[galaxy-dev] Galaxy Main cloudlaunch stall
I've searched the list to see if anyone specifically mentions not being able to use the cloud launchhttps://main.g2.bx.psu.edu/cloudlaunch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ 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/
Re: [galaxy-dev] Galaxy Main cloudlaunch stall
Thanks. The requests will be coming from kennedykrieger.org. On Jan 18, 2013, at 12:36 PM, Dannon Baker dannonba...@me.com wrote: Should definitely be stable enough to use in a classroom and that it isn't working for you is definitely unexpected; it's the only way I've launched instances for many months now. I'm digging through logs to see if I can find any indication of why your particular requests are having issues. On Jan 18, 2013, at 12:33 PM, Matthew Shirley mshir...@jhmi.edu wrote: Thanks, Quang. That's not exactly what I'm looking for. My motivation is to teach an entire class how to start a Galaxy cluster on their own, with minimal knowledge of AWS or systems administration. The cloudlaunch feature on the main psx site seems to fit this purpose exactly, but does not work reliably for me. I've just tried using Chrome 24.0 with no success. I'm using no browser plugins, and this is a clean installation with javascript enabled. The cloudlaunch page just sits there and tells me Launch Pending, please be patient. and I have - it's been over an hour. Any help figuring this out is appreciated. If this feature is just not mature enough to use in a classroom, that would be an acceptable answer as well. On Jan 18, 2013, at 11:40 AM, Quang Trinh quang.tr...@gmail.com wrote: Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote: Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ 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/ ___ 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/
Re: [galaxy-dev] Galaxy Main cloudlaunch stall
Thanks, Quang. That's not exactly what I'm looking for. My motivation is to teach an entire class how to start a Galaxy cluster on their own, with minimal knowledge of AWS or systems administration. The cloudlaunch feature on the main psx site seems to fit this purpose exactly, but does not work reliably for me. I've just tried using Chrome 24.0 with no success. I'm using no browser plugins, and this is a clean installation with javascript enabled. The cloudlaunch page just sits there and tells me Launch Pending, please be patient. and I have - it's been over an hour. Any help figuring this out is appreciated. If this feature is just not mature enough to use in a classroom, that would be an acceptable answer as well. On Jan 18, 2013, at 11:40 AM, Quang Trinh quang.tr...@gmail.commailto:quang.tr...@gmail.com wrote: Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote: Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ 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/ ___ 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/
Re: [galaxy-dev] Defunct munge processes using Torque PBS
Hi Nate. I do understand that this is not a bug directly stemming from the Galaxy code base. Munge is really just a tool to pass user credentials between systems during job submission to the PBS server. Galaxy is spooling jobs through the PBS job runner, which presumably indirectly calls munge through jobs submission to the PBS server. I'm just not sure why the munge process is sometimes becoming corrupt. This is an issue since I rapidly reach my max number of threads for the Galaxy user on my head node. At this point I guess I'll try downloading the latest stable version of Torque and build RPMs. I have been using what is in EPEL for RHEL6. Thanks for the reply, and any other thoughts are still appreciated! On Dec 7, 2012, at 10:51 AM, Nate Coraor n...@bx.psu.edu wrote: On Dec 6, 2012, at 2:34 PM, Matthew Shirley wrote: I am fairly new to PBS management, so I can't rule out some misconfiguration, but I have a strange issue when running Galaxy with the PBS job runner. It seems that munge spawns a bunch of defunct processes after running Galaxy on my cluster: `ps axjf`: 1 25992 25991 25991 ? -1 Sl 7 8:48 python ./scripts/paster.py serve universe_wsgi.ini --daemon 25992 26032 25991 25991 ? -1 Z7 0:00 \_ [munge] defunct 25992 26034 25991 25991 ? -1 Z7 0:00 \_ [munge] defunct 25992 26036 25991 25991 ? -1 Z7 0:00 \_ [munge] defunct Now, these processes are being spawned by Galaxy, and I can't figure out why. Can anyone provide some insight or clues about where to start debugging this? Thanks, Hi Matt, I'm not sure what munge is, it's not something provided with Galaxy. Googling suggests it might be an authentication tool used in some HPC environments. Without having any familiarity with it, I can't say what process in Galaxy would be interacting with it, especially since that interaction must occur implicitly somewhere down the chain of normal Galaxy operations. --nate Matt ___ 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/
