Re: [Dspace-tech] java.io.IOException on Dspace 3.1
On Fri, May 03, 2013 at 07:11:26PM +, Pottinger, Hardy J. wrote: Hi, in an effort to share as much information as we have, here's our latest thinking on this. However, do note, I'm talking about an esoteric/intermittent error that looks just like the much more straightforward error that Peter mentions below. It is well worth your time to troubleshoot as Peter suggests, because a simple permissions issue is easily repaired. However, the error described by Amy [1] is another thing altogether. In troubleshooting it earlier this year, I brought an article [2] to the attention of Mark Wood in Indiana as well as a few sysadmins here. After reading this article, I realized we actually have a bit of an oddity in our server setup. The server that hosts our repository runs on RHEL5, which is 32-bit, but it has a special PAE kernel, which means it's running enough 64-bit Linux to address more RAM. Our sysadmin searched around and discovered another article [3], which generically warns of Java issues on a PAE kernel. So, our plan at this point is to try testing DSpace on a 64-bit machine, using Java 7, and a specifically-tuned installation of Tomcat, to make the best utilization of available memory. Last I heard, Mark was also planning on migrating to 64-bit machine. FWIW scholarworks.iupui.edu migrated a week and a half ago to an AMD Opteron 2356 (64-bit instruction set) on an x86_64 kernel with no complaints so far. savage ~ # uname -a Linux savage 3.7.10-gentoo #1 SMP Tue Mar 12 08:50:14 EDT 2013 x86_64 Quad-Core AMD Opteron(tm) Processor 2356 AuthenticAMD GNU/Linux savage linux # java -version java version 1.6.0_27 OpenJDK Runtime Environment (IcedTea6 1.12.4) (Gentoo build 1.6.0_27-b27) OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode) -- Mark H. Wood, Lead System Programmer mw...@iupui.edu Machines should not be friendly. Machines should be obedient. signature.asc Description: Digital signature -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] java.io.IOException on Dspace 3.1
Hi, in an effort to share as much information as we have, here's our latest thinking on this. However, do note, I'm talking about an esoteric/intermittent error that looks just like the much more straightforward error that Peter mentions below. It is well worth your time to troubleshoot as Peter suggests, because a simple permissions issue is easily repaired. However, the error described by Amy [1] is another thing altogether. In troubleshooting it earlier this year, I brought an article [2] to the attention of Mark Wood in Indiana as well as a few sysadmins here. After reading this article, I realized we actually have a bit of an oddity in our server setup. The server that hosts our repository runs on RHEL5, which is 32-bit, but it has a special PAE kernel, which means it's running enough 64-bit Linux to address more RAM. Our sysadmin searched around and discovered another article [3], which generically warns of Java issues on a PAE kernel. So, our plan at this point is to try testing DSpace on a 64-bit machine, using Java 7, and a specifically-tuned installation of Tomcat, to make the best utilization of available memory. Last I heard, Mark was also planning on migrating to 64-bit machine. Anyway, this is another shot in the dark, but you may want to try upgrading your hardware and using a newer version of Java... it might just help with this little problem. If you do find anything, please do keep the community posted. The ticket Amy mentioned earlier [1] is a good place to do that, and replying to this thread on the mail list would help, too. Thanks! [1] https://jira.duraspace.org/browse/DS-1143 [2] http://blog.thetaphi.de/2012/07/use-lucenes-mmapdirectory-on-64bit.html [3] https://kb.groundworkopensource.com/display/SUPPORT/Using+the+32-bit+PAE+ke rnel+can+cause+JAVA+errors -- HARDY POTTINGER pottinge...@umsystem.edu University of Missouri Library Systems http://lso.umsystem.edu/~pottingerhj/ https://MOspace.umsystem.edu/ No matter how far down the wrong road you've gone, turn back. --Turkish proverb On 5/3/13 1:42 PM, Peter Dietz pdiet...@gmail.com wrote: Hi Will, This might sound like very basic stack-overflow 101 advice, but I would double check filesystem permissions. A while ago, I was sure that the dspace-user owned all of the files, but then I actually checked, and found that some files in our assetstore were owned by root. After chown'ing them to the dspace-user, this problem disappeared for us. Another one of my theories is that our SAN/NAS was having intermittent connectivity issues, but our sys-admin showed me otherwise. Peter Dietz On Fri, May 3, 2013 at 2:24 PM, Lana, Amy la...@missouri.edu wrote: Hi Will, We¹ve had this problem for a while now as well (https://jira.duraspace.org/browse/DS-1143). It¹s my understanding that work trying to fix the issue continues; if you could add your information to the existing ticket, it may help with the diagnosis. Sorry we¹ve no solution at this point. Amy Amy Lana University of Missouri Libraries la...@missouri.edu / 573-882-4757 tel:573-882-4757 http://mulibraries.missouri.edu http://mulibraries.missouri.edu/ https://mospace.umsystem.edu From: Will Clarke [mailto:clark...@wfu.edu] Sent: Friday, May 03, 2013 1:11 PM To: dspace-tech@lists.sourceforge.net Subject: [Dspace-tech] java.io.IOException on Dspace 3.1 We've just upgraded to dspace 3.1 and when trying to add items we are now getting this error. Can anyone help? java.io.IOException: No such file or directoryCocoon stacktrace [hide] Error calling continuation context:/resource://aspects/Submission/submission.js - 507:-1 processPage context:/resource://aspects/Submission/sitemap.xmap - 93:44 map:call context:/resource://aspects/Submission/sitemap.xmap - 92:61 map:match context:/resource://aspects/Submission/sitemap.xmap - 60:48 map:select type=AuthenticatedSelector context:/jndi:/localhost/aspects/aspects.xmap - 89:72 map:mount context:/jndi:/localhost/aspects/aspects.xmap - 79:34 map:select type=parameter context:/jndi:/localhost/aspects/aspects.xmap - 78:36 map:match type=AspectMatcher context:/jndi:/localhost/sitemap.xmap - 485:100 map:mount context:/jndi:/localhost/sitemap.xmap - 484:49 map:match context:/resource://aspects/Statistics/sitemap.xmap - 285:31 map:serialize type=xml context:/resource://aspects/Statistics/sitemap.xmap - 37:19 map:generate context:/resource://aspects/Workflow/sitemap.xmap - 139:38 map:serialize type=xml context:/resource://aspects/Workflow/sitemap.xmap - 76:26 map:generate context:/jndi:/localhost/aspects/aspects.xmap - 85:34 map:serialize type=xml context:/jndi:/localhost/aspects/aspects.xmap - 84:43 map:transform type=PageNotFound context:/jndi:/localhost/aspects/aspects.xmap - 83:22 map:generate context:/jndi:/localhost/themes/Mirage/sitemap.xmap - 164:34 map:serialize type=xhtml context:/jndi:/localhost/themes/Mirage/sitemap.xmap - 158:33 map:transform type=i18n
Re: [Dspace-tech] java.io.IOException on Dspace 3.1
Very odd indeed. I seem to have confirmed that it is a permissions issue - but using chown to make dspace the owner did not do the trick. I made the asset directory world-writeable (don't do this on yours) and uploaded a file. the new file was owned by tomcat6. Did I miss something in the dspace setup as far as the dspace user and the tomcat user goes? -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] java.io.IOException on Dspace 3.1
On Fri, May 3, 2013 at 10:20 PM, Will Clarke clark...@wfu.edu wrote: Very odd indeed. I seem to have confirmed that it is a permissions issue - but using chown to make dspace the owner did not do the trick. I made the asset directory world-writeable (don't do this on yours) and uploaded a file. the new file was owned by tomcat6. Did I miss something in the dspace setup as far as the dspace user and the tomcat user goes? So you're running tomcat as the tomcat6 user while the dspace user owns your dspace installation directory? They both need to be the same user. So either run Tomcat as dspace or chown -R your dspace installation directory to tomcat6. This is an important consideration mentioned more than once in the installation chapter because it's known to cause permission issues: https://wiki.duraspace.org/display/DSDOC3x/Installation This needs to be the same user that Tomcat (or Jetty etc.) will run as Note that DSpace will need to run as the same user as Tomcat, so you might want to install and run Tomcat as a user called 'dspace'. Set the environment variable TOMCAT_USER appropriately. Regards, ~~helix84 Compulsory reading: DSpace Mailing List Etiquette https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
