[ncl-install] NCL/PyNGL Anaconda test - Some result
Kevin Hallock
hallock at ucar.edu
Wed Mar 16 10:23:33 MDT 2016
Hi Shi-Pei,
I wanted to let you know that I was able to reproduce the segfaults you experienced when running “ncl maponly_3.ncl” and “ncl mptick_5.ncl” using the Anaconda linux-64 build of NCL, and I am currently looking into possible solutions.
Thank you for reporting this issue!
Kevin
> On Mar 14, 2016, at 11:33 PM, Shi-Pei Hsu <hsushipei1 at gmail.com> wrote:
>
> 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 <mailto: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 <mailto: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 <http://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 <http://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 <mailto: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 <http://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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