Out of Memory Error (Galaxy Local Instance) - File Download
Hi, We have run into a an error when trying to download a previously uploaded file from our local galaxy instance (lives in a 512 MB VM). The error is at the end of this message. In a previous thread, Nate advised setting use_debug = False in universe_wsgi.ini. Is this because the debugging code is causing the error but otherwise download would be fine? Also, is 512 MB enough for a VM? (Out setup has actual jobs being submitted to the cluster) -John Error Traceback: View as: Interactive<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> | Text<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> | XML<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> (full)<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> ⇝ MemoryError: out of memory URL:http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam Moduleweberror.evalexception.middleware:364in respond <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> [https://mail.ad.uab.edu/owa/attachment.ashx?id=RgAAAADwtwsGAIuwS4Yj8heXBrQ8BwBfPEvHhIGISJMpl3DamZ28AAAADucKAAAn9mSYf%2brbTqKQMfWLxCs%2bAAACFAODAAAJ&attcnt=1&attid0=EACqVATCvqm6R6pDXKPldx%2f%2b] <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> view<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam>
<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> app_iter =self.application(environ,detect_start_response) Module paste.debug.prints:98 in__call__ <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> [https://mail.ad.uab.edu/owa/attachment.ashx?id=RgAAAADwtwsGAIuwS4Yj8heXBrQ8BwBfPEvHhIGISJMpl3DamZ28AAAADucKAAAn9mSYf%2brbTqKQMfWLxCs%2bAAACFAODAAAJ&attcnt=1&attid0=EACqVATCvqm6R6pDXKPldx%2f%2b] <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> view<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> environ, self.app) Module paste.wsgilib:544 inintercept_output <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> [https://mail.ad.uab.edu/owa/attachment.ashx?id=RgAAAADwtwsGAIuwS4Yj8heXBrQ8BwBfPEvHhIGISJMpl3DamZ28AAAADucKAAAn9mSYf%2brbTqKQMfWLxCs%2bAAACFAODAAAJ&attcnt=1&attid0=EACqVATCvqm6R6pDXKPldx%2f%2b] <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> view<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> output.write(item) MemoryError: out of memory
John David Osborne wrote:
Hi,
We have run into a an error when trying to download a previously uploaded file from our local galaxy instance (lives in a 512 MB VM). The error is at the end of this message. In a previous thread, Nate advised setting use_debug = False in universe_wsgi.ini. Is this because the debugging code is causing the error but otherwise download would be fine?
Hi John, That's correct, debug = True will cause the entire response to be loaded into memory, so once all available memory and swap is consumed, the process will crash.
Also, is 512 MB enough for a VM? (Out setup has actual jobs being submitted to the cluster)
Sure, it should be okay if you're not doing anything locally (make sure you set set_metadata_externally = True). --nate
-John
Error Traceback: View as: Interactive<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> | Text<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> | XML<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> (full)<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> ⇝ MemoryError: out of memory URL:http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam Moduleweberror.evalexception.middleware:364in respond <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> [https://mail.ad.uab.edu/owa/attachment.ashx?id=RgAAAADwtwsGAIuwS4Yj8heXBrQ8BwBfPEvHhIGISJMpl3DamZ28AAAADucKAAAn9mSYf%2brbTqKQMfWLxCs%2bAAACFAODAAAJ&attcnt=1&attid0=EACqVATCvqm6R6pDXKPldx%2f%2b] <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> view<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam>
<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> app_iter =self.application(environ,detect_start_response) Module paste.debug.prints:98 in__call__ <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> [https://mail.ad.uab.edu/owa/attachment.ashx?id=RgAAAADwtwsGAIuwS4Yj8heXBrQ8BwBfPEvHhIGISJMpl3DamZ28AAAADucKAAAn9mSYf%2brbTqKQMfWLxCs%2bAAACFAODAAAJ&attcnt=1&attid0=EACqVATCvqm6R6pDXKPldx%2f%2b] <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> view<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> environ, self.app) Module paste.wsgilib:544 inintercept_output <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> [https://mail.ad.uab.edu/owa/attachment.ashx?id=RgAAAADwtwsGAIuwS4Yj8heXBrQ8BwBfPEvHhIGISJMpl3DamZ28AAAADucKAAAn9mSYf%2brbTqKQMfWLxCs%2bAAACFAODAAAJ&attcnt=1&attid0=EACqVATCvqm6R6pDXKPldx%2f%2b] <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> view<http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> <http://galaxy.uabgrid.uab.edu/datasets/ba1915f3923e3bf1/display?to_ext=sam> output.write(item) MemoryError: out of memory
___________________________________________________________ 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 (2)
-
John David Osborne -
Nate Coraor