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Hi Daniela, Daniel, 

Thanks for your help in the matter, but I'm still experiencing issues with running simulations on GRID. The permissions issue isn't resolved yet. I'm still getting the following error message when I try to upload a file on UKI-LT2-QMUL2-disk. 

2021-10-06 22:18:18 UTC dirac-dms-add-file/DataManager/putAndRegister [140605462013760] DEBUG: Failed to put file to Storage Element. dummy1.txt: Permission denied ( 13 : Failed to copy file dummy1.txt to destination url srm://se03.esc.qmul.ac.uk:8444/srm/managerv2?SFN=/vo.moedal.org/vo.moedal.org/user/a/aditya.upreti/dummy1.txt: [13] [gfalt_copy_file][perform_copy][srm_plugin_filecopy][srm_do_transfer][gfalt_copy_file][perform_copy][perform_local_copy] Could not open destination: [streamed_copy][gfal_plugin_openG][gfal_gridftp_openG][gfal_gridftp_openG] globus_ftp_client: the server responded with an error 530 530-Login incorrect. : globus_gss_assist: Error invoking callout  530-globus_callout_module: The callout returned an error  530-an unknown error occurred  530 End.   )


2021-10-06 22:18:18 UTC dirac-dms-add-file [140605462013760] ERROR: Error: failed to upload /vo.moedal.org/user/a/aditya.upreti/dummy1.txt to UKI-LT2-QMUL2-disk


The job fails with the same permissions issue when I use the following code (DiracFile to get the output). I tried this approach as an alternative to submitting it via a JDL script as I described earlier. 

  j = Job()

  j.name = job_name

  j.application = Executable()

  j.application.exe = File(sh_run_ganga_name)

  j.application.args = []

  j.inputfiles = [LocalFile(cfg_path), LocalFile(cfg_ganga_pgun_name), LocalFile(input3Dpath+input3Dhist)]

  j.outputfiles =[DiracFile(outputfile)]

  j.backend = Dirac()

  j.submit()


('/vo.moedal.org/user/a/aditya.upreti/32164/32164451/MonopoleData_2_100_default_0.root','/scratch/condor/dir_11177/WcfLDmo4Uszn8FVDjqQVj3jqav4PzpABFKDm9FCSDmABFKDmtftwXo/DIRAC_YjF9xbpilot/32164451/MonopoleData_2_100_default_0.root','UKI-LT2-QMUL2-disk',guid='F11FBC28-DC8A-C4ED-2292-AF1995B2A826',catalog='[]', checksum = 'b8149d64')
dm.putAndRegister failed with message Failed to put file to Storage Element. Permission denied ( 13 : Failed to copy file

Then, I tried to get the output files locally using LocalFile instead of DiracFile, using the following lines of code

 j = Job()

 j.name = job_name

 j.application = Executable()

 j.application.exe = File(sh_run_ganga_name)

 j.application.args = []

 j.inputfiles = [LocalFile(cfg_path), LocalFile(cfg_ganga_pgun_name), LocalFile(input3Dpath+input3Dhist)]

 j.outputfiles =[LocalFile('/eos/experiment/moedal/aditya/GRID_outputs/test/'+outputfile)]

 j.backend = Dirac()

 j.submit()


and it gives me the following error message in std.out. The simulation stops and job fails halfway. 

UTC dirac-jobexec/Subprocess ERROR: Maximum output buffer length reached
2021-10-05 22:30:19 UTC dirac-jobexec/Script ERROR: System call execution failed:
Reached maximum allowed length (52428800 bytes) for called function return value for '['/scratch/condor/dir_7759/OGNNDmQ46rznOOVDjqUTj3jq6xrg1pABFKDm2f6LDmABFKDmuey6Zn/DIRAC__a2iHspilot/32155611/exe-script.py']' call
2021-10-05 22:30:19 UTC dirac-jobexec/Script ERROR: Non-zero status while executing /scratch/condor/dir_7759/OGNNDmQ46rznOOVDjqUTj3jq6xrg1pABFKDm2f6LDmABFKDmuey6Zn/DIRAC__a2iHspilot/32155611/exe-script.py exited with status 9

Please let me know if there's anything else I can provide to help us debug these errors. 

Best Regards

Aditya Upreti | Ph.D. Candidate / Research Assistant

Divider line

Department of Physics 

102 Gallalee Hall

Tuscaloosa, AL 35404 

Phone 205-886-2914

Divider line

The University of Alabama box A with stacked words logo


From: Daniela Bauer <daniela.bauer.grid@googlemail.com>
Sent: Monday, September 27, 2021 4:37 AM
To: Aditya Upreti <aupreti@crimson.ua.edu>
Cc: Daniel Traynor <d.traynor@qmul.ac.uk>; Simon Fayer <simon.fayer05@imperial.ac.uk>
Subject: Re: Issue regrading GRID
 
Hi Aditya,

I don't know Ganga, but in DIRAC there is the concept of an OutputSandbox: This is for small files, and you can retrieve them via dirac-wms-job-get-output. For the actual data, you should use the various data handling mechanism within DIRAC which will upload your data to an SE. There is some documentation here:
https://www.gridpp.ac.uk/wiki/DIRAC_Data_Handling_within_a_Job

Regards,
Daniela

On Mon, 27 Sept 2021 at 05:54, Aditya Upreti <aupreti@crimson.ua.edu> wrote:
Hi Daniela, 

Sorry for the late reply. 
Okay, I can try writing to RALPP. Do I have to mention RALPP in the OutputSandbox instead of UKI-LT2-QMUL2-disk?

Also, I am able to submit jobs via the Ganga interface using a python submit script and getting the output file locally using 
"j = Job()
j.outputfiles = [LocalFile(outputfile)]"

which outputs the file locally, but I'm not sure why I'm failing to do that with a JDL script directly, bypassing Ganga. (as with Ganga, I get some python dependency errors like 'no module named six'. etc, when submitting the jobs"). 

Best Regards

Aditya Upreti | Ph.D. Candidate / Research Assistant

Divider line

Department of Physics 

102 Gallalee Hall

Tuscaloosa, AL 35404 

Phone 205-886-2914

Divider line

The University of Alabama box A with stacked words logo



From: Daniela Bauer <daniela.bauer.grid@googlemail.com>
Sent: Thursday, September 23, 2021 4:20 AM
To: Daniel Traynor <d.traynor@qmul.ac.uk>
Cc: Aditya Upreti <aupreti@crimson.ua.edu>; Simon Fayer <simon.fayer05@imperial.ac.uk>
Subject: Re: Issue regrading GRID
 
@Aditya Upreti
: In the meantime, do you want to try and write to RALPP ? You should be able to copy the data later if needed.

Regards,
Daniela

On Wed, 22 Sept 2021 at 18:38, Daniel Traynor <d.traynor@qmul.ac.uk> wrote:
not yet.

* Dr Daniel Traynor, Grid cluster system manager
* Tel +44(0)20 7882 6560, Particle Physics,QMUL


________________________________________
From: Daniela Bauer <daniela.bauer.grid@googlemail.com>
Sent: 22 September 2021 18:33
To: Aditya Upreti
Cc: Daniel Traynor; Simon Fayer
Subject: Re: Issue regrading GRID

This is a question for Dan - we need to work out where the permission denied comes from.
@Dan: Any idea ?

Cheers,
Daniela


On Tue, 21 Sept 2021 at 21:59, Aditya Upreti <aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu>> wrote:
Hi all,

Any resolution on this issue?
Thanks!

Best Regards

Aditya Upreti | Ph.D. Candidate / Research Assistant

[Divider line]

Department of Physics

The University of Alabama<https://www.ua.edu/>

102 Gallalee Hall

Tuscaloosa, AL 35404

Phone 205-886-2914

aupreti@crimson.ua.edu

[Divider line]

[The University of Alabama box A with stacked words logo]<https://www.ua.edu/>

________________________________
From: Aditya Upreti <aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu>>
Sent: Monday, September 20, 2021 10:53 AM
To: Daniela Bauer <daniela.bauer.grid@googlemail.com<mailto:daniela.bauer.grid@googlemail.com>>
Cc: Daniel Traynor <d.traynor@qmul.ac.uk<mailto:d.traynor@qmul.ac.uk>>; Simon Fayer <simon.fayer05@imperial.ac.uk<mailto:simon.fayer05@imperial.ac.uk>>
Subject: Re: Issue regrading GRID

Hi Daniela,

I tried those commands and it still gives me the same error messages (attached).

Best Regards

Aditya Upreti | Ph.D. Candidate / Research Assistant

[Divider line]

Department of Physics

The University of Alabama<https://www.ua.edu/>

102 Gallalee Hall

Tuscaloosa, AL 35404

Phone 205-886-2914

aupreti@crimson.ua.edu

[Divider line]

[The University of Alabama box A with stacked words logo]<https://www.ua.edu/>

________________________________
From: Daniela Bauer <daniela.bauer.grid@googlemail.com<mailto:daniela.bauer.grid@googlemail.com>>
Sent: Monday, September 20, 2021 10:42 AM
To: Aditya Upreti <aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu>>
Cc: Daniel Traynor <d.traynor@qmul.ac.uk<mailto:d.traynor@qmul.ac.uk>>; Simon Fayer <simon.fayer05@imperial.ac.uk<mailto:simon.fayer05@imperial.ac.uk>>
Subject: Re: Issue regrading GRID

Hi Aditya,

This looks like a straight forward permissions error, so Dan needs to have a look to see why you wouldn't be allowed to access the disk.
Could you please run one last test ?
In a clean window (no ganga setup) can you please run:
export VOMS_USERCONF=/cvmfs/grid.cern.ch/etc/grid-security/vomses<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgrid.cern.ch%2Fetc%2Fgrid-security%2Fvomses&data=04%7C01%7Caupreti%40crimson.ua.edu%7C820b3cbda3094ab4ba6f08d97c4d4ce7%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677493735006265%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2B7w7RwLzWRK1VxCdBifcehs8C%2Fs2Yo93kgkyBZG0zAk%3D&reserved=0>
export X509_VOMSES=/cvmfs/grid.cern.ch/etc/grid-security/vomses<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgrid.cern.ch%2Fetc%2Fgrid-security%2Fvomses&data=04%7C01%7Caupreti%40crimson.ua.edu%7C820b3cbda3094ab4ba6f08d97c4d4ce7%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677493735016224%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=UAN1oqkRXIHRpucTITosJv6HoL2K2p4GUBtDNS6zPj0%3D&reserved=0>
source /cvmfs/dirac.egi.eu/dirac/bashrc_gridpp<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdirac.egi.eu%2Fdirac%2Fbashrc_gridpp&data=04%7C01%7Caupreti%40crimson.ua.edu%7C820b3cbda3094ab4ba6f08d97c4d4ce7%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677493735016224%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Zw9tTNin1Xb%2B8u0ymD8I8yadbMvyWfqcusi9nPLXQq4%3D&reserved=0>
dirac-proxy-init -g vo.moedal.org_user
and the copy command again (maybe with a slightly different file name to avoid any potential override conflicts).

The ganga DIRAC version is very old, and while I don't think it matters in this case, I want to make sure.

Regards,
Daniela

On Mon, 20 Sept 2021 at 16:20, Aditya Upreti <aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu>> wrote:
Hi Daniela,

I used the command dirac-dms-add-file and I'm still unable to upload a file.
Attached is the output in a text file.

Best Regards

Aditya Upreti | Ph.D. Candidate / Research Assistant

[Divider line]

Department of Physics

The University of Alabama<https://www.ua.edu/>

102 Gallalee Hall

Tuscaloosa, AL 35404

Phone 205-886-2914

aupreti@crimson.ua.edu

[Divider line]

[The University of Alabama box A with stacked words logo]<https://www.ua.edu/>

________________________________
From: Daniela Bauer <daniela.bauer.grid@googlemail.com<mailto:daniela.bauer.grid@googlemail.com>>
Sent: Monday, September 20, 2021 9:58 AM
To: Daniel Traynor <d.traynor@qmul.ac.uk<mailto:d.traynor@qmul.ac.uk>>
Cc: Aditya Upreti <aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu>>; Simon Fayer <simon.fayer05@imperial.ac.uk<mailto:simon.fayer05@imperial.ac.uk>>
Subject: Re: Issue regrading GRID

Hi Dan, Aditya,

@Aditya Upreti<mailto:aupreti@crimson.ua.edu> Could you please try to upload a file using:
dirac-proxy-info
dirac-dms-file-add -ddd  /vo.moedal.org/user/a/aditya.upreti/dummy1.txt<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvo.moedal.org%2Fuser%2Fa%2Faditya.upreti%2Fdummy1.txt&data=04%7C01%7Caupreti%40crimson.ua.edu%7C820b3cbda3094ab4ba6f08d97c4d4ce7%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677493735026179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=j4ZoYVGkSdrkjPtarCj20yFtIj3fjOXaG%2B1q56iaE30%3D&reserved=0> dummy.txt UKI-LT2-QMUL2-disk and email the output back ?
Just renewing your certificate should not make any difference.

@Dan: Can you see a permissions error for this user somewhere ?


Regards,
Daniela



On Mon, 20 Sept 2021 at 15:28, Daniel Traynor <d.traynor@qmul.ac.uk<mailto:d.traynor@qmul.ac.uk>> wrote:
We have user directories for moedal and i see attempts to writes the jobs output on disk there for several users e.g.

ls /mnt/lustre_3/storm_3/vo.moedal.org/vo.moedal.org/user/a/aditya.upreti/<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvo.moedal.org%2Fvo.moedal.org%2Fuser%2Fa%2Faditya.upreti%2F&data=04%7C01%7Caupreti%40crimson.ua.edu%7C820b3cbda3094ab4ba6f08d97c4d4ce7%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677493735026179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3hxegJTr14RK0ili3pKZWh3qmwE7%2BudrYf24aADsrEU%3D&reserved=0>
30272  30348  31778  31780  31781  31783  31784  31793  31798  31805  31829  31861  GRID  tmp

but recent directories are empty. The last successful wite was on the 13th July (directory 30348)

dan


* Dr Daniel Traynor, Grid cluster system manager
* Tel +44(0)20 7882 6560, Particle Physics,QMUL


________________________________________
From: Daniela Bauer <daniela.bauer.grid@googlemail.com<mailto:daniela.bauer.grid@googlemail.com>>
Sent: 20 September 2021 14:21
To: Aditya Upreti
Cc: Simon Fayer; Daniel Traynor
Subject: Re: Issue regrading GRID

Hi Aditya,

I'll try to disentangle this.
Looking at the JDL I can see on the server you seem to have your output files specified both in the OutputData and the OutputSandbox field.
Listing them in OutputData means DIRAC will try to write it to a storage element (SE), which you need to specify. I think you initially specified QMUL. I've cc'ed the QMUL admin to check if moedal users are meant to use this SE (@Dan: Should they ?). If yes, you'd need to debug with him to see why you can't write there.
If all you want to do is ship a couple of log files back, then just use OutputSandbox (but never in combination with OutputData), which you can retrieve with dirac-wms-job-get-output. Just be aware that output sandboxes are limited in size (< 10MB) and tend not to scale.
If you have any question wrt DIRAC, I would encourage you to use the DIRAC mailing list: gridpp-dirac-users@imperial.ac.uk<mailto:gridpp-dirac-users@imperial.ac.uk><mailto:gridpp-dirac-users@imperial.ac.uk<mailto:gridpp-dirac-users@imperial.ac.uk>>
as I am not always online and (as you will have seen), there can be quite a delay between you sending and me seeing this email.

Hope that helps,
Daiela

On Fri, 17 Sept 2021 at 17:53, Aditya Upreti <aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu><mailto:aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu>>> wrote:
​Hi Daniela,

Hope you are doing well.
I am getting the following error message after my simulation completes running on Grid.

Failed to upload output data file Encountered 1 errors
Could not putAndRegister file std.out with LFN /vo.moedal.org/user/a/aditya.upreti/31829/31829313/std.out<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvo.moedal.org%2Fuser%2Fa%2Faditya.upreti%2F31829%2F31829313%2Fstd.out&data=04%7C01%7Caupreti%40crimson.ua.edu%7C820b3cbda3094ab4ba6f08d97c4d4ce7%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677493735026179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=rB%2BUj5bFMRgprSiftesgzQgUVovZHQld5VzSRjUGr38%3D&reserved=0><http://vo.moedal.org/user/a/aditya.upreti/31829/31829313/std.out<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvo.moedal.org%2Fuser%2Fa%2Faditya.upreti%2F31829%2F31829313%2Fstd.out&data=04%7C01%7Caupreti%40crimson.ua.edu%7C820b3cbda3094ab4ba6f08d97c4d4ce7%7C2a00728ef0d040b4a4e8ce433f3fbca7%7C0%7C0%7C637677493735036136%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Y0tzOs96lKNi%2BxYZ6UFpFBkv02rxR8CKfscfQEIq%2BPE%3D&reserved=0>> to UKI-LT2-QMUL2-disk with GUID E7D2E680-3F6A-B9AB-6969-CF91C330F037 trying failover storage
No failover SEs defined for JobWrapper, cannot try to upload output file std.out anywhere else.
Failed to upload OutputData
JobWrapper failed to process output files
Traceback (most recent call last):
  File "/scratch/tmp/OD6MDmdLVlzn5Wq3smovVnomg01fWmABFKDmqGGKDmABFKDmTORfJm/DIRAC_ZJLEU2pilot/job/Wrapper/Wrapper_31829313", line 197, in execute
    raise JobWrapperError(result['Message'])
JobWrapperError: Failed to upload OutputData

The output sandbox only contains the std.out and std.err files and not the output root files. Would you be able to help me resolve this error? Please let me know if you need more information/input files.

Thank you!

Best Regards

Aditya Upreti | Ph.D. Candidate / Research Assistant

[Divider line]

Department of Physics

The University of Alabama<https://www.ua.edu/>

102 Gallalee Hall

Tuscaloosa, AL 35404

Phone 205-886-2914

aupreti@crimson.ua.edu<mailto:aupreti@crimson.ua.edu>

[Divider line]

[The University of Alabama box A with stacked words logo]<https://www.ua.edu/>



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Tel: Working from home, please use email.
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Tel: Working from home, please use email.
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Imperial College
London, SW7 2BW
Tel: Working from home, please use email.
http://www.hep.ph.ic.ac.uk/~dbauer/