[MITgcm-support] output using diagnostics package

q li qliuri at yahoo.com
Wed Jul 29 12:50:47 EDT 2009


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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