# No subject

Thu Oct 27 09:13:38 EDT 2011

```Alternatively, you can balance the fluxes only at every time step, using the flags described in the documentation:
<http://mitgcm.org/public/r2_manual/latest/online_documents/node236.html#SECTION00731560000000000000>

M.

On Sep 2, 2012, at 11:13 PM, Chun-Yan Zhou wrote:

> Hi all,
> I did a regional model with south and east boundary driven by boundary velocity, but the mean eta increase slowly along with time. So I meed to modify the south boundary v velocity and east boundary u velocity in order to get flux in and flux out balance.
>
> The south boundary has 174 points and 40 layers while east boundary has 226 points and 40 layers.
> my understanding after looking through the manual is that
> south boundary : the flux in each grid = hfacc*drf*dxg*masks*vsouth
> east boundary :  the flux in each grid =  hfacc*drf*dyg*maskw*ueast
> Therefore, I compute the flux in and flux out the model area as follows,but I am not sure I use the right formula, because there is also hfacs,hfacw,drc parameters. Can anyone confirm whether the formula is right or wrong?
>
> vin=0;
> for i=1:174
> for k=1:40
> end
> end
>
> uout=0;
> for j=1:226
> for k=1:40
> end
> end
>
>
>
>
> Chunyan Zhou
> Division of Civil Engineering
> School of Engineering, Physics and Mathematics
> College of Art, Science and Engineering
> Fulton Building,G19
> University of Dundee
> Dundee, UK DD1 4HN
> Tel. 01382 385431
>
>
>
> ________________________________________
> From: mitgcm-support-request at mitgcm.org [mitgcm-support-request at mitgcm.org]
> Sent: 24 August 2012 02:43
> To: mitgcm-support at mitgcm.org
> Subject: MITgcm-support Digest, Vol 110, Issue 17
>
> Send MITgcm-support mailing list submissions to
>       mitgcm-support at mitgcm.org
>
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> or, via email, send a message with subject or body 'help' to
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>
> than "Re: Contents of MITgcm-support digest..."
>
>
> Today's Topics:
>
>  1. using gather/scatter to work with global fields (Katherine Quinn)
>  2. Re: using gather/scatter to work with global fields
>     (Matthew Mazloff)
>  3. Re: using gather/scatter to work with global fields
>     (Katherine Quinn)
>  4. Re: using gather/scatter to work with global fields
>     (Matthew Mazloff)
>  5. vertical velocities in high-res runs (Andreas Klocker)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 23 Aug 2012 13:40:55 -0400
> From: Katherine Quinn <kquinn at aer.com>
> To: mitgcm-support at mitgcm.org
> Subject: [MITgcm-support] using gather/scatter to work with global
>       fields
> Message-ID: <50366B27.4040901 at aer.com>
> Content-Type: text/plain; CHARSET=US-ASCII; format=flowed
>
> Hi all,
> Within the MITgcm code (not matlab) I need to gather tiled variables
> into a global array, specifically I'm trying to gather XC and YC.  I'm
> using the subroutine gather_2d_r4, which suggests "barrier calls" before
> and after but it seems no matter what various barrier calls I use, when
> I look at the global array there's chunks of tiles missing.  Other
> relevant info - the MITgcm setup is for ecco version 4 runs, with
> all_exch2 turned on.
> Here's the relevant portions of my code, please suggest what I'm doing
> wrong:
>
> C     == Global variables ===
> #include "SIZE.h"
> #include "EEPARAMS.h"
> #include "EESUPPORT.h"
> #include "PARAMS.h"
> #ifdef ALLOW_EXCH2
> # include "W2_EXCH2_SIZE.h"
> # include "W2_EXCH2_TOPOLOGY.h"
> # include "W2_EXCH2_PARAMS.h"
> #endif /* ALLOW_EXCH2 */
> #include "EEBUFF_SCPU.h"
> #include "GRID.h"
>
> C     INPUT/OUTPUT PARAMETERS:
> C     == Routine arguments ==
> C     myThid - Thread number for this instance of the routine.
>      INTEGER  myThid
>
> C     LOCAL VARIABLES:
>      LOGICAL zeroBuff, useExch2ioLayOut
>      INTEGER xSize, ySize
> #ifdef ALLOW_EXCH2
>      _RL  XC_global(exch2_global_Nx,exch2_global_Ny)
>      _RL  YC_global(exch2_global_Nx,exch2_global_Ny)
> #else  /* ALLOW_EXCH2 */
>      _RS  XC_global(Nx,Ny)
>      _RS  YC_global(Nx,Ny)
> #endif /* ALLOW_EXCH2 */
>
> C Set dimensions and flags (e.g. mdsio_write_field.F)
>      xSize = Nx
>      ySize = Ny
>      useExch2ioLayOut = .FALSE.
>      zeroBuff = .TRUE.
> #ifdef ALLOW_EXCH2
>      IF ( W2_useE2ioLayOut ) THEN
>         xSize = exch2_global_Nx
>         ySize = exch2_global_Ny
>         useExch2ioLayOut = .TRUE.
>      ENDIF
> #endif /* ALLOW_EXCH2 */
>
> C gather XC and YC into global model grid
>
>      CALL BAR2( myThid )
>      _BEGIN_MASTER( myThid )
>      CALL GATHER_2D_R4(
>     O                  XC_global,
>     I                  XC,
>     I                  xSize, ySize,
>     I                  useExch2ioLayOut,
>     I                  zeroBuff,
>     I                  myThid )
>      _END_MASTER( myThid )
>      CALL BAR2( myThid )
>
>      _BEGIN_MASTER( myThid )
>      CALL GATHER_2D_R4(
>     O                  YC_global,
>     I                  YC,
>     I                  xSize, ySize,
>     I                  useExch2ioLayOut,
>     I                  zeroBuff,
>     I                  myThid )
>      _END_MASTER( myThid )
>      CALL BAR2( myThid )
>
>
>
> --
> Katherine J. Quinn
> Atmospheric and Environmental Research         voice: 781-761-2234
> 131 Hartwell Avenue                              fax: 781-761-2299
> Lexington, MA  02421-3126                     e-mail: kquinn at aer.com
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 23 Aug 2012 11:03:09 -0700
> From: Matthew Mazloff <mmazloff at ucsd.edu>
> To: <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] using gather/scatter to work with global
>       fields
> Message-ID: <C862A330-E66C-42A4-BE97-E2F1F95842B2 at ucsd.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hi Katherine
>
> Do you have
> defined.  If you do, perhaps try it with it undefined.
>
> -Matt
>
>
>
> On Aug 23, 2012, at 10:40 AM, Katherine Quinn wrote:
>
>> Hi all,
>> Within the MITgcm code (not matlab) I need to gather tiled variables
>> into a global array, specifically I'm trying to gather XC and YC.
>> I'm using the subroutine gather_2d_r4, which suggests "barrier
>> calls" before and after but it seems no matter what various barrier
>> calls I use, when I look at the global array there's chunks of tiles
>> missing.  Other relevant info - the MITgcm setup is for ecco version
>> 4 runs, with all_exch2 turned on.
>> Here's the relevant portions of my code, please suggest what I'm
>> doing wrong:
>>
>> C     == Global variables ===
>> #include "SIZE.h"
>> #include "EEPARAMS.h"
>> #include "EESUPPORT.h"
>> #include "PARAMS.h"
>> #ifdef ALLOW_EXCH2
>> # include "W2_EXCH2_SIZE.h"
>> # include "W2_EXCH2_TOPOLOGY.h"
>> # include "W2_EXCH2_PARAMS.h"
>> #endif /* ALLOW_EXCH2 */
>> #include "EEBUFF_SCPU.h"
>> #include "GRID.h"
>>
>> C     INPUT/OUTPUT PARAMETERS:
>> C     == Routine arguments ==
>> C     myThid - Thread number for this instance of the routine.
>>    INTEGER  myThid
>>
>> C     LOCAL VARIABLES:
>>    LOGICAL zeroBuff, useExch2ioLayOut
>>    INTEGER xSize, ySize
>> #ifdef ALLOW_EXCH2
>>    _RL  XC_global(exch2_global_Nx,exch2_global_Ny)
>>    _RL  YC_global(exch2_global_Nx,exch2_global_Ny)
>> #else  /* ALLOW_EXCH2 */
>>    _RS  XC_global(Nx,Ny)
>>    _RS  YC_global(Nx,Ny)
>> #endif /* ALLOW_EXCH2 */
>>
>> C Set dimensions and flags (e.g. mdsio_write_field.F)
>>    xSize = Nx
>>    ySize = Ny
>>    useExch2ioLayOut = .FALSE.
>>    zeroBuff = .TRUE.
>> #ifdef ALLOW_EXCH2
>>    IF ( W2_useE2ioLayOut ) THEN
>>       xSize = exch2_global_Nx
>>       ySize = exch2_global_Ny
>>       useExch2ioLayOut = .TRUE.
>>    ENDIF
>> #endif /* ALLOW_EXCH2 */
>>
>> C gather XC and YC into global model grid
>>
>>    CALL BAR2( myThid )
>>    _BEGIN_MASTER( myThid )
>>    CALL GATHER_2D_R4(
>>   O                  XC_global,
>>   I                  XC,
>>   I                  xSize, ySize,
>>   I                  useExch2ioLayOut,
>>   I                  zeroBuff,
>>   I                  myThid )
>>    _END_MASTER( myThid )
>>    CALL BAR2( myThid )
>>
>>    _BEGIN_MASTER( myThid )
>>    CALL GATHER_2D_R4(
>>   O                  YC_global,
>>   I                  YC,
>>   I                  xSize, ySize,
>>   I                  useExch2ioLayOut,
>>   I                  zeroBuff,
>>   I                  myThid )
>>    _END_MASTER( myThid )
>>    CALL BAR2( myThid )
>>
>>
>>
>> --
>> Katherine J. Quinn
>> Atmospheric and Environmental Research         voice: 781-761-2234
>> 131 Hartwell Avenue                              fax: 781-761-2299
>> Lexington, MA  02421-3126                     e-mail: kquinn at aer.com
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 23 Aug 2012 14:50:53 -0400
> From: Katherine Quinn <kquinn at aer.com>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] using gather/scatter to work with global
>       fields
> Message-ID: <50367B8D.4000106 at aer.com>
> Content-Type: text/plain; CHARSET=US-ASCII; format=flowed
>
> Hi Matt,
> Any other ideas?  All this barrier, process, tiles stuff is driving me
> batty.
> cheers, Katy
>
> Katherine Quinn wrote:
>> Matthew Mazloff mmazloff at ucsd.edu
>> Thu Aug 23 14:03:09 EDT 2012
>>
>> Hi Katherine
>>
>> Do you have
>> defined.  If you do, perhaps try it with it undefined.
>>
>> -Matt
>>
>> Katherine Quinn wrote:
>>> Hi all,
>>> Within the MITgcm code (not matlab) I need to gather tiled variables
>>> into a global array, specifically I'm trying to gather XC and YC.  I'm
>>> using the subroutine gather_2d_r4, which suggests "barrier calls"
>>> before and after but it seems no matter what various barrier calls I
>>> use, when I look at the global array there's chunks of tiles missing.
>>> Other relevant info - the MITgcm setup is for ecco version 4 runs,
>>> with all_exch2 turned on.
>>> Here's the relevant portions of my code, please suggest what I'm doing
>>> wrong:
>>>
>>> C     == Global variables ===
>>> #include "SIZE.h"
>>> #include "EEPARAMS.h"
>>> #include "EESUPPORT.h"
>>> #include "PARAMS.h"
>>> #ifdef ALLOW_EXCH2
>>> # include "W2_EXCH2_SIZE.h"
>>> # include "W2_EXCH2_TOPOLOGY.h"
>>> # include "W2_EXCH2_PARAMS.h"
>>> #endif /* ALLOW_EXCH2 */
>>> #include "EEBUFF_SCPU.h"
>>> #include "GRID.h"
>>>
>>> C     INPUT/OUTPUT PARAMETERS:
>>> C     == Routine arguments ==
>>> C     myThid - Thread number for this instance of the routine.
>>>     INTEGER  myThid
>>>
>>> C     LOCAL VARIABLES:
>>>     LOGICAL zeroBuff, useExch2ioLayOut
>>>     INTEGER xSize, ySize
>>> #ifdef ALLOW_EXCH2
>>>     _RL  XC_global(exch2_global_Nx,exch2_global_Ny)
>>>     _RL  YC_global(exch2_global_Nx,exch2_global_Ny)
>>> #else  /* ALLOW_EXCH2 */
>>>     _RS  XC_global(Nx,Ny)
>>>     _RS  YC_global(Nx,Ny)
>>> #endif /* ALLOW_EXCH2 */
>>>
>>> C Set dimensions and flags (e.g. mdsio_write_field.F)
>>>     xSize = Nx
>>>     ySize = Ny
>>>     useExch2ioLayOut = .FALSE.
>>>     zeroBuff = .TRUE.
>>> #ifdef ALLOW_EXCH2
>>>     IF ( W2_useE2ioLayOut ) THEN
>>>        xSize = exch2_global_Nx
>>>        ySize = exch2_global_Ny
>>>        useExch2ioLayOut = .TRUE.
>>>     ENDIF
>>> #endif /* ALLOW_EXCH2 */
>>>
>>> C gather XC and YC into global model grid
>>>
>>>     CALL BAR2( myThid )
>>>     _BEGIN_MASTER( myThid )
>>>     CALL GATHER_2D_R4(
>>>    O                  XC_global,
>>>    I                  XC,
>>>    I                  xSize, ySize,
>>>    I                  useExch2ioLayOut,
>>>    I                  zeroBuff,
>>>    I                  myThid )
>>>     _END_MASTER( myThid )
>>>     CALL BAR2( myThid )
>>>
>>>     _BEGIN_MASTER( myThid )
>>>     CALL GATHER_2D_R4(
>>>    O                  YC_global,
>>>    I                  YC,
>>>    I                  xSize, ySize,
>>>    I                  useExch2ioLayOut,
>>>    I                  zeroBuff,
>>>    I                  myThid )
>>>     _END_MASTER( myThid )
>>>     CALL BAR2( myThid )
>>>
>>>
>>>
>>
>
> --
> Katherine J. Quinn
> Atmospheric and Environmental Research         voice: 781-761-2234
> 131 Hartwell Avenue                              fax: 781-761-2299
> Lexington, MA  02421-3126                     e-mail: kquinn at aer.com
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 23 Aug 2012 18:37:05 -0700
> From: Matthew Mazloff <mmazloff at ucsd.edu>
> To: <mitgcm-support at mitgcm.org>
> Subject: Re: [MITgcm-support] using gather/scatter to work with global
>       fields
> Message-ID: <E0AC6D20-5E4E-418E-A32D-3BA2433A04A7 at ucsd.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hi Katy,
>
> The only time I've seen this before is if the model run ends before it
> has had time to finish writing some of the output.  If this is showing
> up in writing of XC and YC, are you running many timesteps?  I could
> see this happening if you only run 1 timestep -- try running for longer.
>
> Otherwise, I am afraid I am out of ideas.
>
> -Matt
>
>
> On Aug 23, 2012, at 11:50 AM, Katherine Quinn wrote:
>
>> Hi Matt,
>> Any other ideas?  All this barrier, process, tiles stuff is driving
>> me batty.
>> cheers, Katy
>>
>> Katherine Quinn wrote:
>>> Matthew Mazloff mmazloff at ucsd.edu
>>> Thu Aug 23 14:03:09 EDT 2012
>>> Hi Katherine
>>> Do you have
>>> defined.  If you do, perhaps try it with it undefined.
>>> -Matt
>>> Katherine Quinn wrote:
>>>> Hi all,
>>>> Within the MITgcm code (not matlab) I need to gather tiled
>>>> variables into a global array, specifically I'm trying to gather
>>>> XC and YC.  I'm using the subroutine gather_2d_r4, which suggests
>>>> "barrier calls" before and after but it seems no matter what
>>>> various barrier calls I use, when I look at the global array
>>>> there's chunks of tiles missing.  Other relevant info - the MITgcm
>>>> setup is for ecco version 4 runs, with all_exch2 turned on.
>>>> Here's the relevant portions of my code, please suggest what I'm
>>>> doing wrong:
>>>>
>>>> C     == Global variables ===
>>>> #include "SIZE.h"
>>>> #include "EEPARAMS.h"
>>>> #include "EESUPPORT.h"
>>>> #include "PARAMS.h"
>>>> #ifdef ALLOW_EXCH2
>>>> # include "W2_EXCH2_SIZE.h"
>>>> # include "W2_EXCH2_TOPOLOGY.h"
>>>> # include "W2_EXCH2_PARAMS.h"
>>>> #endif /* ALLOW_EXCH2 */
>>>> #include "EEBUFF_SCPU.h"
>>>> #include "GRID.h"
>>>>
>>>> C     INPUT/OUTPUT PARAMETERS:
>>>> C     == Routine arguments ==
>>>> C     myThid - Thread number for this instance of the routine.
>>>>    INTEGER  myThid
>>>>
>>>> C     LOCAL VARIABLES:
>>>>    LOGICAL zeroBuff, useExch2ioLayOut
>>>>    INTEGER xSize, ySize
>>>> #ifdef ALLOW_EXCH2
>>>>    _RL  XC_global(exch2_global_Nx,exch2_global_Ny)
>>>>    _RL  YC_global(exch2_global_Nx,exch2_global_Ny)
>>>> #else  /* ALLOW_EXCH2 */
>>>>    _RS  XC_global(Nx,Ny)
>>>>    _RS  YC_global(Nx,Ny)
>>>> #endif /* ALLOW_EXCH2 */
>>>>
>>>> C Set dimensions and flags (e.g. mdsio_write_field.F)
>>>>    xSize = Nx
>>>>    ySize = Ny
>>>>    useExch2ioLayOut = .FALSE.
>>>>    zeroBuff = .TRUE.
>>>> #ifdef ALLOW_EXCH2
>>>>    IF ( W2_useE2ioLayOut ) THEN
>>>>       xSize = exch2_global_Nx
>>>>       ySize = exch2_global_Ny
>>>>       useExch2ioLayOut = .TRUE.
>>>>    ENDIF
>>>> #endif /* ALLOW_EXCH2 */
>>>>
>>>> C gather XC and YC into global model grid
>>>>
>>>>    CALL BAR2( myThid )
>>>>    _BEGIN_MASTER( myThid )
>>>>    CALL GATHER_2D_R4(
>>>>   O                  XC_global,
>>>>   I                  XC,
>>>>   I                  xSize, ySize,
>>>>   I                  useExch2ioLayOut,
>>>>   I                  zeroBuff,
>>>>   I                  myThid )
>>>>    _END_MASTER( myThid )
>>>>    CALL BAR2( myThid )
>>>>
>>>>    _BEGIN_MASTER( myThid )
>>>>    CALL GATHER_2D_R4(
>>>>   O                  YC_global,
>>>>   I                  YC,
>>>>   I                  xSize, ySize,
>>>>   I                  useExch2ioLayOut,
>>>>   I                  zeroBuff,
>>>>   I                  myThid )
>>>>    _END_MASTER( myThid )
>>>>    CALL BAR2( myThid )
>>>>
>>>>
>>>>
>>
>> --
>> Katherine J. Quinn
>> Atmospheric and Environmental Research         voice: 781-761-2234
>> 131 Hartwell Avenue                              fax: 781-761-2299
>> Lexington, MA  02421-3126                     e-mail: kquinn at aer.com
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 24 Aug 2012 11:43:15 +1000
> From: Andreas Klocker <andreas.klocker at anu.edu.au>
> To: mitgcm-support at mitgcm.org
> Subject: [MITgcm-support] vertical velocities in high-res runs
> Message-ID: <5036DC33.3080200 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi everyone,
>
> I've got a little problem with vertical velocities in I high-res run which I don't understand and I have no idea how to get rid of that problem.
>
> The model is a channel with realistic topography, 1/20 deg resolution, 150 vertical layers, see below data file for more info.
>
> The problem: As you can see in the attached figure of the vertical velocity I always get two lines (which not quite follow isopycnals) which have very strong grid-scale vertical velocities along them which do not make sense. I tried both advection scheme 7 and 33 and it doesn't make much of a difference. When I add more Smagorinsky visc. the whole velocity filed gets much smoother and less energetic but the problem of the grid-scale noise doesn't change. If I use KPP it produces large vertical diff. in those regions but the problem doesn't go away...I'm not sure what else to try...
>
> Has anyone got an idea what could cause that problem and how to solve it?
>
> cheers,
> Andreas
>
> # Continuous equation parameters
> &PARM01
> tRef               = 150*5.0,
> sRef               = 150*34.5,
> viscAr= 5.6614e-04,
> diffKrT=1.e-5,
> diffKrS=1.e-5,
> no_slip_sides=.FALSE.,
> no_slip_bottom=.TRUE.,
> rhonil=1027.5,
> rhoConstFresh=999.8,
> eosType='JMD95Z',
> # hFacMinDr=50.,
> # hFacMin=0.5,
> hFacInf=0.01,
> hFacSup=2.,
> select_rStar=2,
> nonlinFreeSurf=4,
> implicitDiffusion=.TRUE.,
> implicitViscosity=.TRUE.,
> # ivdc_kappa=100.,
> viscC4Leith=2.,
> viscC4Leithd=2.,
> viscC2Leith=1.5,
> viscC2Leithd=1.5,
> viscA4GridMax=0.5,
> viscC2Smag=1.5,
> # viscA4=2.0E8,
> # viscAhD=60,
> useAreaViscLength=.TRUE.,
> sideDragFactor=0.,
> # highOrderVorticity  = .TRUE.,
> useAbsVorticity=.TRUE.,
> selectVortScheme=2,
> selectKEscheme=3,
> StaggerTimeStep=.TRUE.,
> vectorInvariantMomentum=.TRUE.,
> implicitFreeSurface=.TRUE.,
> exactConserv=.TRUE.,
> # debuglevel=4,
> convertFW2Salt=-1
> useRealFreshWaterFlux=.TRUE.,
> useSingleCPUio=.TRUE.,
> globalFiles=.TRUE.,
> allowFreezing=.TRUE.,
> # useJamartWetPoints=.TRUE.,
> &
>
> --
> ===============================================
> Dr. Andreas Klocker
> Research Fellow
>
> Center of Excellence for Climate System Science
> &
> Geophysical Fluid Dynamics Group
> Research School of Earth Sciences
> Room J7.221, Jaeger 7 Building
> The Australian National University
> Canberra ACT 0200 Australia
>
> T:     +61 2 6125 0920
> M:     +61 437 870 182
> W:     http://web.mit.edu/aklocker/www/
> skype: andiklocker
> ===============================================
>
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
> End of MITgcm-support Digest, Vol 110, Issue 17
> ***********************************************
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
> _______________________________________________
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> http://mitgcm.org/mailman/listinfo/mitgcm-support

```