[MITgcm-support] Forcing files in data.dic (biogeochemistry)
Jonny Williams
Jonny.Williams at bristol.ac.uk
Mon Aug 4 08:41:14 EDT 2014
Thanks for that Martin.
I'm currently using the following submit command...
*qsub archer_script*
... where the contents of *archer_script *is below. Do you know where I
should insert the *-g*?
Thanks!
START
*#!/bin/bash --login*
*#PBS -N run.bio*
*#PBS -l select=2*
*#PBS -l walltime=48:0:0*
*#PBS -A n02-STATOIL*
*# Make sure any symbolic links are resolved to absolute path*
*export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)*
*# Change to the direcotry that the job was submitted from*
*cd $PBS_O_WORKDIR*
*# Set the number of threads to 1*
*# This prevents any system libraries from automatically*
*# using threading.*
*export OMP_NUM_THREADS=1*
*# Launch the parallel job*
*aprun -n 48 ./mitgcmuv*
END
On 4 August 2014 12:42, Martin Losch <Martin.Losch at awi.de> wrote:
> Hi Jonny,
>
> it’s probably something really small. Can you convince your compiler
> (maybe through the -g flag) to convert the routine names into something
> human-readable? Then it would be easier to find the problem. It’s probably
> a line like this one: WRITE(fn,'(A,I10.10)') 'pickup_dic.', myIter
>
> Martin
>
> On Aug 4, 2014, at 1:01 PM, Jonny Williams <Jonny.Williams at bristol.ac.uk>
> 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 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) 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
> >>> 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
> >>
> >> --
> >> 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 list
> >>
> >> MITgcm-support at mitgcm.org
> >> http://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
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