ERROR: LVD not found

[m_migliavacca1@campus_unimib_it]

Dear all,

I am trying to run CLM with my own climate forcing (ENSEMBLES) over Europe, I got the following error:

(shr_dmodel_readLBUB) reading file: /gpfs/scratch/userjrc/jrcccu10/CLM/InputENS/atm/datm7/CLM1PT_data/ENSEMBLES_E_101x120/clm1pt-2000-01.nc 31
(shr_dmodel_readLBUB) reading file: /gpfs/scratch/userjrc/jrcccu10/CLM/InputENS/atm/datm7/CLM1PT_data/ENSEMBLES_E_101x120/clm1pt-2000-01.nc 1
(shr_stream_findBounds) ERROR: LVD not found, all data is before yearFirst
(shr_sys_abort) ERROR: (shr_stream_findBounds) ERROR: LVD not found, all data is before yearFirst
(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping


It seems that te error is in a mismatch between the first year in my forcing and the first year expected by CLM. However, I carefully checked dates in my configuratione and data streams and seems ok. Does anyone have an idea?
Please find below the atm log file.
thanks
mirco

jrcccu10@sp0201 /gpfs/scratch/userjrc/jrcccu10/ProvaRegion/run> cat atm.log.111004-165341
(datm_comp_init) atm_in = datm_atm_in
(datm_comp_init) decomp = 1d
(datm_comp_init) iradsw = 1
(datm_comp_init) factorFn = unused
(datm_comp_init) restfilm = undefined
(datm_comp_init) restfils = undefined
(datm_comp_init) presaero = T
(shr_strdata_readnml) reading input namelist file: datm_atm_in
(shr_stream_init) Reading file clm1PT.ENSEMBLES_E_101x120.stream.txt
(shr_file_freeUnit) unit 97 was not in use
(shr_stream_init) Reading file presaero.stream.txt
(shr_file_freeUnit) unit 97 was not in use
(datm_comp_init) atm mode = CLMNCEP
(shr_strdata_init) calling shr_dmodel_mapSet for fill
(shr_strdata_init) calling shr_dmodel_mapSet for remap
(shr_strdata_print) ----------------------------------------------------------
(shr_strdata_print) name = ATM data
(shr_strdata_print) dataMode = CLMNCEP
(shr_strdata_print) domainFile = /gpfs/scratch/userjrc/jrcccu10/CLM/InputENS/atm/datm7/domain.clm/domain.lnd.ENSEMBLES_E_101x120_gx1v6.nc
(shr_strdata_print) nxg = 120
(shr_strdata_print) nyg = 101
(shr_strdata_print) io_type = 6
(shr_strdata_print) num_iotasks = 1
(shr_strdata_print) io_root = 0
(shr_strdata_print) io_stride = 4
(shr_strdata_print) num_agg = 0
(shr_strdata_print) eccen = 1.670772E-02
(shr_strdata_print) mvelpp = 4.934468E+00
(shr_strdata_print) lambm0 = -3.250364E-02
(shr_strdata_print) obliqr = 4.091238E-01
(shr_strdata_print) nstreams = 2
(shr_strdata_print) streams ( 1) = clm1PT.ENSEMBLES_E_101x120.stream.txt 1 2000 2000
(shr_strdata_print) taxMode ( 1) = cycle
(shr_strdata_print) dtlimit ( 1) = 1.500000E+00
(shr_strdata_print) strnxg ( 1) = 120
(shr_strdata_print) strnyg ( 1) = 101
(shr_strdata_print) dofill ( 1) = F
(shr_strdata_print) fillalgo( 1) = nn
(shr_strdata_print) fillmask( 1) = nomask
(shr_strdata_print) fillread( 1) = NOT_SET
(shr_strdata_print) fillwrit( 1) = NOT_SET
(shr_strdata_print) domaps ( 1) = F
(shr_strdata_print) mapalgo ( 1) = bilinear
(shr_strdata_print) mapmask ( 1) = nomask
(shr_strdata_print) mapread ( 1) = NOT_SET
(shr_strdata_print) mapwrit ( 1) = NOT_SET
(shr_strdata_print) tintalgo( 1) = linear
(shr_strdata_print)
(shr_strdata_print) streams ( 2) = presaero.stream.txt 1 2000 2000
(shr_strdata_print) taxMode ( 2) = cycle
(shr_strdata_print) dtlimit ( 2) = 1.500000E+00
(shr_strdata_print) strnxg ( 2) = 9
(shr_strdata_print) strnyg ( 2) = 14
(shr_strdata_print) dofill ( 2) = T
(shr_strdata_print) fillalgo( 2) = nn
(shr_strdata_print) fillmask( 2) = nomask
(shr_strdata_print) fillread( 2) = NOT_SET
(shr_strdata_print) fillwrit( 2) = NOT_SET
(shr_strdata_print) domaps ( 2) = T
(shr_strdata_print) mapalgo ( 2) = bilinear
(shr_strdata_print) mapmask ( 2) = nomask
(shr_strdata_print) mapread ( 2) = NOT_SET
(shr_strdata_print) mapwrit ( 2) = NOT_SET
(shr_strdata_print) tintalgo( 2) = linear
(shr_strdata_print)
(shr_strdata_print) nvectors = 0
(shr_strdata_print) ----------------------------------------------------------
(datm_comp_init) initialize gsmaps
(datm_comp_init) copy domains
(datm_comp_init) allocate AVs
(datm_comp_init) flds_strm = strm_tbot:strm_wind:strm_shum:strm_swdn:strm_precn
(shr_dmodel_readLBUB) reading file: /gpfs/scratch/userjrc/jrcccu10/CLM/InputENS/atm/datm7/CLM1PT_data/ENSEMBLES_E_101x120/clm1pt-2000-01.nc 31
(shr_dmodel_readLBUB) reading file: /gpfs/scratch/userjrc/jrcccu10/CLM/InputENS/atm/datm7/CLM1PT_data/ENSEMBLES_E_101x120/clm1pt-2000-01.nc 1
(shr_stream_findBounds) ERROR: LVD not found, all data is before yearFirst
(shr_sys_abort) ERROR: (shr_stream_findBounds) ERROR: LVD not found, all data is before yearFirst
(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping

 

[slevis]

A visitor and I encountered this error last summer. I asked her if she remembered how we solved it:


Yes, we did encounter this error. I have some notes as to what we did, but didn't write down our final solution. However, from my notes it looks like we solved this problem by adjusting the dates in the datm.buildnml.csh file where we tell it the streams (for this case, it was ozone.stream.txt). We changed the dates from 1 1 1 to 1 2004 2004. We also had to add time units to my ozone data file, but if I remember correctly, that did not solve this problem. The error message was generated from file /models/csm_share/shr/shr_stream_mod, and it was around line 1094.


I hope that her response helps...

Sam

 

[m_migliavacca1@campus_unimib_it]

Thanks Sam,

I am not sure that in my case the problem is this, as you can see below the stream is set exactly how you suggest, I do not understand if the problem is in the meteorological forcing stream clm1PT.ENSEMBLES_E_101x120 or in the
presaero stream. The only strange thing I see at the moment is that in the aerosol deposition netCDF the dates are set as 0001-01-01. Could be this the problem?
thank you very much
mirco



shr_strdata_print) streams ( 1) = clm1PT.ENSEMBLES_E_101x120.stream.txt 1 2000 2000
(shr_strdata_print) taxMode ( 1) = cycle
(shr_strdata_print) dtlimit ( 1) = 1.500000E+00
(shr_strdata_print) strnxg ( 1) = 120
(shr_strdata_print) strnyg ( 1) = 101
(shr_strdata_print) dofill ( 1) = F
(shr_strdata_print) fillalgo( 1) = nn
(shr_strdata_print) fillmask( 1) = nomask
(shr_strdata_print) fillread( 1) = NOT_SET
(shr_strdata_print) fillwrit( 1) = NOT_SET
(shr_strdata_print) domaps ( 1) = F
(shr_strdata_print) mapalgo ( 1) = bilinear
(shr_strdata_print) mapmask ( 1) = nomask
(shr_strdata_print) mapread ( 1) = NOT_SET
(shr_strdata_print) mapwrit ( 1) = NOT_SET
(shr_strdata_print) tintalgo( 1) = linear
(shr_strdata_print)
(shr_strdata_print) streams ( 2) = presaero.stream.txt 1 2000 2000

 

[m_migliavacca1@campus_unimib_it]

Hi Sam,

I've fixed the error, the problem was first in the offset parameter in the datm namelist and second in the aerosol deposition input file in which the dates are computed since 0001-01-01 instead od 2000-01-01 (for my case). Please note that this file was generated with the the ./getregional_datasets.pl script with -sim_year 2000.

I have a question one question and one more error:

-question:

it's about the aerosol deposition produced by ./getregional_datasets.pl and by aerosol deposition NCL tool. Is it possible to regrid/interpolate my aerosol deposition in order to be consistent to my own grid. I am not able to regrid the data to a different resolution than the f09 with the ncl tool. My own resolution is 0.25x0.25 and I have both the grid file and the domain.

Error:
Now I am able to initialize the model but I get this error in the first time step:


0-127: Signal received: SIGTRAP - Trace trap
0-127: Signal generated for floating-point exception:
0-127: FP invalid operation
0-127:
0-127: Instruction that generated the exception:
0-127: fmul fr03,fr02,fr03
0-127: Source Operand values:
0-127: fr02 = NaNS
0-127: fr03 = 1.00000000000000e+00
0-127:
0-127: Traceback:
0-127: Offset 0x00001be4 in procedure __subgridavemod_NMOD_p2g_1d, near line 1017 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/subgridAveMod.F90
0-127: Offset 0x00000514 in procedure *__subgridavemod_NMOD_p2g_1d_stub_in___histfilemod_NMOD_hist_update_hbuf_field_1d, near line -1 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/histFileMod.F90
0-127: Offset 0x00000af8 in procedure __histfilemod_NMOD_hist_update_hbuf_field_1d, near line 1170 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/histFileMod.F90
0-127: Offset 0x0000023c in procedure __histfilemod_NMOD_hist_update_hbuf, near line 1090 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/histFileMod.F90
0-127: Offset 0x00000294 in procedure __clm_driver_NMOD_clm_driver2, near line 819 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/clm_driver.F90
0-127: Offset 0x000000a0 in procedure __clm_comp_NMOD_clm_run2, near line 276 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/clm_comp.F90
0-127: Offset 0x00001588 in procedure __lnd_comp_mct_NMOD_lnd_run_mct, near line 675 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/cpl_mct/lnd_comp_mct.F90
0-127: Offset 0x00014c48 in procedure ccsm_driver, near line 1666 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/drv/driver/ccsm_driver.F90
0-127: --- End of call chain ---
0-127:
INFO: 0031-639 Exit status from pm_respond = 0
77098E-01 1.00000000000000000

Thank you very much for the help
mirco

 

[slevis]

I'm not very familiar with the aerosol deposition. I will tell you what I remember:

In a 2010 version of CLM4 I think that I regridded the aerosol deposition file from one resolution to another to do my simulation.

In the current version (still CLM4 but in the CESM1_0_3 release) I believe that the model regrids the aerosol deposition data at run time.

I cannot help you with the error that you got. Clearly there's a NaN in one of the model variables. You'll have to debug the model to find which of your changes causes this.

Sam

 

[m_migliavacca1@campus_unimib_it]

Hi Sam,

I see what you say, in fact in the guide is suggested that both for aerosol and nitrogen depositions the regridding and interpolation are performed during the model run.
However, it seems that for my case the best solution for running the model is is to regrid and interpolate aerosol and nitrogen deposition with the NCL tools, otherwise does not work.

However I still get errors, I am running (for year 2000) a COLDSTART case to generate a restart file to use later with interpininc to create the initial considitions. The model stops during the initialization of the lnd component when (I think) is reading the nitrogen deposition file (just generated by NCLscripts). The error is somewhere into the shr_stream_readTCoord but I am not able to understand the error.

Please find below the piece of lnd.log file and the namelist I am using

lnd.log

------------------------------------------------------------
Successfully initialized variables for accumulation

Setting initial data to non-spun up values

ndepdyn stream settings:
stream_year_first_ndep = 0
stream_year_last_ndep = 0
model_year_align_ndep = 1
stream_fldFileName_ndep = /gpfs/scratch/userjrc/jrcccu10/CLM/InputENS/lnd/clm2/ndepdata/ndep_clm_simyr2000_ENSEMBLES_E_101x120.nc


(shr_stream_set) size of filename = 1
(shr_stream_set) filename = /gpfs/scratch/userjrc/jrcccu10/CLM/InputENS/lnd/clm2/ndepdata/ndep_clm_simyr2000_ENSEMBLES_E_101x120.nc
(shr_strdata_print) ----------------------------------------------------------
(shr_strdata_print) name = CLMNDEP data
(shr_strdata_print) dataMode = NULL
(shr_strdata_print) domainFile = null
(shr_strdata_print) nxg = 120
(shr_strdata_print) nyg = 101
(shr_strdata_print) io_type = 6
(shr_strdata_print) num_iotasks = 1
(shr_strdata_print) io_root = 0
(shr_strdata_print) io_stride = 4
(shr_strdata_print) num_agg = 0
(shr_strdata_print) eccen = 1.000000E+36
(shr_strdata_print) mvelpp = 1.000000E+36
(shr_strdata_print) lambm0 = 1.000000E+36
(shr_strdata_print) obliqr = 1.000000E+36
(shr_strdata_print) nstreams = 1
(shr_strdata_print) streams ( 1) = null
(shr_strdata_print) taxMode ( 1) = extend
(shr_strdata_print) dtlimit ( 1) = 1.000000E+30
(shr_strdata_print) strnxg ( 1) = 120
(shr_strdata_print) strnyg ( 1) = 101
(shr_strdata_print) dofill ( 1) = F
(shr_strdata_print) fillalgo( 1) = none
(shr_strdata_print) fillmask( 1) = nomask
(shr_strdata_print) fillread( 1) = NOT_SET
(shr_strdata_print) fillwrit( 1) = NOT_SET
(shr_strdata_print) domaps ( 1) = F
(shr_strdata_print) mapalgo ( 1) = bilinear
(shr_strdata_print) mapmask ( 1) = dstmask
(shr_strdata_print) mapread ( 1) = NOT_SET
(shr_strdata_print) mapwrit ( 1) = NOT_SET
(shr_strdata_print) tintalgo( 1) = linear
(shr_strdata_print)
(shr_strdata_print) nvectors = 0
(shr_strdata_print) ----------------------------------------------------------
(shr_sys_abort) ERROR: (shr_stream_readTCoord) ERROR: nf90_inq_varid
(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping


NAMELIST

cat >! lnd_in

 

[m_migliavacca1@campus_unimib_it]

Sam,

just to give more info, if I don't use the nitrogen deposition I can initialize the model but then I run into this error at the first time step (I think is a segmentation fault error):


79:(seq_frac_check) [atm init] ofrac min/max = 0.00000000000000000 0.916666666666666852
79:(seq_frac_check) [atm init] lfrin min/max = 0-127: Fortran language trap: integer division by zero
0-127:
0-127: Traceback:
64-95: Signal received: SIGTRAP - Trace trap
0-127: Offset 0x00000180 in procedure __accumulmod_NMOD_update_accum_field_sl, near line 507 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/accumulMod.F90
0-127:
0-127: Offset 0x00000788 in procedure __accfldsmod_NMOD_updateaccflds, near line 390 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/accFldsMod.F90
0-127: Offset 0x000001b4 in procedure __clm_driver_NMOD_clm_driver2, near line 811 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/clm_driver.F90
0-127: Offset 0x00000074 in procedure __clm_comp_NMOD_clm_run2, near line 276 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/clm_comp.F90
0-127: Offset 0x00000cc8 in procedure __lnd_comp_mct_NMOD_lnd_run_mct, near line 675 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/lnd/clm/src/main/cpl_mct/lnd_comp_mct.F90
0-127: Offset 0x0000e140 in procedure ccsm_driver, near line 1666 in file /gpfs/scratch/userjrc/jrcccu10/CLM_Kloster/models/drv/driver/ccsm_driver.F90
0-127: --- End of call chain ---
64-95:
INFO: 0031-639 Exit status from pm_respond = 0
0.833333333333331899E-01 1.00000000000000000

thanks,
mirco

 

[slevis]

I hope that the info in your last posting will help you with your debugging.

Sam

 

[m_migliavacca1@campus_unimib_it]

Hi Sam,

problem fixed running again the NCL script for the extraction of nitrogen depositions.
I am running in another error now but I'll open a new post later if I am not able to fix it,
thanks