[MITgcm-support] MITgcm-support Digest, Vol 163, Issue 3

Julian Mak j.mak at ed.ac.uk
Tue Jan 10 09:19:37 EST 2017 

Maybe not the reason, but one of the problems I just had was that there 
were old, non-linked files (in this case two *.F files) in the ./build 
directory that seems to take precedence over the ones in ../code/ when 
using "make". Not sure why "make Clean" or "make CLEAN" weren't deleting 
them (not that I know/remember why they were there in the first place) 
but deleting them and recompiling as normal registers the changes, with 
the relevant things appearing as linked files as they should.


Julian


On 10/01/17 14:01, Baker, Jon wrote:
> That's fantastic! Thanks for all your responses. Hopefully, this will 
> solve my issue, although I have definitely been linking the build and 
> inputs directories, after compiling the model, prior to running. 
> Perhaps, I have been compiling incorrectly, or not linking the SIZE.h 
> file since this is in the code directory. I will update you on the 
> cause of the error as soon as I have access to the supercomputer. Many 
> thanks for your advice!
>
> Cheers,
> Jon
>
> ------------------------------------------------------------------------
> *From:* mitgcm-support-request at mitgcm.org 
> <mitgcm-support-request at mitgcm.org>
> *Sent:* 09 January 2017 20:31:36
> *To:* mitgcm-support at mitgcm.org
> *Subject:* MITgcm-support Digest, Vol 163, Issue 3
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> Today's Topics:
>
>    1. Re: MITgcm-support Digest, Vol 163, Issue 1 (Edward W Doddridge)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 Jan 2017 20:31:13 +0000
> From: Edward W Doddridge <ewd at mit.edu>
> To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] MITgcm-support Digest, Vol 163, Issue 1
> Message-ID: <96574F33-EB03-4FA6-8F88-5823DE5B1B82 at mit.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Jon,
>
> The fact that the model is still looking for 20 (or 128) grid spacings 
> suggests to me that you haven?t recompiled the model after making the 
> changes in SIZE.h. The changes in that file will only have an effect 
> when the model is compiled, not at run time.
>
> Cheers,
> Ed
>
>
> ________________________________
> Edward Doddridge
> Postdoctoral researcher
> Earth, Atmospheric and Planetary Sciences
> Massachusetts Institute of Technology
>
> www.doddridge.me<http://www.doddridge.me>
>
> On 9 Jan 2017, at 15:23, Baker, Jon 
> <jb812 at exeter.ac.uk<mailto:jb812 at exeter.ac.uk>> wrote:
>
> Hi Martin and Malte,
>
> Thanks for your quick responses! The specific error message from 
> running the natl_box (and the biogeochem tutorials) was as follows:
>
> S/R LOAD_GRID_SPACING: No value for delX at i =   11
>
> This error message is then repeated for i=11 to i=20 where 20 was the 
> number of grid points in the x-direction in the original setup of the 
> natl_box tutorial.
>
> I received the same type of error message in the biogeochem tutorial 
> when I tried to change it from a global setup to a basin setup.
> <http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CX.htm>
>
>
> I changed the SIZE.h file to the appropriate Nx and Ny for the 
> specified delX and delY (certainly in the biogeochem tutorial and I 
> believe in the natl_box tutorial too). When I changed delX from 
> delX=20*2 to delX=10*2, I altered sNx in SIZE.h from 20 to 10 to 
> reflect this change (and made the appropriate change in sNy too). 
> Thus, Nx= 10 = sNx*nSx*nPx .
>
> For the biogeochem tutorial, the &PARM04 in the data file for the 
> particular setup (global) I am using has:
> delX=128*2.8125
> delY=64*2.8125
>
> and the SIZE.h file has sNx=64, sNy=32 and nSx=2,nSy=2 and nPx=1,nPy=1.
>
> However, when I change delX to delX=24*281 in the data file and change 
> sNx to sNx=12 in SIZE.h, and alter the size of the input files, I 
> receive the error above repeated for i=25 to i=128.
>
> Unfortunately, the supercomputer I am using has been shutdown today 
> but I hope to be able to use it again asap. I therefore do not have 
> access to the files currently to show you SIZE.h. I will try using 
> dxspacing (and dyspacing) to see if it still gives me an error and 
> check the natl_box experiment again when I have access.
>
> I found that the error comes from the following MITgcm code:
>
>
> $Header: /u/gcmpack/MITgcm/model/src/load_grid_spacing.F
>
> C--   Check delX grid-spacing:
>        
> n<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/GU.htm> 
> = 0
>        DO 
> i<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CX.htm>=1,gridNx<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/1QN.htm 
> <http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CX.htm%3E=1,gridNx%3Chttp://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/1QN.htm>>
> C-    check that delX has been set
>         IF ( 
> delX<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/VK.htm>(i<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CX.htm>).EQ.UNSET_RL<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CPH.htm 
> <http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/VK.htm%3E%28i%3Chttp://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CX.htm%3E%29.EQ.UNSET_RL%3Chttp://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CPH.htm>> 
> ) THEN
>          
> n<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/GU.htm> 
> = 
> n<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/GU.htm>+1
> WRITE(msgBuf<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/AD.htm>,'(2A,I5)') 
> 'S/R LOAD_GRID_SPACING:',
>      &       ' No value for delX at i =', 
> i<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CX.htm>
>          CALL 
> PRINT_ERROR<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/CVQ.htm>( 
> msgBuf<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/AD.htm>, 
> myThid<http://mitgcm.org/public/r2_manual/latest/code_reference/vdb/names/AE.htm> 
> )
>         ENDIF
>
> However, I am still unsure why I get this error message if I have 
> changed SIZE.h correctly. In fact in the biogeochem setup I am running
> (a modified version of the tutorial), changing sNx or sNy in SIZE.h to 
> any value does not produce an error, despite keeping delX and
> delY constant
>
> (i.e.
>
> delX=128*2.8125,
>
> delY=64*2.8125 were not changed) which I find strange. Yet as soon as 
> delX is changed in the
>
> data file, the
>
> error occurs regardless of whether the SIZE.h file is changed correctly.
>
>
> Thanks in advance for your help!
>
> Cheers,
> Jon
>
>
>
>
>
>
>
>
> ________________________________
> From: 
> mitgcm-support-request at mitgcm.org<mailto:mitgcm-support-request at mitgcm.org> 
> <mitgcm-support-request at mitgcm.org<mailto:mitgcm-support-request at mitgcm.org>>
> Sent: 09 January 2017 17:00:02
> To: mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>
> Subject: MITgcm-support Digest, Vol 163, Issue 1
>
> Send MITgcm-support mailing list submissions to
> mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mitgcm.org/mailman/listinfo/mitgcm-support
> or, via email, send a message with subject or body 'help' to
> mitgcm-support-request at mitgcm.org<mailto:mitgcm-support-request at mitgcm.org>
>
> You can reach the person managing the list at
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MITgcm-support digest..."
>
>
> Today's Topics:
>
>    1. Re: ABNORMAL END: S/R LOAD_GRID_SPACING (when changing number
>       of grid points) (Baker, Jon)
>    2. Re: ABNORMAL END: S/R LOAD_GRID_SPACING (when changing number
>       of grid points) (Martin Losch)
>    3. Re: ABNORMAL END: S/R LOAD_GRID_SPACING (when changing number
>       of grid points) (Malte Jansen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 Jan 2017 12:24:13 +0000
> From: "Baker, Jon" <jb812 at exeter.ac.uk<mailto:jb812 at exeter.ac.uk>>
> To: "mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>" 
> <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
> Subject: Re: [MITgcm-support] ABNORMAL END: S/R LOAD_GRID_SPACING
>         (when changing number of grid points)
> Message-ID:
> <HE1PR0301MB215597E946C56C453F462A7BCE640 at HE1PR0301MB2155.eurprd03.prod.outlook.com<mailto:HE1PR0301MB215597E946C56C453F462A7BCE640 at he1pr0301mb2155.eurprd03.prod.outlook.com>>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
>
> I am attempting to edit the geometry in several of the tutorials (e.g. 
> natl_box and biogeochem) to an idealised setup but I keep getting the 
> following runtime error: S/R LOAD_GRID_SPACING.
>
>
> I have altered the input files and the SIZE.h file to the appropriate 
> domain size, although this does not appear to be the cause of the 
> error. The error is caused by altering delX and delY in the data file 
> to the appropriate number of grid points e.g. in the natl_box 
> tutorial, delX= 20*2, but if I change the number of grid points (e.g. 
> to delX= 10*2), the aforementioned error occurs!
>
>
> Perhaps some other files need to be altered (in addition to SIZE.h and 
> the input files). Any help would be greatly appreciated.
>
>
> Cheers,
>
> Jon
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>
> Message: 2
> Date: Mon, 9 Jan 2017 13:44:20 +0100
> From: Martin Losch <martin.losch at awi.de<mailto:martin.losch at awi.de>>
> To: MITgcm Support 
> <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
> Subject: Re: [MITgcm-support] ABNORMAL END: S/R LOAD_GRID_SPACING
>         (when changing number of grid points)
> Message-ID: 
> <0E7B3F23-D96C-433D-896D-B3DF3AFD5BAC at awi.de<mailto:0E7B3F23-D96C-433D-896D-B3DF3AFD5BAC at awi.de>>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Jon,
>
> could you provide more details of the error messages? The S/R 
> LOAD_GRID_SPACING has several different checks.
>
> As a general rule, Nx = sNx*nSx*nPx should be the same as the number 
> delX that you provide. In natl_box Nx = 20, so delX = 20*2, (twenty 
> time 2 degrees in this case).
>
> Whenever dx is constant, I use dxSpacing = 2 (and dySpacing) instead 
> of delX = ?Nx?*2, this avoids having to specify the grid dimension in 
> ?data"
>
> Martin
>
> > On 9 Jan 2017, at 13:24, Baker, Jon 
> <jb812 at exeter.ac.uk<mailto:jb812 at exeter.ac.uk>> wrote:
> >
> > Hi all,
> >
> > I am attempting to edit the geometry in several of the tutorials 
> (e.g. natl_box and biogeochem) to an idealised setup but I keep 
> getting the following runtime error: S/R LOAD_GRID_SPACING.
> >
> > I have altered the input files and the SIZE.h file to the 
> appropriate domain size, although this does not appear to be the cause 
> of the error. The error is caused by altering delX and delY in the 
> data file to the appropriate number of grid points e.g. in the 
> natl_box tutorial, delX= 20*2, but if I change the number of grid 
> points (e.g. to delX= 10*2), the aforementioned error occurs!
> >
> > Perhaps some other files need to be altered (in addition to SIZE.h 
> and the input files). Any help would be greatly appreciated.
> >
> > Cheers,
> > Jon
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org<mailto:MITgcm-support at mitgcm.org>
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 9 Jan 2017 15:26:11 +0000
> From: Malte Jansen <mfj at uchicago.edu<mailto:mfj at uchicago.edu>>
> To: "mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>" 
> <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
> Subject: Re: [MITgcm-support] ABNORMAL END: S/R LOAD_GRID_SPACING
>         (when changing number of grid points)
> Message-ID: 
> <AC5DBF6A-40BD-42A8-9303-0343E77F96E4 at uchicago.edu<mailto:AC5DBF6A-40BD-42A8-9303-0343E77F96E4 at uchicago.edu>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Jon,
> It would help if you provide your SIZE.h file and the &PARM04 part of 
> the data file that you are using.
> Also: Is there anything more to the error message?
> -Malte
>
>
> On Jan 9, 2017, at 6:24 AM, Baker, Jon 
> <jb812 at exeter.ac.uk<mailto:jb812 at exeter.ac.uk><mailto:jb812 at exeter.ac.uk>> 
> wrote:
>
> Hi all,
>
> I am attempting to edit the geometry in several of the tutorials (e.g. 
> natl_box and biogeochem) to an idealised setup but I keep getting the 
> following runtime error: S/R LOAD_GRID_SPACING.
>
> I have altered the input files and the SIZE.h file to the appropriate 
> domain size, although this does not appear to be the cause of the 
> error. The error is caused by altering delX and delY in the data file 
> to the appropriate number of grid points e.g. in the natl_box 
> tutorial, delX= 20*2, but if I change the number of grid points (e.g. 
> to delX= 10*2), the aforementioned error occurs!
>
> Perhaps some other files need to be altered (in addition to SIZE.h and 
> the input files). Any help would be greatly appreciated.
>
> Cheers,
> Jon
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org<mailto:MITgcm-support at mitgcm.org><mailto:MITgcm-support at mitgcm.org>
> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
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-- 
Julian Mak,
School of Mathematics,
The University of Edinburgh,
James Clerk Maxwell Building,
The King's Buildings,
Edinburgh, EH9 3FD
e-mail: j.mak at ed.ac.uk
tel: +44 131 650 5040
www: https://sites.google.com/site/julianclmak/home

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