Teaching Galaxy

Question: Teaching Galaxy

6.1 years ago by

Larry Reiter • 100 wrote:

Tried to teach a class today on ChipSeq analysis, but the local Cloud install is broken and then the Penn server froze on us. Is there something I should know? LTR -- Lawrence T. Reiter, Ph.D. Associate Professor, Department of Neurology 855 Monroe Ave., Link 415 Memphis, TN 38163 901-448-2635 (Office) 901-448-7440 (FAX) 901-448-7443 (Lab) e-mail: lreiter@uthsc.edu Reiter Faculty Page <http: www.uthsc.edu="" neuroscience="" faculty="" l_reiter.php=""> Reiter Citation Index <http: scholar.google.com="" citations?user="-kaQJ14AAAAJ&hl=en"> Tooth Study <http: tinyurl.com="" 88f688l="">

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modified 6.1 years ago by Lei Yan • 130 • written 6.1 years ago by Larry Reiter • 100

6.1 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

Can you describe more about what is broken with your cloud install? Regarding main - the server has been under heavy load today and, while it shouldn't remain frozen, might be slow to dispatch and, depending on the type, execute) jobs. -Dannon

ADD COMMENT • link written 6.1 years ago by Dannon Baker ♦ 3.7k

Dannon, Thanks for getting back to me. Both the local cloud install and the main server are frozen. Well, not exactly frozen. I can still rename or delete jobs, etc. I can even switch histories and such, but I can't get it to run even simple jobs - like taking a demo file and running Fastq Groomer. I realize the load is high today on the main server, but we were able to get jobs to run right up until we tried to MAP using Bowtie for Illumina. At that point, all members of the class - and me - could not go any further (i.e. jobs are grey and never start to run). Class ended almost three hours ago. Does this help? LTR -- Lawrence T. Reiter, Ph.D. Associate Professor, Department of Neurology 855 Monroe Ave., Link 415 Memphis, TN 38163 901-448-2635 (Office) 901-448-7440 (FAX) 901-448-7443 (Lab) e-mail: lreiter@uthsc.edu Reiter Faculty Page <http: www.uthsc.edu="" neuroscience="" faculty="" l_reiter.php=""> Reiter Citation Index <http: scholar.google.com="" citations?user="-kaQJ14AAAAJ&hl=en"> Tooth Study <http: tinyurl.com="" 88f688l="">

ADD REPLY • link written 6.1 years ago by Larry Reiter • 100

I also had a similar issue. I thought it has to do with the hurricane in the east coat and never bothered to ask. Even small analyses (such as running the RNA-seq analysis exercise by Jeremy Goecks) were stalled; in a couple of instances for a day or more. Thanks. Tilahun

ADD REPLY • link written 6.1 years ago by Tilahun Abebe • 40

Main will complete the jobs eventually, though obviously that's not particularly useful in the context of your class today. How is your cloud instance set up? Cloud or local instances should be the best and most reliable option for teaching with and I'd definitely like to figure out why yours failed. -Dannon

ADD REPLY • link written 6.1 years ago by Dannon Baker ♦ 3.7k

Dannon, Maybe you can, but not through me. I'm just a lowly user and biologist. You would have to contact the guy who did the installation and runs the server: Lei Yan (leiyan2000@gmail.com) I would think he would be receptive to some help, so you should mail him. LTR -- Lawrence T. Reiter, Ph.D. Associate Professor, Department of Neurology 855 Monroe Ave., Link 415 Memphis, TN 38163 901-448-2635 (Office) 901-448-7440 (FAX) 901-448-7443 (Lab) e-mail: lreiter@uthsc.edu Reiter Faculty Page <http: www.uthsc.edu="" neuroscience="" faculty="" l_reiter.php=""> Reiter Citation Index <http: scholar.google.com="" citations?user="-kaQJ14AAAAJ&hl=en"> Tooth Study <http: tinyurl.com="" 88f688l="">

ADD REPLY • link written 6.1 years ago by Larry Reiter • 100

It looks like both the main server and our local install are frozen. Nothing has run since we started yesterday at about 11:30am. Anybody know why? LTR -- Lawrence T. Reiter, Ph.D. Associate Professor, Department of Neurology 855 Monroe Ave., Link 415 Memphis, TN 38163 901-448-2635 (Office) 901-448-1160 (FAX) 901-448-7443 (Lab) e-mail: lreiter@uthsc.edu Reiter Faculty Page <http: www.uthsc.edu="" neuroscience="" faculty="" l_reiter.php=""> Reiter Citation Index <http: scholar.google.com="" citations?user="-kaQJ14AAAAJ&hl=en">

ADD REPLY • link written 6.1 years ago by Larry Reiter • 100

6.1 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

NGS jobs are experiencing significant delays at this time due to load -- we're looking into it. Regarding the local install I'd have to recommend pinging the administrator on site there -- they should be able to help out. -Dannon

ADD COMMENT • link written 6.1 years ago by Dannon Baker ♦ 3.7k

6.1 years ago by

Lei Yan • 130

Lei Yan • 130 wrote:

Dear Dannon, My name is Lei Yan, and I am a systems administrator at UTHSC. I installed a Cloud Galaxy on the Amazon EC2 about two months ago, and most functions work well at that time. http://galaxycloud.genenetwork.org/ But from the day before yesterday, jobs were hung up always. In my opinion, I didnt find any reasons, because all look correct from Galaxy Admin page (see attachments please). Would you please help us to check it? I can give you the administrator password if you need. Thanks so much. Lei Yan leiyan2000@gmail.com UTHSC

ADD COMMENT • link written 6.1 years ago by Lei Yan • 130

Lei - It looks like you have two worker nodes, but both are currently listed as non-idle, yet have low load. My guess is that something has gone wrong with the SGE configuration causing jobs to simply wait in the queue. If you look at the contents of qconf and qstat on the admin page, does it look like there are jobs backed up and/or worker nodes processing the queue? Depending on how comfortable you are working with SGE, it might be easiest to just click "restart" for SGE in the admin panel and see if everything goes back to normal. -Dannon

ADD REPLY • link written 6.1 years ago by Dannon Baker ♦ 3.7k

Dear Dannon, We appreciate your helps. It looks like jobs can run now. But I found a strange thing here, and I dont know it is an error or not, please see attachments (marked with a red arrow). Would you please help us to check it? Thanks again. Dear Larry, Does the cloud galaxy work for you now? Lei Yan leiyan2000@gmail.com UTHSC

ADD REPLY • link written 6.1 years ago by Lei Yan • 130

I'm out of town till Tuesday. Lawrence T Reiter, PhD UTHSC, Memphis, TN Dear Dannon, We appreciate your helps. It looks like jobs can run now. But I found a strange thing here, and I dont know it is an error or not, please see attachments (marked with a red arrow). Would you please help us to check it? Thanks again. Dear Larry, Does the cloud galaxy work for you now? Lei Yan leiyan2000@gmail.com<mailto:leiyan2000@gmail.com> UTHSC Lei - It looks like you have two worker nodes, but both are currently listed as non-idle, yet have low load. My guess is that something has gone wrong with the SGE configuration causing jobs to simply wait in the queue. If you look at the contents of qconf and qstat on the admin page, does it look like there are jobs backed up and/or worker nodes processing the queue? Depending on how comfortable you are working with SGE, it might be easiest to just click "restart" for SGE in the admin panel and see if everything goes back to normal. -Dannon <2012-11-09 16-30-41.png> <2012-11-09 16-29-09.png> <2012-11-09 16-27-29.png>

ADD REPLY • link written 6.1 years ago by Larry Reiter • 100

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