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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi All,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for your help Gerald and Luca, adding an [env] section
with a PythonPath has fixed my problem. This is a little odd as I can see the
PythonPath is set to “.” by default in the debug trace when no
PythonPath is set, but I am happy it’s working now!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Should I be logging these segfault cases as bugs somewhere so
they can be addressed at some stage in the future?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Next problem:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>This link:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'><a
href="http://shilpa.media.osaka-cu.ac.jp/zoo/?request=Execute&service=WPS&version=1.0.0&Identifier=Distance&DataInputs=InputEntity1=Reference@xlink:href=http://carto.languedoc-roussillon.ecologie.gouv.fr/webservices/wfs/diren_general/%3FVERSION%3D1.1.0%26service%3DWFS%26request%3DGetFeature%26typename%3DZnieff1%26maxfeatures%3D1;InputEntity2=Reference@xlink:href=http://carto.languedoc-roussillon.ecologie.gouv.fr/webservices/wfs/diren_general/%3FVERSION%3D1.1.0%26service%3DWFS%26request%3DGetFeature%26typename%3DZnieff2%26maxfeatures%3D1">http://shilpa.media.osaka-cu.ac.jp/zoo/?request=Execute&service=WPS&version=1.0.0&Identifier=Distance&DataInputs=InputEntity1=Reference@xlink:href=http://carto.languedoc-roussillon.ecologie.gouv.fr/webservices/wfs/diren_general/%3FVERSION%3D1.1.0%26service%3DWFS%26request%3DGetFeature%26typename%3DZnieff1%26maxfeatures%3D1;InputEntity2=Reference@xlink:href=http://carto.languedoc-roussillon.ecologie.gouv.fr/webservices/wfs/diren_general/%3FVERSION%3D1.1.0%26service%3DWFS%26request%3DGetFeature%26typename%3DZnieff2%26maxfeatures%3D1</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Does not work with the default Distance.zfg from Subversion on
my server. When I debug this is because a segfault is caused (due to the VALUE
being null I think?). Would it be possible to get the set of zfcg files from
the shipla server? The Bounding box example with the xlink works, so I can
reverse engineer each zfcg if I need to.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for your help so far, <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<h5 style='mso-margin-top-alt:12.0pt;margin-right:0cm;margin-bottom:12.0pt;
margin-left:0cm;background:white'><span style='font-size:11.0pt;font-family:
"Calibri","sans-serif";color:#1F497D;font-weight:normal'>Cheers,<o:p></o:p></span></h5>
<h5 style='margin:0cm;margin-bottom:.0001pt;background:white'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;
font-weight:normal'>James Sewell<o:p></o:p></span></h5>
<h5 style='margin:0cm;margin-bottom:.0001pt;background:white'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;
font-weight:normal'>LISAsoft Developer<o:p></o:p></span></h5>
<h5 style='margin:0cm;margin-bottom:.0001pt;background:white'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;
font-weight:normal'>+61 (3) 8680 3200 / +61 414 688 892<o:p></o:p></span></h5>
<p class=MsoNormal><span style='font-family:"Calibri","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Gérald Fenoy
[mailto:gerald.fenoy@geolabs.fr] <br>
<b>Sent:</b> Sunday, 16 May 2010 12:15 AM<br>
<b>To:</b> James.Sewell@lisasoft.com<br>
<b>Subject:</b> Re: [ZOO-Discuss] ZOO and segfaults<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi James,<o:p></o:p></p>
<div>
<p class=MsoNormal>sorry for my late answer.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>I'm not sure to know how to solve your issue, but can you
tell me what is the PYTHONPATH set in your main configuration file in the
specific env section if you get any ?<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Indeed, it seems that there is some problem if you don't set
the PYTHONPATH in the env section of your main configuration file
unfortunately.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Please try to add the following section at the end of your
main configuration file corresponding to your specific Python installation :<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>[env] <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>PYTHONPATH=<YOUR_PYTHONPATH><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Please let me know if this solve your issue.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Hope to hear from you,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>best regards,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal>Le 14 mai 2010 à 09:20, <a
href="mailto:James.Sewell@lisasoft.com">James.Sewell@lisasoft.com</a> a écrit :<o:p></o:p></p>
</div>
<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
<div>
<div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hey
all,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>After
having worked out my previous problem (segfaults caused by an older version of
CURL) I am faced with a new problem. I am now getting segfaults caused by
calls to free(). I get these problems when trying to run an Execute (I am
testing with the python hello world at the moment).<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>A
portion of the backtrace when debugging with gdb is below. It looks like
calling free on<span class=apple-converted-space> </span></span><span
style='font-size:11.0pt;font-family:"Courier New"'>python_path</span><span
class=apple-converted-space><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> </span></span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>is the culprit.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>***
glibc detected *** ./zoo_loader_capture: free(): invalid pointer:
0x000000000042515b ***<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>..<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>#4
0x00007ffff4c5be53 in free () from /lib/libc.so.6</span><span style='font-size:
11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>No
symbol table info available.</span><span style='font-size:11.0pt;font-family:
"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>#5
0x00000000004117a3 in zoo_python_support (main_conf=<value optimised
out>, request=0x631830, s=0x642150,</span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
real_inputs=<value optimised out>, real_outputs=0x7fffffff0820) at
service_internal_python.c:178</span><span style='font-size:11.0pt;font-family:
"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
m = 0x632e30</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
inputs = 0x651a60</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
outputs = <value optimised out></span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
tmp = <value optimised out></span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
python_path = 0x42515b "."</span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
pModule = <value optimised out></span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>
pFunc = <value optimised out></span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'>…</span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New"'> </span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I
have replicated this behavior on a CentOS 64bit machine and a Ubuntu 32bit
machine. The Java hello world runs fine, although it looks like some of
the other processes (Distance etc..) have other problems causing segfaults for
other reasons (a call to xmlNewText which seems to be in the libxml2 library in
the case of Distance).<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I
can stop the free errors by setting MALLOC_CHECK_ =0, but that doesn’t
seem like a very good solution.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Can
anyone shed any light on why this is happening? Has anyone managed a successful
install of the subversion head which can process python? I can run all these
requests from<span class=apple-converted-space> </span></span><span
style='font-size:11.0pt;font-family:"Courier New"'>shilpa.media.osaka-cu.ac.jp/zoo/?</span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>, so I am also
curious about what version this is running. I can see some differences on this box
to the head (the Distance process only requires one Input as an example).<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I
am more than happy to provide more debugging output if anyone would like some.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<h5 style='margin-bottom:12.0pt;background:white;background-image:initial;
background-repeat:initial;background-attachment:initial;-webkit-background-clip: initial;
-webkit-background-origin: initial;background-position:initial initial'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;
font-weight:normal'>Cheers,</span><o:p></o:p></h5>
<h5 style='margin:0cm;margin-bottom:.0001pt;background:white;background-image:
initial;background-repeat:initial;background-attachment:initial;-webkit-background-clip: initial;
-webkit-background-origin: initial;background-position:initial initial'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;
font-weight:normal'>James Sewell</span><o:p></o:p></h5>
<h5 style='margin:0cm;margin-bottom:.0001pt;background:white;background-image:
initial;background-repeat:initial;background-attachment:initial;-webkit-background-clip: initial;
-webkit-background-origin: initial;background-position:initial initial'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;
font-weight:normal'>LISAsoft Developer</span><o:p></o:p></h5>
<h5 style='margin:0cm;margin-bottom:.0001pt;background:white;background-image:
initial;background-repeat:initial;background-attachment:initial;-webkit-background-clip: initial;
-webkit-background-origin: initial;background-position:initial initial'><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;
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