[MITgcm-support] Forcing files in data.dic (biogeochemistry)
Jonny Williams
Jonny.Williams at bristol.ac.uk
Thu Aug 14 05:35:18 EDT 2014
Hi Jean-Michel
Thanks again for your input on this. It seems that my problem simply
related to the fact that I wasn't specifying niter0! It seems to be working
fine now which is great. The pickupSuff option is very helpful, and worked
even when I was changing timestep length, which has caused me problems in
the past.
Thanks again
Jonny
On 12 August 2014 16:17, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
> Hi Jonny,
>
> Just 2 comments:
> 1) regarding this:
> > Is there anything I need to do apart from set pickupSuff='ckptA', in the
> > PARM03 namelist for this to work? Do I also need to set niter0 also as I
> > have needed to in the past? I have attached my data file in case this is
> of
> > any use?
> You need to specify when the simulation starts (either startTime or
> nIter0),
> unless you want to use the default (startTime = baseTime , nIter0=0).
> This is not affected by setting (or not) pickupSuff.
> All these parameters are reported in the "Model configuration" part of
> the standard output file (STDOUT.*).
>
> 2) regarding the problem you described:
> I would need more information (data.pkg, data.ptracers, data.gchem,
> data.dic, data.obcs) to have a chance to check what's might be happening.
>
> Cheers,
> Jean-Michel
>
> On Mon, Aug 11, 2014 at 06:19:27PM +0100, Jonny Williams wrote:
> > Hi Jean-Michel
> >
> > Thanks very much indeed for that, I wasn't aware of your suggestion (a)
> >
> > Unfortunately I am still having issues with restarting my model with the
> > DIC, GCHEM and PTRACERS packages turned on.
> >
> > What seems to be happening is that when I restart from a pickup, all of
> the
> > ptracers*.nc output gets initialised to zeros around the edges. The
> > alkalinity, PO4 etc seem to be able to recover but the DIC variable
> simply
> > goes to NaNs everywhere apart from at the edges, where it is always zero.
> >
> > I am assuming that this problem must have something to do with the OBCS
> > package?
> >
> > Is there anything I need to do apart from set pickupSuff='ckptA', in the
> > PARM03 namelist for this to work? Do I also need to set niter0 also as I
> > have needed to in the past? I have attached my data file in case this is
> of
> > any use?
> >
> > The modules themselves are working fine, it's just that they don't know
> how
> > to get going from pickups I think! The model runs fine and gives
> reasonable
> > output when starting from scratch (i.e. niter0=0).
> >
> > Thank you!
> >
> > Jonny
> >
> >
> > On 5 August 2014 17:14, Jean-Michel Campin <jmc at ocean.mit.edu> wrote:
> >
> > > Hi Jonny,
> > >
> > > Just a comment regarding the symbolic link for pickup files:
> > > a) you could by-pass this symbolic link step and specify,
> > > in main parameter file "data", in 3rd namelist (/PARM03/):
> > > pickupSuff='ckptA',
> > > so that the model will load-in pickup*.ckptA.* files instead of
> > > pickup*.[nIter0].* files (pickup*.0000012960.* in your case).
> > > b) an other option, if you want to keep the set of pickup files
> > > that you use to restart, is to rename all the pickup*.ckptA.* files
> > > to pickup*.[nIter0].* (I often do that, so that I can re-run
> > > some segments of a multi-segment simulation).
> > > You could find the script "rn_pickup" in MITgcm_contrib/jmc_script
> > > that will do this renaming (just typing "rn_pickup" prints
> > > how to use it; and in your case, "rn_pickup A" should do the
> > > remaning).
> > >
> > > Cheers,
> > > Jean-Michel
> > >
> > > On Mon, Aug 04, 2014 at 12:01:23PM +0100, Jonny Williams wrote:
> > > > ... as often happens though, I have now uncovered a further error
> which
> > > > occurs when I try to restart the model using global pickup files.
> > > >
> > > > Previously, when I have run without the biogeochemistry packages
> (DIC,
> > > > PTRACERS, GCHM) I created a symbolic link such as this...
> > > >
> > > > *pickup_dic.0000012960.meta -> pickup_dic.ckptA.meta*
> > > >
> > > > ... to indicate that I want to use the ckptA file to restart the run
> from
> > > > timestep 12960. I now that I also have pickup files called
> > > >
> > > > *pickup_ptracers.ckptA.meta/data *
> > > > and
> > > > *pickup_dic.ckptA.meta/data *
> > > >
> > > > *... *for the DIC and PTRACERS packages.
> > > >
> > > > I have created 2 further sets symbolic links thus...
> > > >
> > > > *pickup_dic.0000012960.meta/data -> pickup_dic.ckptA.meta/data*
> > > > and
> > > > *pickup_ptracers.0000012960.meta/data ->
> pickup_ptracers.ckptA.meta/data*
> > > >
> > > > Unfortunately I am getting the following error out and the model is
> not
> > > > running...
> > > >
> > > > *forrtl: severe (64): input conversion error, unit -5, file Internal
> > > > Formatted Read*
> > > > *Image PC Routine Line
> > > Source
> > > > *
> > > > *mitgcmuv 0000000000BAB3FE Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 0000000000BA973A Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 000000000051D78C Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 00000000005CE598 Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 00000000007410B0 Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 000000000070FE8E Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 0000000000735AD2 Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 000000000075BCEF Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 000000000075BF19 Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 00000000006A2B14 Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 0000000000400F26 Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 0000000000C5DBA4 Unknown Unknown
> > > > Unknown*
> > > > *mitgcmuv 0000000000400D8D Unknown Unknown
> > > > Unknown*
> > > >
> > > > Is there anything else that anyone can think of that I need to do to
> get
> > > > this restart to restart successfully?
> > > >
> > > > Many thanks
> > > >
> > > > Jonny
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On 4 August 2014 11:29, Jonny Williams <Jonny.Williams at bristol.ac.uk
> >
> > > wrote:
> > > >
> > > > > Hi there
> > > > >
> > > > > I thought that I would update this thread since I have now found a
> > > > > solution to this problem. I found the solution in this
> > > > > <http://mitgcm.org/pipermail/mitgcm-support/2008-April/005351.html
> >
> > > thread
> > > > > from the MITgcm support list archive.
> > > > >
> > > > > Basically, the interaction of the biogeochemistry packages (DIC,
> GCHEM,
> > > > > PTRACERS) and the OBCS boundary condition package were
> incompatible and
> > > > > adding the following line in my data.obcs file fixed the problem...
> > > > >
> > > > > *OBCSfixTopo=.TRUE.,*
> > > > >
> > > > > Thanks to everyone for your help again.
> > > > >
> > > > > Jonny
> > > > >
> > > > >
> > > > > On 31 July 2014 12:00, Jonny Williams <
> Jonny.Williams at bristol.ac.uk>
> > > > > wrote:
> > > > >
> > > > >> Hi Christoph
> > > > >>
> > > > >> Many thanks for your email, I really appreciate it.
> > > > >>
> > > > >> I am now able to run the model which is great! I am getting
> plausible
> > > > >> values for alkalinity, PO4, DOP and O2 and these evolve through
> time
> > > as I
> > > > >> would expect.
> > > > >>
> > > > >> Note that I am running with an empty *DIC_FORCING* namelist in
> > > *data.dic*.
> > > > >> it seems that I need to include this namelist even though it is
> empty.
> > > > >>
> > > > >> *&DIC_FORCING*
> > > > >>
> > > > >> *&*
> > > > >>
> > > > >>
> > > > >> Unfortunately, although the DIC field is being initialised
> correctly
> > > > >> (using the values specified in *data.ptracers*), the DIC field
> rapidly
> > > > >> becomes unphysical, giving NaNs everywhere (even over land!) after
> > > about 25
> > > > >> timesteps of 24s each.
> > > > >>
> > > > >> The NaNs seems to 'propagate' from the corners of the domain as
> the
> > > > >> simulation proceeds. I have attached an image of the domain after
> 13
> > > > >> timesteps which clearly shows the unphysical nature of the output!
> > > > >>
> > > > >> I assume that there must be something that I am missing in my
> setup
> > > > >> regarding DIC?
> > > > >>
> > > > >> Thanks again
> > > > >>
> > > > >> Jonny
> > > > >>
> > > > >>
> > > > >>
> > > > >>
> > > > >> On 31 July 2014 11:17, Christoph Voelker <
> christoph.voelker at awi.de>
> > > > >> wrote:
> > > > >>
> > > > >>> Hi Jonny,
> > > > >>>
> > > > >>> the fractional sea-ice area, supplied via the sea-ice file (or
> > > > >>> calculated in the sea-ice module) is used for reducing the
> air-sea
> > > gas
> > > > >>> exchange in the presence of sea-ice. The simple assumption here
> is
> > > that sea
> > > > >>> ice is impermeable, so the flux comes just from the non-covered
> part
> > > of the
> > > > >>> ocean surface. You can certainly set all values in the file to
> zero;
> > > then
> > > > >>> the ocean can exchange CO2 unhampered. Maybe you can even just
> leave
> > > the
> > > > >>> filename blank, but I am not sure about that; I usually don't
> > > specify the
> > > > >>> file, but I always use the sea-ice package.
> > > > >>>
> > > > >>> Concerning the silica file: You don't have to specify it. If you
> > > leave
> > > > >>> it away, what you do is that you neglect the contribution of
> silicic
> > > acid
> > > > >>> to the alkalinity, which in many parts of the surface ocean is
> > > small. But
> > > > >>> it is not so small in the Southern Ocean, and also to some
> extent in
> > > the
> > > > >>> North Pacific.
> > > > >>> The contribution of silicic acid to alkalinity is used in the
> > > > >>> calculation of the equilibrium carbonate chemistry, which is
> called
> > > when
> > > > >>> the model calculates air-sea flux. Neglecting it will lead to a
> > > small bias
> > > > >>> in equilibrium DIC values where Si is high.
> > > > >>>
> > > > >>>
> > > > >>> Hope that helps a bit,
> > > > >>> Cheers, Christoph
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> On 7/31/14 11:45 AM, Jonny Williams wrote:
> > > > >>>
> > > > >>> Hi Manfredi
> > > > >>>
> > > > >>> Thank you very much for your very helpful email!
> > > > >>>
> > > > >>> I should clarify my model set up. Although I am using a regional
> > > model
> > > > >>> which is based on an Arctic configuration I am now using it for a
> > > different
> > > > >>> part of the world.
> > > > >>>
> > > > >>> Also, I have the sea ice package switched off. Perhaps I need to
> > > > >>> specify a sea ice file which is simply all zeros?
> > > > >>>
> > > > >>> Finally do I need to supply a silica file (like sillev1.bin in
> the
> > > > >>> tutorial model)?
> > > > >>>
> > > > >>> Many thanks again
> > > > >>>
> > > > >>> Jonny
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> On 30 July 2014 19:31, Manfredi Manizza <mmanizza at ucsd.edu>
> wrote:
> > > > >>>
> > > > >>>> Hi Jonny,
> > > > >>>>
> > > > >>>> yes, you are correct that namelist below works fine for the
> > > > >>>> verification experiment where you run the 2.8 by 2.8 global
> > > > >>>> setup with dimensions 28 by 64 by 12 of input filles for sea-ice
> > > cover
> > > > >>>> and for windspeed
> > > > >>>>
> > > > >>>> For your (coarse-res ?) Arctic set-up, you will read wind speed
> via
> > > > >>>> the EXF package directly from re-analyzed products (NCEP,
> ECMWF,
> > > JRA-25)
> > > > >>>>
> > > > >>>> For the fraction of sea- ice (or sea ice cover) you will pass
> to the
> > > > >>>> biogeochemical routine the variable that is computed
> > > > >>>> by the sea-ice model that its is coupled in your run to the
> ocean
> > > > >>>> physical model.
> > > > >>>>
> > > > >>>> In this case you do not have to generate any input files with
> > > specificy
> > > > >>>> dimensions becuase in the data.exf file you should have
> > > > >>>> all details needed to interpolate on the fly your forcing
> > > accordingly
> > > > >>>> to your Arctic domain.
> > > > >>>>
> > > > >>>> Debugging tip :
> > > > >>>>
> > > > >>>> Just make sure that in the dic package the sea-ice coverage is
> > > > >>>> correctly read in order to compute the gas transfer velocity
> > > > >>>> and the amount of irradiance use to compute the Net Community
> > > > >>>> Production that has to be masked at the surface
> > > > >>>> by the sea-ice fraction. Running 2-3 time steps with printout
> > > linese of
> > > > >>>> the variables always helps
> > > > >>>> to figure out that all works OK and the two parts of the code
> talk
> > > to
> > > > >>>> each other.
> > > > >>>>
> > > > >>>> I hope this helps.
> > > > >>>>
> > > > >>>> Manfredi
> > > > >>>>
> > > > >>>>
> > > > >>>>
> > > > >>>> On 07/30/2014 07:45 AM, Jonny Williams wrote:
> > > > >>>>
> > > > >>>> Hi there
> > > > >>>>
> > > > >>>> I am currently trying to incorporate the GCHEM, PTRACERS and
> DIC
> > > > >>>> packages into my setup of the MITgcm. I already have it
> successfully
> > > > >>>> working in regional model using the OBCS and EXF forcing
> packages.
> > > > >>>>
> > > > >>>> in the ~/MITgcm/verification/tutorial_global_oce_biogeo
> example,
> > > the
> > > > >>>> data.dic file calls for the following files in the DIC_FORCING
> > > namelist
> > > > >>>>
> > > > >>>> &DIC_FORCING
> > > > >>>> DIC_iceFile='fice.bin',
> > > > >>>> DIC_windFile='tren_speed.bin',
> > > > >>>> DIC_silicaFile='sillev1.bin',
> > > > >>>> &
> > > > >>>>
> > > > >>>> What I cannot work out however is what size these files should
> be
> > > in
> > > > >>>> my setup. From trial and error, I think the ice and wind files
> are
> > > monthly
> > > > >>>> climatologies (longitude x latitude x 12 months) and the sillev1
> > > file
> > > > >>>> (silica data file, according to the manual
> > > > >>>> <
> > > http://mitgcm.org/public/r2_manual/latest/online_documents/manual.pdf
> >)
> > > > >>>> is of the form longitude x latitude x 15 levels.
> > > > >>>>
> > > > >>>> Does anyone know what size they should be? Should they have the
> > > same
> > > > >>>> number of elements as the underlying grid, or is it staggered?
> > > > >>>>
> > > > >>>> This raises a more generic issue in that clearly the binary
> input
> > > > >>>> files are not self-describing (like, say, NetCDF) and so having
> to
> > > > >>>> reverse-engineer what size forcing and boundary condition files
> > > should is
> > > > >>>> not uncommon for me.
> > > > >>>>
> > > > >>>> I may well be going about this in the wrong way so any
> suggestions
> > > > >>>> about how to avoid this situation in future would be
> appreciated :)
> > > > >>>>
> > > > >>>> Many thanks, as always
> > > > >>>>
> > > > >>>> Jonny
> > > > >>>>
> > > > >>>> --
> > > > >>>> Dr Jonny Williams
> > > > >>>> School of Geographical Sciences
> > > > >>>> University of Bristol
> > > > >>>> University Road
> > > > >>>> BS8 1SS
> > > > >>>>
> > > > >>>> +44 (0)117 3318352 <%2B44%20%280%29117%203318352>
> > > > >>>> jonny.williams at bristol.ac.uk
> > > > >>>> bit.ly/jonnywilliams
> > > > >>>>
> > > > >>>>
> > > > >>>> _______________________________________________
> > > > >>>> MITgcm-support mailing listMITgcm-support at mitgcm.orghttp://
> > > mitgcm.org/mailman/listinfo/mitgcm-support
> > > > >>>>
> > > > >>>>
> > > > >>>> --
> > > > >>>> Dr. Manfredi Manizza
> > > > >>>> Geosciences Research Division
> > > > >>>> Scripps Institution of Oceanography
> > > > >>>> University of California San Diego
> > > > >>>> 9500 Gilman Drive La Jolla, CA 92093-0244
> > > > >>>> email : mmanizza at ucsd.edu
> > > > >>>> tel : +1-858-534-7094
> > > > >>>> web : http://bluemoon.ucsd.edu/mmanizza/
> > > > >>>>
> > > > >>>>
> > > > >>>> _______________________________________________
> > > > >>>> MITgcm-support mailing list
> > > > >>>> MITgcm-support at mitgcm.org
> > > > >>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
> > > > >>>>
> > > > >>>>
> > > > >>>
> > > > >>>
> > > > >>> --
> > > > >>> Dr Jonny Williams
> > > > >>> School of Geographical Sciences
> > > > >>> University of Bristol
> > > > >>> University Road
> > > > >>> BS8 1SS
> > > > >>>
> > > > >>> +44 (0)117 3318352
> > > > >>> jonny.williams at bristol.ac.uk
> > > > >>> bit.ly/jonnywilliams
> > > > >>>
> > > > >>>
> > > > >>> _______________________________________________
> > > > >>> MITgcm-support mailing listMITgcm-support at mitgcm.orghttp://
> > > mitgcm.org/mailman/listinfo/mitgcm-support
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> --
> > > > >>> Christoph Voelker
> > > > >>> Alfred Wegener Institute for Polar and Marine Research
> > > > >>> Am Handelshafen 12
> > > > >>> 27570 Bremerhaven, Germany
> > > > >>> e: Christoph.Voelker at awi.de
> > > > >>> t: +49 471 4831 1848
> > > > >>>
> > > > >>>
> > > > >>> _______________________________________________
> > > > >>> MITgcm-support mailing list
> > > > >>> MITgcm-support at mitgcm.org
> > > > >>> http://mitgcm.org/mailman/listinfo/mitgcm-support
> > > > >>>
> > > > >>>
> > > > >>
> > > > >>
> > > > >> --
> > > > >> Dr Jonny Williams
> > > > >> School of Geographical Sciences
> > > > >> University of Bristol
> > > > >> University Road
> > > > >> BS8 1SS
> > > > >>
> > > > >> +44 (0)117 3318352
> > > > >> jonny.williams at bristol.ac.uk
> > > > >> bit.ly/jonnywilliams
> > > > >>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Dr Jonny Williams
> > > > > School of Geographical Sciences
> > > > > University of Bristol
> > > > > University Road
> > > > > BS8 1SS
> > > > >
> > > > > +44 (0)117 3318352
> > > > > jonny.williams at bristol.ac.uk
> > > > > bit.ly/jonnywilliams
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Dr Jonny Williams
> > > > School of Geographical Sciences
> > > > University of Bristol
> > > > University Road
> > > > BS8 1SS
> > > >
> > > > +44 (0)117 3318352
> > > > jonny.williams at bristol.ac.uk
> > > > bit.ly/jonnywilliams
> > >
> > > > _______________________________________________
> > > > MITgcm-support mailing list
> > > > MITgcm-support at mitgcm.org
> > > > http://mitgcm.org/mailman/listinfo/mitgcm-support
> > >
> > >
> > > _______________________________________________
> > > MITgcm-support mailing list
> > > MITgcm-support at mitgcm.org
> > > http://mitgcm.org/mailman/listinfo/mitgcm-support
> > >
> >
> >
> >
> > --
> > Dr Jonny Williams
> > School of Geographical Sciences
> > University of Bristol
> > University Road
> > BS8 1SS
> >
> > +44 (0)117 3318352
> > jonny.williams at bristol.ac.uk
> > bit.ly/jonnywilliams
>
>
> > _______________________________________________
> > MITgcm-support mailing list
> > MITgcm-support at mitgcm.org
> > http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
--
Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS
+44 (0)117 3318352
jonny.williams at bristol.ac.uk
bit.ly/jonnywilliams
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