Re: [galaxy-dev] Error while uploading
Hi Luciano, I had a similar problem with our local instance of Galaxy. In our case, the /tmp directory was filling up, causing the job to abort. We had Galaxy running on a partition with tons of disk space, but the partition on which /tmp was located had substantially less free disk space. Try running the "df" command from the Linux command line. If you don't know how to interpret its output, let me know. Certain tasks that run on behalf of Galaxy, like gzip for decompressing large datasets, will store intermediate temporary data in /tmp instead of a subdirectory within your Galaxy installation. Let me know if that solves your issue, Dan ________________________________________ Message: 1 Date: Sat, 10 Mar 2012 17:25:38 -0600 From: Luciano Cosme <cosme.simple@gmail.com> To: Galaxy-dev <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Error while uploading Message-ID: <CAMASfsjdm0UDciVqk7P-mPijr8UaLxe0zX7SZuG4UPsQJ_NxBQ@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I uploaded 11 files today (1 to 2Gb compressed files) to my local instance without a problem (as admin). Then I got this error message below and it get stuck at "This dataset is uploading" and I could not upload the last files. Is there anything I can do to solve it? What I notice is that I can still upload small files, before I concatenate them. I have 15 time points and some of them have up to 20 files, so it is easier to concatenate them and them upload. Thank you. Luciano
You can change the default location of tmp files by modifying the environment; we ran into this with samtools directly dumping temp sort files to a local node, causing the job to shut down. Setting TMPDIR worked for me. chris On Mar 11, 2012, at 5:10 PM, Dorset, Daniel C wrote:
Hi Luciano,
I had a similar problem with our local instance of Galaxy. In our case, the /tmp directory was filling up, causing the job to abort. We had Galaxy running on a partition with tons of disk space, but the partition on which /tmp was located had substantially less free disk space. Try running the "df" command from the Linux command line. If you don't know how to interpret its output, let me know.
Certain tasks that run on behalf of Galaxy, like gzip for decompressing large datasets, will store intermediate temporary data in /tmp instead of a subdirectory within your Galaxy installation.
Let me know if that solves your issue,
Dan ________________________________________
Message: 1 Date: Sat, 10 Mar 2012 17:25:38 -0600 From: Luciano Cosme <cosme.simple@gmail.com> To: Galaxy-dev <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Error while uploading Message-ID: <CAMASfsjdm0UDciVqk7P-mPijr8UaLxe0zX7SZuG4UPsQJ_NxBQ@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1"
Hi, I uploaded 11 files today (1 to 2Gb compressed files) to my local instance without a problem (as admin). Then I got this error message below and it get stuck at "This dataset is uploading" and I could not upload the last files. Is there anything I can do to solve it? What I notice is that I can still upload small files, before I concatenate them. I have 15 time points and some of them have up to 20 files, so it is easier to concatenate them and them upload. Thank you.
Luciano
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On Mar 12, 2012, at 2:23 PM, Fields, Christopher J wrote:
You can change the default location of tmp files by modifying the environment; we ran into this with samtools directly dumping temp sort files to a local node, causing the job to shut down. Setting TMPDIR worked for me.
Hi Chris, Thanks for pointing this out, I've added it to the cluster wiki page: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Galaxy_Configurat... --nate
chris
On Mar 11, 2012, at 5:10 PM, Dorset, Daniel C wrote:
Hi Luciano,
I had a similar problem with our local instance of Galaxy. In our case, the /tmp directory was filling up, causing the job to abort. We had Galaxy running on a partition with tons of disk space, but the partition on which /tmp was located had substantially less free disk space. Try running the "df" command from the Linux command line. If you don't know how to interpret its output, let me know.
Certain tasks that run on behalf of Galaxy, like gzip for decompressing large datasets, will store intermediate temporary data in /tmp instead of a subdirectory within your Galaxy installation.
Let me know if that solves your issue,
Dan ________________________________________
Message: 1 Date: Sat, 10 Mar 2012 17:25:38 -0600 From: Luciano Cosme <cosme.simple@gmail.com> To: Galaxy-dev <galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Error while uploading Message-ID: <CAMASfsjdm0UDciVqk7P-mPijr8UaLxe0zX7SZuG4UPsQJ_NxBQ@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1"
Hi, I uploaded 11 files today (1 to 2Gb compressed files) to my local instance without a problem (as admin). Then I got this error message below and it get stuck at "This dataset is uploading" and I could not upload the last files. Is there anything I can do to solve it? What I notice is that I can still upload small files, before I concatenate them. I have 15 time points and some of them have up to 20 files, so it is easier to concatenate them and them upload. Thank you.
Luciano
___________________________________________________________ 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:
___________________________________________________________ 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:
participants (3)
-
Dorset, Daniel C -
Fields, Christopher J -
Nate Coraor