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
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.simple@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
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 jredmond@wustl.edu
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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.simple@gmail.commailto:cosme.simple@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.edumailto: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
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 jredmond@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****
jredmond@wustl.edu****
*From:* galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@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.simple@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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Redmond, James