I'm on cloudman, trying to upload files, and I'm getting this error message:
"No space left on device" transferring a 1 GB file to my instance, but the cloudman console says I have more than 5 GB left?
Is this a bad error message?
Is there some other file you want to see?
@bffo
[cid:BF845074-1348-4A8F-87D2-6AACAD1313E7@wtgc.org]
[cid:11E8AB13-A630-4638-8A1F-BF9E3AE526DF@wtgc.org]
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
Hey Francis,
There's a bug in the current release of cloudman that causes files fetched by galaxy (this doesn't affect direct http or ftp upload) to use the root volume as temporary storage, which has very little space. This is fixed in the next release scheduled to coincide with the galaxy-dist release. Until that's available, I'd recommend using one of the other upload options. If this isn't possible, let me know and I'll try to figure out another workaround. Sorry for the trouble!
-Dannon
On Oct 24, 2013, at 8:45 AM, Francis Ouellette francis@oicr.on.ca wrote:
I'm on cloudman, trying to upload files, and I'm getting this error message:
"No space left on device" transferring a 1 GB file to my instance, but the cloudman console says I have more than 5 GB left?
Is this a bad error message?
Is there some other file you want to see?
@bffo
<Screenshot 2013-10-24 13.06.12.png>
<Screenshot 2013-10-24 13.40.31.png>
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
Hi Francis, This is an issue with where Galaxy stores temporary files that are being uploaded via the web interface from an ftp site. Namely, it sticks them into /tmp rather than the path pointed to by TEMP. Cloud instances have limited space on the root image and thus the error.
Until this is fixed, do you have an option to upload the file via an FTP client or from a non-ftp site?
On Thu, Oct 24, 2013 at 2:45 PM, Francis Ouellette francis@oicr.on.cawrote:
I'm on cloudman, trying to upload files, and I'm getting this error message:
"No space left on device" transferring a 1 GB file to my instance, but the cloudman console says I have more than 5 GB left?
Is this a bad error message?
Is there some other file you want to see?
@bffo
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
One quick additional comment -- you may want to ssh in to the instance and remove any large upload files that were created in /tmp by galaxy, or other things might also start failing.
On Oct 26, 2013, at 3:03 PM, Dannon Baker siryoplait@gmail.com wrote:
Hey Francis,
There's a bug in the current release of cloudman that causes files fetched by galaxy (this doesn't affect direct http or ftp upload) to use the root volume as temporary storage, which has very little space. This is fixed in the next release scheduled to coincide with the galaxy-dist release. Until that's available, I'd recommend using one of the other upload options. If this isn't possible, let me know and I'll try to figure out another workaround. Sorry for the trouble!
-Dannon
On Oct 24, 2013, at 8:45 AM, Francis Ouellette francis@oicr.on.ca wrote:
I'm on cloudman, trying to upload files, and I'm getting this error message:
"No space left on device" transferring a 1 GB file to my instance, but the cloudman console says I have more than 5 GB left?
Is this a bad error message?
Is there some other file you want to see?
@bffo
<Screenshot 2013-10-24 13.06.12.png>
<Screenshot 2013-10-24 13.40.31.png>
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
Actually figured out the issue … I was out of space, but the cloudman console was wrong, and I was out of disk space.
This also happened to many of the students, and unfortunately, although you can allocate more space, after the fact, it does "reboot" your instance.
The workshop went well in most cases, although cloudman failed for about 4 of the 42 instances we started, and eventually (on second or third retry) for all of them … but that took a while.
I think that overall it was a great experience for student, and big thank you to Jeremy for his RNA-Seq page
https://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise
(pages are currently not found right now?)
@bffo
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
On 2013-10-24, at 8:45 AM, Francis Ouellette <francis@oicr.on.camailto:francis@oicr.on.ca> wrote:
I'm on cloudman, trying to upload files, and I'm getting this error message:
"No space left on device" transferring a 1 GB file to my instance, but the cloudman console says I have more than 5 GB left?
Is this a bad error message?
Is there some other file you want to see?
@bffo
[cid:BF845074-1348-4A8F-87D2-6AACAD1313E7@wtgc.org]
[cid:11E8AB13-A630-4638-8A1F-BF9E3AE526DF@wtgc.org]
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
Thank you all for feedback … Workshop eneded yesterday, so hopefully students read this list (as I advised them to do :-), and I will know better next class I run!
Cheers to all,
@bffo
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
On 2013-10-26, at 3:13 PM, Dannon Baker <siryoplait@gmail.commailto:siryoplait@gmail.com> wrote:
One quick additional comment -- you may want to ssh in to the instance and remove any large upload files that were created in /tmp by galaxy, or other things might also start failing.
On Oct 26, 2013, at 3:03 PM, Dannon Baker <siryoplait@gmail.commailto:siryoplait@gmail.com> wrote:
Hey Francis,
There's a bug in the current release of cloudman that causes files fetched by galaxy (this doesn't affect direct http or ftp upload) to use the root volume as temporary storage, which has very little space. This is fixed in the next release scheduled to coincide with the galaxy-dist release. Until that's available, I'd recommend using one of the other upload options. If this isn't possible, let me know and I'll try to figure out another workaround. Sorry for the trouble!
-Dannon
On Oct 24, 2013, at 8:45 AM, Francis Ouellette <francis@oicr.on.camailto:francis@oicr.on.ca> wrote:
I'm on cloudman, trying to upload files, and I'm getting this error message:
"No space left on device" transferring a 1 GB file to my instance, but the cloudman console says I have more than 5 GB left?
Is this a bad error message?
Is there some other file you want to see?
@bffo
<Screenshot 2013-10-24 13.06.12.png>
<Screenshot 2013-10-24 13.40.31.png>
-- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://usegalaxy.org/. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
galaxy-user@lists.galaxyproject.org
-
Dannon Baker -
Enis Afgan -
Francis Ouellette