Re: [Treebase-devel] Fwd: [[treebase-bugs] #7718] error message when submitting nexus file

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Bill,

This is disk space issue.  The tomcat log was growing very large as it is currently logging every single query. 

I am currently working on:
1) excluding all application messages from catalina.out. There is a a separate treebase.log for this, which is properly rotated.
2) get catalina.out into log rotation (not straightforward, most scenarios require a tomcat restart)
3) disk space monitoring checks submitted to nagios.

Anyways, for the moment, I've moved the old tomcat log and started a new one, which freed up 4 GB of space.

-Jon

On Apr 1, 2010, at 9:42 AM, William Piel wrote:

> 
> Hi Jon,
> 
> Is this a RAM outage or a disc space issue?
> 
> "No space left on device at org.apache.commons.fileupload.FileUploadBase.parseRequest"
> 
> bp
> 
> 
> 
> Begin forwarded message:
> 
>> From: "Torbjørn Ekrem via RT" <bu...@tr...>
>> Date: April 1, 2010 8:31:41 AM CDT
>> To: undisclosed-recipients: ;
>> Subject: [[treebase-bugs] #7718] error message when submitting nexus file 
>> Reply-To: bu...@tr...
>> 
>> 
>> Thu Apr 01 09:31:40 2010: Request 7718 was acted upon.
>> Transaction: Ticket created by Tor...@vm...
>>       Queue: Treebase-bugs
>>     Subject: error message when submitting nexus file
>>       Owner: Nobody
>>  Requestors: Tor...@vm...
>>      Status: new
>> Ticket <URL: https://help.nescent.org/Ticket/Display.html?id=7718 >
>> 
>> 
>> Hi,
>> 
>> I tried to upload a nexus-file that is successfully parsed in Mesquite today,
>> and got the below error message. Is there anything that I might have overlooked
>> or is this perhaps a bug. The file is not very large (about 270 kb) and include
>> taxa, characters and trees blocks.
>> 
>> Best regards,
>> Torbjørn
>> 
>> -- 
>> Dr. Torbjørn Ekrem
>> Systematikk og evolusjonsgruppa
>> NTNU Vitenskapsmuseet         
>> Seksjon for naturhistorie      
>> 7491 Trondheim                 
>> 
>> Systematics and Evolution Group
>> Museum of Natural History and Archaeology
>> Norwegian University of Science and Technology
>> NO-7491 Trondheim, Norway
>> 
>> Tel: +47 73 59 78 12
>> Email: Tor...@vm...Web: www.ntnu.no/~torbjoe
>> Uncaught Exception Encountered
>> 
>> 
>> org.springframework.web.multipart.MultipartException: Could not parse multipart
>> servlet request; nested exception is
>> org.apache.commons.fileupload.FileUploadBase$IOFileUploadException: Processing
>> of multipart/form-data request failed. No space left on device Caused by:
>> org.apache.commons.fileupload.FileUploadBase$IOFileUploadException: Processing
>> of multipart/form-data request failed. No space left on device at
>> org.apache.commons.fileupload.FileUploadBase.parseRequest(FileUploadBase.java:359)
>> at
>> org.apache.commons.fileupload.servlet.ServletFileUpload.parseRequest(ServletFileUpload.java:126)
>> at
>> org.cipres.treebase.web.controllers.AjaxMultipartResolver.resolveMultipart(AjaxMultipartResolver.java:35)
>> at
>> org.springframework.web.servlet.DispatcherServlet.checkMultipart(DispatcherServlet.java:980)
>> at
>> org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:834)
>> at
>> org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
>> at
>> org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
>> at
>> org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at
>> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>> at
>> org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
>> at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at
>> org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
>> at
>> org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>> at
>> org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>> at
>> org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
>> at
>> org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>> at
>> com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
>> at
>> com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>> at
>> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264)
>> at
>> org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
>> at
>> org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
>> at
>> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
>> at
>> org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110)
>> at
>> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
>> at
>> org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81)
>> at
>> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
>> at
>> org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217)
>> at
>> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
>> at
>> org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191)
>> at
>> org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
>> at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148)
>> at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
>> at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
>> at
>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
>> at
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
>> at
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
>> at
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
>> at
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
>> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
>> at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873)
>> at
>> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
>> at
>> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
>> at
>> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
>> at
>> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
>> at java.lang.Thread.run(Thread.java:636) Caused by: java.io.IOException: No
>> space left on device at java.io.FileOutputStream.writeBytes(Native Method) at
>> java.io.FileOutputStream.write(FileOutputStream.java:297) at
>> org.apache.commons.io.output.ByteArrayOutputStream.writeTo(ByteArrayOutputStream.java:217)
>> at
>> org.apache.commons.io.output.DeferredFileOutputStream.thresholdReached(DeferredFileOutputStream.java:124)
>> at
>> org.apache.commons.io.output.ThresholdingOutputStream.checkThreshold(ThresholdingOutputStream.java:220)
>> at
>> org.apache.commons.io.output.ThresholdingOutputStream.write(ThresholdingOutputStream.java:127)
>> at org.apache.commons.fileupload.util.Streams.copy(Streams.java:101) at
>> org.apache.commons.fileupload.util.Streams.copy(Streams.java:64) at
>> org.apache.commons.fileupload.FileUploadBase.parseRequest(FileUploadBase.java:354)
>> ... 56 more Cookies:
>> itemToHighlight=[http%3A//www.treebase.org/treebase-web/user/uploadFile.html]
>> JSESSIONID=[4159496F4E66A78FD91DB3E51F4833F3]
>> 
> 
> 
> 
> 
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-------------------------------------------------------
Jon Auman
Systems Administrator
National Evolutionary Synthesis Center
Duke University
http:www.nescent.org
jon...@ne...
------------------------------------------------------