Sorry for the confusion - this was moved back to galaxy-dev. -Scott
----- Original Message ----- > > This has been forwarded from galaxy-dev. > > -Scott > > ----- Forwarded Message ----- > From: "Scott McManus" <scottmcma...@gatech.edu> > To: "Daniel Patrick Sullivan" <dansulli...@gmail.com> > Cc: galaxy-...@lists.bx.psu.edu > Sent: Wednesday, August 1, 2012 4:46:26 PM > Subject: Re: [galaxy-dev] PBS Server Throwing Errors > > > Hi Dan- > > Thanks again for your great hospitality at UCI! > > It looks like you've done most of the sane things, and a quick > check looks like the PBS egg is requesting protocol version 1 > while the server supports protocol version 2. One possibility > is that there is a protocol mismatch, which could be the result > of using an old library. We can check if the egg is at fault > first - try the following link for compiling the pbs_python.py > egg yourself and try the example to see if the connection and > a simple stats-gathering operation (the examples/pbsnodes-a.py > script from pbs_python) works: > https://subtrac.sara.nl/oss/pbs_python/wiki/TorqueInstallation > > -Scott > > ----- Original Message ----- > > Hi, Galaxy Community, > > > > Greetings from The University of Chicago; I hope all who attended > > the > > Galaxy conference enjoyed it as much as I did. I have searched the > > mailing list archives as well as Google to a resolve problem I am > > seeing, however I am somewhat at a loss as to the next course of > > action I should be taking to bring this issue to a close. I am > > hoping > > that one of the bright minds on this mailing list could help me > > shed > > some light on the solution to my problem, or at least help me > > identify > > a root cause. I have configured Galaxy to integrate with TORQUE > > (version 4.0.2) server, and successfully built the PBS python egg > > as > > specified in the Galaxy documentation. I am using Python version > > 2.6 > > and the latest build of Galaxy. Whenever I launch a job from the > > Galaxy UI, I get the following error message(s) on the PBS server: > > > > 07/30/2012 > > 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting > > version numbers, 1 detected, 2 expected > > 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply > > code=15058(Bad DIS based Request Protocol MSG=cannot decode > > message), > > aux=0, type=AlternateUserAuthentication, from galaxy@ > > 07/30/2012 > > 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting > > version numbers, 1 detected, 2 expected > > 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply > > code=15058(Bad DIS based Request Protocol MSG=cannot decode > > message), > > aux=0, type=QueueJob, from galaxy@ > > 07/30/2012 > > 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting > > version numbers, 1 detected, 2 expected > > 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply > > code=15058(Bad DIS based Request Protocol MSG=cannot decode > > message), > > aux=0, type=Disconnect, from galaxy@ > > 07/30/2012 15:43:01;0002;PBS_Server;Svr;PBS_Server;Torque Server > > Version = 4.0.2, loglevel = 1 > > > > One thing I did notice, that suggests there might be a problem, is > > that there is no hostname after the galaxy@; most of the other > > messages in this log file have a host name appended to log entry, > > i.e.: > > > > 07/30/2012 15:43:38;0100;PBS_Server;Req;;Type StatusJob request > > received from root@sc01, sock=10 > > > > I have completed a tcpdump on the schedule node, and I can > > definitely > > see bi-directional traffic between the Galaxy server and the > > scheduler > > node on TCP port 15001. In addition to this, I have installed the > > TORQUE client tools on on the Galaxy server, and can spawn an > > interactive job with qsub -I, as well as check the status of queued > > jobs using qstat (from the Galaxy server). This suggests to me > > that > > there a potential problem with the PBS Egg, although I am not > > certain. > > Has anybody seen something like this before, or could somebody > > point > > me in the right direction? We do have a support contract with > > Adaptive Computing, and I am opening a ticket with them as well, > > however I wanted to reach out to the Galaxy community to cover all > > of > > my bases. Thank-you so much for taking the time to read my email. > > > > Dan Sullivan > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
