[MITgcm-support] EXF and Calendar Package
Andres Fernandez
andres.fernandez at nyu.edu
Thu Aug 7 20:18:22 EDT 2014
It seems that by turning OBCS = FALSE in data.pkg it solves the problem;
One needs to #undef USE_EXF_INTERPOLATION or else it does not work.
Cheers,
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, Aug 7, 2014 at 6:52 PM, Andres Fernandez <andres.fernandez at nyu.edu>
wrote:
> Thank you all for your tremendous support !
>
> Things seem to be moving forward. I just do not seem to be able to
> successfully run a basic evaporation forcing (EXF_READ_EVAP) I have done
> the following:
>
> in the EXE_OPTIONS.h I added the following:
>
> C Bulk formulae related flags.
> #undef ALLOW_ATM_TEMP
> #undef ALLOW_ATM_WIND
> #undef ALLOW_DOWNWARD_RADIATION
> #undef ALLOW_RUNOFF
> C I added EXF_READ_EVAP below
> #define EXF_READ_EVAP
>
>
> I compiled....
>
> and then the data.exf file I have and the data file are the following:
> https://www.dropbox.com/sh/l3ajr61zbb7v94u/AADX32m0dSoDj69apzgFlfvLa
>
> I have no latitude and longitude information on the model; that is why I
> commented out longitude and latitude. I also added #undef
> USE_EXF_INTERPOLATION because it required latitude longitude, if I am not
> mistaken?
>
> and I get an error:
>
>
> forrtl: severe (24): end-of-file during read
>
> the STDOUT ends here:
> (PID.TID 0000.0001) EXF_READPARMS: reading EXF_NML_01
> (PID.TID 0000.0001) EXF_READPARMS: reading EXF_NML_02
> (PID.TID 0000.0001) EXF_READPARMS: reading EXF_NML_03
> (PID.TID 0000.0001) EXF_READPARMS: reading EXF_NML_04
> (PID.TID 0000.0001) EXF_READPARMS: reading EXF_NML_OBCS
>
>
> Thank you for all your help!
>
> *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, Aug 7, 2014 at 1:42 AM, Jean-Michel Campin <jmc at ocean.mit.edu>
> wrote:
>
>> Hi All,
>>
>> I am not going to comment too much on this specific error message
>> (since, given the information in this message, it's going to be
>> very difficult to reproduce it from a fresh built) but rather on
>> the circumstances where a full cleaning ("make Clean" or even the
>> stronger "make CLEAN") is needed.
>>
>> It's generally OK to just type "make" when changes have been made in
>> some source files (*.h or *.F) while keeping the location of any source
>> file unchanged.
>>
>> Otherwise, any time one or more source file is moved around (for instance,
>> added to one of the setup-specific local dir that is given in the "-mods"
>> argument list of genmake2) or a package is added (to the packages.conf
>> file) or a preprocessor (CPP) header file (*_OPTIONS.h) is changed,
>> or, for adjoint built, a flow directive or AD diff list is changed,
>> then it's safer to go for a full clean: "make Clean"
>> before re-building a new executable (make makefile ; make depend ; make).
>>
>> And finally, it could be very useful to check for any error (not so much
>> warnings that are more dependent on the preprocessor CPP version and
>> default options) at the "make depend" stage (although a fail at this stage
>> might not prevent to continue the building sequence): these errors
>> are generally easy to figure out and therefore easy to fix.
>>
>> Note that, in the special case of an OpenAD built (without a "make depend"
>> stage), the remarks above don't apply and a full cleaning might be safer
>> (to be confirmed).
>>
>> Cheers,
>> Jean-Michel
>>
>> On Wed, Aug 06, 2014 at 07:17:47PM -0400, Andres Fernandez wrote:
>> > 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
>> > > > >>>>>
>> > > > >>>>> > _______________________________________________
>> > > > >>>>> > MITgcm-support mailing list
>> > > > >>>>> > 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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