[MITgcm-support] MITgcm-support Digest, Vol 163, Issue 20
Baker, Jon
jb812 at exeter.ac.uk
Mon Jan 30 15:59:35 EST 2017
Hi Martin,
Sorry for the delayed reply. I was having some issues running the model in full but have now tried commenting out the hydrogThetaFile and hydrogSaltFile in data. The model now runs fully with no issues. Thanks for your invaluable help!
Cheers,
Jon
________________________________
From: mitgcm-support-request at mitgcm.org <mitgcm-support-request at mitgcm.org>
Sent: 27 January 2017 13:10:26
To: mitgcm-support at mitgcm.org
Subject: MITgcm-support Digest, Vol 163, Issue 20
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Today's Topics:
1. bathymetry file in a .bin format (smaeilpour)
2. Using xarray with MITgcm (Liam Brannigan)
3. ABNORMAL END: S/R INI_THETA (when changing geometry) (Baker, Jon)
4. Re: ABNORMAL END: S/R INI_THETA (when changing geometry)
(Martin Losch)
----------------------------------------------------------------------
Message: 1
Date: Thu, 26 Jan 2017 20:32:19 +0000 (UTC)
From: smaeilpour <saeid_gal at yahoo.com>
To: <mitgcm-support at mitgcm.org>
Cc: dmenemenlis at gmail.com
Subject: [MITgcm-support] bathymetry file in a .bin format
Message-ID: <201875127.1897538.1485462739775 at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8
Hi MITgcm experts and dear all,
i created a file (in .asc format) by GEBCO Grid Demonstrator Software, so i converted it to a TXT format, now for creating a bathymetry file for MITgcm Model, should values be positive (+) or negative (-) in water? as regards, the ocean surface is at z=0, and land values should be zero (0).
could you please write me the commands in MATLAB that i can create a bathymetry file in a binary format (e.g. .bin)? or what way is easy for making it?
thank you in advance.
Best,
saeid
------------------------------
Message: 2
Date: Fri, 27 Jan 2017 07:29:32 +0000
From: Liam Brannigan <liam.brannigan at misu.su.se>
To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
Subject: [MITgcm-support] Using xarray with MITgcm
Message-ID: <1485502172687.97887 at misu.su.se>
Content-Type: text/plain; charset="iso-8859-1"
Hi
I've been using the excellent Xarray package (http://xarray.pydata.org/en/stable/) to analyse netcdf outputs from the MITgcm.
The package is very easy to use, but there is one aspect where the way the package works can conflict with the expectations of someone working with MITgcm output. The time variable in the model is 'T', but 'T' in the package refers to a transpose operation rather than a variable.
For example, a dataset object can be created with:
import xarray as xr
ds = xr.open_dataset('state.0000000000.nc')
The X coordinate can then be accessed with either dictionary-style access:
ds['X']
or as an attribute
ds.X
However, reading the time coordinate as ds.T replaces the T coordinate with a transpose of the full dataset and so time should be accessed as ds['T'] or possibly renamed.
More details can be found here:
http://stackoverflow.com/questions/41879269/xarray-dataarray-opens-as-a-dataset/41885639#41885639
Overall, I encourage everyone to try out the package (or Ryan's modified version for binary output http://xmitgcm.readthedocs.io/en/latest/), it makes a lot of the analysis easier and offers an easy route to making your analysis parallel.
Liam
________________________________________
From: mitgcm-support-request at mitgcm.org <mitgcm-support-request at mitgcm.org>
Sent: 24 January 2017 18:00
To: mitgcm-support at mitgcm.org
Subject: MITgcm-support Digest, Vol 163, Issue 18
Send MITgcm-support mailing list submissions to
mitgcm-support at mitgcm.org
To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. Re: Collected output (Camille Mazoyer)
----------------------------------------------------------------------
Message: 1
Date: Tue, 24 Jan 2017 09:35:02 +0100
From: Camille Mazoyer <mazoyer at univ-tln.fr>
To: mitgcm-support at mitgcm.org
Subject: Re: [MITgcm-support] Collected output
Message-ID: <588711B6.2010907 at univ-tln.fr>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"
Hi,
It seems that your script gluemncbig is not where you want.
Could you try on a terminal:
ls ~/MITgcm_c63/utils/python/MITgcmutils/scripts/gluemncbig
to verify it location?
And then, if it's not theren you can use this command to know where it is:
locate gluemncbig
What you can do is copying the script on your working directory and then
use your second command:
python gluemncbig -o a.nc mnc_test_000*/state*
Hope this will fix your problem,
Camille Mazoyer
Le 23/01/2017 21:29, rahele shafiee a ?crit :
> Hi everyone,
> I am running MITgcm model and my output format is as ?.nc? , so
> because of npx*npy=4 , I have to collecte them together. I?m trying by
> using the following commands:
>
> python ~/MITgcm_c63/utils/python/MITgcmutils/scripts/gluemncbig -o
> a.nc mnc_test_000*/state*
> or
> python gluemncbig -o a.nc mnc_test_000*/state*
>
> But I get the following error:
>
> python: can't open file
> '/home/caelinux/MITgcm_c63/utils/python/MITgcmutils/scripts/gluemncbig':
> [Errno 2] No such file or directory
>
> How can I fix it? thank you in advance for attention to this matter
> Regards Rahele
>
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
--
------------------------------------------
Camille Mazoyer
Phd Student
Mediterranean Institute of Oceanography (MIO)
Institut de Math?matiques de Toulon (IMATH)
Universit? de TOULON
Bat X - CS 60584
83041 TOULON cedex 9
France
tel: +33.4.94.14.24.50
Email: mazoyer at univ-tln.fr
http://mio.pytheas.univ-amu.fr/
http://imath.fr/
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Message: 3
Date: Fri, 27 Jan 2017 10:53:01 +0000
From: "Baker, Jon" <jb812 at exeter.ac.uk>
To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
Subject: [MITgcm-support] ABNORMAL END: S/R INI_THETA (when changing
geometry)
Message-ID:
<HE1PR0301MB21556DCB46266198D5064061CE760 at HE1PR0301MB2155.eurprd03.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello,
I am attempting to alter the geometry (number of grid points) of various tutorials and have encountered a new problem. After changing the number of grid points in the data file and SIZE.h file, the following error is shown when I run the global_oce_biogeochemistry and global_oce_latlon tutorials: ABNORMAL END: S/R INI_THETA .
The full error message is as follows:
INI_THETA: found 5875 wet grid-pts with theta=0 identically.
If this is intentional, you need to set checkIniTemp=.false. in "data", namelist PARM05
ABNORMAL END: S/R INI_THETA
I have looked up this error and found that it is because theta(i,j,k,bi,bj)=0. at at least one wet grid point (as described previously: http://mitgcm.org/pipermail/mitgcm-support/2008-June/005539.html).
However, I am having difficulty understanding why this is the case, since I believe tRef is set correctly (presumably this shouldn't change when the horizontal geometry is altered, as long as the vertical grid points remain unchanged). In the biogeochemistry tutorial which has 15 grid points in the vertical, the following setup is used in the data file:
&PARM01
tRef=15*20.,
sRef=15*35.,
Thus, the reference temperature is set to 20C at all 15 vertical grid points. This runs normally for the original geometrical setup (global) but has the above error when the geometry (number of horizontal grid points) is altered.
In the INI_THETA subroutine:
theta<http://mitgcm.org/sealion/code_reference/vdb/names/4N1.htm>(I<http://mitgcm.org/sealion/code_reference/vdb/names/61.htm>,J<http://mitgcm.org/sealion/code_reference/vdb/names/8V.htm>,K<http://mitgcm.org/sealion/code_reference/vdb/names/9C.htm>,bi<http://mitgcm.org/sealion/code_reference/vdb/names/56.htm>,bj<http://mitgcm.org/sealion/code_reference/vdb/names/57.htm>) = tRef<http://mitgcm.org/sealion/code_reference/vdb/names/13O.htm>(K<http://mitgcm.org/sealion/code_reference/vdb/names/9C.htm>)
Therefore, the temperature should not be 0 at any of the wet grid points!
Interestingly, setting tRef=15*0. removes the error, replacing it with a different error:
'ABNORMAL END: S/R INI_SALT'
The natl_box tutorial does not have tRef or sRef defined in the data file and runs normally when I change the number of horizontal grid points.
The above link suggests that 'when you interpolated the temperature field, that you have the model read, you missed at least one point'. However, given the tRef that has been set (tRef=15*20.), interpolation should not be a problem, unless there is another file where the temperature is defined which I am unaware of.
Any help would be greatly appreciated!
Cheers,
Jon
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Message: 4
Date: Fri, 27 Jan 2017 14:00:56 +0100
From: Martin Losch <martin.losch at awi.de>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] ABNORMAL END: S/R INI_THETA (when
changing geometry)
Message-ID: <12DF1F6F-D71B-4C5B-8483-DD2621B2D53E at awi.de>
Content-Type: text/plain; charset="utf-8"
Hi Jon,
since you already invested the time to inspect ini_theta.F, I suggest you have another look. You?ll see that first theta is initialised with tRef, then whatever is in ?hydrogThetaFile? ***overwrites*** theta. Try commenting out ?hydrogThetaFile?, and ?hydrogSaltFile? in ?data.
Martin
> On 27 Jan 2017, at 11:53, Baker, Jon <jb812 at exeter.ac.uk> wrote:
>
> Hello,
>
> I am attempting to alter the geometry (number of grid points) of various tutorials and have encountered a new problem. After changing the number of grid points in the data file and SIZE.h file, the following error is shown when I run the global_oce_biogeochemistry and global_oce_latlon tutorials: ABNORMAL END: S/R INI_THETA .
>
> The full error message is as follows:
>
> INI_THETA: found 5875 wet grid-pts with theta=0 identically.
> If this is intentional, you need to set checkIniTemp=.false. in "data", namelist PARM05
> ABNORMAL END: S/R INI_THETA
>
> I have looked up this error and found that it is because theta(i,j,k,bi,bj)=0. at at least one wet grid point (as described previously: http://mitgcm.org/pipermail/mitgcm-support/2008-June/005539.html).
>
> However, I am having difficulty understanding why this is the case, since I believe tRef is set correctly (presumably this shouldn't change when the horizontal geometry is altered, as long as the vertical grid points remain unchanged). In the biogeochemistry tutorial which has 15 grid points in the vertical, the following setup is used in the data file:
>
> &PARM01
> tRef=15*20.,
> sRef=15*35.,
>
> Thus, the reference temperature is set to 20C at all 15 vertical grid points. This runs normally for the original geometrical setup (global) but has the above error when the geometry (number of horizontal grid points) is altered.
>
> In the INI_THETA subroutine:
> theta(I,J,K,bi,bj) = tRef(K)
> Therefore, the temperature should not be 0 at any of the wet grid points!
>
> Interestingly, setting tRef=15*0. removes the error, replacing it with a different error:
> 'ABNORMAL END: S/R INI_SALT'
>
> The natl_box tutorial does not have tRef or sRef defined in the data file and runs normally when I change the number of horizontal grid points.
>
> The above link suggests that 'when you interpolated the temperature field, that you have the model read, you missed at least one point'. However, given the tRef that has been set (tRef=15*20.), interpolation should not be a problem, unless there is another file where the temperature is defined which I am unaware of.
>
> Any help would be greatly appreciated!
>
> Cheers,
> Jon
>
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
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