[MITgcm-support] MITgcm 40km resolution Arctic simulation

Thu Oct 17 10:36:34 EDT 2013

Ok. I will take a look later today, update config, test and get back.

Dimitris Menemenlis
818-625-6498

On Oct 17, 2013, at 7:34 AM, "Jonny Williams" <Jonny.Williams at bristol.ac.uk<mailto:Jonny.Williams at bristol.ac.uk>> wrote:

sorry yes, the following output is in the STDERR file(s)

(PID.TID 0000.0001) *** ERROR *** S/R INI_PARMS: tauSaltClimRelax > 0 but
(PID.TID 0000.0001) *** ERROR *** S/R INI_PARMS: saltClimFile is undefined
(PID.TID 0000.0001) *** ERROR *** S/R INI_PARMS: detected  1 fatal error(s)
(PID.TID 0000.0001) *** ERROR *** S/R ALL_PROC_DIE: ending the run

In light of this I changed the tauSaltClimRelax  value to zero in my data file in the run directory and I am now getting the following errors in the STDERR file

(PID.TID 0000.0001) *** ERROR *** S/R SEAICE_READPARMS: "SEAICE_freeze" no longer allowed in file "data.seaice"
(PID.TID 0000.0001) *** ERROR *** S/R SEAICE_READPARMS: set instead "SEAICE_tempFrz0" and "SEAICE_dTempFrz_dS"
(PID.TID 0000.0001) ** WARNING ** SEAICE_READPARMS: will use AdvScheme = 2 for HEFF  without any diffusion
(PID.TID 0000.0001) ** WARNING ** SEAICE_READPARMS: will use AdvScheme = 2 for AREA  without any diffusion
(PID.TID 0000.0001) ** WARNING ** SEAICE_READPARMS: will use AdvScheme = 2 for HSNOW without any diffusion
(PID.TID 0000.0001) ** WARNING ** SEAICE_READPARMS: since DIFF1 is set to 0 (= new DIFF1 default value)
(PID.TID 0000.0001) ** WARNING ** INI_MODEL_IO: use tiled-files to write sections (for OBCS)
(PID.TID 0000.0001) *** ERROR *** DIAGNOSTICS_LIST_CHECK: diagnostic "KPPmld  " was retired in favor of "MXLDEPTH"
(PID.TID 0000.0001) *** ERROR *** DIAGNOSTICS_LIST_CHECK: => need to change "data.diagnostics" accordingly
(PID.TID 0000.0001) *** ERROR *** DIAGNOSTICS_LIST_CHECK: diagnostic "KPPghat " was retired in favor of "KPPghatK"
(PID.TID 0000.0001) *** ERROR *** DIAGNOSTICS_LIST_CHECK: => need to change "data.diagnostics" accordingly

I really appreciate your help and perseverance! If we can get this regional Arctic example working then this will stand in brilliant stead for the 'real' research simulations that I wish to perform later, especially if we can get it running at several different resolutions!

Cheers

Jonny

On 17 October 2013 15:12, Menemenlis, Dimitris (3248) <Dimitris.Menemenlis at jpl.nasa.gov<mailto:Dimitris.Menemenlis at jpl.nasa.gov>> wrote:
Is there any more info in STDERR* and tail end of STDOUT*.
The 36-km configuration is also a little out of date
so some parameters have changed name compared
to new code.  I will try to make time to test and update later today.

Sorry for this trouble - especially pkg/seaice has seen a lot of changes
in last couple of years, and many of these changes are not
backward compatible.

Cheers

Dimitris Menemenlis

On Oct 17, 2013, at 7:00 AM, Jonny Williams wrote:

Hi again Dimitris (CC MITgcm)

Some progress. I've downloaded the http://ecco2.jpl.nasa.gov/data1/arctic/code2/ and
http://ecco2.jpl.nasa.gov/data1/arctic/run_template2/ as you suggested and have compiled (I think) successfully.

I put all the files from the "run_template2" directory into a /input directory as I believe is standard.

When I try and run the executable, I get the following error 16 times (one for each of the 16 processors defined in the SIZE.h file, nPx=2, nPy=8)...

ABNORMAL END: S/R INI_PARMS

I assume this means that I am missing a boundary condition file somewhere? Do I need to download some more files from http://ecco2.jpl.nasa.gov/data1/arctic/ ?

Thanks again

Jonny

On 16 October 2013 17:41, Menemenlis, Dimitris (3248) <Dimitris.Menemenlis at jpl.nasa.gov<mailto:Dimitris.Menemenlis at jpl.nasa.gov>> wrote:
Hi Jonny, you need to add
#define OLD_GRID_IO
in CPP_OPTIONS.h

The 40-km set-up hasn't been touched for quite a while so there will be several
options and parameters that are out of date.

If you do manage to get it to work, please send updated code and input files
and I will check them in for next user.

As a possible guideline of things to change, one place that might be helpful is:
http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/MPMice/beaufort
(although there's coupled code stuff there that you don't need).

Also slightly less out of date set-up available here:
http://ecco2.jpl.nasa.gov/data1/arctic/code2/
http://ecco2.jpl.nasa.gov/data1/arctic/run_template2/
This is a 36-km set-up and the nice thing is that there
is open boundary conditions available from ECCO2 project
and a whole bunch of increasingly higher-res configs, all the
way to 1-km horizontal grid spacing ready to go.
Again, if you use any of the above and you find
discrepancies or updates, please let me know and
I will try to help and also update the instructions for next user.

I cc MITgcm support for more suggestions.

Cheers

Dimitris Menemenlis

On Oct 16, 2013, at 4:42 AM, Jonny Williams wrote:

Hi again!

I've now managed to download the files I need I think and have been going through some run-time error

The first error was as follows

S/R INI_PARMS: "thetaMin" no longer allowed, has been replaced by "xgOrigin"
S/R INI_PARMS: "phiMin" no longer allowed, has been replaced by "ygOrigin"

I have managed to get round by replacing thetaMin and phiMin with xgOrigin and ygOrigin respectively.

The second error was as follows

S/R INI_PARMS: tauSaltClimRelax > 0 but
S/R INI_PARMS: saltClimFile is undefined

I have fixed this for now by setting tauSaltClimRelax=0

The error which has floored me now is the following

PGFIO-F-209/OPEN/unit=9/'OLD' specified for file which does not exist.
File name = tile001.mitgrid
In source file mdsio_facef_read.f, at line number 740

The offending line in mdsio_facef_read.f reads

OPEN( dUnit, file=fName(1:iLen), status='old',

I have done a 'grep' search in the arctic40km directory and there is no mention of tile001.mitgrid at all so perhaps this code is out of date?

Do you have any ideas about how to fix this issue?

Many thanks once again. I'm looking forward to getting this model running!

Jonny

On 11 October 2013 21:00, Menemenlis, Dimitris (3248) <Dimitris.Menemenlis at jpl.nasa.gov<mailto:Dimitris.Menemenlis at jpl.nasa.gov>> wrote:
Hi Johnny, the files you are looking for appear to be available here:
http://mit.ecco-group.org/datasets/MITgcm_input_files/MITgcm_contrib/arctic40km/input/

Cheers

Dimitris Menemenlis

On Oct 11, 2013, at 10:20 AM, Jinlun Zhang wrote:

Hi Jonny, I doubt it is still available. But I am not sure and referring this to Dimitris. Dimitris, could you help Jonny - thanks.
Best,
Jinlun

On 10/11/2013 2:10 AM, Jonny Williams wrote:
Dear Dr Zhang

I am a postdoc researcher at the University of Bristol in the UK and I am starting to work on regional ocean modelling. I am trying to download and run the "arctic40km" configuration and the documentation for this states that users should contact you when trying to do this.

I have downloaded the base directory (cvs co -d arctic40km MITgcm_contrib/arctic40km) but when I try to download the input data (wget -nd -r -A"*.bin" http://channel.mit.edu/datasets/MITgcm_input_files/MITgcm_contrib/arctic40km/input) the download fails with the following error...

"Connecting to channel.mit.edu<http://channel.mit.edu/>|18.83.0.150|:80... failed: Connection timed out."

Do you know is it still possible to run this example?

Many thanks for any assistance that you are able to provide!

Best wishes

Jonny Williams

--
Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS

+44 (0)117 3318352<tel:%2B44%20%280%29117%203318352>
jonny.williams at bristol.ac.uk<mailto:jonny.williams at bristol.ac.uk>
bit.ly/jonnywilliams<http://bit.ly/jonnywilliams>

--
Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS

+44 (0)117 3318352
jonny.williams at bristol.ac.uk<mailto:jonny.williams at bristol.ac.uk>
bit.ly/jonnywilliams<http://bit.ly/jonnywilliams>
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