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HPS-SOFTWARE  November 2013

HPS-SOFTWARE November 2013

Subject:

Re: Running SLIC Locally

From:

Sho Uemura <[log in to unmask]>

Reply-To:

Software for the Heavy Photon Search Experiment <[log in to unmask]>

Date:

Thu, 7 Nov 2013 11:21:35 -0800

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (372 lines)

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+look+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
>                                                >>
>                                                >> ________________________________
>                                                >>
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>                                                >>
>                                                >>
>                                                >> ________________________________
>                                                >>
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