[ecco-support] Getting ECCO_v4_r3 running
Wang, Ou (329B)
Ou.Wang at jpl.nasa.gov
Wed Aug 2 12:20:25 EDT 2017
Hi Emma,
1) There is no need to provide the start and end dates for 'sss_AQanom' and ‘sss_AQmean’; the model will use the model start and end dates. Did your model stop if the start and end dates were not specified?
2) This is an oversight. I have renamed the files in input_ecco/input_nsidc/ from NOAA_NSIDC_DAILY_MAPPED_TO_LLC90_yyyy.bin to NOAA_NSIDC_DAILY_MAPPED_TO_LLC90_yyyy.
3) This is not an error. The cost function “sshv4-lsc’ uses the datafile of the cost functions 'sshv4-tp’, 'sshv4-ers’, and 'sshv4-gfo’ (indices 12-14).
Best,
Ou
From: <ecco-support-bounces at mit.edu<mailto:ecco-support-bounces at mit.edu>> on behalf of Emma Boland <emmomp at bas.ac.uk<mailto:emmomp at bas.ac.uk>>
Reply-To: "ECCO support list, wider membership" <ecco-support at mit.edu<mailto:ecco-support at mit.edu>>
Date: Tuesday, August 1, 2017 at 6:16 AM
To: "ecco-support at mit.edu<mailto:ecco-support at mit.edu>" <ecco-support at mit.edu<mailto:ecco-support at mit.edu>>
Subject: Re: [ecco-support] Getting ECCO_v4_r3 running
I have found several errors in data.ecco.
1. The cost functions 'sss_AQanom' and 'sss_AQmean' (indexes 19 and 20) are missing start and end dates. I have set these to 20110901 and 20131201 respectively, based on the filenames of the input, monthlyAQ_v3_092011-122013_yyyy. Is this correct?
2. The NOAA_NSIDC_DAILY_MAPPED_TO_LLC90_yyyy.bin inputs (from input_ecco/input_nsidc/) need to be renamed without the extension '.bin' to end _yyyy so they can be read.
3. The cost function 'sshv4-lsc' (index 15) does not appear to have a datafile, gencost_datafile(15) is NOT defined. I'm getting a runtime error that says: "** WARNING ** ECCO_CHECK_FILES: no data so gencost gets switched off" which I assume is related to this. I can't see an obvious datafile to point it to in the input directories - is this missing/obsolete?
Thanks,
Emma
On 01/08/17 12:48, Emma Boland wrote:
Ok, I've fixed it by remaking data.seaice by editing an old version. I think the problem is that the r3 data.seaice contains some erroneous control characters - if you type 'cat -v data.seaice' in a linux command line you can see the extra character '^M' everywhere - according to wikipedia this is a carriage return in macos, dos etc. I would advise you replace the version in the CVS repository with a corrected one.
Emma
On 01/08/17 11:32, Emma Boland wrote:
Hi Ou,
It is definitely a problem with data.seaice, as if I replace it with the r2 data.seaice it starts running. I've tried deleting whitespace, replacing the / with & for the namelist terminator, I've added a blank SEAICE_PARM03 namelist... Nothing seems to work. I guess there is something funny with the format somewhere in the file but I can't see what.
I'm pretty sure /tmp/F011.QAAa36052 is just a temporary, local, copy of data.seaice generated at runtime.
Here is STDERR.0000:
(PID.TID 0000.0001) ** WARNING ** S.Edge of facet # 1 disconnected (facet_link= 0.00)
(PID.TID 0000.0001) ** WARNING ** S.Edge of facet # 2 disconnected (facet_link= 0.00)
(PID.TID 0000.0001) ** WARNING ** E.Edge of facet # 4 disconnected (facet_link= 0.00)
(PID.TID 0000.0001) ** WARNING ** E.Edge of facet # 5 disconnected (facet_link= 0.00)
(PID.TID 0000.0001) ** WARNING ** INI_PARMS: Ignores diffKrT (or Kp,Kz) setting in file "data" with ALLOW_3D_DIFFKR
(PID.TID 0000.0001) ** WARNING ** INI_PARMS: Ignores diffKrS (or Kp,Kz) setting in file "data" and uses diffKrFile
The end of STDOUT.0000:
(PID.TID 0000.0001) SEAICE_READPARMS: opening data.seaice
(PID.TID 0000.0001) OPEN_COPY_DATA_FILE: opening file data.seaice
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) // Parameter file "data.seaice"
(PID.TID 0000.0001) // =======================================================
(PID.TID 0000.0001) ># SEAICE parameters
(PID.TID 0000.0001) > &SEAICE_PARM01
(PID.TID 0000.0001) > SEAICEpresH0=2.,
(PID.TID 0000.0001) > SEAICEpresPow0=1,
(PID.TID 0000.0001) > SEAICEpresPow1=1,
(PID.TID 0000.0001) > SEAICE_strength = 2.25e4,
(PID.TID 0000.0001) > SEAICE_area_max = 0.97,
(PID.TID 0000.0001) > SEAICE_no_slip = .TRUE.,
(PID.TID 0000.0001) > SEAICE_drag=0.001,
(PID.TID 0000.0001) > OCEAN_drag=0.001,
(PID.TID 0000.0001) > SEAICEuseTILT=.FALSE.,
(PID.TID 0000.0001) > SEAICE_multDim=1,
(PID.TID 0000.0001) > SEAICErestoreUnderIce=.TRUE.,
(PID.TID 0000.0001) > SEAICE_salt0=4.,
(PID.TID 0000.0001) > LSR_ERROR = 2.e-4,
(PID.TID 0000.0001) > SEAICEuseDYNAMICS = .TRUE.,
(PID.TID 0000.0001) > MIN_ATEMP = -40.,
(PID.TID 0000.0001) > MIN_TICE = -40.,
(PID.TID 0000.0001) > SEAICEadvScheme = 30,
(PID.TID 0000.0001) > SEAICEuseFluxForm = .TRUE.,
(PID.TID 0000.0001) > SEAICEadvSnow = .TRUE.,
(PID.TID 0000.0001) > SEAICEdiffKhHeff = 400.,
(PID.TID 0000.0001) > SEAICEdiffKhArea = 400.,
(PID.TID 0000.0001) > SEAICEdiffKhSnow = 400.,
(PID.TID 0000.0001) > SEAICEuseFlooding = .TRUE.,
(PID.TID 0000.0001) > SEAICE_mcPheePiston= 3.858024691358025E-05,
(PID.TID 0000.0001) > SEAICE_frazilFrac = 1.,
(PID.TID 0000.0001) > SEAICE_mcPheeTaper = 0.,
(PID.TID 0000.0001) > SEAICE_areaLossFormula=2,
(PID.TID 0000.0001) > SEAICEheatConsFix = .TRUE.,
(PID.TID 0000.0001) > SEAICE_tempFrz0 = -1.96,
(PID.TID 0000.0001) > SEAICE_dTempFrz_dS = 0.,
(PID.TID 0000.0001) > SEAICEuseMetricTerms = .TRUE.,
(PID.TID 0000.0001) > SEAICE_clipVelocities = .TRUE.,
(PID.TID 0000.0001) >#take 33% out of (1-albedo)
(PID.TID 0000.0001) > SEAICE_dryIceAlb = 0.84,
(PID.TID 0000.0001) > SEAICE_wetIceAlb = 0.78,
(PID.TID 0000.0001) > SEAICE_drySnowAlb = 0.90,
(PID.TID 0000.0001) > SEAICE_wetSnowAlb = 0.8 ,
(PID.TID 0000.0001) >#default albedos
(PID.TID 0000.0001) > SEAICE_dryIceAlb_south = 0.75,
(PID.TID 0000.0001) > SEAICE_wetIceAlb_south = 0.66,
(PID.TID 0000.0001) > SEAICE_drySnowAlb_south = 0.84,
(PID.TID 0000.0001) > SEAICE_wetSnowAlb_south = 0.7,
(PID.TID 0000.0001) > /
(PID.TID 0000.0001) >#
(PID.TID 0000.0001) > &SEAICE_PARM02
(PID.TID 0000.0001) > /
(PID.TID 0000.0001) >#
(PID.TID 0000.0001) > &SEAICE_PARM03
(PID.TID 0000.0001) > /
(PID.TID 0000.0001)
And my error log file just says the error I originally posted again and again.
Thanks,
Emma
Hi Emma,
It is not obvious from your description what caused the crash. Can you post your STDERR.0000 and the end part of STDOUT.0000, as well as your log file. Also, what is the temporary file /tmp/F011.QAAa36052? Is it just a copy of data.seaice?
Ou Wang
From: <ecco-support-bounces at mit.edu<mailto:ecco-support-bounces at mit.edu><mailto:ecco-support-bouncesatmit.edu>> on behalf of Emma Boland <emmomp at bas.ac.uk<mailto:emmomp at bas.ac.uk><mailto:emmompatbas.ac.uk>>
Reply-To: "ECCO support list, wider membership" <ecco-support at mit.edu<mailto:ecco-support at mit.edu><mailto:ecco-supportatmit.edu>>
Date: Wednesday, July 26, 2017 at 5:36 AM
To: "ecco-support at mit.edu<mailto:ecco-support at mit.edu><mailto:ecco-supportatmit.edu>" <ecco-support at mit.edu<mailto:ecco-support at mit.edu><mailto:ecco-supportatmit.edu>>
Subject: [ecco-support] Getting ECCO_v4_r3 running
Hi Guys,
I'm attempting to get r3 running on the ARCHER machine in the UK. All I've altered are SIZE.h and data.exch2. It's crashing during reading of the namelists - STDOUT implies this is reading data.seaice. I'm getting errors of the sort:
lib-4001 : UNRECOVERABLE library error
A READ operation tried to read past the end-of-file.
Encountered during a namelist READ from unit 11
Fortran unit 11 is connected to a sequential formatted text file:
"/tmp/F011.QAAa36052"
Looking at data.seaice I can't see anything obviously wrong. Is this something anyone else has come across? And just because STDOUT ends after reading data.seaice, is this a guarantee that this is the true cause of the crash (i.e. is the buffer necessarily up to date when it crashes)?
Thanks,
Emma
--
Dr Emma Boland
Physical Oceanographer
Polar Oceans Group
British Antarctic Survey
Phone: 01223 221276
Web: www.antarctica.ac.uk/about_bas/contact/staff/profile/eboland<http://www.antarctica.ac.uk/about_bas/contact/staff/profile/eboland><https://www.bas.ac.uk/profile/emmomp/><https://www.bas.ac.uk/profile/emmomp/>
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Dr Emma Boland
Physical Oceanographer
Polar Oceans Group
British Antarctic Survey
Phone: 01223 221276
Web: www.antarctica.ac.uk/about_bas/contact/staff/profile/eboland<https://www.bas.ac.uk/profile/emmomp/>
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This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
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--
Dr Emma Boland
Physical Oceanographer
Polar Oceans Group
British Antarctic Survey
Phone: 01223 221276
Web: www.antarctica.ac.uk/about_bas/contact/staff/profile/eboland<https://www.bas.ac.uk/profile/emmomp/>
________________________________
This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
________________________________
_______________________________________________
ecco-support mailing list
ecco-support at mit.edu<mailto:ecco-support at mit.edu>http://mailman.mit.edu/mailman/listinfo/ecco-support
--
Dr Emma Boland
Physical Oceanographer
Polar Oceans Group
British Antarctic Survey
Phone: 01223 221276
Web: www.antarctica.ac.uk/about_bas/contact/staff/profile/eboland<https://www.bas.ac.uk/profile/emmomp/>
________________________________
This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.
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