<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div>I made a mistake sending this mail to James only...<br><div><br><div>Début du message réexpédié :</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>De : </b></span><span style="font-family:'Helvetica'; font-size:medium;">Gérald Fenoy <<a href="mailto:gerald.fenoy@geolabs.fr">gerald.fenoy@geolabs.fr</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date : </b></span><span style="font-family:'Helvetica'; font-size:medium;">15 mai 2010 16:14:59 HAEC<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>À : </b></span><span style="font-family:'Helvetica'; font-size:medium;">"<a href="mailto:James.Sewell@lisasoft.com">James.Sewell@lisasoft.com</a>" <<a href="mailto:James.Sewell@lisasoft.com">James.Sewell@lisasoft.com</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Objet : </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Rép : [ZOO-Discuss] ZOO and segfaults</b><br></span></div><br><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi James,<div>sorry for my late answer.</div><div><br></div><div>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 ?</div><div><br></div><div>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.</div><div><br></div><div>Please try to add the following section at the end of your main configuration file corresponding to your specific Python installation :</div><div><br></div><div>[env] </div><div>PYTHONPATH=<YOUR_PYTHONPATH></div><div><br></div><div>Please let me know if this solve your issue.</div><div><br></div><div>Hope to hear from you,</div><div>best regards,</div><div><br><div><div>Le 14 mai 2010 à 09:20, <a href="mailto:James.Sewell@lisasoft.com">James.Sewell@lisasoft.com</a> a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-US" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; ">Hey all,<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; 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></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; 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 style="font-family: 'Courier New'; ">python_path</span><span class="Apple-converted-space"> </span>is the culprit.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; ">*** glibc detected *** ./zoo_loader_capture: free(): invalid pointer: 0x000000000042515b ***<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; ">..<span style="font-family: 'Courier New'; "><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; ">#4 0x00007ffff4c5be53 in free () from /lib/libc.so.6<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; ">No symbol table info available.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; ">#5 0x00000000004117a3 in zoo_python_support (main_conf=<value optimised out>, request=0x631830, s=0x642150,<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> real_inputs=<value optimised out>, real_outputs=0x7fffffff0820) at service_internal_python.c:178<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> m = 0x632e30<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> inputs = 0x651a60<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> outputs = <value optimised out><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> tmp = <value optimised out><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> python_path = 0x42515b "."<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> pModule = <value optimised out><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "> pFunc = <value optimised out><o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; ">…<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-family: 'Courier New'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; 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></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; 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></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; 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 style="font-family: 'Courier New'; ">shilpa.media.osaka-cu.ac.jp/zoo/?</span>, 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></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; ">I am more than happy to provide more debugging output if anyone would like some.<o:p></o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><h5 style="margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-image: initial; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: white; background-position: initial initial; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); font-weight: normal; ">Cheers,<o:p></o:p></span></h5><h5 style="margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: 'Times New Roman', serif; margin-top: 0cm; margin-bottom: 0.0001pt; background-image: initial; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: white; background-position: initial initial; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); font-weight: normal; ">James Sewell<o:p></o:p></span></h5><h5 style="margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: 'Times New Roman', serif; margin-top: 0cm; margin-bottom: 0.0001pt; background-image: initial; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: white; background-position: initial initial; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); font-weight: normal; ">LISAsoft Developer<o:p></o:p></span></h5><h5 style="margin-right: 0cm; margin-left: 0cm; font-size: 10pt; font-family: 'Times New Roman', serif; margin-top: 0cm; margin-bottom: 0.0001pt; background-image: initial; background-repeat: initial; background-attachment: initial; -webkit-background-clip: initial; -webkit-background-origin: initial; background-color: white; background-position: initial initial; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); font-weight: normal; ">+61 (3) 8680 3200 / +61 414 688 892<o:p></o:p></span></h5><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div>_______________________________________________<br>Zoo-discuss mailing list<br><a href="mailto:Zoo-discuss@gisws.media.osaka-cu.ac.jp" style="color: blue; text-decoration: underline; ">Zoo-discuss@gisws.media.osaka-cu.ac.jp</a><br><a href="http://gisws.media.osaka-cu.ac.jp/mailman/listinfo/zoo-discuss" style="color: blue; text-decoration: underline; ">http://gisws.media.osaka-cu.ac.jp/mailman/listinfo/zoo-discuss</a><br></div></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-size: 12px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="font-size: medium; ">Djay</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="font-size: medium; ">Just a ZOO Tribe member</span></div><div><span class="Apple-style-span" style="font-size: medium; "><a href="mailto:gerald.fenoy@geolabs.fr">gerald.fenoy@geolabs.fr</a></span></div></span></div></span></div></div></span>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-size: 12px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="font-size: medium; ">Djay</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-style-span" style="font-size: medium; ">Just a ZOO Tribe member</span></div><div><span class="Apple-style-span" style="font-size: medium; "><a href="mailto:gerald.fenoy@geolabs.fr">gerald.fenoy@geolabs.fr</a></span></div></span></div></span></div></div></span>
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