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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 07:48:23 -0800

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (271 lines)

Then copy the LCDD schemas and GDML schemas to the same directory and 
point to that. Odd, I thought it worked for me (latest ilcinstall from 
SVN).

On Thu, 7 Nov 2013, Kyle McCarty 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
>>>>
>>>> ________________________________
>>>>
>>>> Use REPLY-ALL to reply to list
>>>>
>>>> To unsubscribe from the HPS-SOFTWARE list, click the following link:
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>>>>
>>>>
>>>>
>>>> ________________________________
>>>>
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>>>> To unsubscribe from the HPS-SOFTWARE list, click the following link:
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>>>>
>>>> <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>
>>>>
>>>>
>>>>
>>>> ########################################################################
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>>>>
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>>
>
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