NOC-MSM / pyBDY

pyBDY: a Python based regional NEMO model configuration toolbox.
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Pynemo can't find bathymetry #63

Closed jenjar93 closed 4 years ago

jenjar93 commented 4 years ago

@thopri Hi Tom, I'm currently trying to run pynemo (IMMERSE branch) but am getting a persistent error very early on that says it can't find the Bathymetry variable - despite that the variable exists in bathy_meter.nc file. Originally I thought it was a mask issue but it still fails both with/without bdy_mask.nc. Any ideas? We've run it with two domains that both worked with a previous version of pynemo: one of these examples, including the nrct.log, can be found on livljobs at /projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3

Thanks! Jenny

thopri commented 4 years ago

Hi Jenny,

unfortunate I don't have access to the accord folder on projectsa. can you send me the log file? Hopefully its a simple issue!

Many Thanks

Tom

Dr Thomas Prime Applied Modeller Marine Data Products Team UK National Oceanography Centre, European Way, Southampton SO14 3ZH

E: thopri@noc.ac.ukmailto:thopri@noc.ac.uk noc.ac.ukhttp://noc.ac.uk/ | @NOCnewshttps://twitter.com/nocnews | Subscribe to NOCmail e-alertshttps://public.govdelivery.com/accounts/UKNOC/subscriber/new

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From: jenjar93 notifications@github.com Sent: 16 July 2020 12:07 To: NOC-MSM/PyNEMO PyNEMO@noreply.github.com Cc: Prime, Thomas D. thopri@noc.ac.uk; Mention mention@noreply.github.com Subject: [NOC-MSM/PyNEMO] Pynemo can't find bathymetry (#63)

@thoprihttps://github.com/thopri Hi Tom, I'm currently trying to run pynemo (IMMERSE branch) but am getting a persistent error very early on that says it can't find the Bathymetry variable - despite that the variable exists in bathy_meter.nc file. Originally I thought it was a mask issue but it still fails both with/without bdy_mask.nc. Any ideas? We've run it with two domains that both worked with a previous version of pynemo: one of these examples, including the nrct.log, can be found on livljobs at /projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3

Thanks! Jenny

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This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. The National Oceanography Centre (NOC) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. NOC does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to NOC business are solely those of the author and do not represent the views of NOC.

jenjar93 commented 4 years ago

Hi Tom

No problem, please find attached the log file and a screenshot of the command line errors that pop up.

Thanks Jenny

From: thopri notifications@github.com Reply to: NOC-MSM/PyNEMO reply@reply.github.com Date: Thursday, 16 July 2020 at 13:39 To: NOC-MSM/PyNEMO PyNEMO@noreply.github.com Cc: jenjar93 j.jardine@liverpool.ac.uk, Author author@noreply.github.com Subject: Re: [NOC-MSM/PyNEMO] Pynemo can't find bathymetry (#63)

Hi Jenny,

unfortunate I don't have access to the accord folder on projectsa. can you send me the log file? Hopefully its a simple issue!

Many Thanks

Tom

Dr Thomas Prime Applied Modeller Marine Data Products Team UK National Oceanography Centre, European Way, Southampton SO14 3ZH

E: thopri@noc.ac.ukmailto:thopri@noc.ac.uk noc.ac.ukhttp://noc.ac.uk/ | @NOCnewshttps://twitter.com/nocnews | Subscribe to NOCmail e-alertshttps://public.govdelivery.com/accounts/UKNOC/subscriber/new

DISCLAIMER:

This communication (including any attachments) is intended for the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the National Oceanography Centre. In the event that this communication has incorrectly been addressed to you, it is likewise subject to protection under confidentiality and should not be disclosed. In either event if you have received this communication in error, please permanently delete it from your system and promptly notify the sender. You should not copy it or use it for any purpose nor disclose or distribute its contents to any other person.


From: jenjar93 notifications@github.com Sent: 16 July 2020 12:07 To: NOC-MSM/PyNEMO PyNEMO@noreply.github.com Cc: Prime, Thomas D. thopri@noc.ac.uk; Mention mention@noreply.github.com Subject: [NOC-MSM/PyNEMO] Pynemo can't find bathymetry (#63)

@thoprihttps://github.com/thopri Hi Tom, I'm currently trying to run pynemo (IMMERSE branch) but am getting a persistent error very early on that says it can't find the Bathymetry variable - despite that the variable exists in bathy_meter.nc file. Originally I thought it was a mask issue but it still fails both with/without bdy_mask.nc. Any ideas? We've run it with two domains that both worked with a previous version of pynemo: one of these examples, including the nrct.log, can be found on livljobs at /projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3

Thanks! Jenny

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/NOC-MSM/PyNEMO/issues/63, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AJ2BRDWPCDEXRTDVDRGDIL3R33NP3ANCNFSM4O4BL6QA.

This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. The National Oceanography Centre (NOC) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. NOC does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to NOC business are solely those of the author and do not represent the views of NOC.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/NOC-MSM/PyNEMO/issues/63#issuecomment-659383893, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AM4P2SX2VOSVOMOCYDIVO7DR33YG5ANCNFSM4O4BL6QA.

thopri commented 4 years ago

This is due to the NC file being used not having a units attribute for the bathy variable. Without it it makes the program crash. Adding this attribute should fix the problem. I will also amend the code so that it will log a warning instead of crashing.