[MITgcm-support] Adding multiple tracers to MITgcm

Wed Nov 15 17:51:39 EST 2017

Hi Dhruv,

One possible explanation could be the following:
 - you compile with maskLEN set to 3 in RBCS_SIZE.h, either because you
   are using the default RBCS_SIZE.h (from pkg/rbcs) or because you did
   not change it from the single ptracer case.
 - but at run-time, as you try to read RBCS_PARM01, this line:
>  relaxMaskFile(4)='tracer_mask.bin',
   cause an error since relaxMaskFile has only maskLEN size.
   If you were compiling with some check-bounds option, this would produce
   a more explicit error message like this one:
> At line 2058 of file rbcs_readparms.f (unit = 11, file = 'scratch1.000000000')
> Fortran runtime error: Index 1 out of range for namelist variable relaxmaskfile

If this is the case, you could either:
 - recompile with a customized RBCS_SIZE.h in which maskLEN = 4
 or
 - since you are using the same binary mask-file (in your case: tracer_mask.bin)
   for both tracers, you could just comment out this line:
>  relaxMaskFile(4)='tracer_mask.bin',
   and the same mask will be used for both tracers.
   Note that this setting is reported in STDOUT:
> (PID.TID 0000.0001)  ---  RBCS_INIT_FIXED: setting RBCS mask  ---
   so you should be able to check.

Cheers,
Jean-Michel

On Wed, Nov 15, 2017 at 03:09:20PM -0500, Dhruv Balwada wrote:
> Hi Jean-Michel, 
> 
> Thanks for the suggestions. I incorporated them both. 
> Here is the STDOUT output (attached file as well). 
> (PID.TID 0000.0001)  PTRACERS_READPARMS: finished reading data.ptracers
> (PID.TID 0000.0001)  RBCS_READPARMS: opening data.rbcs
> (PID.TID 0000.0001)  OPEN_COPY_DATA_FILE: opening file data.rbcs
> (PID.TID 0000.0001) // =======================================================
> (PID.TID 0000.0001) // Parameter file "data.rbcs"
> (PID.TID 0000.0001) // =======================================================
> (PID.TID 0000.0001) > &RBCS_PARM01
> (PID.TID 0000.0001) >  rbcsForcingPeriod=0.,
> (PID.TID 0000.0001) >  useRBCptracers=.TRUE.,
> (PID.TID 0000.0001) >  relaxMaskFile(3)='tracer_mask.bin',
> (PID.TID 0000.0001) >  relaxMaskFile(4)='tracer_mask.bin',
> (PID.TID 0000.0001) > &
> (PID.TID 0000.0001) > &RBCS_PARM02
> (PID.TID 0000.0001) >  useRBCptrnum(1)=.TRUE.,
> (PID.TID 0000.0001) >  tauRelaxPTR(1)=1000.,
> (PID.TID 0000.0001) >  relaxPtracerFile(1)='tracer_relax.bin',
> (PID.TID 0000.0001) >  useRBCptrnum(2)=.TRUE.,
> (PID.TID 0000.0001) >  tauRelaxPTR(2)=1000.,
> (PID.TID 0000.0001) >  relaxPtracerFile(2)='tracer_relax.bin',
> (PID.TID 0000.0001) > &
> (PID.TID 0000.0001)
> "STDOUT.0000" 304L, 16658C                                                                                                              304,1         Bot
> 
> I have the simulation running with one tracer. Am I supposed to define some extra flags when I use more than one tracer? 
> There is no error in STDERR.0000 
> 
> Thanks,
> Dhruv
> 
> 
> 
> > On Nov 15, 2017, at 2:50 PM, Jean-Michel Campin <jmc at mit.edu> wrote:
> > 
> > Hi Dhruv,
> > 
> > 2 (short) suggestions:
> > 
> > 1) rbcsForcingPeriod is a real parameter, so I would try to specify:
> >>  rbcsForcingPeriod=0.,
> >   instead of:
> >>  rbcsForcingPeriod=0,
> > 
> > 2) If you want to be sure that your are getting everything written in STDOUT.#####
> >  (not retained in an IO buffer and lost as the model stops) you could specify:
> >  a) in "eedata":
> >> debugMode=.TRUE.,
> >  b) in "data", PARM01 namelist:
> >> debugLevel=2,
> > This will flush the IO buffer so that it should be easier to see 
> > where the model stops.
> > 
> > Cheers,
> > Jean-Michel
> > 
> > On Wed, Nov 15, 2017 at 01:30:37PM -0500, Dhruv Balwada wrote:
> >> Hello,
> >> 
> >> I am doing an experiment with MITgcm using multiple tracers that are restored at a certain boundary. I am using the rbcs and ptracers package. The simulations works when I only restore one of the tracers, but when I add multiple tracers to the data.rbcs file I start getting the error - 
> >> 
> >> 'forrtl: severe (19): invalid reference to variable in NAMELIST input, unit 11, file /var/tmpdata/fortew5BaY, line 5, position 18
> >> Image              PC                Routine            Line        Source
> >> libifcore.so.5     00002B14AF4B7A28  Unknown               Unknown  Unknown
> >> ???
> >> 
> >> I think this error implies that there is some typo in the data files, and probably in data.rbcs because that where the STDOUT stopped. However, I can???t find any thing that seems out of place. 
> >> Here is the text from data.rbcs - 
> >> &RBCS_PARM01
> >>  rbcsForcingPeriod=0,
> >>  useRBCptracers=.TRUE.,
> >>  relaxMaskFile(3)='tracer_mask.bin',
> >>  relaxMaskFile(4)='tracer_mask.bin',
> >> &
> >> &RBCS_PARM02
> >>  useRBCptrnum(1)=.TRUE.,
> >>  tauRelaxPTR(1)=1000.,
> >>  relaxPtracerFile(1)='tracer_relax.bin',
> >>  useRBCptrnum(2)=.TRUE.,
> >>  tauRelaxPTR(2) =100000.,
> >>  relaxPtracerFile(2)='tracer_relax.bin',
> >> &
> >> 
> >> And here is the text from data.ptracers -
> >> &PTRACERS_PARM01
> >>  PTRACERS_Iter0=4147200,
> >>  PTRACERS_numInUse=3,
> >>  PTRACERS_names(1)='TRAC01',
> >>  PTRACERS_names(2)='TRAC02',
> >>  PTRACERS_names(3)='TRAC03',
> >> &
> >> 
> >> 
> >> Any suggestions would be appreciated. 
> >> 
> >> Thank you,
> >> Dhruv 
> > 
> >> _______________________________________________
> >> MITgcm-support mailing list
> >> MITgcm-support at mitgcm.org
> >> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support
> > 
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> 

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