<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Shi-Pei,<div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Thank you for reporting this issue!</div><div class=""><br class=""></div><div class="">Kevin</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 14, 2016, at 11:33 PM, Shi-Pei Hsu <<a href="mailto:hsushipei1@gmail.com" class="">hsushipei1@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Mary,<div class=""><br class=""></div><div class="">Sorry I forgot to provide the environment variable of NCL in conda:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo; color: rgb(175, 173, 36);" class=""><span style="" class="">(ncl_test)</span>[hsushipei@master ncl_testing_code]$<span style="" class=""> ncl -V</span></div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class="">r16433</div><div style="margin: 0px; line-height: normal; font-family: Menlo; color: rgb(175, 173, 36);" class=""><span style="" class="">(ncl_test)</span>[hsushipei@master ncl_testing_code]$<span style="" class=""> which ncl</span></div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class="">~/miniconda2/envs/ncl_test/bin/ncl</div><div style="margin: 0px; line-height: normal; font-family: Menlo; color: rgb(175, 173, 36);" class=""><span style="" class="">(ncl_test)</span>[hsushipei@master ncl_testing_code]$<span style="" class=""> env | grep NCARG</span></div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class="">OLD_NCARG_ROOT=/data5/hsushipei/software/ncl-6.2.0</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class="">NCARG_ROOT=/home/hsushipei/miniconda2/envs/ncl_test</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" class="">Best,</font></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" class=""><br class=""></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" class="">Shi-Pei</font></div></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Mar 15, 2016 at 1:24 PM, Shi-Pei Hsu <span dir="ltr" class=""><<a href="mailto:hsushipei1@gmail.com" target="_blank" class="">hsushipei1@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Hi Mary,<div class=""><br class=""></div><div class="">For NCL tests:</div><div class=""><br class=""></div><div class="">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 "<a href="http://www.ncl.ucar.edu/Download/build_from_src.shtml#pkgconfig" target="_blank" class="">Build NCL from source</a>".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</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class="">$ 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</div></div><div class=""><br class=""></div><div class="">but failed due to dependency conflict:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; line-height: normal; font-family: Menlo;" class="">The following specifications were found to be in conflict:</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""> - cairo 1.12.18* -> freetype 2.4*|2.5*|2.5.*</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""> - cairo 1.12.18* -> libpng 1.5.13|1.6.*|1.6.17</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""> - cairo 1.12.18* -> pixman 0.26.2</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""> - freetype 2.5.5* -> libpng 1.6.*</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""> - libpng 1.2.50*</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class=""> - ncl dev* -> libpng</div><div style="margin: 0px; line-height: normal; font-family: Menlo;" class="">Use "conda info <package>" to see the dependencies for each package.</div></div><div class=""><br class=""></div><div class="">I guess maybe this is because the cairo was previously built with libpng-1.6.x.</div><div class=""><br class=""></div><div class="">Thanks!!</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""><br class=""></div><div class="">She-Pei </div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Mar 14, 2016 at 8:05 AM, Mary Haley <span dir="ltr" class=""><<a href="mailto:haley@ucar.edu" target="_blank" class="">haley@ucar.edu</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class="gmail_default" style="font-size:small">She-Pei,</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">Thanks so much for testing our conda installation, and providing a summary of the results.</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">NCL tests:</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">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"?</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">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.</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">To make sure your environment looks okay, could you email me the following output, from your "ncl_test" conda environment:</div><div class="gmail_default" style="font-size:small"> </div><div class="gmail_default" style="font-size:small"> ncl -V</div><div class="gmail_default" style="font-size:small"> which ncl</div><div class="gmail_default" style="font-size:small"> env | grep NCARG</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">PyNGL/PyNIO tests:</div><div class="gmail_default" style="font-size:small"><br class="">I think the failure on the opendap test is because that file no longer exists, but we'll look into this.</div>
<div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">The errors about NetCDF not supporting 64-bit longs may be coming from a test that is expected to fail (the "<a href="http://test2.7.sh/" target="_blank" class="">test2.7.sh</a>" is a PyNIO test suite, by the way, and not a PyNGL test suite).</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">Do you have a full output file that you could email me from the <a href="http://test2.7.sh/" target="_blank" class="">test2.7.sh</a> run, so I can see which tests are failing? You can just mail it to me if you prefer.</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small">--Mary</div><div class="gmail_default" style="font-size:small"><br class=""></div><div class="gmail_default" style="font-size:small"><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote"><div class=""><div class="">On Sat, Mar 12, 2016 at 10:58 PM, Shi-Pei Hsu <span dir="ltr" class=""><<a href="mailto:hsushipei1@gmail.com" target="_blank" class="">hsushipei1@gmail.com</a>></span> wrote:<br class=""></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class=""><div class=""><div dir="ltr" class="">Hi NCL-install team,<div class=""> 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). </div><div class=""> 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.</div><div class=""><br class=""></div><div class=""><table border="1" cellspacing="0" cellpadding="0" width="100%" style="width:556px;border-collapse:collapse;border:none" class=""><tbody class=""><tr class=""><td width="199" colspan="2" valign="top" style="width:199.25pt;border:1pt solid windowtext;padding:0cm 5.4pt" class=""><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" class="">NCL</span></p></td><td width="215" colspan="2" valign="top" style="width:215.25pt;border-style:solid solid solid none;border-top-color:windowtext;border-right-color:windowtext;border-bottom-color:windowtext;border-top-width:1pt;border-right-width:1pt;border-bottom-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" class="">PyNIO+PyNGL</span></p></td></tr><tr class=""><td width="155" valign="top" style="width:154.9pt;border-style:none solid solid;border-right-color:windowtext;border-bottom-color:windowtext;border-left-color:windowtext;border-right-width:1pt;border-bottom-width:1pt;border-left-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" style="font-size:13pt" class="">Functionality testing</span></p></td><td width="44" valign="top" style="width:44.35pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" class="">Result</span></p><div style="text-align: center;" class=""><span lang="EN-US" class=""> </span><br class="webkit-block-placeholder"></div></td><td width="174" valign="top" style="width:174.4pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" style="font-size:13pt" class="">Functionality testing</span></p></td><td width="41" valign="top" style="width:40.85pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" class="">Result</span></p><div style="text-align: center;" class=""><span lang="EN-US" class=""> </span><br class="webkit-block-placeholder"></div></td></tr><tr class=""><td width="155" valign="top" style="width:154.9pt;border-style:none solid solid;border-right-color:windowtext;border-bottom-color:windowtext;border-left-color:windowtext;border-right-width:1pt;border-bottom-width:1pt;border-left-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" style="font-size:10pt;font-family:Courier" class="">“ng4ex gsun01n –clean” </span><span lang="EN-US" style="font-size:10pt" class="">command</span><span lang="EN-US" style="font-size:10pt" class=""></span></p></td><td width="44" valign="top" style="width:44.35pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" class="">Passed</span></p></td><td width="174" valign="top" style="width:174.4pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" class="">In python shell, type“import Nio” and “import Ngl”</span></p></td><td width="41" valign="top" style="width:40.85pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" class="">No error message</span></p></td></tr><tr class=""><td width="155" valign="top" style="width:154.9pt;border-style:none solid solid;border-right-color:windowtext;border-bottom-color:windowtext;border-left-color:windowtext;border-right-width:1pt;border-bottom-width:1pt;border-left-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" style="font-size:10pt" class="">Run examples provided by NCL website. For example, “maponly_3.ncl” and “mptick5.ncl”</span><span lang="EN-US" class=""></span></p></td><td width="44" valign="top" style="width:44.35pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" class="">Got output: “Segmentation fault”</span></p></td><td width="174" valign="top" style="width:174.4pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" class="">Run file “<a href="http://test2.7.sh/" target="_blank" class="">test2.7.sh</a>” provided in PyNGL source code package.</span></p></td><td width="41" valign="top" style="width:40.85pt;border-style:none solid solid none;border-bottom-color:windowtext;border-bottom-width:1pt;border-right-color:windowtext;border-right-width:1pt;padding:0cm 5.4pt" class=""><p class="MsoNormal"><span lang="EN-US" class="">Output message is below:</span></p></td></tr></tbody></table>
</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">ma_test.py:10: RuntimeWarning: tempnam is a potential security risk to your program</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""> filename = os.tempnam(None, 'test_')</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">......</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">----------------------------------------------------------------------</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">Ran 6 tests in 0.024s</i></font></div><div style="margin: 0px; line-height: normal; min-height: 21px;" class=""><font face="georgia, serif" class=""><i class=""><br class=""></i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">OK</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">warning:Can't map type, netCDF does not support 64 bit longs, NCL will try to promote type to double, errors may occur</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">warning:Can't map type, netCDF does not support 64 bit longs, NCL will try to promote type to double, errors may occur</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">warning:Can't map type, netCDF does not support 64 bit longs, NCL will try to promote type to double, errors may occur</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">warning:Can't map type, netCDF does not support 64 bit longs, NCL will try to promote type to double, errors may occur</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">Nio.NIOError: coercing 8-byte long data to 4-byte integer variable (v44): possible data loss due to overflow</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">test_mfio.py:10: RuntimeWarning: tempnam is a potential security risk to your program</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""> filename = os.tempnam(None, 'test_')</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">..........</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">----------------------------------------------------------------------</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">Ran 10 tests in 0.081s</i></font></div><div style="margin: 0px; line-height: normal; min-height: 21px;" class=""><font face="georgia, serif" class=""><i class=""><br class=""></i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">OK</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">var-sub-test.py:10: RuntimeWarning: tempnam is a potential security risk to your program</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""> filename = os.tempnam(None, 'test_')</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">....</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">----------------------------------------------------------------------</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">Ran 4 tests in 0.015s</i></font></div><div style="margin: 0px; line-height: normal; min-height: 21px;" class=""><font face="georgia, serif" class=""><i class=""><br class=""></i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">OK</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">syntax error, unexpected WORD_STRING, expecting WORD_WORD</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">context: Error { code = 1; message = "Cannot locate resource: <a href="http://test.opendap.org/opendap/hyrax/data/nc/123.nc.dds" target="_blank" class="">http://test.opendap.org/opendap/hyrax/data/nc/123.nc.dds</a>"^;};</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">fatal:Could not open (<a href="http://test.opendap.org/opendap/data/nc/123.nc" target="_blank" class="">http://test.opendap.org/opendap/data/nc/123.nc</a>)</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">Traceback (most recent call last):</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""> File "test-opendap2.py", line 20, in <module></i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""> f = Nio.open_file(url + filename)</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""> File "/home/hsushipei/miniconda2/envs/pyngl_test/lib/python2.7/site-packages/PyNIO/Nio.py", line 735, in open_file</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""> file = _Nio.open_file(filename,mode,options,history,format)</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class="">Nio.NIOError: Unable to open file</i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""><br class=""></i></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" size="4" class="">Thanks!</font><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" size="4" class=""><br class=""></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" size="4" class="">Best regards,</font></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" size="4" class=""><br class=""></font></div><div style="margin: 0px; line-height: normal;" class=""><font face="arial, helvetica, sans-serif" size="4" class="">She-Pei</font><br class=""></div><div style="margin: 0px; line-height: normal;" class=""><font face="georgia, serif" class=""><i class=""><br class=""></i></font></div></div></div>
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