Hi Shane, This happens to us sometimes when the SGE daemons on the node/s in question have terminated for some reason. I would make sure they are running on the nodes in question and re-launch them if not. That usually works for me. Cheers, - Jason de Koning, University at Albany On Mar 30, 2005, at 1:20 PM, Shane Brubaker wrote: > > Hi, I have some SGE jobs which stay in a "dr" state and will not go > away. I have issued a qdel command on these jobs, so they are in a > "deleted, running" > state. Usually such jobs will go away after a few minutes, but these > won't. I also can't delete that queue now because it has jobs in it. > > These happened to be fairly long jobs that ran a day or two. Also, > these jobs do not show up on the actual nodes, so they aren't really > running anymore. They only > appear in qstat. > > Any help would be much appreciated. > > > Thank You, > Shane Brubaker > JGI > > At 09:09 AM 3/30/2005, you wrote: >> Send Bioclusters mailing list submissions to >> bioclusters at bioinformatics.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://bioinformatics.org/mailman/listinfo/bioclusters >> or, via email, send a message with subject or body 'help' to >> bioclusters-request at bioinformatics.org >> >> You can reach the person managing the list at >> bioclusters-owner at bioinformatics.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Bioclusters digest..." >> >> >> Today's Topics: >> >> 1. Re: alternative DHCP implementations? >> (jason.calvert at novartis.com) >> 2. Re: alternative DHCP implementations? (Lars G. T. Jorgensen) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 30 Mar 2005 11:43:17 -0400 >> From: jason.calvert at novartis.com >> Subject: Re: [Bioclusters] alternative DHCP implementations? >> To: "Clustering, compute farming & distributed computing in >> life >> science informatics" <bioclusters at bioinformatics.org> >> Message-ID: >> <OFE1C386E6.4CD361C1-ON85256FD4.00560E7A >> -85256FD4.00565C5B at EU.novartis.net> >> >> Content-Type: text/plain; charset="us-ascii" >> >> There are scripts within the OSCAR release to do this for you. You >> can >> start the scripts, power on the nodes in the order you wish, and then >> assign them to auto generated hostnames. The scripts output the >> dhcp.conf >> file. >> >> I would think you could pull them out of oscar pretty easily. >> >> Jason >> >> >> >> >> Chris Dagdigian <dag at sonsorol.org> >> Sent by: >> bioclusters- >> bounces+jason.calvert=pharma.novartis.com at bioinformatics.org >> 03/29/2005 02:27 PM >> Please respond to "Clustering, compute farming & distributed >> computing in >> life science informatics" >> >> >> To: adamm at menlo.com, "Clustering, compute farming & >> distributed computing in >> life science informatics" <bioclusters at bioinformatics.org> >> cc: (bcc: Jason Calvert/PH/Novartis) >> Subject: Re: [Bioclusters] alternative DHCP >> implementations? >> >> >> >> >> Agreed. It was just a shortcut. We already do allocation of IP based >> on >> MAC address but that only works when you know the MAC address >> information ahead of time. This is rare especially on whitebox >> cluster >> projects where people don't put the MAC on the product packaging or on >> the chassis itself. Some vendors do a good job of making the data easy >> to find and others simply don't bother. >> >> A dhcp server handing out dynamic-range leases in a predictable manner >> is what allowed us to easily map MAC address to node position and >> nodename simply by powering on the nodes for PXE boot in the order in >> which they are racked and stacked. Once this was done we had the >> MAC->Node mapping data we needed to generate the static allocation >> entries. >> >> A workaround for non-predictable allocation is to simply power on the >> cluster in the order in which you want things named, then parse the >> dhcpd leases file for both the MAC address *and* the timestamp >> representing the lease handout. That would allow you to map MAC -> >> Node >> without having to care about hostnames for the first pass MAC >> collection >> phase. Then you build the static-by-mac entries into the conf file >> and >> problem solved. If we stick with ISC DHCP this is a possibility... >> >> c >> >> Adam S. Moskowitz wrote: >> > Chris, >> > >> > >> >>We are thinking about trying to find a replacement DHCP server that >> has >> >>a predictable method of allocating dynamic IP addresses (even if >> only >> >>for the initial cluster deployment) >> > >> > >> > I think it's a bad idea to rely on such behavior. I don't remember >> what >> > the RFC says, but in general, unless the RFC guarantees an >> > implementation should behave a particular way, you are asking for >> > trouble to rely on specific behavior. >> > >> > A great example of this is how round-robin DNS used to work and >> then how >> > it changed and lots of things broke. >> > >> > DHCP isn't meant to do what you're asking it to do, so I strongly >> > suggest you not use it to solve that particular problem. >> > >> > That said, DHCP supports a mechanism for binding specific IP >> addresses >> > to specific MAC addresses, even though the assignment is still done >> > dynamically. Yes, this is a bit more work, but at least it's >> guaranteed >> > behavior. >> _______________________________________________ >> Bioclusters maillist - Bioclusters at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bioclusters >> >> >> >> >> ______________________________________________________________________ >> The Novartis email address format has changed to >> firstname.lastname at novartis.com. Please update your address book >> accordingly. >> ______________________________________________________________________ >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://bioinformatics.org/pipermail/bioclusters/attachments/20050330/ >> 217cb3f0/attachment-0001.htm >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 30 Mar 2005 14:55:55 +0200 >> From: "Lars G. T. Jorgensen" <lars at binf.ku.dk> >> Subject: Re: [Bioclusters] alternative DHCP implementations? >> To: "Clustering, compute farming & distributed computing in >> life >> science informatics" <bioclusters at bioinformatics.org> >> Message-ID: <424AA1DB.8000702 at binf.ku.dk> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Chris Dagdigian wrote: >> >> > >> > >> > Agreed. It was just a shortcut. We already do allocation of IP based >> > on MAC address but that only works when you know the MAC address >> > information ahead of time. This is rare especially on whitebox >> > cluster projects where people don't put the MAC on the product >> > packaging or on the chassis itself. Some vendors do a good job of >> > making the data easy to find and others simply don't bother. >> > >> > A dhcp server handing out dynamic-range leases in a predictable >> manner >> > is what allowed us to easily map MAC address to node position and >> > nodename simply by powering on the nodes for PXE boot in the order >> in >> > which they are racked and stacked. Once this was done we had the >> > MAC->Node mapping data we needed to generate the static allocation >> > entries. >> > >> > A workaround for non-predictable allocation is to simply power on >> the >> > cluster in the order in which you want things named, then parse the >> > dhcpd leases file for both the MAC address *and* the timestamp >> > representing the lease handout. That would allow you to map MAC -> >> > Node without having to care about hostnames for the first pass MAC >> > collection phase. Then you build the static-by-mac entries into the >> > conf file and problem solved. If we stick with ISC DHCP this is a >> > possibility... >> >> Or buy an switch with a bit of inteligence that can dump the machines >> MAC addresses based on ports. >> >> > >> > c >> > >> > Adam S. Moskowitz wrote: >> > >> >> Chris, >> >> >> >> >> >>> We are thinking about trying to find a replacement DHCP server >> that >> >>> has a predictable method of allocating dynamic IP addresses (even >> if >> >>> only for the initial cluster deployment) >> >> >> >> >> >> >> >> I think it's a bad idea to rely on such behavior. I don't remember >> what >> >> the RFC says, but in general, unless the RFC guarantees an >> >> implementation should behave a particular way, you are asking for >> >> trouble to rely on specific behavior. >> >> >> >> A great example of this is how round-robin DNS used to work and >> then how >> >> it changed and lots of things broke. >> >> >> >> DHCP isn't meant to do what you're asking it to do, so I strongly >> >> suggest you not use it to solve that particular problem. >> >> >> >> That said, DHCP supports a mechanism for binding specific IP >> addresses >> >> to specific MAC addresses, even though the assignment is still done >> >> dynamically. Yes, this is a bit more work, but at least it's >> guaranteed >> >> behavior. >> > >> > _______________________________________________ >> > Bioclusters maillist - Bioclusters at bioinformatics.org >> > https://bioinformatics.org/mailman/listinfo/bioclusters >> > >> >> >> -- >> Mvh|Regards, Lars >> System Administrator, Phone: 3532 1349, Room: 318 >> >> Bioinformatics Centre, University of Copenhagen, >> Universitetsparken 15 >> DK-2100 Copenhagen >> DENMARK >> >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Bioclusters maillist - Bioclusters at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bioclusters >> >> >> End of Bioclusters Digest, Vol 5, Issue 28 >> ****************************************** > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters >