<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I upgraded to 1.997. Accessing the browser through mod_perl seems to be working fine now, with sessions locking as expected. However, the default link (cgi-bin/gb2/gbrowse) comes up with an error, reported in the server log as:<div><div>[Thu Jul 30 14:19:44 2009] [error] [client xx] (13)Permission denied: exec of '/usr/lib/cgi-bin/gb2/gbrowse' failed</div><div>[Thu Jul 30 14:19:44 2009] [error] [client xx] Premature end of script headers: gbrowse</div><div><br></div><div>fast-cgi access also returns an error:</div><div><div>[Thu Jul 30 14:21:19 2009] [warn] (104)Connection reset by peer: mod_fcgid: read data from fastcgi server error.</div><div>[Thu Jul 30 14:21:19 2009] [error] [client xx] Premature end of script headers: gbrowse</div><div>[Thu Jul 30 14:21:22 2009] [notice] mod_fcgid: process /usr/lib/cgi-bin/gb2/gbrowse(23135) exit(communication error), terminated by calling exit(), return code: 255</div><div><br></div><div>Of course, those are superfluous now that mod_perl works. I installed everything with root permission and to the default destinations, so I'm not sure what's causing those errors.</div><div><br></div><div>Thanks again,</div><div>Joe</div><div><br></div><div><br></div><div><br></div></div><div><br></div><div><div>On 30 Jul 2009, at 12:41, Lincoln Stein wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Joseph,<br><br>I believe I have fixed this bug. Please try version 1.997 that I just uploaded to CPAN.<br><br>Lincoln<br><br><div class="gmail_quote">On Thu, Jul 30, 2009 at 10:10 AM, joseph franklin <span dir="ltr"><<a href="mailto:joseph.franklin@yale.edu">joseph.franklin@yale.edu</a>></span> wrote:<br> <blockquote class="gmail_quote" style="border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); margin-top: 0pt; margin-right: 0pt; margin-bottom: 0pt; margin-left: 0.8ex; padding-left: 1ex; position: static; z-index: auto; "><div style="">Lincoln,<div>As far as I know, everything I'm doing related to session locking is the default, except that I added the "session lock type = nfs" line to try to make sure that it isn't using flock:</div> <div><br></div><div><div># session settings</div><div>session lock type = nfs</div><div class="im"><div>session driver = driver:file;serializer:default</div><div>session args = Directory /var/tmp/gbrowse2/sessions</div> <div><br></div></div><div><div>Since this problem is limited to the mod_perl and fcgi modes, is there something specific to those packages that needs to be specified for proper session locking? (I know very little about insides of those modules or apache2).</div> <div><br></div><div>Let me know if I can provide any more info. Thanks-</div><div>Joe</div></div><div><div></div><div class="h5"><div><br></div><div><br></div><div><div>On 29 Jul 2009, at 16:10, Lincoln Stein wrote:</div> <br><blockquote type="cite">This is unpleasant news; I thought the session locking was pretty well tested. Can you describe how to reproduce this bug?<br><br>Lincoln<br><br><div class="gmail_quote">On Tue, Jul 28, 2009 at 12:26 PM, joseph franklin <span dir="ltr"><<a href="mailto:joseph.franklin@yale.edu" target="_blank">joseph.franklin@yale.edu</a>></span> wrote:<br> <blockquote class="gmail_quote" style="border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); margin-top: 0pt; margin-right: 0pt; margin-bottom: 0pt; margin-left: 0.8ex; padding-left: 1ex; position: static; z-index: auto; ">(Now that I've recovered the browser installation, I'll post my original question)<br> <br> When I use either ModPerl or Fast-CGI in Gbrowse2 (1.996), track loading and refresh are both nicely accelerated. However, in either of these modes, it seems like the session locks get overwritten, rather than created, when a new user accesses the browser (the landmarks, tracks, etc. are lost for the first user). The default installation (localhost/cgi-bin/gb2/) appears to be locking sessions normally.<br> <br> Realizing that GBrowse 2 is pre-release, I'd love to hear if anyone has any easy suggestions (or perhaps this is a bug).<br> <br> I'm running this on Ubuntu 9.04 (webserver: Apache/2.2.11 (Ubuntu) PHP/5.2.6-3ubuntu4.1 with Suhosin-Patch mod_perl/2.0.4 Perl/v5.10.0 Server).<br> <br> Here is my GBrowse.conf session settings stanza:<br> # session settings<br> session driver = driver:file;serializer:default<br> session args = Directory /var/tmp/gbrowse2/sessions<br> <br> <br> /var/tmp/gbrowse2/sessions and /var/tmp/gbrowse2/locks are both writable to the server, and indeed written to when any new session is started (except in the mod_perl or fcgi cases, when relevant session/lock files are overwritten).<br> <br> <br> Thanks,<br> joe<br> <br> <br> <br> ________________________________<br> Joe Franklin<br> Department of Cell Biology<br> Yale University School of Medicine<br> 295 Congress Ave, BCMM 137<br> New Haven, CT 06519<br> USA<br><font color="#888888"> <br> <a href="mailto:joseph.franklin@yale.edu" target="_blank">joseph.franklin@yale.edu</a><br> 407 341 3263 (cell)<br> 203 654 7494 (google voice)<br> <br> </font></blockquote></div><br><br clear="all"> <br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br>Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br> 416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca" target="_blank">Renata.Musa@oicr.on.ca</a>><br> </blockquote></div><br><div> <span style="font-size: 12px;"><div style=""><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Sans'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style=""> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Sans'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style=""> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Sans'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style=""> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Sans'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style=""> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Sans'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style=""> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Lucida Sans'; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style=""> <div><div><div style="font-size: 11px;">________________________________</div><div>Joe Franklin</div><div>Department of Cell Biology</div><div>Yale University School of Medicine</div><div>295 Congress Ave, BCMM 137</div><div> New Haven, CT 06519</div><div>USA</div><div><br></div></div><div><a href="mailto:joseph.franklin@yale.edu" target="_blank">joseph.franklin@yale.edu</a></div><div>407 341 3263 (cell)</div>203 654 7494 (google voice)<br></div> </div></span></div></span></div></span></div></span></div></span></div></span></div></span> </div><br></div></div></div></div></blockquote></div><br><br clear="all"><br>-- <br>Lincoln D. Stein<br>Director, Informatics and Biocomputing Platform<br> Ontario Institute for Cancer Research<br>101 College St., Suite 800<br>Toronto, ON, Canada M5G0A3<br>416 673-8514<br>Assistant: Renata Musa <<a href="mailto:Renata.Musa@oicr.on.ca">Renata.Musa@oicr.on.ca</a>><br></blockquote></div>]</div></body></html>