[MITgcm-support] output using diagnostics package
q li
qliuri at yahoo.com
Fri Jul 31 11:04:55 EDT 2009
Hi Jean-Michel,
You are right. I put them in one file. It works.
Here is the STDERR file. The 2D domain is 4096x300. It runs using MPI on 32 cpus.
The DIAGNOSTICS_SIZE.h is followed. I did not change anything. It says the maximum. It looks all works for my 4 point output.
Many thanks. Have a great weekend.
Li
> more STDE*
::::::::::::::
STDERR.0000
::::::::::::::
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 23 ETAN has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 30 UVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 31 VVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 32 WVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 26 THETA has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 23 ETAN has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 30 UVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 31 VVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 32 WVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 26 THETA has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 23 ETAN has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 30 UVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 31 VVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 32 WVEL has already been set
(PID.TID 0000.0001) - WARNING - SETDIAG: Stats-Diag # 26 THETA has already been set
::::::::::::::
Here is the DIAGNOSTICS_SIZE.h.
C $Header: /u/gcmpack/MITgcm/verification/global_ocean.cs32x15/code/DIAGNOSTICS_SIZE.h,v 1.1 2006/06/08 00:54:30 jmc Exp $
C $Name: $
C Diagnostics Array Dimension
C ---------------------------
C ndiagMax :: maximum total number of available diagnostics
C numlists :: maximum number of diagnostics list (in data.diagnostics)
C numperlist :: maximum number of active diagnostics per list (data.diagnostics)
C numLevels :: maximum number of levels to write (data.diagnostics)
C numdiags :: maximum size of the storage array for active 2D/3D diagnostics
C nRegions :: maximum number of regions (statistics-diagnostics)
C sizRegMsk :: maximum size of the regional-mask (statistics-diagnostics)
C nStats :: maximum number of statistics (e.g.: aver,min,max ...)
C diagSt_size:: maximum size of the storage array for statistics-diagnostics
C Note : may need to increase "numdiags" when using several 2D/3D diagnostics,
C and "diagSt_size" (statistics-diags) since values here are deliberately small.
INTEGER ndiagMax
INTEGER numlists, numperlist, numLevels
INTEGER numdiags
INTEGER nRegions, sizRegMsk, nStats
INTEGER diagSt_size
PARAMETER( ndiagMax = 500 )
PARAMETER( numlists = 10, numperlist = 50, numLevels=2*Nr )
PARAMETER( numdiags = 40*Nr )
PARAMETER( nRegions = 10 , sizRegMsk = 3 , nStats = 4 )
PARAMETER( diagSt_size = 10*Nr )
CEH3 ;;; Local Variables: ***
CEH3 ;;; mode:fortran ***
CEH3 ;;; End: ***
________________________________
From: Jean-Michel Campin <jmc at ocean.mit.edu>
To: mitgcm-support at mitgcm.org
Sent: Thursday, July 30, 2009 5:23:11 PM
Subject: Re: [MITgcm-support] output using diagnostics package
Hi Li,
Do you see something in one of the STDERR.* ?
Not sure, but a copy of our DIAGNOSTICS_SIZE.h could help.
Not related to this problem, but just 2 suggestions:
1) You probably don't need to define a 3-D "regMask" array, and
could drop the 3rd dimension (since you are using
> nSetRegMskFile=1,
2) And if you prefer, you could chose to put all those output in the 1rst file
> stat_region(1,1)= 1, 2, 3 , 4,
since the list of variables + frequency is identical in all 4 output files.
You could also turn on MNC to get NetCDF file instead of ASCII output.
Cheers,
Jean-Michel
On Thu, Jul 30, 2009 at 01:04:51PM -0700, q li wrote:
> Hi Jean-Michel,
>
> I can only output 2 stat files. If I remove stat_fields(1,3) and stat_fields(1,4) from data.diagnostics, it worked fine. But when I add them, an error appears:
>
> forrtl: severe (104): incorrect STATUS= specifier value for connected file, unit 11, file ~/MITgcm/diagn/runEWH/statA3.0000000000.txt
>
> I set 5 different points in the model domain in Matlab.
>
> nx=2^12; ny=1; nz=300;
> regMask=zeros(nx,ny,nz);
> regMask(xA1,1,:)=1; regMask(xA2,1,:)=2; regMask(xA3,1,:)=3;
> regMask(xP1,1,:)=4; regMask(xP2,1,:)=5;
>
> And here is my data.diagnostics:
>
> &DIAG_STATIS_PARMS
> #- regional mask: 3 lat. band: 1 : y <= -24 ; 2 : -24<y<24 ; 3 : 24 <= y
> diagSt_regMaskFile='regMask.bin',
> nSetRegMskFile=1,
> set_regMask(1)= 1, 1, 1, 1, 1, 1,
> val_regMask(1)= 0.,1., 2., 3., 4., 5.,
> #---
> stat_fields(1,1)= 'ETAN ','UVEL ','VVEL ','WVEL ', 'THETA ',
> stat_fname(1)= 'statA1',
> stat_region(1,1)= 1,
> stat_freq(1)= -60.,
> stat_phase(1)= 0.,
>
> stat_fields(1,2)= 'ETAN ','UVEL ','VVEL ','WVEL ', 'THETA ',
> stat_fname(2)= 'statA2',
> stat_region(1,2)= 2,
> stat_freq(2)= -60.,
> stat_phase(2)= 0.,
>
> stat_fields(1,3)= 'ETAN ','UVEL ','VVEL ','WVEL ', 'THETA ',
> stat_fname(3)= 'statA3',
> stat_region(1,3)= 3,
> stat_freq(3)= -60.,
> stat_phase(3)= 0.,
>
> stat_fields(1,4)= 'ETAN ','UVEL ','VVEL ','WVEL ', 'THETA ',
> stat_fname(4)= 'statP1',
> stat_region(1,4)= 4,
> stat_freq(4)= -60.,
> stat_phase(4)= 0.,
> &
>
> Do you have any idea what is happening?
>
> Best,
>
> Li
>
>
>
>
>
> ________________________________
> From: Jean-Michel Campin <jmc at ocean.mit.edu>
> To: mitgcm-support at mitgcm.org
> Sent: Wednesday, July 29, 2009 4:34:32 PM
> Subject: Re: [MITgcm-support] output using diagnostics package
>
> 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
> >
> >
> >
> >
> > _______________________________________________
> > 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
>
>
>
>
> _______________________________________________
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mitgcm.org/pipermail/mitgcm-support/attachments/20090731/1f3de938/attachment.htm>
More information about the MITgcm-support
mailing list