[MITgcm-support] EXF and Calendar Package
Martin Losch
Martin.Losch at awi.de
Wed Aug 6 03:16:31 EDT 2014
Hi Andres,
the files you posted do compile on my computer, but you didn’t post the correct data/input files.
I wonder why you have 40 CPUs for a 100 by 80 domain. For testing I would use 1CPU and then run the model interactively. That’s what I did (nPx/nPy=1, nSx=5, nSy=8).
The “data”-file does not contain the appropriate delR. I replaced it with the “data.odt” that you posted earlier (not a good idea to post an ascii file in a specific text editor format). Then I have no problems reading the file, except that you put in namelist parameters, that do not exist:
(PID.TID 0000.0001)
(PID.TID 0000.0001) INI_PARMS ; starts to read PARM01
(PID.TID 0000.0001) INI_PARMS ; read PARM01 : OK
(PID.TID 0000.0001) INI_PARMS ; starts to read PARM02
(PID.TID 0000.0001) INI_PARMS ; read PARM02 : OK
(PID.TID 0000.0001) INI_PARMS ; starts to read PARM03
(PID.TID 0000.0001) INI_PARMS ; read PARM03 : OK
(PID.TID 0000.0001) INI_PARMS ; starts to read PARM04
(PID.TID 0000.0001) INI_PARMS ; read PARM04 : OK
(PID.TID 0000.0001) INI_PARMS ; starts to read PARM05
At line 3212 of file ini_parms.f (unit = 11, file = '/var/folders/r2/jkk7t8vd2vjcb7h_gp0_g19h0000gq/T/gfortrantmp0GwsWQ')
Fortran runtime error: Cannot match namelist object name evapfile
BTW, that’s also what your system error file dotEfile.odt suggests.
Please have a look at model/src/ini_parms.F to find out which parameters you can specifiy in the namelists in “data”
- after commenting out
# evapfile='evaporation_data.bin'
# precipfile=‘precipitation_data.bin’
The model stops here:
from PACKAGES_CHECK: run-time control flag useGMRedi is set
but pkg/gmredi was not compiled (ALLOW_GMREDI undef).
==> Re-compile with pkg "gmredi" in file "packages.conf"
S/R ALL_PROC_DIE: ending the run
STOP ABNORMAL END: S/R PACKAGE_ERROR_MSG
I guess the error message is self-explanatory, and then after commenting out useGMredi = .TRUE. in data.pkg, I get
CONFIG_CHECK: #undef ALLOW_NONHYDROSTATIC and
CONFIG_CHECK: nonHydrostatic is TRUE
CONFIG_CHECK: detected 1 fatal error(s)
S/R ALL_PROC_DIE: ending the run
STOP ABNORMAL END: S/R CONFIG_CHECK
again, it should be clear what this means (if you want to use nonHydrostatic=.TRUE. you have to set ALLOW_NONHYDROSTATAIC in CPP_OPTIONS.h). It also tells me, that you posted a combination of CPP-flags and namelist parameters that are not compatible. Either that’s a mistake or you haven’t even gotten that far.
Hope that helps,
Martin
On Aug 6, 2014, at 12:11 AM, Andres Fernandez <andres.fernandez at nyu.edu> wrote:
> Hi Martin, I have been trying to work off of global_with_exf .... Have not succeeded yet.
>
> Here is the link with my input directories and code directories:
>
> https://www.dropbox.com/sh/l3ajr61zbb7v94u/AADX32m0dSoDj69apzgFlfvLa
>
> Thank you in advance!
> Andres
>
> Andres Fernandez
> Undergraduate Chemical Engineering
> New York University Abu Dhabi - 2015
> Mobile (USA): +1 646 717 2231
>
> *Think before printing. The environment is in our hands
>
>
>
> On Tue, Aug 5, 2014 at 2:27 AM, Martin Losch <Martin.Losch at awi.de> wrote:
> Hi Andres,
>
> dz(k+1)/dz(k) < sqrt(2) is a rule of thumb (that you should follow). The finite volume discretization requires some averaging to grid cell interfaces and currently (and I don’t believe that this will change) this averaging requires that the grid spacing varies smoothly to avoid large discretrization errors. The same is true for the horizontal grid spacing, but in the horizontal very irregular grid appear unnatural, right?
>
> Can you gzip/tar your code and input directories and put them somewhere to download and look at (please don’t send large files to this list)?
>
> For problems like yours, it makes sense to start from a working example and change it file by file to the actual configuration that you want to run, so that you can identify the problems individually.
>
> Martin
>
> On Aug 5, 2014, at 12:46 AM, Andres Fernandez <andres.fernandez at nyu.edu> wrote:
>
> > Data file, STDOUT.0000 and the .e file that is generated are attached...
> > the STDERR.0000 is blank, so i did not attach it.
> >
> > @Nicolas, I was not aware of this limitation of irregular spacing. Any comments from other users?
> >
> >
> > Thank you all!
> >
> >
> > Andres Fernandez
> > Undergraduate Chemical Engineering
> > New York University Abu Dhabi - 2015
> > Mobile (USA): +1 646 717 2231
> >
> > *Think before printing. The environment is in our hands
> >
> >
> >
> > On Mon, Aug 4, 2014 at 5:23 PM, Dustin Carroll <dcarroll at uoregon.edu> wrote:
> > Hi Andres,
> >
> > It would be helpful for you to share your data file…plus the last few lines from STDOUT.0000 and the output from STDERR.0000.
> >
> > Dustin
> >
> > On Aug 4, 2014, at 7:15 PM, Andres Fernandez <andres.fernandez at nyu.edu> wrote:
> >
> >> Dear Dustin,
> >> I realized I had a comma missing in the list when copying you the delR declaration. I have an irregular spacing declared as follows: So, thank you.
> >>
> >> delR= 5.0,
> >> 5.0,
> >> 5.0,
> >> 5.0,
> >> 5.0,
> >> 5.0,
> >> 5.0,
> >> 5.0,
> >> 5.0,
> >> 5.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 10.0,
> >> 50.0,
> >> 50.0,
> >> 50.0,
> >> 50.0,
> >> 50.0,
> >> &
> >>
> >>
> >>
> >>
> >> ** I do still get an error though!
> >>
> >> forrtl: severe (24): end-of-file during read, unit 11, file .../fortzlTn72 line 8, position 0
> >> "" ... / fort5xkez2
> >> "" .../ fort2YWOn2fort5xkez2
> >> and a bunch more files..
> >>
> >> Unsure if you could assist with this error?
> >>
> >> @Jean- Michel, I have ran a couple models before and the struggle I have right now is with external forcing, I want to add precipitation and evaporation and I am not succeeding. I have not found any comprehensive information on the manual.
> >>
> >>
> >>
> >> Andres Fernandez
> >> Undergraduate Chemical Engineering
> >> New York University Abu Dhabi - 2015
> >> Mobile (USA): +1 646 717 2231
> >>
> >> *Think before printing. The environment is in our hands
> >>
> >>
> >>
> >> On Mon, Aug 4, 2014 at 3:58 PM, Dustin Carroll <dcarroll at uoregon.edu> wrote:
> >> Hi Andres,
> >>
> >> The vertical grid spacing (delZ, delP, or delR) is set in your data file. You can specific with a *.bin file, i.e delRfile=‘dz. bin’
> >>
> >> or without a bin file...delR=100*10
> >>
> >> Cheers,
> >> Dustin
> >>
> >>
> >>
> >>
> >> On Aug 4, 2014, at 5:43 PM, Andres Fernandez <andres.fernandez at nyu.edu> wrote:
> >>
> >>> Dear support,
> >>>
> >>> I get the (PID.TID 0001.0001) *** ERROR *** S/R INI_PARMS: No value for delZ/delP/delR at k = 16 ....25
> >>> I am unsure where to set these initial conditions... or is this when I build it?
> >>>
> >>> Did I build it incorrectly?
> >>>
> >>> Thank you
> >>>
> >>> Andres Fernandez
> >>> Undergraduate Chemical Engineering
> >>> New York University Abu Dhabi - 2015
> >>> Mobile (USA): +1 646 717 2231
> >>>
> >>> *Think before printing. The environment is in our hands
> >>>
> >>>
> >>>
> >>> On Thu, Jul 31, 2014 at 8:34 PM, Dustin Carroll <dcarroll at uoregon.edu> wrote:
> >>> Hi Andres,
> >>>
> >>> You can debug this further by looking at your STDERR.0000 file for more specific error information... also take a look at STDOUT.0000 to see where your model crashed. You probably have a syntax error in one of your data files.
> >>>
> >>> Cheers,
> >>> Dustin
> >>>
> >>>
> >>> On Jul 31, 2014, at 9:21 PM, Andres Fernandez <andres.fernandez at nyu.edu> wrote:
> >>>
> >>>> So I recompiled the executable; and placed it in my input folder;
> >>>>
> >>>> I have the following folders:
> >>>>
> >>>> data
> >>>> data.cal
> >>>> data.exf
> >>>> data.obcs
> >>>> data.pkg
> >>>> data.rbcs
> >>>> eedata
> >>>> eedata.mth
> >>>> executable
> >>>> (some binary files)
> >>>>
> >>>> And I get this error when I run:
> >>>> ABNORMAL END: S/R INI_PARMS
> >>>>
> >>>> Thank you for your assistance.
> >>>>
> >>>>
> >>>> Best,
> >>>> Andres
> >>>>
> >>>> Andres Fernandez
> >>>> Mobile (USA): +1 646 717 2231
> >>>>
> >>>> *Think before printing. The environment is in our hands
> >>>>
> >>>>
> >>>>
> >>>> On Thu, Jul 31, 2014 at 3:46 PM, Dustin Carroll <dcarroll at uoregon.edu> wrote:
> >>>> Hi Andres,
> >>>>
> >>>> also, under code/packages.conf add the line:
> >>>>
> >>>> cal
> >>>>
> >>>> and recompile. Then you should be fine with useEXF=.TRUE., in your data.pkg file.
> >>>>
> >>>> Cheers,
> >>>>
> >>>>
> >>>> Dustin
> >>>>
> >>>> On Jul 31, 2014, at 3:53 PM, Andres Fernandez <andres.fernandez at nyu.edu> wrote:
> >>>>
> >>>>> Thank you!
> >>>>> So building a code with the following packages should allow me to use external forcing correctly?
> >>>>>
> >>>>> # Packages
> >>>>> &PACKAGES
> >>>>> useOBCS=.TRUE.,
> >>>>> usePtracers=.FALSE.,
> >>>>> useRBCS=.FALSE.,
> >>>>> useEXF=.TRUE.,
> >>>>> #useLayers=.TRUE.,
> >>>>> &
> >>>>>
> >>>>> Best,
> >>>>> Andres
> >>>>>
> >>>>> Andres Fernandez
> >>>>> Undergraduate Chemical Engineering
> >>>>> New York University Abu Dhabi - 2015
> >>>>> Mobile (USA): +1 646 717 2231
> >>>>>
> >>>>> *Think before printing. The environment is in our hands
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Thu, Jul 31, 2014 at 12:08 PM, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
> >>>>> Hi Andres,
> >>>>>
> >>>>> Since pkg/exf requires the use of calendar package (pkg/cal),
> >>>>> this later (pkg/cal) is always compiled (MITgcm/pkg/pkg_depend)
> >>>>> and used (in: model/src/packages_boot.F: IF (useEXF) useCAL = .TRUE.)
> >>>>> anytime pkg/exf is compiled and used.
> >>>>>
> >>>>> Cheers,
> >>>>> Jean-Michel
> >>>>>
> >>>>> On Thu, Jul 31, 2014 at 11:30:08AM -0400, Andres Fernandez wrote:
> >>>>> > Dear MITgcm support,
> >>>>> >
> >>>>> > I have been trying to run the external forcing package; and I have yet to
> >>>>> > succeed, but I was wondering if a reason why it is not working is because I
> >>>>> > do not have the calendar package?
> >>>>> >
> >>>>> > Thank you,
> >>>>> >
> >>>>> > *Andres Fernandez*
> >>>>> > Mobile (USA): +1 646 717 2231
> >>>>> >
> >>>>> > *Think before printing. The environment is in our hands
> >>>>>
> >>>>> > _______________________________________________
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> >>>>> > MITgcm-support at mitgcm.org
> >>>>> > http://mitgcm.org/mailman/listinfo/mitgcm-support
> >>>>>
> >>>>>
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> > <STDOUT.0000.odt><DATA.odt><dotEfile.odt>_______________________________________________
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