[MITgcm-support] EXF and Calendar Package

Andres Fernandez andres.fernandez at nyu.edu
Wed Aug 6 19:17:47 EDT 2014 

When I  add gmredi to packages.conf  I get the following error when
compiling:

Any comments on this? How do define the type?

mredi_calc_diff.f(3305): error #6404: This name does not have a type, and
must have an explicit type.   [GAD_TR1]
           IF (tracerIdentity .LT. GAD_TR1) THEN
-----------------------------------^
compilation aborted for gmredi_calc_diff.f (code 1)
make[1]: *** [gmredi_calc_diff.o] Error 1
make[1]: *** Waiting for unfinished jobs....






*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 Wed, Aug 6, 2014 at 3:16 AM, Martin Losch <Martin.Losch at awi.de> wrote:

> 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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> > >>>>>
> > >>>>>
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> > >
> <STDOUT.0000.odt><DATA.odt><dotEfile.odt>_______________________________________________
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