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.file.readline(self.length - 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
>
> ****
>
> ** **
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
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>
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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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