[MITgcm-support] output using diagnostics package
Jean-Michel Campin
jmc at ocean.mit.edu
Wed Jul 29 16:34:32 EDT 2009
Hi Li,
Fortran Unit 11 is used to read parameter files (all the data*).
Looks like the namelist termination (for the 1rst namelist:
DIAGNOSTICS_LIST) is missing in file "data.diagnostics".
> I don't quite understand three parameters in data.diagnostics: nSetRegMskFile,
> set_regMask and val_regMask. Could anyone help me out?
You can find few emails (in Apr 2009) on the support list about
Regional statistics diag (regon-mask).
And an example in MITgcm/verification/aim.5l_cs/input.thSI
with matlab script (mk3regions_mask.m) to generate the region-mask file.
Cheers,
Jean-Michel
On Wed, Jul 29, 2009 at 09:50:47AM -0700, q li wrote:
> Experts,
>
> I am trying to output only UVEL and THETA for the whole domain (2D model) every hour, and also UVEL and THETA for 4 locations every 1 minute in order to compare to observations. Thank Jean-Michel for telling me the diagnostics package was designed for it. I got following error information from the server. I don't know why and I cannot find any help file for it either. Is anything wrong with my diagnostics.size file? I don't quite understand three parameters in data.diagnostics: nSetRegMskFile, set_regMask and val_regMask. Could anyone help me out?
>
> Best,
>
> Li
>
> Error output from the server: (MPI run on 32 cpus)
>
> ~/MITgcm/SCS/diagn/run> more *.err
> forrtl: severe (24): end-of-file during read, unit 11, file /tmp/pbs.16613.a330/fortZROgSu, line 18, position 0
> Image PC Routine Line Source
> mitgcmuv 4000000000439F50 Unknown Unknown Unknown
> mitgcmuv 4000000000437A60 Unknown Unknown Unknown
> mitgcmuv 4000000000391D10 Unknown Unknown Unknown
> mitgcmuv 40000000002FBA10 Unknown Unknown Unknown
> mitgcmuv 40000000002FA9A0 Unknown Unknown Unknown
> mitgcmuv 4000000000339400 Unknown Unknown Unknown
> mitgcmuv 400000000003EC60 Unknown Unknown Unknown
> mitgcmuv 40000000002C3B10 Unknown Unknown Unknown
> mitgcmuv 40000000002B0DA0 Unknown Unknown Unknown
> mitgcmuv 40000000002E3590 Unknown Unknown Unknown
> mitgcmuv 4000000000204F50 Unknown Unknown Unknown
> mitgcmuv 4000000000003ED0 Unknown Unknown Unknown
> libc.so.6.1 2000000003BB1C50 Unknown Unknown Unknown
> mitgcmuv 4000000000003CC0 Unknown Unknown Unknown
> forrtl: severe (24): end-of-file during read, unit 11, file /tmp/pbs.16613.a330/fortC73lfs, line 18, position 0
> Image PC Routine Line Source
> mitgcmuv 4000000000439F50 Unknown Unknown Unknown
> mitgcmuv 4000000000437A60 Unknown Unknown Unknown
> mitgcmuv 4000000000391D10 Unknown Unknown Unknown
> mitgcmuv 40000000002FBA10 Unknown Unknown Unknown
> mitgcmuv 40000000002FA9A0 Unknown Unknown Unknown
> mitgcmuv 4000000000339400 Unknown Unknown Unknown
> mitgcmuv 400000000003EC60 Unknown Unknown Unknown
> mitgcmuv 40000000002C3B10 Unknown Unknown Unknown
> mitgcmuv 40000000002B0DA0 Unknown Unknown Unknown
> mitgcmuv 40000000002E3590 Unknown Unknown Unknown
> mitgcmuv 4000000000204F50 Unknown Unknown Unknown
> mitgcmuv 4000000000003ED0 Unknown Unknown Unknown
> libc.so.6.1 2000000003BB1C50 Unknown Unknown Unknown
> mitgcmuv 4000000000003CC0 Unknown Unknown Unknown
> forrtl: severe (24): end-of-file during read, unit 11, file /tmp/pbs.16613.a330/fortu2M8R0, line 18, position 0
> Image PC Routine Line Source
> mitgcmuv 4000000000439F50 Unknown Unknown Unknown
> mitgcmuv 4000000000437A60 Unknown Unknown Unknown
> mitgcmuv 4000000000391D10 Unknown Unknown Unknown
> mitgcmuv 40000000002FBA10 Unknown Unknown Unknown
> mitgcmuv 40000000002FA9A0 Unknown Unknown Unknown
> mitgcmuv 4000000000339400 Unknown Unknown Unknown
> mitgcmuv 400000000003EC60 Unknown Unknown Unknown
> mitgcmuv 40000000002C3B10 Unknown Unknown Unknown
> mitgcmuv 40000000002B0DA0 Unknown Unknown Unknown
> mitgcmuv 40000000002E3590 Unknown Unknown Unknown
> mitgcmuv 4000000000204F50 Unknown Unknown Unknown
> mitgcmuv 4000000000003ED0 Unknown Unknown Unknown
> libc.so.6.1 2000000003BB1C50 Unknown Unknown Unknown
> mitgcmuv 4000000000003CC0 Unknown Unknown Unknown
> forrtl: severe (24): end-of-file during read, unit 11, file /tmp/pbs.16613.a330/fortIhTnQJ, line 18, position 0
> Image PC Routine Line Source
> mitgcmuv 4000000000439F50 Unknown Unknown Unknown
> mitgcmuv 4000000000437A60 Unknown Unknown Unknown
> mitgcmuv 4000000000391D10 Unknown Unknown Unknown
> mitgcmuv 40000000002FBA10 Unknown Unknown Unknown
> mitgcmuv 40000000002FA9A0 Unknown Unknown Unknown
> mitgcmuv 4000000000339400 Unknown Unknown Unknown
> mitgcmuv 400000000003EC60 Unknown Unknown Unknown
> mitgcmuv 40000000002C3B10 Unknown Unknown Unknown
> mitgcmuv 40000000002B0DA0 Unknown Unknown Unknown
> mitgcmuv 40000000002E3590 Unknown Unknown Unknown
> mitgcmuv 4000000000204F50 Unknown Unknown Unknown
> mitgcmuv 4000000000003ED0 Unknown Unknown Unknown
> libc.so.6.1 2000000003BB1C50 Unknown Unknown Unknown
> mitgcmuv 4000000000003CC0 Unknown Unknown Unknown
> forrtl: severe (24): end-of-file during read, unit 11, file /tmp/pbs.16613.a330/fortyjeMpE, line 18, position 0
> Image PC Routine Line Source
> mitgcmuv 4000000000439F50 Unknown Unknown Unknown
> mitgcmuv 4000000000437A60 Unknown Unknown Unknown
> mitgcmuv 4000000000391D10 Unknown Unknown Unknown
> mitgcmuv 40000000002FBA10 Unknown Unknown Unknown
> mitgcmuv 40000000002FA9A0 Unknown Unknown Unknown
> mitgcmuv 4000000000339400 Unknown Unknown Unknown
> mitgcmuv 400000000003EC60 Unknown Unknown Unknown
> mitgcmuv 40000000002C3B10 Unknown Unknown Unknown
> mitgcmuv 40000000002B0DA0 Unknown Unknown Unknown
> mitgcmuv 40000000002E3590 Unknown Unknown Unknown
> mitgcmuv 4000000000204F50 Unknown Unknown Unknown
> mitgcmuv 4000000000003ED0 Unknown Unknown Unknown
> libc.so.6.1 2000000003BB1C50 Unknown Unknown Unknown
> mitgcmuv 4000000000003CC0 Unknown Unknown Unknown
> MPI: MPI_COMM_WORLD rank 21 has terminated without calling MPI_Finalize()
> MPI: aborting job
>
>
>
> setup in data.dignostics:
>
>
> (PID.TID 0000.0001) DIAGNOSTICS_READPARMS: opening data.diagnostics
> (PID.TID 0000.0001) OPEN_COPY_DATA_FILE: opening file data.diagnostics
> (PID.TID 0000.0001) // =======================================================
> (PID.TID 0000.0001) // Parameter file "data.diagnostics"
> (PID.TID 0000.0001) // =======================================================
> (PID.TID 0000.0001) ># Diagnostic Package Choices
> (PID.TID 0000.0001) >#-----------------
> (PID.TID 0000.0001) ># for each output-stream:
> (PID.TID 0000.0001) ># filename(n) : prefix of the output file name (only 8.c long) for outp.stream n
> (PID.TID 0000.0001) ># frequency(n):< 0 : write snap-shot output every |frequency| seconds
> (PID.TID 0000.0001) ># > 0 : write time-average output every frequency seconds
> (PID.TID 0000.0001) ># timePhase(n) : write at time = timePhase + multiple of |frequency|
> (PID.TID 0000.0001) ># averagingFreq(n) : frequency (in s) for periodic averaging interval
> (PID.TID 0000.0001) ># averagingPhase(n): phase (in s) for periodic averaging interval
> (PID.TID 0000.0001) ># repeatCycle(n) : number of averaging intervals in 1 cycle
> (PID.TID 0000.0001) ># levels(:,n) : list of levels to write to file (Notes: declared as REAL)
> (PID.TID 0000.0001) ># when this entry is missing, select all common levels of this list
> (PID.TID 0000.0001) ># fields(:,n) : list of diagnostics fields (8.c) (see "available_diagnostics.log"
> (PID.TID 0000.0001) ># file for the list of all available diag. in this particular config)
> (PID.TID 0000.0001) >#-----------------
> (PID.TID 0000.0001) > &DIAGNOSTICS_LIST
> (PID.TID 0000.0001) ># diag_mnc = .FALSE.,
> (PID.TID 0000.0001) ># dumpAtLast = .TRUE.,
> (PID.TID 0000.0001) > fields(1,1) = 'UVEL ','THETA ',
> (PID.TID 0000.0001) > filename(1) = 'UT',
> (PID.TID 0000.0001) > frequency(1) = -10800.0D+0,
> (PID.TID 0000.0001) >
> (PID.TID 0000.0001) >
> (PID.TID 0000.0001) ># Parameter for Diagnostics of per level statistics:
> (PID.TID 0000.0001) >#-----------------
> (PID.TID 0000.0001) ># for each output-stream:
> (PID.TID 0000.0001) ># stat_fname(n) : prefix of the output file name (only 8.c long) for outp.stream n
> (PID.TID 0000.0001) ># stat_freq(n):< 0 : write snap-shot output every |stat_freq| seconds
> (PID.TID 0000.0001) ># > 0 : write time-average output every stat_freq seconds
> (PID.TID 0000.0001) ># stat_phase(n) : write at time = stat_phase + multiple of |stat_freq|
> (PID.TID 0000.0001) ># stat_region(:,n) : list of "regions" (default: 1 region only=global)
> (PID.TID 0000.0001) ># stat_fields(:,n) : list of diagnostics fields (8.c) (see "available_diagnostics.log"
> (PID.TID 0000.0001) ># file for the list of all available diag. in this particular config)
> (PID.TID 0000.0001) >#-----------------
> (PID.TID 0000.0001) > &DIAG_STATIS_PARMS
> (PID.TID 0000.0001) > diagSt_regMaskFile='regMask.bin',
> (PID.TID 0000.0001) > nSetRegMskFile=1,
> (PID.TID 0000.0001) > set_regMask(1)= 1, 1, 1,
> (PID.TID 0000.0001) > val_regMask(1)= 1., 2., 3.,
> (PID.TID 0000.0001) >#---
> (PID.TID 0000.0001) > stat_fields(1,1)= 'UVEL ','THETA ',
> (PID.TID 0000.0001) > stat_fname(1)= 'dynStDiag',
> (PID.TID 0000.0001) > stat_freq(1)= -600.,
> (PID.TID 0000.0001) >
> (PID.TID 0000.0001) > &
> (PID.TID 0000.0001) >
> (PID.TID 0000.0001)
> (PID.TID 0000.0001) S/R DIAGNOSTICS_READPARMS, read namelist "diagnostics_list": start
> (PID.TID 0000.0001) S/R DIAGNOSTICS_READPARMS, read namelist "diagnostics_list": OK
> (PID.TID 0000.0001) S/R DIAGNOSTICS_READPARMS, read namelist "DIAG_STATIS_PARMS": start
>
>
>
>
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