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

Mon Mar 14 23:24:41 MDT 2016

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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