6.x.
>
> Thanks!!
>
> Best regards,
>
> She-Pei
>
>
>
>
> On Mon, Mar 14, 2016 at 8:05 AM, Mary Haley <haley at ucar.edu> wrote:
>
>> She-Pei,
>>
>> Thanks so much for testing our conda installation, and providing a
>> summary of the results.
>>
>> NCL tests:
>>
>> Is the conda version of NCL causing a segmentation fault on all examples,
>> or just a subset of them? I couldn't reproduce the results when I tried the
>> conda ncl on mptick_5.ncl and maponly_3.ncl.  Also, are you getting any
>> errors from running these tests, or just a "segmentation fault"?
>>
>> It's quite possible that this problem is from an environment issue, for
>> example, if NCARG_ROOT is set incorrectly, or else other NCARG_XXXX
>> environment variables are set that are not consistent with the "conda" path.
>>
>> To make sure your environment looks okay, could you email me the
>> following output, from your "ncl_test" conda environment:
>>
>>   ncl -V
>>   which ncl
>>   env | grep NCARG
>>
>> PyNGL/PyNIO tests:
>>
>> I think the failure on the opendap test is because that file no longer
>> exists, but we'll look into this.
>>
>> The errors about NetCDF not supporting 64-bit longs may be coming from a
>> test that is expected to fail (the "test2.7.sh" is a PyNIO test suite,
>> by the way, and not a PyNGL test suite).
>>
>> Do you have a full output file that you could email me from the
>> test2.7.sh run, so I can see which tests are failing? You can just mail
>> it to me if you prefer.
>>
>> --Mary
>>
>>
>>
>> On Sat, Mar 12, 2016 at 10:58 PM, Shi-Pei Hsu <hsushipei1 at gmail.com>
>> wrote:
>>
>>> Hi NCL-install team,
>>>         I'm running a 64-bit Linux and I chose Miniconda as environment
>>> and package manager. The environment set-up and installation of both NCL
>>> and PyNGL works successfully (No error messages came out).
>>>         After NCL and PyNGL are installed, I've done some simple
>>> functionality testing for them.(I guess this section will be the next
>>> goal?) Tests I've done are shown in the table below.
>>>
>>> NCL
>>>
>>> PyNIO+PyNGL
>>>
>>> Functionality testing
>>>
>>> Result
>>>
>>>
>>>
>>> Functionality testing
>>>
>>> Result
>>>
>>>
>>>
>>> “ng4ex gsun01n –clean” command
>>>
>>> Passed
>>>
>>> In python shell, type“import Nio” and “import Ngl”
>>>
>>> No error message
>>>
>>> Run examples provided by NCL website. For example, “maponly_3.ncl” and
>>> “mptick5.ncl”
>>>
>>> Got output: “Segmentation fault”
>>>
>>> Run file “test2.7.sh” provided in PyNGL source code package.
>>>
>>> Output message is below:
>>>
>>> *ma_test.py:10: RuntimeWarning: tempnam is a potential security risk to
>>> your program*
>>>
>>> *  filename = os.tempnam(None, 'test_')*
>>>
>>> *......*
>>>
>>> *----------------------------------------------------------------------*
>>>
>>> *Ran 6 tests in 0.024s*
>>>
>>>
>>> *OK*
>>>
>>> *warning:Can't map type, netCDF does not support 64 bit longs, NCL will
>>> try to promote type to double, errors may occur*
>>>
>>> *warning:Can't map type, netCDF does not support 64 bit longs, NCL will
>>> try to promote type to double, errors may occur*
>>>
>>> *warning:Can't map type, netCDF does not support 64 bit longs, NCL will
>>> try to promote type to double, errors may occur*
>>>
>>> *warning:Can't map type, netCDF does not support 64 bit longs, NCL will
>>> try to promote type to double, errors may occur*
>>>
>>> *Nio.NIOError: coercing 8-byte long data to 4-byte integer variable
>>> (v44): possible data loss due to overflow*
>>>
>>> *test_mfio.py:10: RuntimeWarning: tempnam is a potential security risk
>>> to your program*
>>>
>>> *  filename = os.tempnam(None, 'test_')*
>>>
>>> *..........*
>>>
>>> *----------------------------------------------------------------------*
>>>
>>> *Ran 10 tests in 0.081s*
>>>
>>>
>>> *OK*
>>>
>>> *var-sub-test.py:10: RuntimeWarning: tempnam is a potential security
>>> risk to your program*
>>>
>>> *  filename = os.tempnam(None, 'test_')*
>>>
>>> *....*
>>>
>>> *----------------------------------------------------------------------*
>>>
>>> *Ran 4 tests in 0.015s*
>>>
>>>
>>> *OK*
>>>
>>> *syntax error, unexpected WORD_STRING, expecting WORD_WORD*
>>>
>>> *context: Error { code = 1; message = "Cannot locate resource:
>>> http://test.opendap.org/opendap/hyrax/data/nc/123.nc.dds
>>> <http://test.opendap.org/opendap/hyrax/data/nc/123.nc.dds>"^;};*
>>>
>>> *fatal:Could not open (http://test.opendap.org/opendap/data/nc/123.nc
>>> <http://test.opendap.org/opendap/data/nc/123.nc>)*
>>>
>>> *Traceback (most recent call last):*
>>>
>>> *  File "test-opendap2.py", line 20, in <module>*
>>>
>>> *    f = Nio.open_file(url + filename)*
>>>
>>> *  File
>>> "/home/hsushipei/miniconda2/envs/pyngl_test/lib/python2.7/site-packages/PyNIO/Nio.py",
>>> line 735, in open_file*
>>>
>>> *    file = _Nio.open_file(filename,mode,options,history,format)*
>>>
>>> *Nio.NIOError: Unable to open file*
>>>
>>>
>>> Thanks!
>>>
>>>
>>> Best regards,
>>>
>>>
>>> She-Pei
>>>
>>>
>>>
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>>>
>>
>
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