Re: [galaxy-dev] [galaxy-bugs] galaxy.genenetwork.org
Dear Dannon and James, On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker <dannonbaker@me.com> wrote:
• I installed a Cloud Galaxy instance one month ago, and a user
reported that it still has some problems. At that time, I found that it can be upgraded to new version in the administration page, so I did so. But its log showed that it “has error”, and the service cannot start. I then tried to reboot the machine, but Galaxy still could not start and the service is not responding.
Can you share the cloud log? This would be the best place to look to find out what the errors are.
For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”.
• Then I tried to build a new Cloud Galaxy, but after trying at
least 8 times it still didn’t work. Each time, after I launched the Cloud Galaxy instance, even its State is "running" and the "Status Checks" is "2/2 checks passed”, but it would still not respond if I opened “http:// ******.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on the cloud".
Can you share any more information about this? Can you confirm that you're using the supported AMI, have launched with the correct security groups, etc? For future reference, just using usegalaxy.org/cloudlaunchis probably the easiest way to make sure you avoid any launch issues. Are you able to SSH in to the instance?
I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to "Welcome to Galaxy on the cloud".
Could you please give us some suggestions or let us know who we should contact about this issue?
Sending email directly to galaxy-bugs, as you have, for stuff you'd rather not share with the wider community is the best bet. For anything that isn't sensitive, emailing galaxy-dev is useful if you're working with customized or local/cloud installs.
I cannot find any telephone number on the Galaxy community pages, and it would be better if I could talk to someone about the problem over the phone.
Would it be helpful to chat over IRC and debug this? See the "IRC Channel" information on http://wiki.galaxyproject.org/Get%20Involved.
-Dannon
Thanks so much for your help. Lei Yan leiyan2000@gmail.com UTHSC
有olb吃掉 Yunbo Xu 817 Hickman rd, Apt A-23 Augusta,GA 30904 706 - 877 3892 On Dec 11, 2012, at 4:13 PM, Lei Yan <leiyan2000@gmail.com> wrote:
Dear Dannon and James,
On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker <dannonbaker@me.com> wrote:
• I installed a Cloud Galaxy instance one month ago, and a user reported that it still has some problems. At that time, I found that it can be upgraded to new version in the administration page, so I did so. But its log showed that it “has error”, and the service cannot start. I then tried to reboot the machine, but Galaxy still could not start and the service is not responding.
Can you share the cloud log? This would be the best place to look to find out what the errors are.
For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”.
• Then I tried to build a new Cloud Galaxy, but after trying at least 8 times it still didn’t work. Each time, after I launched the Cloud Galaxy instance, even its State is "running" and the "Status Checks" is "2/2 checks passed”, but it would still not respond if I opened “http://******.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on the cloud".
Can you share any more information about this? Can you confirm that you're using the supported AMI, have launched with the correct security groups, etc? For future reference, just using usegalaxy.org/cloudlaunch is probably the easiest way to make sure you avoid any launch issues. Are you able to SSH in to the instance?
I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to "Welcome to Galaxy on the cloud".
Could you please give us some suggestions or let us know who we should contact about this issue?
Sending email directly to galaxy-bugs, as you have, for stuff you'd rather not share with the wider community is the best bet. For anything that isn't sensitive, emailing galaxy-dev is useful if you're working with customized or local/cloud installs.
I cannot find any telephone number on the Galaxy community pages, and it would be better if I could talk to someone about the problem over the phone.
Would it be helpful to chat over IRC and debug this? See the "IRC Channel" information on http://wiki.galaxyproject.org/Get%20Involved.
-Dannon
Thanks so much for your help.
Lei Yan leiyan2000@gmail.com UTHSC <1.log.zip> <2.ami.png> <2.instanceconfiguration.png> <2.securitygroups.png> ___________________________________________________________ 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:
Dear all, Recently I tried this for several times: https://main.g2.bx.psu.edu/cloudlaunch But each time it just show up “Launch Pending, please be patient”, and then it would still not respond (please see attachment). Could somebody help us for this problem? If you need, I can give you our AWS secret keys. Thanks so much. Lei Yan leiyan2000@gmail.com UTHSC On Tue, Dec 11, 2012 at 3:13 PM, Lei Yan <leiyan2000@gmail.com> wrote:
Dear Dannon and James,
On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker <dannonbaker@me.com> wrote:
• I installed a Cloud Galaxy instance one month ago, and a user
reported that it still has some problems. At that time, I found that it can be upgraded to new version in the administration page, so I did so. But its log showed that it “has error”, and the service cannot start. I then tried to reboot the machine, but Galaxy still could not start and the service is not responding.
Can you share the cloud log? This would be the best place to look to find out what the errors are.
For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”.
• Then I tried to build a new Cloud Galaxy, but after trying at
least 8 times it still didn’t work. Each time, after I launched the Cloud Galaxy instance, even its State is "running" and the "Status Checks" is "2/2 checks passed”, but it would still not respond if I opened “http:// ******.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on the cloud".
Can you share any more information about this? Can you confirm that you're using the supported AMI, have launched with the correct security groups, etc? For future reference, just using usegalaxy.org/cloudlaunchis probably the easiest way to make sure you avoid any launch issues. Are you able to SSH in to the instance?
I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to "Welcome to Galaxy on the cloud".
Could you please give us some suggestions or let us know who we should contact about this issue?
Sending email directly to galaxy-bugs, as you have, for stuff you'd rather not share with the wider community is the best bet. For anything that isn't sensitive, emailing galaxy-dev is useful if you're working with customized or local/cloud installs.
I cannot find any telephone number on the Galaxy community pages, and it would be better if I could talk to someone about the problem over the phone.
Would it be helpful to chat over IRC and debug this? See the "IRC Channel" information on http://wiki.galaxyproject.org/Get%20Involved.
-Dannon
Thanks so much for your help.
Lei Yan leiyan2000@gmail.com UTHSC
I don't see any failures in the recent logs. Has cloudlaunch worked for you before? A few more questions: When did this occur? Were you restarting an existing cluster, or starting a new one? Using existing keypairs or a new one? And, do the instances actually start even though there's no web response (if you look in the AWS terminal manually)? -Dannon On Jan 11, 2013, at 2:08 PM, Lei Yan <leiyan2000@gmail.com> wrote:
Dear all,
Recently I tried this for several times: https://main.g2.bx.psu.edu/cloudlaunch But each time it just show up “Launch Pending, please be patient”, and then it would still not respond (please see attachment). Could somebody help us for this problem? If you need, I can give you our AWS secret keys. Thanks so much.
Lei Yan leiyan2000@gmail.com UTHSC
On Tue, Dec 11, 2012 at 3:13 PM, Lei Yan <leiyan2000@gmail.com> wrote: Dear Dannon and James,
On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker <dannonbaker@me.com> wrote:
• I installed a Cloud Galaxy instance one month ago, and a user reported that it still has some problems. At that time, I found that it can be upgraded to new version in the administration page, so I did so. But its log showed that it “has error”, and the service cannot start. I then tried to reboot the machine, but Galaxy still could not start and the service is not responding.
Can you share the cloud log? This would be the best place to look to find out what the errors are.
For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”.
• Then I tried to build a new Cloud Galaxy, but after trying at least 8 times it still didn’t work. Each time, after I launched the Cloud Galaxy instance, even its State is "running" and the "Status Checks" is "2/2 checks passed”, but it would still not respond if I opened “http://******.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on the cloud".
Can you share any more information about this? Can you confirm that you're using the supported AMI, have launched with the correct security groups, etc? For future reference, just using usegalaxy.org/cloudlaunch is probably the easiest way to make sure you avoid any launch issues. Are you able to SSH in to the instance?
I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to "Welcome to Galaxy on the cloud".
Could you please give us some suggestions or let us know who we should contact about this issue?
Sending email directly to galaxy-bugs, as you have, for stuff you'd rather not share with the wider community is the best bet. For anything that isn't sensitive, emailing galaxy-dev is useful if you're working with customized or local/cloud installs.
I cannot find any telephone number on the Galaxy community pages, and it would be better if I could talk to someone about the problem over the phone.
Would it be helpful to chat over IRC and debug this? See the "IRC Channel" information on http://wiki.galaxyproject.org/Get%20Involved.
-Dannon
Thanks so much for your help.
Lei Yan leiyan2000@gmail.com UTHSC <2013-01-11 10-30-41.png>
Hi Dannon, Thanks so much. On Fri, Jan 11, 2013 at 1:25 PM, Dannon Baker <dannonbaker@me.com> wrote:
I don't see any failures in the recent logs. Has cloudlaunch worked for you before?
Yes, but cloudlaunch worked for me only at the first time. I tried it for test at the first time. Then I deleted it, and I would launch a regular Galaxy instance. But it always failed after that.
A few more questions:
When did this occur?
This occurred in recent 2 weeks, including today. Were you restarting an existing cluster, or starting a new one?
No. Using existing keypairs or a new one?
Tried both.
And, do the instances actually start even though there's no web response (if you look in the AWS terminal manually)?
I don’t think it actually start, because there is not any Galaxy instance in the AWS ec2 console.
-Dannon
On Jan 11, 2013, at 2:08 PM, Lei Yan <leiyan2000@gmail.com> wrote:
Dear all,
Recently I tried this for several times: https://main.g2.bx.psu.edu/cloudlaunch But each time it just show up “Launch Pending, please be patient”, and then it would still not respond (please see attachment). Could somebody help us for this problem? If you need, I can give you our AWS secret keys. Thanks so much.
Lei Yan leiyan2000@gmail.com UTHSC
On Tue, Dec 11, 2012 at 3:13 PM, Lei Yan <leiyan2000@gmail.com> wrote: Dear Dannon and James,
On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker <dannonbaker@me.com> wrote:
• I installed a Cloud Galaxy instance one month ago, and a user
reported that it still has some problems. At that time, I found that it can be upgraded to new version in the administration page, so I did so. But its log showed that it “has error”, and the service cannot start. I then tried to reboot the machine, but Galaxy still could not start and the service is not responding.
Can you share the cloud log? This would be the best place to look to find out what the errors are.
For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”.
• Then I tried to build a new Cloud Galaxy, but after trying at
least 8 times it still didn’t work. Each time, after I launched the Cloud Galaxy instance, even its State is "running" and the "Status Checks" is "2/2 checks passed”, but it would still not respond if I opened “http:// ******.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on the cloud".
Can you share any more information about this? Can you confirm that you're using the supported AMI, have launched with the correct security groups, etc? For future reference, just using usegalaxy.org/cloudlaunchis probably the easiest way to make sure you avoid any launch issues. Are you able to SSH in to the instance?
I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to "Welcome to Galaxy on the cloud".
Could you please give us some suggestions or let us know who we should contact about this issue?
Sending email directly to galaxy-bugs, as you have, for stuff you'd rather not share with the wider community is the best bet. For anything that isn't sensitive, emailing galaxy-dev is useful if you're working with customized or local/cloud installs.
I cannot find any telephone number on the Galaxy community pages, and it would be better if I could talk to someone about the problem over the phone.
Would it be helpful to chat over IRC and debug this? See the "IRC Channel" information on http://wiki.galaxyproject.org/Get%20Involved.
-Dannon
Thanks so much for your help.
Lei Yan leiyan2000@gmail.com UTHSC <2013-01-11 10-30-41.png>
participants (3)
-
Dannon Baker -
Lei Yan -
Yunbo Xu