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From: Conrad H. <co...@cg...> - 2010-02-09 02:20:07
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Sorry about the false alarm. The whole thing is my fault because I installed Opal2 as user "root". The installed tree was not writable by the tomcat server, hence the error. Reinstalling as the correct user fixed everything. Thank you for your help and the great software. Conrad On 2/4/10 4:59 PM, Sriram Krishnan wrote: > Note that version 1.9.5 didn't use Hibernate and HSQL - all Opal state > was stored in memory, which was lost when Tomcat was restarted. > > The HSQL files should be in $CATALINA_HOME/webapps/opal2/WEB-INF/data/. > Does that exist for you? > > A good test would be install this in a fresh version of Tomcat. I just > downloaded an Opal installation from SourceForge and installed it inside > a fresh version of Tomcat 5.5.28, and did the exact same changes you > did, and everything worked fine. It is possible that there may be some > conflicts with other web applications deployed inside your Tomcat > instance. If you can't get Opal installed on a vanilla fresh Tomcat, we > can help you debug that. > > Thanks, > Sriram > > On Feb 4, 2010, at 4:31 PM, Conrad Huang wrote: > >> I did not touch etc/hibernate-opal.cfg.xml. The only two files from >> the standard 2.2 distribution that I modified were etc/opal.properties >> and build.properties. In opal.properties, the only item I changed was >> "tomcat.url", which I set to be the same as on 1.9.5. The >> build.properties file for 1.9.5 and 2.2 are the same except for >> "version". >> >> I guess I'm unclear on where the HSQL databases are for 1.9.5 and 2.2 >> are. On 1.9.5, in etc/opal.properties, I have >> >> database.use=false >> >> On 2.2, in etc/hibernate-opal.cfg.xml, I have >> >> <property name="connection.url">jdbc:hsqldb:file:data/opaldb</property> >> >> Where on the file system should these databases live, given these >> settings? >> >> Thanks. >> >> Conrad >> >> On 2/4/10 4:08 PM, Sriram Krishnan wrote: >>> Hi Conrad, >>> >>> Just to elaborate on Jane's question - did you modify the >>> etc/hibernate-opal.cfg.xml as well? I would recommend default the >>> default configuration (i.e. using the HSQL database) first, and checking >>> if everything works out of the box. >>> >>> Once that works, you can try connecting to another database. Also note >>> that the database schemas for Opal 1.9.5 and Opal 2.X are different. So >>> if you are using the same database instance, please use a different >>> database name in the "connection.url". >>> >>> Let us know if that helps. >>> Sriram >>> >>> On Feb 4, 2010, at 3:19 PM, Jane Ren wrote: >>> >>>> Hi Conrad, >>>> >>>> Are you using the default database? >>>> >>>> Jane >>>> ________________________________________ >>>> From: Conrad Huang [co...@cg...] >>>> Sent: Thursday, February 04, 2010 2:34 PM >>>> To: opa...@li... >>>> Subject: [Opaltoolkit-users] Problem installing Opal 2.X >>>> >>>> I've been using Opal 1.9.5 for a while and it works very well for us. >>>> Now that 2.2 is out, I'd like to migrate to the newer version while >>>> keeping the old one up and running for legacy users. Following the >>>> instructions, I managed to get through "edit etc/opal.properties and >>>> build.properties" and "ant install", but starting tomcat at that point >>>> generates the attached error log. The old 1.9.5 services are working >>>> fine, but services deployed for 2.2 generate similar exceptions about >>>> "Connections could not be acquired from the underlying database!" Can >>>> someone please point me towards where I went wrong? Thanks. >>>> >>>> Conrad >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> >>>> The Planet: dedicated and managed hosting, cloud storage, colocation >>>> Stay online with enterprise data centers and the best network in the >>>> business >>>> Choose flexible plans and management services without long-term >>>> contracts >>>> Personal 24x7 support from experience hosting pros just a phone call >>>> away. >>>> http://p.sf.net/sfu/theplanet-com >>>> _______________________________________________ >>>> Opaltoolkit-users mailing list >>>> Opa...@li... >>>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users >>> > |
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From: Sriram K. <sr...@sd...> - 2010-02-05 01:00:09
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Note that version 1.9.5 didn't use Hibernate and HSQL - all Opal state was stored in memory, which was lost when Tomcat was restarted. The HSQL files should be in $CATALINA_HOME/webapps/opal2/WEB-INF/ data/. Does that exist for you? A good test would be install this in a fresh version of Tomcat. I just downloaded an Opal installation from SourceForge and installed it inside a fresh version of Tomcat 5.5.28, and did the exact same changes you did, and everything worked fine. It is possible that there may be some conflicts with other web applications deployed inside your Tomcat instance. If you can't get Opal installed on a vanilla fresh Tomcat, we can help you debug that. Thanks, Sriram On Feb 4, 2010, at 4:31 PM, Conrad Huang wrote: > I did not touch etc/hibernate-opal.cfg.xml. The only two files from > the standard 2.2 distribution that I modified were etc/ > opal.properties and build.properties. In opal.properties, the only > item I changed was "tomcat.url", which I set to be the same as on > 1.9.5. The build.properties file for 1.9.5 and 2.2 are the same > except for "version". > > I guess I'm unclear on where the HSQL databases are for 1.9.5 and > 2.2 are. On 1.9.5, in etc/opal.properties, I have > > database.use=false > > On 2.2, in etc/hibernate-opal.cfg.xml, I have > > <property name="connection.url">jdbc:hsqldb:file:data/opaldb</ > property> > > Where on the file system should these databases live, given these > settings? > > Thanks. > > Conrad > > On 2/4/10 4:08 PM, Sriram Krishnan wrote: >> Hi Conrad, >> >> Just to elaborate on Jane's question - did you modify the >> etc/hibernate-opal.cfg.xml as well? I would recommend default the >> default configuration (i.e. using the HSQL database) first, and >> checking >> if everything works out of the box. >> >> Once that works, you can try connecting to another database. Also >> note >> that the database schemas for Opal 1.9.5 and Opal 2.X are >> different. So >> if you are using the same database instance, please use a different >> database name in the "connection.url". >> >> Let us know if that helps. >> Sriram >> >> On Feb 4, 2010, at 3:19 PM, Jane Ren wrote: >> >>> Hi Conrad, >>> >>> Are you using the default database? >>> >>> Jane >>> ________________________________________ >>> From: Conrad Huang [co...@cg...] >>> Sent: Thursday, February 04, 2010 2:34 PM >>> To: opa...@li... >>> Subject: [Opaltoolkit-users] Problem installing Opal 2.X >>> >>> I've been using Opal 1.9.5 for a while and it works very well for >>> us. >>> Now that 2.2 is out, I'd like to migrate to the newer version while >>> keeping the old one up and running for legacy users. Following the >>> instructions, I managed to get through "edit etc/opal.properties and >>> build.properties" and "ant install", but starting tomcat at that >>> point >>> generates the attached error log. The old 1.9.5 services are working >>> fine, but services deployed for 2.2 generate similar exceptions >>> about >>> "Connections could not be acquired from the underlying database!" >>> Can >>> someone please point me towards where I went wrong? Thanks. >>> >>> Conrad >>> >>> ------------------------------------------------------------------------------ >>> >>> The Planet: dedicated and managed hosting, cloud storage, colocation >>> Stay online with enterprise data centers and the best network in the >>> business >>> Choose flexible plans and management services without long-term >>> contracts >>> Personal 24x7 support from experience hosting pros just a phone call >>> away. >>> http://p.sf.net/sfu/theplanet-com >>> _______________________________________________ >>> Opaltoolkit-users mailing list >>> Opa...@li... >>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users >> |
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From: Conrad H. <co...@cg...> - 2010-02-05 00:55:54
|
I did not touch etc/hibernate-opal.cfg.xml. The only two files from the standard 2.2 distribution that I modified were etc/opal.properties and build.properties. In opal.properties, the only item I changed was "tomcat.url", which I set to be the same as on 1.9.5. The build.properties file for 1.9.5 and 2.2 are the same except for "version". I guess I'm unclear on where the HSQL databases are for 1.9.5 and 2.2 are. On 1.9.5, in etc/opal.properties, I have database.use=false On 2.2, in etc/hibernate-opal.cfg.xml, I have <property name="connection.url">jdbc:hsqldb:file:data/opaldb</property> Where on the file system should these databases live, given these settings? Thanks. Conrad On 2/4/10 4:08 PM, Sriram Krishnan wrote: > Hi Conrad, > > Just to elaborate on Jane's question - did you modify the > etc/hibernate-opal.cfg.xml as well? I would recommend default the > default configuration (i.e. using the HSQL database) first, and checking > if everything works out of the box. > > Once that works, you can try connecting to another database. Also note > that the database schemas for Opal 1.9.5 and Opal 2.X are different. So > if you are using the same database instance, please use a different > database name in the "connection.url". > > Let us know if that helps. > Sriram > > On Feb 4, 2010, at 3:19 PM, Jane Ren wrote: > >> Hi Conrad, >> >> Are you using the default database? >> >> Jane >> ________________________________________ >> From: Conrad Huang [co...@cg...] >> Sent: Thursday, February 04, 2010 2:34 PM >> To: opa...@li... >> Subject: [Opaltoolkit-users] Problem installing Opal 2.X >> >> I've been using Opal 1.9.5 for a while and it works very well for us. >> Now that 2.2 is out, I'd like to migrate to the newer version while >> keeping the old one up and running for legacy users. Following the >> instructions, I managed to get through "edit etc/opal.properties and >> build.properties" and "ant install", but starting tomcat at that point >> generates the attached error log. The old 1.9.5 services are working >> fine, but services deployed for 2.2 generate similar exceptions about >> "Connections could not be acquired from the underlying database!" Can >> someone please point me towards where I went wrong? Thanks. >> >> Conrad >> >> ------------------------------------------------------------------------------ >> >> The Planet: dedicated and managed hosting, cloud storage, colocation >> Stay online with enterprise data centers and the best network in the >> business >> Choose flexible plans and management services without long-term contracts >> Personal 24x7 support from experience hosting pros just a phone call >> away. >> http://p.sf.net/sfu/theplanet-com >> _______________________________________________ >> Opaltoolkit-users mailing list >> Opa...@li... >> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users > |
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From: Sriram K. <sr...@sd...> - 2010-02-05 00:08:21
|
Hi Conrad, Just to elaborate on Jane's question - did you modify the etc/ hibernate-opal.cfg.xml as well? I would recommend default the default configuration (i.e. using the HSQL database) first, and checking if everything works out of the box. Once that works, you can try connecting to another database. Also note that the database schemas for Opal 1.9.5 and Opal 2.X are different. So if you are using the same database instance, please use a different database name in the "connection.url". Let us know if that helps. Sriram On Feb 4, 2010, at 3:19 PM, Jane Ren wrote: > Hi Conrad, > > Are you using the default database? > > Jane > ________________________________________ > From: Conrad Huang [co...@cg...] > Sent: Thursday, February 04, 2010 2:34 PM > To: opa...@li... > Subject: [Opaltoolkit-users] Problem installing Opal 2.X > > I've been using Opal 1.9.5 for a while and it works very well for us. > Now that 2.2 is out, I'd like to migrate to the newer version while > keeping the old one up and running for legacy users. Following the > instructions, I managed to get through "edit etc/opal.properties and > build.properties" and "ant install", but starting tomcat at that point > generates the attached error log. The old 1.9.5 services are working > fine, but services deployed for 2.2 generate similar exceptions about > "Connections could not be acquired from the underlying database!" Can > someone please point me towards where I went wrong? Thanks. > > Conrad > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term > contracts > Personal 24x7 support from experience hosting pros just a phone call > away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
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From: Jane R. <j2...@uc...> - 2010-02-04 23:20:30
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Hi Conrad, Are you using the default database? Jane ________________________________________ From: Conrad Huang [co...@cg...] Sent: Thursday, February 04, 2010 2:34 PM To: opa...@li... Subject: [Opaltoolkit-users] Problem installing Opal 2.X I've been using Opal 1.9.5 for a while and it works very well for us. Now that 2.2 is out, I'd like to migrate to the newer version while keeping the old one up and running for legacy users. Following the instructions, I managed to get through "edit etc/opal.properties and build.properties" and "ant install", but starting tomcat at that point generates the attached error log. The old 1.9.5 services are working fine, but services deployed for 2.2 generate similar exceptions about "Connections could not be acquired from the underlying database!" Can someone please point me towards where I went wrong? Thanks. Conrad |
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From: Conrad H. <co...@cg...> - 2010-02-04 22:34:34
|
I've been using Opal 1.9.5 for a while and it works very well for us. Now that 2.2 is out, I'd like to migrate to the newer version while keeping the old one up and running for legacy users. Following the instructions, I managed to get through "edit etc/opal.properties and build.properties" and "ant install", but starting tomcat at that point generates the attached error log. The old 1.9.5 services are working fine, but services deployed for 2.2 generate similar exceptions about "Connections could not be acquired from the underlying database!" Can someone please point me towards where I went wrong? Thanks. Conrad |
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From: Sriram K. <sr...@sd...> - 2010-02-04 19:31:16
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Dear all, We are pleased to announce the release of version 2.2 of the Opal Toolkit. This release improves version 2.1 in the following ways: - Optional auto-generation of service specific WSDLs, based on user- specified application metadata. This update has been contributed by Anthony Bretaudeau from IRISA, France - Support for the DB2 database for state monitoring, in addition to the support for MySQL and PostgreSQL provided in the past - Use of MIME attachments in the Opal dashboard, which leads to better performance and support for larger file uploads - Basic support for Per-IP limits on number of jobs per hour, to stop server overloading - Upgrade of the DRMAA jar to version 6.1 Opal 2.2 can be downloaded from: https://sourceforge.net/projects/opaltoolkit/files . More information about the Opal Toolkit, including relevant documentation, can be found at: http://opal.nbcr.net. Sincerely, Opal Team |
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From: Sriram K. <sr...@sd...> - 2010-01-26 20:00:40
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Hello Rakesh, Answers inline - > I am really sorry to bother you, but didn't get any reply from > mailing list thus writing to you. The mailing list is only open for posting to subscribers. Please sign up at - https://lists.sourceforge.net/lists/listinfo/opaltoolkit- users. It is fairly low traffic. > We have rocks cluster and we are trying to use Opal Toolkit for job > submission for some of our applications. Opal-Toolkit is installed > successfully and working. As Rocks uses SGE by default we have set > the opal.properties to DRMAA. > opal.jobmanager=edu.sdsc.nbcr.opal.manager.DRMAAJobManager > > Secondly, we would using OpenMpi thus have used the configuration > drmaa.pe=orte (Could u advise, if this is ok) We have personally never used it with OpenMpi, but there is no reason why it shouldn't work. Is "orte" the the PE that you use when you run SGE scripts from the command-line? If so, you should use that value. Also make sure that the mpi.run property is set correctly to run MPI programs correctly. > This cluster is primarily being used for BLAST, I would appreciate > if your could advise me on the config.xml file for blast. If you don't need advanced features such as automatic interface generation, I would start with the configs/date_config.xml and modify the "binaryLocation" and "parallel" values. If you want to try automatic interface generation, you could look at configs/ pdb2pqr_config.xml for an example. Hope that helps, Sriram |
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From: Luca C. <luc...@gm...> - 2009-12-01 21:31:14
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If you didn't change the configuration of the DB and if you are running the latest version you should fine a directory inside your tomcat called: webapps/opal2/WEB-INF/data/ or just data/ inside there there are a bunch of text file with the database info. Although I strongly recommend you to use an external data base (see opal doc) and to interface with that howevery you prefer (if you use postgress there are tons of libraries to query it). Sincerely, Luca On Tue, Dec 1, 2009 at 8:37 PM, Malcolm Tobias <mt...@wu...> wrote: > > Luca, > > I wasn't aware of this database, but it sounds like just what I need. > Is this stored on the server somewhere? Is it a flat file, or can you provide > me with some pointers on how I'd go about extracting fields? > > Cheers, > Malcolm > > On Tuesday 01 December 2009 01:25:58 pm Luca Clementi wrote: >> Malcom, >> you can look into Opal database and in the job_info table you have >> both the base_url field where you can get the output directory (in the >> form of http://blabla/app123451523) and then there is the field handle >> that if I'm not wrong it should contain the SGE JobID if you are using >> DRMAA. >> >> Sincerely, >> Luca >> >> On Tue, Dec 1, 2009 at 8:01 PM, Malcolm Tobias <mt...@wu...> wrote: >> > I'd like to be able collect some statistics for the jobs running on our >> > Opal server (e.g. run time, memory usage, some info about the input >> > parameters) and am wondering about the best way to go about this. One >> > important detail is that I'm using the DRMAA Job Manager. It seems like >> > there are multiple approaches, but I'm thinking the cleanest approach >> > might be to parse the temporary directories (where I'd have direct access >> > to the input files), but I'm not sure how to correlate the Opal job >> > number (app1259160756494) with the job number that the queuing system >> > associates with the job. If I had this latter info, I could query the >> > queuing system to find the run time and memory usage. I noticed that >> > this information does show up in the Tomcat logs, but it never shows up >> > at the same time as the Opal job number: >> > >> > 2009-11-25 08:52:36,501 DEBUG >> > edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java >> >:210) - Working >> > directory: >> > /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT/app1259160756494/ >> > ... >> > 2009-11-25 08:52:36,545 INFO >> > edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java >> >:233) - DRMAA job has been submitted with id 4549 >> > >> > I could assume that the line after the launchJob message contains the >> > queuing system job id, but I can imagine this getting screwed up if >> > multiple jobs are running at the same time which is entirely possible. >> > >> > Can anyone recommend a better solution? >> > >> > Would it be possible to include the queuing system job id into the >> > temporary directory somehow (say in a file called jobid)? >> > >> > Thanks in advance, >> > Malcolm >> > >> > >> > >> > -- >> > Malcolm Tobias >> > 314.362.1594 >> > >> > >> > ------------------------------------------------------------------------- >> >----- Join us December 9, 2009 for the Red Hat Virtual Experience, >> > a free event focused on virtualization and cloud computing. >> > Attend in-depth sessions from your desk. Your couch. Anywhere. >> > http://p.sf.net/sfu/redhat-sfdev2dev >> > _______________________________________________ >> > Opaltoolkit-users mailing list >> > Opa...@li... >> > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users > > > > -- > Malcolm Tobias > 314.362.1594 > > |
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From: Malcolm T. <mt...@wu...> - 2009-12-01 19:37:57
|
Luca, I wasn't aware of this database, but it sounds like just what I need. Is this stored on the server somewhere? Is it a flat file, or can you provide me with some pointers on how I'd go about extracting fields? Cheers, Malcolm On Tuesday 01 December 2009 01:25:58 pm Luca Clementi wrote: > Malcom, > you can look into Opal database and in the job_info table you have > both the base_url field where you can get the output directory (in the > form of http://blabla/app123451523) and then there is the field handle > that if I'm not wrong it should contain the SGE JobID if you are using > DRMAA. > > Sincerely, > Luca > > On Tue, Dec 1, 2009 at 8:01 PM, Malcolm Tobias <mt...@wu...> wrote: > > I'd like to be able collect some statistics for the jobs running on our > > Opal server (e.g. run time, memory usage, some info about the input > > parameters) and am wondering about the best way to go about this. One > > important detail is that I'm using the DRMAA Job Manager. It seems like > > there are multiple approaches, but I'm thinking the cleanest approach > > might be to parse the temporary directories (where I'd have direct access > > to the input files), but I'm not sure how to correlate the Opal job > > number (app1259160756494) with the job number that the queuing system > > associates with the job. If I had this latter info, I could query the > > queuing system to find the run time and memory usage. I noticed that > > this information does show up in the Tomcat logs, but it never shows up > > at the same time as the Opal job number: > > > > 2009-11-25 08:52:36,501 DEBUG > > edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java > >:210) - Working > > directory: > > /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT/app1259160756494/ > > ... > > 2009-11-25 08:52:36,545 INFO > > edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java > >:233) - DRMAA job has been submitted with id 4549 > > > > I could assume that the line after the launchJob message contains the > > queuing system job id, but I can imagine this getting screwed up if > > multiple jobs are running at the same time which is entirely possible. > > > > Can anyone recommend a better solution? > > > > Would it be possible to include the queuing system job id into the > > temporary directory somehow (say in a file called jobid)? > > > > Thanks in advance, > > Malcolm > > > > > > > > -- > > Malcolm Tobias > > 314.362.1594 > > > > > > ------------------------------------------------------------------------- > >----- Join us December 9, 2009 for the Red Hat Virtual Experience, > > a free event focused on virtualization and cloud computing. > > Attend in-depth sessions from your desk. Your couch. Anywhere. > > http://p.sf.net/sfu/redhat-sfdev2dev > > _______________________________________________ > > Opaltoolkit-users mailing list > > Opa...@li... > > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users -- Malcolm Tobias 314.362.1594 |
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From: Luca C. <luc...@gm...> - 2009-12-01 19:26:06
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Malcom, you can look into Opal database and in the job_info table you have both the base_url field where you can get the output directory (in the form of http://blabla/app123451523) and then there is the field handle that if I'm not wrong it should contain the SGE JobID if you are using DRMAA. Sincerely, Luca On Tue, Dec 1, 2009 at 8:01 PM, Malcolm Tobias <mt...@wu...> wrote: > > I'd like to be able collect some statistics for the jobs running on our Opal > server (e.g. run time, memory usage, some info about the input parameters) > and am wondering about the best way to go about this. One important detail > is that I'm using the DRMAA Job Manager. It seems like there are multiple > approaches, but I'm thinking the cleanest approach might be to parse the > temporary directories (where I'd have direct access to the input files), but > I'm not sure how to correlate the Opal job number (app1259160756494) with the > job number that the queuing system associates with the job. If I had this > latter info, I could query the queuing system to find the run time and memory > usage. I noticed that this information does show up in the Tomcat logs, but > it never shows up at the same time as the Opal job number: > > 2009-11-25 08:52:36,501 DEBUG > edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java:210) - > Working > directory: /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT/app1259160756494/ > ... > 2009-11-25 08:52:36,545 INFO > edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java:233) - > DRMAA job has been submitted with id 4549 > > I could assume that the line after the launchJob message contains the queuing > system job id, but I can imagine this getting screwed up if multiple jobs are > running at the same time which is entirely possible. > > Can anyone recommend a better solution? > > Would it be possible to include the queuing system job id into the temporary > directory somehow (say in a file called jobid)? > > Thanks in advance, > Malcolm > > > > -- > Malcolm Tobias > 314.362.1594 > > > ------------------------------------------------------------------------------ > Join us December 9, 2009 for the Red Hat Virtual Experience, > a free event focused on virtualization and cloud computing. > Attend in-depth sessions from your desk. Your couch. Anywhere. > http://p.sf.net/sfu/redhat-sfdev2dev > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users > |
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From: Malcolm T. <mt...@wu...> - 2009-12-01 19:24:06
|
Wilfred, On Tuesday 01 December 2009 01:16:44 pm Wilfred Li wrote: > It's probably most portable if you have your application report such > statistics as one of the outputs in the Opal Job output directory. I thought about that, but we're supporting multiple applications, and even if they could all be convinced to add the output, there's no guarantee that they would report things in a consistent way (i.e. max. physical vs. virtual memory), nor is there any guarantee that the output wouldn't change at some point in the future. Finally, there are occasional 'run away' jobs that have to be killed so would never report their usage even thought they had consumed resources. Since the queuing system already has access to all this information I'd like to find a way to leverage it (assuming it's easy enough to do). Thanks for the response. Malcolm -- Malcolm Tobias 314.362.1594 |
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From: Wilfred Li <wi...@sd...> - 2009-12-01 19:17:01
|
Hi, Malcom It's probably most portable if you have your application report such statistics as one of the outputs in the Opal Job output directory. Best regards, Wilfred Sent from my FUZE™ -----Original Message----- From: Malcolm Tobias <mt...@wu...> Sent: 2009年12月1日 上午 11:02 To: Opa...@li... <Opa...@li...> Subject: [Opaltoolkit-users] collecting statistics of Opal jobs I'd like to be able collect some statistics for the jobs running on our Opal server (e.g. run time, memory usage, some info about the input parameters) and am wondering about the best way to go about this. One important detail is that I'm using the DRMAA Job Manager. It seems like there are multiple approaches, but I'm thinking the cleanest approach might be to parse the temporary directories (where I'd have direct access to the input files), but I'm not sure how to correlate the Opal job number (app1259160756494) with the job number that the queuing system associates with the job. If I had this latter info, I could query the queuing system to find the run time and memory usage. I noticed that this information does show up in the Tomcat logs, but it never shows up at the same time as the Opal job number: 2009-11-25 08:52:36,501 DEBUG edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java:210) - Working directory: /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT/app1259160756494/ ... 2009-11-25 08:52:36,545 INFO edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java:233) - DRMAA job has been submitted with id 4549 I could assume that the line after the launchJob message contains the queuing system job id, but I can imagine this getting screwed up if multiple jobs are running at the same time which is entirely possible. Can anyone recommend a better solution? Would it be possible to include the queuing system job id into the temporary directory somehow (say in a file called jobid)? Thanks in advance, Malcolm -- Malcolm Tobias 314.362.1594 ------------------------------------------------------------------------------ Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev _______________________________________________ Opaltoolkit-users mailing list Opa...@li... https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
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From: Malcolm T. <mt...@wu...> - 2009-12-01 19:02:05
|
I'd like to be able collect some statistics for the jobs running on our Opal server (e.g. run time, memory usage, some info about the input parameters) and am wondering about the best way to go about this. One important detail is that I'm using the DRMAA Job Manager. It seems like there are multiple approaches, but I'm thinking the cleanest approach might be to parse the temporary directories (where I'd have direct access to the input files), but I'm not sure how to correlate the Opal job number (app1259160756494) with the job number that the queuing system associates with the job. If I had this latter info, I could query the queuing system to find the run time and memory usage. I noticed that this information does show up in the Tomcat logs, but it never shows up at the same time as the Opal job number: 2009-11-25 08:52:36,501 DEBUG edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java:210) - Working directory: /export/home/opal/jakarta-tomcat-5.0.30/webapps/ROOT/app1259160756494/ ... 2009-11-25 08:52:36,545 INFO edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java:233) - DRMAA job has been submitted with id 4549 I could assume that the line after the launchJob message contains the queuing system job id, but I can imagine this getting screwed up if multiple jobs are running at the same time which is entirely possible. Can anyone recommend a better solution? Would it be possible to include the queuing system job id into the temporary directory somehow (say in a file called jobid)? Thanks in advance, Malcolm -- Malcolm Tobias 314.362.1594 |
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From: Sriram K. <sr...@sd...> - 2009-11-17 18:05:02
|
Hi all, The Opal team will be at the NBCR booth at the Supercomputing Conference in Portland, OR. Please feel free to stop by booth number 1838 if you are attending. We are planning on doing some demos/ presentation - but most importantly, would love to interact with our users in person. Thanks, Sriram |
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From: Sriram K. <sr...@sd...> - 2009-11-04 16:36:33
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Hi Malcolm, The hard limit is being set programmatically via DRMAA. However, as the note says, only some schedulers support it. We have also noticed that SGE simply ignores this - which is consistent with what you have seen. As a solution, you might want to write a cron script that looks at the hard limit and purges jobs from the queue if it is old. Thanks, Sriram On Nov 4, 2009, at 7:27 AM, Malcolm Tobias wrote: > > I'm running Opal 2.0 and using the DRMAAJobManager to interface with > Sun Grid > Engine (SGE). I've got the opal.hard_limit set to 3600s: > > # specify in seconds the hard limit for how long a job can run > # only applicable if either DRMAA or Globus is being used, and if > # the scheduler supports it > opal.hard_limit=3600 > > but occasionally encounter 'run away' jobs that are never killed: > > [mtobias@sccne ~]$ qstat -u opal > job-ID prior name user state submit/start at > queue > slots ja-task-ID > ----------------------------------------------------------------------------------------------------------------- > 3058 0.55500 pdb2pqr.py opal r 11/02/2009 14:34:19 > all.q@compute-0-10.local 1 > > I've tried looking in the $TOMCAT/webapps/ROOT directory where the > job data is > stored, but I don't see any file that looks like a batch script to > examine to > see if it's limiting the CPU time limit. > > I've also looked at the compute-node that the job is running on and > examined > the 'trace' file which appears to be where SGE is setting up the > job. It > seems like it's setting some ridiculous limits: > > 11/02/2009 14:34:19 [400:22267]: setting limits > 11/02/2009 14:34:19 [400:22267]: RLIMIT_CPU setting: (soft > 18446744073709551615 > hard 18446744073709551615) resulting: (soft 18446744073709551615 hard > 18446744073709551615) > > Any ideas on what might be going wrong or how to debug this further? > > Malcolm > > -- > Malcolm Tobias > 314.362.1594 > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
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From: Malcolm T. <mt...@wu...> - 2009-11-04 15:41:22
|
I'm running Opal 2.0 and using the DRMAAJobManager to interface with Sun Grid Engine (SGE). I've got the opal.hard_limit set to 3600s: # specify in seconds the hard limit for how long a job can run # only applicable if either DRMAA or Globus is being used, and if # the scheduler supports it opal.hard_limit=3600 but occasionally encounter 'run away' jobs that are never killed: [mtobias@sccne ~]$ qstat -u opal job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 3058 0.55500 pdb2pqr.py opal r 11/02/2009 14:34:19 all.q@compute-0-10.local 1 I've tried looking in the $TOMCAT/webapps/ROOT directory where the job data is stored, but I don't see any file that looks like a batch script to examine to see if it's limiting the CPU time limit. I've also looked at the compute-node that the job is running on and examined the 'trace' file which appears to be where SGE is setting up the job. It seems like it's setting some ridiculous limits: 11/02/2009 14:34:19 [400:22267]: setting limits 11/02/2009 14:34:19 [400:22267]: RLIMIT_CPU setting: (soft 18446744073709551615 hard 18446744073709551615) resulting: (soft 18446744073709551615 hard 18446744073709551615) Any ideas on what might be going wrong or how to debug this further? Malcolm -- Malcolm Tobias 314.362.1594 |
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From: Sriram K. <sr...@sd...> - 2009-10-08 21:33:03
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We are pleased to announce the release of version 2.1 of the Opal Toolkit. This release improves version 2.0 in the following ways: - Improved Ajax-based dashboard that enables searching applications by their metadata - Use of C3P0 for providing production-level connection pooling for state management, and addition of support for MySQL database back-end (contributed by Anthony Bretaudeau) - Addition of two new job managers - for Condor and the Community Scheduler Framework (CSF4) - Updated user guide consistent with all new features Bug fixes include removal of the hardcoding of opal URL in the dashboard code, and fixing of the default HSQL configuration to write data to within the opal2 webapp. Opal 2.1 can be downloaded from here: https://sourceforge.net/projects/opaltoolkit/files/ . Sincerely, Opal Team |
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From: Sriram K. <sr...@sd...> - 2009-09-18 14:09:53
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Hi Malcolm, The AppService is the generic interface on the server-side. To give you a more specific answer, we would need to know what language/client you are using. All Java documentation can be found here: http://www.nbcr.net/software/opal/docs/2.0/index.html , and all Python docs are here: http://www.nbcr.net/software/opal/docs/2.0/opal-py-index.html . Thanks, Sriram On Sep 18, 2009, at 9:40 AM, Malcolm Tobias wrote: > > Sriram, > > Thanks for the response. > > I'm not developing this interface myself, but from talking to the > developers I > take it we're currently using AppService. Can you point me to some > documentation for GenericServiceClient or some examples of it's use? > > Thanks again, > Malcolm > > > On Wednesday 16 September 2009 04:55:31 pm Sriram Krishnan wrote: >> Hi Malcom, >> >> The num.procs in the opal.properties is the maximum number of >> processors available on the system. You can set the number of >> processors on a per application basis from the command-line (or via a >> SOAP call), as long as it is less than the num.procs specified in the >> opal.properties. >> >> Are you using the GenericServiceClient to launch your parallel jobs? >> If so, use the "-n" parameter to set the number of processors. You >> can >> also set the number of processors via the dashboard. >> >> Let us know if that works. >> >> Cheers, >> Sriram >> >> On Sep 16, 2009, at 3:29 PM, Malcolm Tobias wrote: >>> I've got a working Opal server and I'm now trying to configure it to >>> run >>> parallel jobs. In my etc/opal.properties I have: >>> >>> # parallel parameters >>> num.procs=4 >>> mpi.run=/export/apps/openmpi-1.3.3/bin/mpirun >>> >>> I verified that these values did find their way into tomcat: >>> >>> jakarta-tomcat-5.0.30/webapps/opal2/WEB-INF/classes/opal.properties >>> >>> but when we attempt to run parallel jobs, the command that gets >>> generated is: >>> >>> 2009-09-16 15:19:32,613 DEBUG >>> edu >>> .sdsc >>> .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: >>> 171) - >>> CMD: /export/apps/openmpi-1.3.3/bin/mpirun -machinefile $TMPDIR/ >>> machines -np >>> 1 /export/apps/apbs_svn_20090915/bin/apbs 1ABF.in >>> >>> I know that it's picking up the <parallel>true</parallel> in the >>> service >>> configuration file since it's including the mpirun command, but why >>> isn't the >>> number of processors agreeing with 'num.procs'? >>> >>> Thanks for your help. >>> >>> Malcolm >>> >>> -- >>> Malcolm Tobias >>> 314.362.1594 >>> >>> >>> ------------------------------------------------------------------------- >>> ----- Come build with us! The BlackBerry® Developer Conference >>> in SF, >>> CA is the only developer event you need to attend this year. >>> Jumpstart >>> your >>> developing skills, take BlackBerry mobile applications to market and >>> stay >>> ahead of the curve. Join us from November 9-12, 2009. Register >>> now! >>> http://p.sf.net/sfu/devconf >>> _______________________________________________ >>> Opaltoolkit-users mailing list >>> Opa...@li... >>> https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users > > > > -- > Malcolm Tobias > 314.362.1594 |
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From: Malcolm T. <mt...@wu...> - 2009-09-18 14:06:52
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Sriram, Thanks for the response. I'm not developing this interface myself, but from talking to the developers I take it we're currently using AppService. Can you point me to some documentation for GenericServiceClient or some examples of it's use? Thanks again, Malcolm On Wednesday 16 September 2009 04:55:31 pm Sriram Krishnan wrote: > Hi Malcom, > > The num.procs in the opal.properties is the maximum number of > processors available on the system. You can set the number of > processors on a per application basis from the command-line (or via a > SOAP call), as long as it is less than the num.procs specified in the > opal.properties. > > Are you using the GenericServiceClient to launch your parallel jobs? > If so, use the "-n" parameter to set the number of processors. You can > also set the number of processors via the dashboard. > > Let us know if that works. > > Cheers, > Sriram > > On Sep 16, 2009, at 3:29 PM, Malcolm Tobias wrote: > > I've got a working Opal server and I'm now trying to configure it to > > run > > parallel jobs. In my etc/opal.properties I have: > > > > # parallel parameters > > num.procs=4 > > mpi.run=/export/apps/openmpi-1.3.3/bin/mpirun > > > > I verified that these values did find their way into tomcat: > > > > jakarta-tomcat-5.0.30/webapps/opal2/WEB-INF/classes/opal.properties > > > > but when we attempt to run parallel jobs, the command that gets > > generated is: > > > > 2009-09-16 15:19:32,613 DEBUG > > edu > > .sdsc > > .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: > > 171) - > > CMD: /export/apps/openmpi-1.3.3/bin/mpirun -machinefile $TMPDIR/ > > machines -np > > 1 /export/apps/apbs_svn_20090915/bin/apbs 1ABF.in > > > > I know that it's picking up the <parallel>true</parallel> in the > > service > > configuration file since it's including the mpirun command, but why > > isn't the > > number of processors agreeing with 'num.procs'? > > > > Thanks for your help. > > > > Malcolm > > > > -- > > Malcolm Tobias > > 314.362.1594 > > > > > > ------------------------------------------------------------------------- > >----- Come build with us! The BlackBerry® Developer Conference in SF, > > CA is the only developer event you need to attend this year. Jumpstart > > your > > developing skills, take BlackBerry mobile applications to market and > > stay > > ahead of the curve. Join us from November 9-12, 2009. Register > > now! > > http://p.sf.net/sfu/devconf > > _______________________________________________ > > Opaltoolkit-users mailing list > > Opa...@li... > > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users -- Malcolm Tobias 314.362.1594 |
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From: Sriram K. <sr...@sd...> - 2009-09-16 21:55:56
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Hi Malcom, The num.procs in the opal.properties is the maximum number of processors available on the system. You can set the number of processors on a per application basis from the command-line (or via a SOAP call), as long as it is less than the num.procs specified in the opal.properties. Are you using the GenericServiceClient to launch your parallel jobs? If so, use the "-n" parameter to set the number of processors. You can also set the number of processors via the dashboard. Let us know if that works. Cheers, Sriram On Sep 16, 2009, at 3:29 PM, Malcolm Tobias wrote: > > I've got a working Opal server and I'm now trying to configure it to > run > parallel jobs. In my etc/opal.properties I have: > > # parallel parameters > num.procs=4 > mpi.run=/export/apps/openmpi-1.3.3/bin/mpirun > > I verified that these values did find their way into tomcat: > > jakarta-tomcat-5.0.30/webapps/opal2/WEB-INF/classes/opal.properties > > but when we attempt to run parallel jobs, the command that gets > generated is: > > 2009-09-16 15:19:32,613 DEBUG > edu > .sdsc > .nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java: > 171) - > CMD: /export/apps/openmpi-1.3.3/bin/mpirun -machinefile $TMPDIR/ > machines -np > 1 /export/apps/apbs_svn_20090915/bin/apbs 1ABF.in > > I know that it's picking up the <parallel>true</parallel> in the > service > configuration file since it's including the mpirun command, but why > isn't the > number of processors agreeing with 'num.procs'? > > Thanks for your help. > > Malcolm > > -- > Malcolm Tobias > 314.362.1594 > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > _______________________________________________ > Opaltoolkit-users mailing list > Opa...@li... > https://lists.sourceforge.net/lists/listinfo/opaltoolkit-users |
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From: Malcolm T. <mt...@wu...> - 2009-09-16 20:29:58
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I've got a working Opal server and I'm now trying to configure it to run parallel jobs. In my etc/opal.properties I have: # parallel parameters num.procs=4 mpi.run=/export/apps/openmpi-1.3.3/bin/mpirun I verified that these values did find their way into tomcat: jakarta-tomcat-5.0.30/webapps/opal2/WEB-INF/classes/opal.properties but when we attempt to run parallel jobs, the command that gets generated is: 2009-09-16 15:19:32,613 DEBUG edu.sdsc.nbcr.opal.manager.DRMAAJobManager.launchJob(DRMAAJobManager.java:171) - CMD: /export/apps/openmpi-1.3.3/bin/mpirun -machinefile $TMPDIR/machines -np 1 /export/apps/apbs_svn_20090915/bin/apbs 1ABF.in I know that it's picking up the <parallel>true</parallel> in the service configuration file since it's including the mpirun command, but why isn't the number of processors agreeing with 'num.procs'? Thanks for your help. Malcolm -- Malcolm Tobias 314.362.1594 |
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From: Sriram K. <sr...@sd...> - 2009-09-14 22:47:48
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Hello Anthony, Thanks for your comments. Responses inline - > -First, I've found a bug in my "typed WSDL addon": on a freshly > installed opal2 with the addon, you cannot deploy any service. So I > attach a patched file to put in OpalSOAPRequestFilter package. > Briefly, the problem was that the file WEB-INF/server-config.wsdd > (which is used by the filter) doesn't exists when no service is > deployed. Thanks. I will take a look at this once we are done with Opal release 2.1. A release candidate should be available soon, and we are hoping for a 2.1 release before the end of the month. > -I see you've included c3p0 and mysql connector packages (which is > great!), but their are not the latest versions available (0.9.1.1 > instead of 0.9.1.2 for c3p0 and 5.1.0 instead of 5.1.8 for mysql). I > have no particular problem with these older versions but I was > wondering if there was a reason for that... No particular reason. I had c3p0 version 0.9.1.1 and mysql version 5.1.0 working for another project - so decided to use that. However, I upgraded to the latest versions in SVN like you suggested, and everything still works fine. > -Speaking about c3p0, I've seen you haven't included the > "c3p0.preferredTestQuery=SELECT 1;" property. Is this intended? It > can be defined in $OPAL_SOURCES/etc/hibernate-opal.cfg.xml using > "<property name="c3p0.preferredTestQuery">SELECT 1;</property>". > Looking at the doc, it seems like it makes testing database > availability faster. This was an oversight on my part. It is now checked into SVN, and the performance does seem to be slightly better on initial testing. > -There's also a new bug in svn: our servers are not running on the > 8080 port, so the dashboard has some problems with it (maybe you are > aware of it?). From what I have seen, there's at least one hard- > coded 8080 port in webapps/opal2/dashboard-jsp/serviceList.jsp on > line 51 (there may be the same bug in other files). Making this > configurable would be quite useful! I fixed this in SVN. Now the serviceList.jsp uses the OPAL_URL parameter in the web.xml. I will add some documentation on how to configure this in the very near future. > Apart from that, Opal2 is running smoothly and the new application > list is great! > > You told me you could give me commit access to svn: if you're still > ok with that, do I need to create a sourceforge account? Yes, please. Send me an email with your SourceForge account, and I can give you access. We should also talk about protocols, practices, etc for committing code. Cheers, Sriram |
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From: Luca C. <luc...@gm...> - 2009-09-13 22:35:18
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On Fri, Sep 11, 2009 at 2:22 AM, Anthony Bretaudeau <ant...@ir...> wrote: > Hi! > > -There's also a new bug in svn: our servers are not running on the 8080 > port, so the dashboard has some problems with it (maybe you are aware of > it?). From what I have seen, there's at least one hard-coded 8080 port in > webapps/opal2/dashboard-jsp/serviceList.jsp on line 51 (there may be the > same bug in other files). Making this configurable would be quite useful! > Hey, That's my bad. It is from my last modification I made for the new service list. The second part of the URL at line 51 should be fetched from the OpalUrl param in the web.xml. Now on this computer I don't have any development tools, when I get a new computer if still there I will take a look at it. Sincerely, Luca |
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From: Anthony B. <ant...@ir...> - 2009-09-11 09:22:14
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi!<br>
I've finally installed svn version of Opal2 on a test server and I have
a few comments/questions:<br>
<br>
-First, I've found a bug in my "typed WSDL addon": on a freshly
installed opal2 with the addon, you cannot deploy any service. So I
attach a patched file to put in OpalSOAPRequestFilter package. Briefly,
the problem was that the file WEB-INF/server-config.wsdd (which is used
by the filter) doesn't exists when no service is deployed.<br>
<br>
-I see you've included c3p0 and mysql connector packages (which is
great!), but their are not the latest versions available (0.9.1.1
instead of 0.9.1.2 for c3p0 and 5.1.0 instead of 5.1.8 for mysql). I
have no particular problem with these older versions but I was
wondering if there was a reason for that...<br>
-Speaking about c3p0, I've seen you haven't included the
"c3p0.preferredTestQuery=SELECT 1;" property. Is this intended? It can
be defined in $OPAL_SOURCES/etc/hibernate-opal.cfg.xml using
"<property name="c3p0.preferredTestQuery">SELECT
1;</property>". Looking at the doc, it seems like it makes
testing database availability faster.<br>
<br>
-There's also a new bug in svn: our servers are not running on the 8080
port, so the dashboard has some problems with it (maybe you are aware
of it?). From what I have seen, there's at least one hard-coded 8080
port in webapps/opal2/dashboard-jsp/serviceList.jsp on line 51 (there
may be the same bug in other files). Making this configurable would be
quite useful!<br>
<br>
Apart from that, Opal2 is running smoothly and the new application list
is great!<br>
<br>
You told me you could give me commit access to svn: if you're still ok
with that, do I need to create a sourceforge account?<br>
<br>
Cheers<br>
Anthony<br>
<br>
Sriram Krishnan wrote:
<blockquote cite="mid:0EA...@sd..."
type="cite">Hello Anthony,
<div><br>
</div>
<div>I have committed your changes into SVN, and also added
configuration and jars for c3p0 and mysql. I tested everything and it
seems to be working fine. Please check out the latest version from SVN
and let me know if there are any issues.</div>
<div><br>
</div>
<div>This will be part of the next Opal release that we are planning
for end of this month. Thanks again for your contribution!</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Sriram</div>
<div><br>
<div>
<div>On Sep 2, 2009, at 5:28 AM, Anthony Bretaudeau wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000"> Hi!<br>
After testing, I've managed to make job exec time visualization work
with the following code (replace line 389 with it in
src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java):<br>
<br>
}else if (dialect.equals("org.hibernate.dialect.MySQLDialect")){<br>
//this is MySQL<br>
query = "select jobInfo.start_time_date as date, " +<br>
//number of day <br>
" avg( ( last_update_date - start_time_date ) * 86400 +
" +<br>
//plus number of seconds (epoch returns seconds!)<br>
" ( time_to_sec(last_update_time) -
time_to_sec(start_time_time) )) as average " + queryTail;<br>
}<br>
<br>
Feel free to include this in next release if it can help other users.<br>
Thanks.<br>
Anthony<br>
<br>
Anthony Bretaudeau a écrit :
<blockquote cite="mid:4A9...@ir..." type="cite">
<pre wrap="">Oh yes, the exec time has a problem. I hadn't noticed that.
Is this the only SQL request using local SQL dialect? In this case,
something like "unix_timestamp( last_update_time - start_time_time ) as
average" should work for MySQL (copying the rest of the request from
PostgreSQL). If I have time, I'll try to test it.
Thanks
Anthony
Luca Clementi a écrit :
</pre>
<blockquote type="cite">
<pre wrap="">Anthony Bretaudeau wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi!
We've had a problem using MySQL database for storing opal2 jobs data
instead of the default HSQLDB.
It turned out it was a timeout problem which is quite well described
at the following address:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/">http://www.databasesandlife.com/automatic-reconnect-from-hibernate-to-mysql/</a>.
Briefly: mysql closes connection after an 8h timeout (which is quite
frequent for us, but not for servers where there is more activity).
We solved it by using c3p0 to manage database connection.
Here is what we have done to use it:
</pre>
</blockquote>
<pre wrap="">Anthony,
I expect the dashboard to have some problem visualizing the exec time
of your jobs.
Have a look at line 365:
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/tags/opal2-core-2.0.0/src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java?revision=381&view=markup">http://opaltoolkit.svn.sourceforge.net/viewvc/opaltoolkit/tags/opal2-core-2.0.0/src/edu/sdsc/nbcr/opal/dashboard/persistence/DBManager.java?revision=381&view=markup</a>
Unfortunately I could not find a way to make the query working using
Hibernate SQL and I had to use the local SQL dialect.
Given that I think we should start using some connection manager since
it is also recommended by the Hibernate guys.
Sincerely,
Luca
</pre>
<blockquote type="cite">
<pre wrap="">-Added c3p0 package in $opal_sources/lib/ and modified build.xml
consequently
-Created $opal_sources /etc/c3p0.properties and added "
c3p0.preferredTestQuery=SELECT 1; " in it.
-In build.xml, after <include name="OpalState.hbm.xml"/> added
<include name="c3p0.properties"/>
-In $OPAL_SOURCES/etc/hibernate-opal.cfg.xml, replaced:
<!-- JDBC connection pool (use the built-in) -->
<!--<property name="connection.pool_size">1</property>-->
By these lines:
<!-- JDBC connection pool (use c3p0) -->
<property name="c3p0.min_size">1</property>
<property name="c3p0.max_size">20</property>
<property name="c3p0.timeout">1800</property>
<property name="c3p0.max_statements">50</property>
<property name="c3p0.idle_test_period">1800</property>
<property
name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
Maybe it would be a good idea to include it in a future version of opal?
Bye!
</pre>
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