<div dir="ltr">Hi Mary,<div><br></div><div>Sorry I forgot to provide the environment variable of NCL in conda:</div><div><br></div><div><p style="margin:0px;line-height:normal;font-family:Menlo;color:rgb(175,173,36)"><span style="color:rgb(0,0,0)">(ncl_test)</span>[hsushipei@master ncl_testing_code]$<span style="color:rgb(0,0,0)"> ncl -V</span></p>
<p style="margin:0px;line-height:normal;font-family:Menlo">r16433</p>
<p style="margin:0px;line-height:normal;font-family:Menlo;color:rgb(175,173,36)"><span style="color:rgb(0,0,0)">(ncl_test)</span>[hsushipei@master ncl_testing_code]$<span style="color:rgb(0,0,0)"> which ncl</span></p>
<p style="margin:0px;line-height:normal;font-family:Menlo">~/miniconda2/envs/ncl_test/bin/ncl</p>
<p style="margin:0px;line-height:normal;font-family:Menlo;color:rgb(175,173,36)"><span style="color:rgb(0,0,0)">(ncl_test)</span>[hsushipei@master ncl_testing_code]$<span style="color:rgb(0,0,0)"> env | grep NCARG</span></p>
<p style="margin:0px;line-height:normal;font-family:Menlo">OLD_NCARG_ROOT=/data5/hsushipei/software/ncl-6.2.0</p>
<p style="margin:0px;line-height:normal;font-family:Menlo">NCARG_ROOT=/home/hsushipei/miniconda2/envs/ncl_test</p><p style="margin:0px;line-height:normal;font-family:Menlo"><br></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif">Best,</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif">Shi-Pei</font></p></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 15, 2016 at 1:24 PM, Shi-Pei Hsu <span dir="ltr"><<a href="mailto:hsushipei1@gmail.com" target="_blank">hsushipei1@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Mary,<div><br></div><div>For NCL tests:</div><div><br></div><div>After some more example-testing and comparison, I found that the error message, "Segmentation fault (Core dumped)", would emerge if "png" was specified in function "gsn_open_wks" while "x11", PostScript, PDF and SVG outputs work fine(but for NCL-6.2.0, they all work successfully.). As a result, I compared the version of cairo, libpng, freetype and pixman of "ncl_test" with "<a href="http://www.ncl.ucar.edu/Download/build_from_src.shtml#pkgconfig" target="_blank">Build NCL from source</a>".I noticed that libpng in conda environment seems too new, with 1.6.7 instead of 1.2.52 that NCL-building documentation mentioned and maybe this is why "Segmentation fault" came out. I tried to install those packages with correct version</div><div><br></div><div><p style="margin:0px;line-height:normal;font-family:Menlo">$ 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</p></div><div><br></div><div>but failed due to dependency conflict:</div><div><br></div><div><p style="margin:0px;line-height:normal;font-family:Menlo">The following specifications were found to be in conflict:</p>
<p style="margin:0px;line-height:normal;font-family:Menlo"> - cairo 1.12.18* -> freetype 2.4*|2.5*|2.5.*</p>
<p style="margin:0px;line-height:normal;font-family:Menlo"> - cairo 1.12.18* -> libpng 1.5.13|1.6.*|1.6.17</p>
<p style="margin:0px;line-height:normal;font-family:Menlo"> - cairo 1.12.18* -> pixman 0.26.2</p>
<p style="margin:0px;line-height:normal;font-family:Menlo"> - freetype 2.5.5* -> libpng 1.6.*</p>
<p style="margin:0px;line-height:normal;font-family:Menlo"> - libpng 1.2.50*</p>
<p style="margin:0px;line-height:normal;font-family:Menlo"> - ncl dev* -> libpng</p>
<p style="margin:0px;line-height:normal;font-family:Menlo">Use "conda info <package>" to see the dependencies for each package.</p></div><div><br></div><div>I guess maybe this is because the cairo was previously built with libpng-1.6.x.</div><div><br></div><div>Thanks!!</div><div><br></div><div>Best regards,</div><div><br></div><div>She-Pei </div><div><br></div><div><br></div><div><br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Mar 14, 2016 at 8:05 AM, Mary Haley <span dir="ltr"><<a href="mailto:haley@ucar.edu" target="_blank">haley@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-size:small">She-Pei,</div><div class="gmail_default" style="font-size:small"><br></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></div><div class="gmail_default" style="font-size:small">NCL tests:</div><div class="gmail_default" style="font-size:small"><br></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></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></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></div><div class="gmail_default" style="font-size:small">PyNGL/PyNIO tests:</div><div class="gmail_default" style="font-size:small"><br>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></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">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></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">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></div><div class="gmail_default" style="font-size:small">--Mary</div><div class="gmail_default" style="font-size:small"><br></div><div class="gmail_default" style="font-size:small"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>On Sat, Mar 12, 2016 at 10:58 PM, Shi-Pei Hsu <span dir="ltr"><<a href="mailto:hsushipei1@gmail.com" target="_blank">hsushipei1@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hi NCL-install team,<div> 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> 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><br></div><div><table border="1" cellspacing="0" cellpadding="0" width="100%" style="width:556px;border-collapse:collapse;border:none"><tbody><tr><td width="199" colspan="2" valign="top" style="width:199.25pt;border:1pt solid windowtext;padding:0cm 5.4pt"><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US">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"><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US">PyNIO+PyNGL</span></p></td></tr><tr><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"><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" style="font-size:13pt">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"><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US">Result</span></p><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US"> </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"><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US" style="font-size:13pt">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"><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US">Result</span></p><p class="MsoNormal" align="center" style="text-align:center"><span lang="EN-US"> </span></p></td></tr><tr><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"><p class="MsoNormal"><span lang="EN-US" style="font-size:10pt;font-family:Courier">“ng4ex gsun01n –clean” </span><span lang="EN-US" style="font-size:10pt">command</span><span lang="EN-US" style="font-size:10pt"></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"><p class="MsoNormal"><span lang="EN-US">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"><p class="MsoNormal"><span lang="EN-US">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"><p class="MsoNormal"><span lang="EN-US">No error message</span></p></td></tr><tr><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"><p class="MsoNormal"><span lang="EN-US" style="font-size:10pt">Run examples provided by NCL website. For example, “maponly_3.ncl” and “mptick5.ncl”</span><span lang="EN-US"></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"><p class="MsoNormal"><span lang="EN-US">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"><p class="MsoNormal"><span lang="EN-US">Run file “<a href="http://test2.7.sh" target="_blank">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"><p class="MsoNormal"><span lang="EN-US">Output message is below:</span></p></td></tr></tbody></table>
</div><div><br></div><div><p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>ma_test.py:10: RuntimeWarning: tempnam is a potential security risk to your program</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i> filename = os.tempnam(None, 'test_')</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>......</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>----------------------------------------------------------------------</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>Ran 6 tests in 0.024s</i></font></p>
<p style="margin:0px;line-height:normal;min-height:21px"><font face="georgia, serif"><i><br></i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>OK</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>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></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>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></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>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></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>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></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>Nio.NIOError: coercing 8-byte long data to 4-byte integer variable (v44): possible data loss due to overflow</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>test_mfio.py:10: RuntimeWarning: tempnam is a potential security risk to your program</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i> filename = os.tempnam(None, 'test_')</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>..........</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>----------------------------------------------------------------------</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>Ran 10 tests in 0.081s</i></font></p>
<p style="margin:0px;line-height:normal;min-height:21px"><font face="georgia, serif"><i><br></i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>OK</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>var-sub-test.py:10: RuntimeWarning: tempnam is a potential security risk to your program</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i> filename = os.tempnam(None, 'test_')</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>....</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>----------------------------------------------------------------------</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>Ran 4 tests in 0.015s</i></font></p>
<p style="margin:0px;line-height:normal;min-height:21px"><font face="georgia, serif"><i><br></i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>OK</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>syntax error, unexpected WORD_STRING, expecting WORD_WORD</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>context: Error { code = 1; message = "Cannot locate resource: <a href="http://test.opendap.org/opendap/hyrax/data/nc/123.nc.dds" target="_blank">http://test.opendap.org/opendap/hyrax/data/nc/123.nc.dds</a>"^;};</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>fatal:Could not open (<a href="http://test.opendap.org/opendap/data/nc/123.nc" target="_blank">http://test.opendap.org/opendap/data/nc/123.nc</a>)</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>Traceback (most recent call last):</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i> File "test-opendap2.py", line 20, in <module></i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i> f = Nio.open_file(url + filename)</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i> File "/home/hsushipei/miniconda2/envs/pyngl_test/lib/python2.7/site-packages/PyNIO/Nio.py", line 735, in open_file</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i> file = _Nio.open_file(filename,mode,options,history,format)</i></font></p>
<p style="margin:0px;line-height:normal"><font face="georgia, serif"><i>Nio.NIOError: Unable to open file</i></font></p><p style="margin:0px;line-height:normal"><font face="georgia, serif"><i><br></i></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" size="4">Thanks!</font><br></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" size="4"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" size="4">Best regards,</font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" size="4"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif" size="4">She-Pei</font><br></p><p style="margin:0px;line-height:normal"><font face="georgia, serif"><i><br></i></font></p></div></div>
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