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Hello all, Using the set of schemas from Sho, SLIC has now been running on the batch system for a good 15 minutes without error so it looks like everything is working now. Thanks for your help, Kyle On Thu, Nov 7, 2013 at 2:29 PM, McCormick, Jeremy I. < [log in to unmask]> wrote: > Thanks for pointing that out Sho. > > The correct schemas are in the gdml2 CVS module and also in the web > location you listed. We should use those and not anything else. Sorry, it > is a bit different than what's provided by Geant4. In fact we use an > entirely different GDML code base than them, though the data format is > (mostly) the same. > > I didn't want to package them with LCDD because they would then be > duplicated between the two CVS modules. > > --Jeremy > > -----Original Message----- > From: Sho Uemura [mailto:[log in to unmask]] > Sent: Thursday, November 07, 2013 11:22 AM > To: McCormick, Jeremy I. > Cc: Kyle McCarty; hps-software > Subject: RE: Running SLIC Locally > > Looks like it. So the schemas at http://www.lcsim.org/schemas/gdml/1.0/ > are what we need to use - the schemas that come with Geant4 and the > schemas available at http://gdml.web.cern.ch/GDML/gdmlschema.html are no > good. I've updated Confluence. > > It would be a lot simpler if the LCDD package came with the correct > version of the GDML schemas. They're different, so it's not duplication, > right? > > On Thu, 7 Nov 2013, McCormick, Jeremy I. wrote: > > > I believe that's due to using an old version of the GDML schema. > > > > -----Original Message----- > > From: Kyle McCarty [mailto:[log in to unmask]] > > Sent: Thursday, November 07, 2013 10:20 AM > > To: McCormick, Jeremy I. > > Cc: hps-software > > Subject: Re: Running SLIC Locally > > > > Hello hps-software, > > > > > > SLIC is indeed running now, but I did get a new error that I have not > seen before. I have included it below: > > > > > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1206 column: 56 no declaration found for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1206 column: 56 attribute 'type' is not declared for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1206 column: 56 attribute 'unit' is not declared for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1206 column: 56 attribute 'value' is not declared for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1209 column: 18 element 'NIL' is not allowed for content model > '((property+),(RL|RLref),(AL|ALref),(T|Tref),(P|Pref),(MEE|MEEref),(D|Dref),(atom|composite+|fraction+))' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1215 column: 56 no declaration found for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1215 column: 56 attribute 'type' is not declared for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1215 column: 56 attribute 'unit' is not declared for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1215 column: 56 attribute 'value' is not declared for element 'NIL' > > error: systemId: > /net/data/taro/kylem/hps-software/hps-detectors/detectors/HPS-Proposal2014-v4-6pt6/HPS-Proposal2014-v4-6pt6.lcdd > line: 1218 column: 18 element 'NIL' is not allowed for content model > '((property+),(RL|RLref),(AL|ALref),(T|Tref),(P|Pref),(MEE|MEEref),(D|Dref),(atom|composite+|fraction+))' > > =>> PBS: job killed: walltime 334 exceeded limit 300 > > > > > > All of the errors seem to be related to the use of 'NIL' within the LCDD > file. Any ideas as to the cause? If it helps, this error did not occur > immediately - it took around 600 events or so beforehand. > > > > > > Thanks, and sorry for all the errors! > > > > > > - Kyle > > > > > > > > On Thu, Nov 7, 2013 at 12:32 PM, McCormick, Jeremy I. < > [log in to unmask]> wrote: > > > > > > Hi, > > > > I believe the issue here was that I removed the GDML schemas from > the LCDD package, as they were duplicated from GDML. Consequently, at > runtime it would only find the LCDD xsd files and not the GDML ones unless > you had manually copied them. The init_ilcsoft.sh script actually sets the > GDML_SCHEMA_DIR to the LCDD base area, so if you had them installed > elsewhere it is possible your configuration was being overridden by this > setting. > > > > Probably the best solution would be having ilcinstall do the > schema installation for both LCDD and GDML automatically. I'm not sure > that the XML parser at this point has the capability to use multiple search > directories or at least right now the only interface to it is the > GDML_SCHEMA_DIR directory. It would be possible to add a macro command > that would allow multiple search directories. > > > > > > -Jeremy > > > > On Nov 7, 2013, at 9:14 AM, Kyle McCarty <[log in to unmask]> > wrote: > > > > > > Hello all, > > > > > > Okay, I reinstalled SLIC and am now using version 3.1.4 > and GEANT4 version 9.6.1. When running the first time, I got the same error > and found that this version of SLIC does not actually have the lcdd XSD > files locally. I downloaded them, and placed them in the GDML_SCHEMA_DIR > directory and now it seems to be working. So, it seems to run SLIC locally > using the current direction set, it is important to have the newest version > of SLIC (apparently as far back as 3.1.1 is having trouble somewhere) and > it seems that it is necessary to download the lcdd XSD files from > http://www.lcsim.org/schemas/lcdd/1.0/ and put them in the same directory. > > > > > > With that done, it now seems to be working. I'll have to > wait until it finishes to see if it worked properly, but it is running and > making SLCIO files. > > > > Thanks for your assistance, > > > > > > Kyle > > > > > > > > On Thu, Nov 7, 2013 at 10:57 AM, Kyle McCarty < > [log in to unmask]> wrote: > > > > > > Hello all, > > > > > > Still the same issue. Using the same echo and > > ls commands as before, I now get as output > > > > > /net/home/mccaky/hps/SimDist/v00-00/geant4/9.6.p01/source/persistency/gdml/schema/ > > CVS > > > > gdml_core.xsd > > gdml_define.xsd > > gdml_extensions.xsd > > gdml_materials.xsd > > gdml_parameterised.xsd > > gdml_replicas.xsd > > gdml_solids.xsd > > gdml.xsd > > > > lcdd_display.xsd > > lcdd_fields.xsd > > lcdd_header.xsd > > lcdd_iddict.xsd > > lcdd_limits.xsd > > lcdd_regions.xsd > > lcdd_sensitive_detectors.xsd > > lcdd.xsd > > > > > > So it is definitely finding the directory and it > has all the XSD files, including the one it is trying to get. It still > complains that it is "unable to connect socket for URL ' > http://www.lcsim.org/schemas/lcdd/1.0/lcdd.xsd'" though. I am going to > try and install SLIC again to make sure that I have the newest version and > that this isn't due to a change between versions. I will let you know when > I have done so and tested it. > > > > Thanks, > > > > Kyle > > > > > > > > On Thu, Nov 7, 2013 at 10:48 AM, Maurik Holtrop < > [log in to unmask]> wrote: > > > > > > Hello Kyle and experts, > > > > The files that Kyle is showing in his > directory do not seem to have one that defines the LCDD schema. Would this > problem be resolved if he copied lcdd.xsd into his directory? > > > > Best, > > Maurik > > > > > > On Nov 7, 2013, at 10:33 AM, Kyle McCarty > <[log in to unmask]> wrote: > > > > > > Hello all, > > > > > > It still seems to be having > trouble. I had the scripts I am passing to the batch system perform the > following commands as a diagnostic: > > > > echo $GDML_SCHEMA_DIR > > ls $GDML_SCHEMA_DIR > > > > > > It gives as output > > > > > /net/home/mccaky/hps/SimDist/v00-00/geant4/9.6.p01/source/persistency/gdml/schema/ > > gdml_core.xsd > > gdml_define.xsd > > gdml_extensions.xsd > > gdml_materials.xsd > > gdml_parameterised.xsd > > gdml_replicas.xsd > > gdml_solids.xsd > > gdml.xsd > > > > > > It is definitely recognizing the > correct path and the schemas from the link Sho provided are all there. > However it gives the error: > > > > unable to connect socket for URL ' > http://www.lcsim.org/schemas/lcdd/1.0/lcdd.xsd' > > > > > > It seems to need a schema that is > neither in the directory nor in the link Sho provided. Note that this > schema does exist, but in the directory > "v00-00/lcdd/v03-02-00_pre1/schemas/lcdd/1.0/". Also, just to check that > this is not the issue, do I have an old version of SLIC that and the schema > setup has changed? I am using SLIC version 3.1.1 and GEANT4 version 9.6.1. > > > > > > Thanks, > > > > Kyle > > > > > > > > On Thu, Nov 7, 2013 at 12:46 AM, > Graf, Norman A. <[log in to unmask]> wrote: > > > > > > Thanks Sho. > > Kyle, can you let us know > whether this resolves your batch > > issue? > > > > Norman > > > > > ________________________________________ > > From: Sho Uemura > > [[log in to unmask]] > > > > Sent: Wednesday, November > 06, 2013 9:39 PM > > To: Graf, Norman A. > > Cc: McCormick, Jeremy I.; > Kyle McCarty; hps-software > > Subject: RE: Running > > SLIC Locally > > > > > > Done. I noticed the GDML > schemas are already part of the ilcinstall tree, > > so it's actually a > one-liner assuming you're using ilcinstall, but I kept > > the existing instructions > and you can decide whether to keep them: > > > > > > https://confluence.slac.stanford.edu/display/ilc/How+can+I+make+SLIC+l > > ook+for+XML+schemas+in+a+local+directory > > > > On Wed, 6 Nov 2013, Graf, > Norman A. wrote: > > > > > Hello Sho, > > > Thanks for looking into > this. Feel free to update the > > > confluence page. > > > Norman > > > > > > > ________________________________________ > > > From: Sho Uemura [ > [log in to unmask]] > > > Sent: Wednesday, > November 06, 2013 6:46 PM > > > To: McCormick, Jeremy I. > > > Cc: Kyle McCarty; Graf, > Norman A.; hps-software > > > Subject: Re: Running > SLIC Locally > > > > > > The Confluence > instructions seem to be out of date: ilcinstall pulls in > > > and installs the LCDD > schemas locally, so there's no need to download > > > those, but you do need > to download the GDML schemas (I imagine it would > > > make sense for > ilcinstall to do this as well, but it doesn't seem to). > > > > > > So download all the > .xsd files under > > > > http://www.lcsim.org/schemas/gdml/1.0/ into a local directory, then set > > > GDML_SCHEMA_DIR to > point to this directory. This is all I need to do to > > > get slic running behind > the JLab firewall. > > > > > > On Tue, 5 Nov 2013, > McCormick, Jeremy I. wrote: > > > > > >> Alright I will double > check that it is still working in my local copy... > > >> > > >> On Nov 5, 2013, at > 11:16 AM, "Kyle McCarty" <[log in to unmask]<mailto:[log in to unmask]>> > wrote: > > >> > > >> Hello Jeremy, > > >> > > >> Running the command " > find /net/data/taro/kylem/schema/ -name "*.xsd" " gives > > >> > > >> > /net/data/taro/kylem/schema/lcdd_iddict.xsd > > >> > /net/data/taro/kylem/schema/lcdd_fields.xsd > > >> > /net/data/taro/kylem/schema/lcdd_limits.xsd > > >> > /net/data/taro/kylem/schema/lcdd_display.xsd > > >> > /net/data/taro/kylem/schema/lcdd_sensitive_detectors.xsd > > >> > /net/data/taro/kylem/schema/lcdd.xsd > > >> > /net/data/taro/kylem/schema/lcdd_header.xsd > > >> > /net/data/taro/kylem/schema/lcdd_regions.xsd > > >> > > >> I believe that batch > system can access the folder. It writes the output log files (like the ones > I sent previously) to the same driver (though a different folder), so it > does seem to be able to read/write to said drive. Also, the schema folder > has read/execute permissions for all user groups, so there shouldn't be any > permission issues. The schema files themselves only had read access for all > user groups. I gave execute access to all user groups for these as well, > but this does not stop the errors. I'm fairly certain that the batch system > is running the processes as me anyway, though, since it can write to an > output folder which only I have write access for. > > >> > > >> - Kyle > > >> > > >> > > >> On Tue, Nov 5, 2013 at > 1:31 PM, McCormick, Jeremy I. <[log in to unmask]<mailto: > [log in to unmask]>> wrote: > > >> Hi, Kyle. > > >> > > >> Sorry you?re having > troubles with this... > > >> > > >> Can you execute this > command to show the contents of your schema dir? > > >> > > >> find > /net/data/taro/kylem/schema/ -name ?*.xsd? > > >> > > >> Please paste that > command output into an email back to us. > > >> > > >> Stupid question: Is > that directory accessible to the batch system? > > >> > > >> Thanks. > > >> > > >> On Nov 5, 2013, at > 8:50 AM, Kyle McCarty <[log in to unmask]<mailto:[log in to unmask]>> wrote: > > >> > > >> Hello Norman, > > >> > > >> The batch system we > use is OpenPBS and works by submitting a shell script to the batch system, > which then distributes the process to a node. I have attached a sample > script that gets passed to the batch system as well as the stdout and > stderr that came from running it. The variable GDML_SCHEMA_DIR correctly > resolves as "/net/data/taro/kylem/schema/" which contains all of the XSD > files. > > >> > > >> Thanks, > > >> > > >> Kyle > > >> > > >> > > >> On Mon, Nov 4, 2013 at > 1:45 PM, Graf, Norman A. <[log in to unmask]<mailto: > [log in to unmask]>> wrote: > > >> Hello Kyle, > > >> As far as I know this > should work. Can you provide more information > > >> on exactly how you are > running slic, where the schemas are located > > >> locally and whether > GDML_SCHEMA_DIR resolves correctly? > > >> Norman > > >> > > >> From: Kyle McCarty > [mailto:[log in to unmask]<mailto:[log in to unmask]>] > > >> Sent: Monday, November > 04, 2013 9:10 AM > > >> To: Graf, Norman A. > > >> Cc: hps-software > > >> Subject: Re: Running > SLIC Locally > > >> > > >> Hello Norman, > > >> I tried your > suggestion and I am still getting a similar problem. It now gives the error: > > >> > > >> fatal error: > systemId: line: 0 column: 0 > > >> unable to connect > socket for URL 'http://www.lcsim.org/schemas/gdml/1.0/gdml.xsd' > > >> fatal error: > systemId: file:///net/home/mccaky/data/schema//lcdd.xsd line: 18 column: 80 > > >> fatal error during > schema scan > > >> > > >> -------- EEEE ------- > G4Exception-START -------- EEEE ------- > > >> *** G4Exception : > > >> issued by : > > >> Failed to get the > world volume. > > >> *** Fatal Exception > *** core dump *** > > >> -------- EEEE -------- > G4Exception-END --------- EEEE ------- > > >> > > >> > > >> *** G4Exception: > Aborting execution *** > > >> The file "lcdd.xsd" > does exist at the indicated directory, so it seems that SLIC is having > trouble finding it there, for some reason. > > >> - Kyle > > >> > > >> On Mon, Nov 4, 2013 at > 11:53 AM, Graf, Norman A. <[log in to unmask]<mailto: > [log in to unmask]>> wrote: > > >> Good Morning Kyle, > > >> Have you tried the > following? > > >> > > >> > https://confluence.slac.stanford.edu/display/ilc/How+can+I+make+SLIC+look+for+XML+schemas+in+a+local+directory > > >> > > >> Norman > > >> > > >> From: > [log in to unmask]<mailto:[log in to unmask]> > [mailto:[log in to unmask]<mailto: > [log in to unmask]>] On Behalf Of Kyle McCarty > > >> Sent: Monday, November > 04, 2013 8:51 AM > > >> To: hps-software > > >> Subject: Running SLIC > Locally > > >> > > >> Hello hps-software, > > >> I am attempting to run > SLIC on a computing cluster, but am running into trouble. The individual > nodes in the cluster do not have access to the internet, and this renders > SLIC unable to access a file " > http://www.lcsim.org/schemas/lcdd/1.0/lcdd.xsd" and subsequently > terminate. Is there a means by which I can get SLIC to not require an > internet connection to run? > > >> Thanks, > > >> > > >> Kyle > > >> > > >> > ________________________________ > > >> > > >> Use REPLY-ALL to reply > to list > > >> > > >> To unsubscribe from > the HPS-SOFTWARE list, click the following link: > > >> > https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1 > > >> > > >> > > >> > > >> > ________________________________ > > >> > > >> Use REPLY-ALL to reply > to list > > >> > > >> To unsubscribe from > the HPS-SOFTWARE list, click the following link: > > >> > https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1 > > >> > > >> < > egs_0.0025x0_450na_100kb_1000.sh <http://egs_0.0025x0_450na_100kb_1000.sh/> > <http://egs_0.0025x0_450na_100kb_1000.sh < > http://egs_0.0025x0_450na_100kb_1000.sh/> > >><egs_0.0025x0_450na_100kb_1000.sh.e98608><egs_0.0025x0_450na_100kb_1000.sh.o98608> > > >> > > >> > > >> > > >> > ######################################################################## > > >> Use REPLY-ALL to reply > to list > > >> > > >> To unsubscribe from > the HPS-SOFTWARE list, click the following link: > > >> > https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1 > > >> > > > > ######################################################################## > > > Use REPLY-ALL to reply > to list > > > > > > To unsubscribe from the > HPS-SOFTWARE list, click the following link: > > > > https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1 > > > > > > > > > > > ________________________________ > > > > Use REPLY-ALL to reply to list > > > > To unsubscribe from the > HPS-SOFTWARE list, click the following link: > > > > https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1 > > > > ###################################################################### > > ## > > Use REPLY-ALL to reply to list > > > > To unsubscribe from the HPS-SOFTWARE list, click the following link: > > https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1 > > > > ######################################################################## > Use REPLY-ALL to reply to list > > To unsubscribe from the HPS-SOFTWARE list, click the following link: > https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1 > ######################################################################## Use REPLY-ALL to reply to list To unsubscribe from the HPS-SOFTWARE list, click the following link: https://listserv.slac.stanford.edu/cgi-bin/wa?SUBED1=HPS-SOFTWARE&A=1