[galaxy-dev] Error on save large file - out of memory

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[galaxy-dev] Error on save large file - out of memory

Dennis Gascoigne-2
When we try to save a large file from galaxy (local instance) we get the following. Server should have plenty of resources.

Cheers
Dennis

MemoryError: out of memory
clear this
clear this
Module weberror.evalexception.middleware:364 in respond         view
<<          try:
                __traceback_supplement__ = errormiddleware.Supplement, self, environ
                app_iter = self.application(environ, detect_start_response)
                try:
                    return_iter = list(app_iter)>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__         view
<<          try:
                status, headers, body = wsgilib.intercept_output(
                    environ, self.app)
                if status is None:
                    # Some error occurred>>  environ, self.app)
Module paste.wsgilib:544 in intercept_output         view
<<      try:
            for item in app_iter:
                output.write(item)
        finally:
            if hasattr(app_iter, 'close'):>>  output.write(item)
MemoryError: out of memory
URL: http://genome.imb.qfab.org:8080/datasets/3197f0f893217878/display?to_ext=fasta File '/home/d.gascoigne/Galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 544 in intercept_output output.write(item) MemoryError: out of memory
<?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.6.1"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py </filename> <line> 98 </line> <function> __call__ </function> <operation> environ, self.app) </operation> <operation_context> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py </filename> <line> 544 </line> <function> intercept_output </function> <operation> output.write(item) </operation> <operation_context> try: for item in app_iter: output.write(item) finally: if hasattr(app_iter, 'close'): </operation_context> </frame> </stack> <exception> <type> MemoryError </type> <value> out of memory </value> </exception> </traceback>
<?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.6.1"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py </filename> <line> 98 </line> <function> __call__ </function> <operation> environ, self.app) </operation> <operation_context> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py </filename> <line> 544 </line> <function> intercept_output </function> <operation> output.write(item) </operation> <operation_context> try: for item in app_iter: output.write(item) finally: if hasattr(app_iter, 'close'): </operation_context> </frame> </stack> <exception> <type> MemoryError </type> <value> out of memory </value> </exception> </traceback>

--
Dennis Gascoigne
0407 639 995
[hidden email]

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Re: [galaxy-dev] Error on save large file - out of memory

Nate Coraor (nate@bx.psu.edu)
Hi Dennis,

Please set use_debug = False in the universe_wsgi.ini config file and
restart Galaxy.

--nate

Dennis Gascoigne wrote:

> When we try to save a large file from galaxy (local instance) we get the
> following. Server should have plenty of resources.
>
> Cheers
> Dennis
>
> MemoryError: out of memory
> clear this
> clear this
> URL:
> http://genome.imb.qfab.org:8080/datasets/3197f0f893217878/display?to_ext=fasta
> Module weberror.evalexception.middleware:364 in respond         view
> <<          try:
>                 __traceback_supplement__ = errormiddleware.Supplement,
> self, environ
>                 app_iter = self.application(environ, detect_start_response)
>                 try:
>                     return_iter = list(app_iter)>>  app_iter =
> self.application(environ, detect_start_response)
> Module paste.debug.prints:98 in __call__         view
> <<          try:
>                 status, headers, body = wsgilib.intercept_output(
>                     environ, self.app)
>                 if status is None:
>                     # Some error occurred>>  environ, self.app)
> Module paste.wsgilib:544 in intercept_output         view
> <<      try:
>             for item in app_iter:
>                 output.write(item)
>         finally:
>             if hasattr(app_iter, 'close'):>>  output.write(item)
> MemoryError: out of memory
> URL:
> http://genome.imb.qfab.org:8080/datasets/3197f0f893217878/display?to_ext=fasta 
> File
> '/home/d.gascoigne/Galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
> line 364 in respond app_iter = self.application(environ,
> detect_start_response) File
> '/home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
> line 98 in __call__ environ, self.app) File
> '/home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py',
> line 544 in intercept_output output.write(item) MemoryError: out of memory
> <?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.6.1">
> Python </language> </sysinfo> <stack> <frame> <module>
> weberror.evalexception.middleware </module> <filename>
> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py
> </filename> <line> 364 </line> <function> respond </function>
> <operation> app_iter = self.application(environ, detect_start_response)
> </operation> <operation_context> try: __traceback_supplement__ =
> errormiddleware.Supplement, self, environ app_iter =
> self.application(environ, detect_start_response) try: return_iter =
> list(app_iter) </operation_context> </frame> <frame> <module>
> paste.debug.prints </module> <filename>
> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py
> </filename> <line> 98 </line> <function> __call__ </function>
> <operation> environ, self.app) </operation> <operation_context> try:
> status, headers, body = wsgilib.intercept_output( environ, self.app) if
> status is None: # Some error occurred </operation_context> </frame>
> <frame> <module> paste.wsgilib </module> <filename>
> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py
> </filename> <line> 544 </line> <function> intercept_output </function>
> <operation> output.write(item) </operation> <operation_context> try: for
> item in app_iter: output.write(item) finally: if hasattr(app_iter,
> 'close'): </operation_context> </frame> </stack> <exception> <type>
> MemoryError </type> <value> out of memory </value> </exception> </traceback>
> <?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.6.1">
> Python </language> </sysinfo> <stack> <frame> <module>
> weberror.evalexception.middleware </module> <filename>
> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py
> </filename> <line> 364 </line> <function> respond </function>
> <operation> app_iter = self.application(environ, detect_start_response)
> </operation> <operation_context> try: __traceback_supplement__ =
> errormiddleware.Supplement, self, environ app_iter =
> self.application(environ, detect_start_response) try: return_iter =
> list(app_iter) </operation_context> </frame> <frame> <module>
> paste.debug.prints </module> <filename>
> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py
> </filename> <line> 98 </line> <function> __call__ </function>
> <operation> environ, self.app) </operation> <operation_context> try:
> status, headers, body = wsgilib.intercept_output( environ, self.app) if
> status is None: # Some error occurred </operation_context> </frame>
> <frame> <module> paste.wsgilib </module> <filename>
> /home/d.gascoigne/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py
> </filename> <line> 544 </line> <function> intercept_output </function>
> <operation> output.write(item) </operation> <operation_context> try: for
> item in app_iter: output.write(item) finally: if hasattr(app_iter,
> 'close'): </operation_context> </frame> </stack> <exception> <type>
> MemoryError </type> <value> out of memory </value> </exception> </traceback>
>
> --
> Dennis Gascoigne
> 0407 639 995
> [hidden email] <mailto:[hidden email]>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev

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