Hi Luciano,

This is about what I thought - it's an issue with the OS configuration, not specifically with Galaxy.

You have two entries in fstab for /tmp. When the OS mounts filesystems, it mounts /dev/sdb1, then tmpfs, and it uses tmpfs because it's the one mounted most recently. Since tmpfs is a memory-based filesystem, you're only getting storage up to some percentage of available RAM plus some percentage of available swap space - it doesn't matter that you're so far from the 100GB limit.

Since Galaxy typically works on large files, I think it would be better to remove the tmpfs /tmp line from your fstab. You'll take a slight performance hit for the first few gigabytes, but you'll have full use of /dev/sdb1's space.

(The other option is to convert /dev/sdb1 to swap space, but I think that'd be a bigger performance hit, since you'll be doing more back-and-forth between disks and RAM.)

Hope this fixes your problem.

Jim Redmond
Department of Developmental Biology
Washington University in St. Louis

On May 22, 2012, at 3:05 PM, "Luciano Cosme" <cosme.sim...@gmail.com> wrote:

Hi,
  # /tmp was on /dev/sdb1 during installation
UUID=a2caec47-a863-42ee-a913-81b6596eeb14 /tmp            ext3    defaults        0       2


# swap was on /dev/sda5 during installation
UUID=5bc28efd-40a3-4ea7-b391-24876e458d77 none            swap    sw              0       0

I created this line in fstab:

tmpfs /tmp     tmpfs nodev,nosuid,size=100G          0 0



Thank you.

Luciano


On Mon, May 21, 2012 at 4:48 PM, Redmond, James <jredm...@wustl.edu> wrote:

Hi Luciano,

 

Just curious, but could you post the /tmp and swap lines from your fstab? I think I see your problem, but I’m not certain. Thanks!

 

Jim Redmond

Department of Developmental Biology

Washington University in St. Louis

Office: +1-314-747-4033

jredm...@wustl.edu

 

 

From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Luciano Cosme
Sent: Monday, May 21, 2012 4:17 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Fwd: Load Files in local instance Ubuntu 12.04 LTS /tmp as /tmpfs

 

Hi,
  Actually Galaxy is using tmpfs mounted on /tmp. I just uploaded a small file and a big file. The small file works fine, but the big file (~20GB) did not. The tmpfs started getting used and stopped at 2.2GB, then I got a error from Galaxy.
Here is the df -h:
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda2       817G  3.9G  771G   1% /
udev             12G  4.0K   12G   1% /dev
tmpfs           101G  2.2G   94G   3% /tmp
tmpfs           4.8G  992K  4.8G   1% /run
none            5.0M     0  5.0M   0% /run/lock
none             12G   76K   12G   1% /run/shm
/dev/sdb2       2.6T  101G  2.4T   4% /home
/dev/sdc1       1.9T  1.6T  301G  84% /media/My Book
/dev/sdb1       101G  2.2G   94G   3% /tmp
 

Then I tried it again and I got same error tmpfs had 4.2GB:
Filesystem      Size  Used Avail Use% Mounted on
/dev/sda2       817G  3.9G  771G   1% /
udev             12G  4.0K   12G   1% /dev
tmpfs           101G  4.2G   92G   5% /tmp
tmpfs           4.8G  992K  4.8G   1% /run
none            5.0M     0  5.0M   0% /run/lock
none             12G   76K   12G   1% /run/shm
/dev/sdb2       2.6T  101G  2.4T   4% /home
/dev/sdc1       1.9T  1.6T  301G  84% /media/My Book
/dev/sdb1       101G  4.2G   92G   5% /tmp

Here is the galaxy error:
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 33382)
Traceback (most recent call last):
  File "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
    self.handle()
  File "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 432, in handle
    BaseHTTPRequestHandler.handle(self)
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
    self.handle_one_request()
  File "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 427, in handle_one_request
    self.wsgi_execute()
  File "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute
    self.wsgi_start_response)
  File "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py", line 202, in __call__
    return app(environ, start_response)
  File "/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__
    return self.app( environ, start_response )
  File "/home/koala2/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py", line 164, in __call__
    app_iter = self.application(environ, start_response)
  File "/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__
    return self.application(environ, replacement_start_response)
  File "/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py", line 226, in __call__
    return self.respond(environ, start_response)
  File "/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py", line 399, in respond
    if self.xmlhttp_key in req.params:
  File "/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py", line 900, in params
    params = self.str_params
  File "/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py", line 892, in str_params
    return NestedMultiDict(self.str_GET, self.str_POST)
  File "/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py", line 818, in str_POST
    keep_blank_values=True)
  File "/usr/lib/python2.7/cgi.py", line 508, in __init__
    self.read_multi(environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 632, in read_multi
    environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 510, in __init__
    self.read_single()
  File "/usr/lib/python2.7/cgi.py", line 647, in read_single
    self.read_lines()
  File "/home/koala2/galaxy-central/lib/galaxy/web/framework/base.py", line 268, in read_lines
    self.read_lines_to_outerboundary()
  File "/usr/lib/python2.7/cgi.py", line 697, in read_lines_to_outerboundary
    line = self.fp.readline(1<<16)
  File "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 467, in readline
    data = "" - self._consumed)
  File "/usr/lib/python2.7/socket.py", line 412, in readline
    bline = buf.readline(size)
OverflowError: signed integer is less than minimum
----------------------------------------

Thank you.

Luciano









---------- Forwarded message ----------
From: Luciano Cosme <cosme.sim...@gmail.com>
Date: Mon, May 21, 2012 at 3:28 PM
Subject: Load Files in local instance Ubuntu 12.04 LTS /tmp as /tmpfs
To: galaxy-dev@lists.bx.psu.edu


Hi,
   I decided to format my PC and reinstall everything. I have Ubuntu 12.04LTS installed in one 1TB hard drive (/ and swap) and the /home folder installed in a 3TB hard drive. I created a /tmp partition of 110GB and a /tmp partion of 110GB, both in the 1TB HD. Then I mounted /tmp as /tmpfs using fstab. Here is the df -h output:

Filesystem      Size  Used Avail Use% Mounted on
/dev/sda2       817G  3.9G  771G   1% /
udev             12G  4.0K   12G   1% /dev
tmpfs           100G   16K  100G   1% /tmp
tmpfs           4.8G  992K  4.8G   1% /run
none            5.0M     0  5.0M   0% /run/lock
none             12G  148K   12G   1% /run/shm
/dev/sdb2       2.6T   99G  2.4T   4% /home
/dev/sdc1       1.9T  1.6T  301G  84% /media/My Book

  Then I try to upload files as administrator on my local instance of galaxy and it fails. Since I even have a swap partition with 100GB and using the /tmp partition I don't know why it is not working. What I notice is that it is using the /tmpfs mounted on /run, which is only 4.8GB. I also tried to change universe.ini to use /tmp as temporary files storage:
# Temporary files are stored in this directory.
new_file_path = /tmp

 I can upload files that are smaller than 4.8GB, but not bigger than it. Previously it was working fine on the other Ubuntu version.  I was using /tmp as tmpfs, but I don't know how to configure the Galaxy to use the the tmpfs mounted at /tmp and not the tmpfs mounted at /run. I asked similar question before and I was able to fix it on Ubuntu 10.04 LTS, but now Ubuntu have this tmpfs mounted on /run, which is not in fstab.
   Thank you.

Luciano

 


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--
Luciano Cosme

---------------------------------------------
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.edu
---------------------------------------------



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