Re: [galaxy-dev] cloudman persist filesystem error
Hi Alexander, I tested the process of persisting file system changes but it all worked as expected. Looking at the log snippet you sent, the only thing that seems off is the very first line: Completed creation of a snapshot for the volume 'None', snap id: 'snap-6f0b211d' - volume should not be None there. Actually, it's incredible that it would be None because a volume must exist in order to create a snapshot... Do you have more content from that log? In the mean time, I added more safeguards if this happens again: https://github.com/galaxyproject/cloudman/commit/337ecb95a04788e540d60be37b4f4f817257b24f On Tue, Jun 30, 2015 at 7:32 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Hi, from IRC this question/bug report: (18:06:13) avowinkel: some cloudman guy here? enis? (18:06:30) avowinkel: AttributeError: 'NoneType' object has no attribute 'id' (18:06:50) avowinkel: when persisting galaxyIndices (18:07:43) avowinkel: snapshot is created, but it crashes when ... somewhen well after that (18:11:08) avowinkel: http://pastebin.com/SDp1p96K (18:11:10) mrscribe: Title: paster.log - Pastebin.com (at pastebin.com) Best, Alexander ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cloudman launch
Hi Enis, thank you. I will try it next time I recreate the cluster. I have some more things: A) I wanted to tell you that I did the update of the galaxyFS with the playbook, by using the role cm.filesystem only. It worked - thanks! B) How could I mount another volume to the upstarting cluster? - name: stuff snap_id: snap-xyz Would that work? E.g when I want this snapshot be mounted as /mnt/stuff C) How can I use the dev branch of galaxy with cloudman? There are some things only in dev I will need. How would that be possible? D) There is an email from me to the list from two days ago. Could you look at that? It's not critical for me, but might lead to a bug. I think that's it so far. If I have more, I'll come back to you ;) 2015-07-02 11:32 GMT-05:00 Enis Afgan enis.af...@irb.hr: Hi Alexander, I traced the code and tried it out and you can override what is defined in the flavor by providing the details in the 'Extra user data' field on the launch form. For example: filesystem_templates: - name: galaxy roles: galaxyTools,galaxyData archive_url: http://s3.amazonaws.com/cloudman/fs-archives/galaxyFS-dev-latest.tar.gz type: archive size: 10 - name: galaxyIndices roles: galaxyIndices snap_id: snap-4b20f451 If you want to use your custom bucket (i.e., if you have modified CloudMan code in some way), you can then specify it in the 'default bucket' form field and place cm.tar.gz and cm_boot.py in that bucket but no need to provide snaps.yaml. If you do not want to use a custom bucket, you can use the current 'Standard' flavor, which defaults to cloudman-test bucket with CloudMan from June 19th (I will not be updating anything about it until after GCC). Hope this helps and let me know if you have more questions, Enis On Thu, Jul 2, 2015 at 9:29 AM, Enis Afgan enis.af...@irb.hr wrote: Hi Alexander, Let me investigate this a bit more and get back to you because I was under the impression I had fixed this. In the mean time, I updated your flavor to specify snap-6f0b211d. On Wed, Jul 1, 2015 at 4:44 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Hi Enis, I am trying to launch my cloudman instance with this launcher again: https://launch.usegalaxy.org/launch You created the flavor for me because it wouldn't load my galaxyIndices from the snaps.yaml in my default bucket. I thought, this problem was fixed, but it still creates a galaxyIndices from the default snapshot (600GB) when using the Standard flavor. When I use my flavor, it loads the snapshot, but it is a little outdated ;) So my question: Is this behaviour expected? If no, are you going to fix it soon? If not, could you update my flavor in the way that galaxyIndices gets created from snap-6f0b211d ? Further: Should I update CM? I am still on the version from Jun 22. I am still not sure what I need to change (my snaps.yaml) in order to have my clean cluster creation still functioning. Thanks, Alexander ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cloudman persist filesystem error
No, I don't have more anymore. If this happens again, I will tell you. 2015-07-02 13:46 GMT-05:00 Enis Afgan enis.af...@irb.hr: Hi Alexander, I tested the process of persisting file system changes but it all worked as expected. Looking at the log snippet you sent, the only thing that seems off is the very first line: Completed creation of a snapshot for the volume 'None', snap id: 'snap-6f0b211d' - volume should not be None there. Actually, it's incredible that it would be None because a volume must exist in order to create a snapshot... Do you have more content from that log? In the mean time, I added more safeguards if this happens again: https://github.com/galaxyproject/cloudman/commit/337ecb95a04788e540d60be37b4f4f817257b24f On Tue, Jun 30, 2015 at 7:32 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Hi, from IRC this question/bug report: (18:06:13) avowinkel: some cloudman guy here? enis? (18:06:30) avowinkel: AttributeError: 'NoneType' object has no attribute 'id' (18:06:50) avowinkel: when persisting galaxyIndices (18:07:43) avowinkel: snapshot is created, but it crashes when ... somewhen well after that (18:11:08) avowinkel: http://pastebin.com/SDp1p96K (18:11:10) mrscribe: Title: paster.log - Pastebin.com (at pastebin.com) Best, Alexander ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] cloudman launch
A) I wanted to tell you that I did the update of the galaxyFS with the playbook, by using the role cm.filesystem only. It worked - thanks! Excellent! B) How could I mount another volume to the upstarting cluster? - name: stuff snap_id: snap-xyz Would that work? E.g when I want this snapshot be mounted as /mnt/stuff With this commit https://github.com/galaxyproject/cloudman/commit/b56a6cd77899ac762d34a747da51ac78a14d3da7, you can (I guess that'll be a goo reason to make a move on the next question :) ) C) How can I use the dev branch of galaxy with cloudman? There are some things only in dev I will need. How would that be possible? You'll need to keep using a custom bucket and place cm.tar.gz and cm_boot.py into that bucket. I'll send you a couple of scripts that will make that super easy. D) There is an email from me to the list from two days ago. Could you look at that? It's not critical for me, but might lead to a bug. Just replied. 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
