Error in getting regional data set

D

devarajun@gmail_com

Dev
Member
Hi I am trying to run CLM4 for the region (lat 7 to8 and longitude 68 to 99): I have used the command below and got the error: Any help in this regard will be highly appreciated: ./getregional_datasets.pl -sw 7,68 -ne 38,99 -id 66x50pt_f05_t12_india -mycsmdata $MYCSMDATA
CESM inputdata root directory: /home/devaraju/CLM4/india_inputdata/
Execute: env S_LAT=7 W_LON=68 N_LAT=38 E_LON=99 SIM_YR=1850 SIM_YR_RNG=constant MASK=tx0.1v2 ID=66x50pt_f05_t12_india RCP=-999.9 RES=0.47x0.63 MYCSMDATA=/home/devaraju/CLM4/india_inputdata/    ncl /home/devaraju/cesm1_0_4/models/lnd/clm/tools/ncl_scripts/getregional_datasets.ncl
 Copyright (C) 1995-2011 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.0.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Extract out regional datasets from global datasets
(0)    Execute:ncks -O -d lsmlat,207,272 -d lsmlon,109,158 /home/devaraju/CLM4/india_inputdata//lnd/clm2/griddata/griddata_0.47x0.63_c070918.nc /home/devaraju/CLM4/india_inputdata//lnd/clm2/griddata/griddata_66x50pt_f05_t12_india.nc
(0)    Execute:ncks -O -d lsmlat,207,272 -d lsmlon,109,158 /home/devaraju/CLM4/india_inputdata//lnd/clm2/griddata/fracdata_0.47x0.63_tx0.1v2_c070928.nc /home/devaraju/CLM4/india_inputdata//lnd/clm2/griddata/fracdata_66x50pt_f05_t12_india_tx0.1v2.nc
(0)    Execute:ncks -O -d lsmlat,207,272 -d lsmlon,109,158 /home/devaraju/CLM4/india_inputdata//lnd/clm2/surfdata/surfdata_0.47x0.63_simyr1850_c100826.nc /home/devaraju/CLM4/india_inputdata//lnd/clm2/surfdata/surfdata_66x50pt_f05_t12_india_simyr1850.nc
(0)    Input global fpftdyn file does not exist or not found: -2147483647
(0)    Input global flndtopo file does not exist or not found: /home/devaraju/CLM4/india_inputdata//lnd/clm2/griddata/topodata_0.47x0.63_USGS_c070918.nc
(0)    Input global faerdep file does not exist or not found: -2147483647
(0)    Input global stream_fldfilename_ndep file does not exist or not found: -2147483647
(0)    Execute:ncks -O -d nj,207,272 -d ni,109,158 /home/devaraju/CLM4/india_inputdata//atm/datm7/domain.lnd.fv0.47x0.63_tx0.1v2_070929.nc /home/devaraju/CLM4/india_inputdata//atm/datm7/domain.clm/domain.lnd.66x50pt_f05_t12_india_tx0.1v2.nc
nco_err_exit(): ERROR Short NCO-generated message (usually name of function that triggered error): nco_create()
nco_err_exit(): ERROR Error code is 2. Translation into English with nc_strerror(2) is "No such file or directory"
fatal:Conditional statements (if and do while) require SCALAR logical values, see all and any functions
fatal:Execute: Error occurred at or near line 229 in file /home/devaraju/cesm1_0_4/models/lnd/clm/tools/ncl_scripts/getregional_datasets.ncl

 
slevis

slevis

Moderator
Staff member
The error explicitly states "No such file or directory" about /home/devaraju/CLM4/india_inputdata//atm/datm7/domain.clm/domain.lnd.66x50pt_f05_t12_india_tx0.1v2.ncCheck the path, file name, and file permissions, try again, and I hope this solves the problem.Sam
 
D

devarajun@gmail_com

Dev
Member
Dear Sam,Thanks  a lot for the reply. I make sure that the file exists now (domain.lnd.66x50pt_f05_t12_india_tx0.1v2.nc). I am now geeting the new error below: ./getregional_datasets.pl -sw 7,68 -ne 38,99 -id 66x50pt_f19_india -mycsmdata $MYCSMDATA
test111CESM inputdata root directory: /home/devaraju/Alaska/input_alaska/inputdata_alaska/
Execute: env S_LAT=7 W_LON=68 N_LAT=38 E_LON=99 SIM_YR=1850 SIM_YR_RNG=constant MASK=tx0.1v2 ID=66x50pt_f19_india RCP=-999.9 RES=0.47x0.63 MYCSMDATA=/home/devaraju/Alaska/input_alaska/inputdata_alaska/    ncl /home/devaraju/Alaska/cesm1_0_4/models/lnd/clm/tools/ncl_scripts/getregional_datasets.ncl
 Copyright (C) 1995-2011 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.0.0
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)    Extract out regional datasets from global datasets
(0)    Execute:ncks -O -d lsmlat,207,272 -d lsmlon,109,158 /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/griddata/griddata_0.47x0.63_c070918.nc /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/griddata/griddata_66x50pt_f19_india.nc
(0)    Execute:ncks -O -d lsmlat,207,272 -d lsmlon,109,158 /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/griddata/fracdata_0.47x0.63_tx0.1v2_c070928.nc /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/griddata/fracdata_66x50pt_f19_india_tx0.1v2.nc
(0)    Execute:ncks -O -d lsmlat,207,272 -d lsmlon,109,158 /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/surfdata/surfdata_0.47x0.63_simyr1850_c100826.nc /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/surfdata/surfdata_66x50pt_f19_india_simyr1850.nc
(0)    Input global fpftdyn file does not exist or not found: -2147483647
(0)    Execute:ncks -O -d lsmlat,207,272 -d lsmlon,109,158 /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/griddata/topodata_0.47x0.63_USGS_c070918.nc /home/devaraju/Alaska/input_alaska/inputdata_alaska//lnd/clm2/griddata/topodata_66x50pt_f19_india.nc
(0)    Input global faerdep file does not exist or not found: -2147483647
(0)    Input global stream_fldfilename_ndep file does not exist or not found: -2147483647
(0)    Execute:ncks -O -d nj,207,272 -d ni,109,158 /home/devaraju/Alaska/input_alaska/inputdata_alaska//atm/datm7/domain.lnd.fv0.47x0.63_tx0.1v2_070929.nc /home/devaraju/Alaska/input_alaska/inputdata_alaska//atm/datm7/domain.clm/domain.lnd.66x50pt_f19_india_tx0.1v2.nc
nco_err_exit(): ERROR Short NCO-generated message (usually name of function that triggered error): nco_create()
nco_err_exit(): ERROR Error code is 2. Translation into English with nc_strerror(2) is "No such file or directory"
fatal:Conditional statements (if and do while) require SCALAR logical values, see all and any functions
fatal:Execute: Error occurred at or near line 229 in file /home/devaraju/Alaska/cesm1_0_4/models/lnd/clm/tools/ncl_scripts/getregional_datasets.ncl

I am sure there is no problem with path, file name, and file permissionsI have the fpftdyn file placed here '/home/devaraju/Alaska/input_alaska/inputdata_alaska/lnd/clm2/surfdata/surfdata.pftdyn_66x50pt_f05_t12_india_simyr1850.nc'and faerdep file placed '/home/devaraju/Alaska/input_alaska/inputdata_alaska/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_monthly_1850_mean_1.9x2.5_c090421.nc'I dont understand it just says file does not exist. Can you please tell me  how to resolve this. Any help will be appreciated. Thanks a lot for your help.   
 
slevis

slevis

Moderator
Staff member
The ncks command that gives the error appears to be looking for two files:/home/devaraju/Alaska/input_alaska/inputdata_alaska//atm/datm7/domain.lnd.fv0.47x0.63_tx0.1v2_070929.nc/home/devaraju/Alaska/input_alaska/inputdata_alaska//atm/datm7/domain.clmIf both are located in the right place and with correct permissions, then I'm not sure what to suggest...Sam
 
D

devarajun@gmail_com

Dev
Member
Dear Sam,Thanks for the reply. I have done it all freshly and it showed me somewhere in the middle(0)    Input global fpftdyn file does not exist or not found: -2147483647
(0)    Input global faerdep file does not exist or not found: -2147483647
(0)    Input global stream_fldfilename_ndep file does not exist or not found: -2147483647 But it says at the end succesfully created regional data sets.Then I moved on to run the model, and I got the error message in the Dear Sam,Thanks for the reply. I have done it all freshly and it showed me somewhere in the middle(0)    Input global fpftdyn file does not exist or not found: -2147483647
(0)    Input global faerdep file does not exist or not found: -2147483647
(0)    Input global stream_fldfilename_ndep file does not exist or not found: -2147483647 But it says at the end succesfully created regional data sets.Then I moved on to run the model, and I got the error message in the cpl.log.130605-182840 file as below:(seq_rearr_gsmapCreate) created new gsmap decomp_type =       2
(seq_rearr_gsmapCreate)   ngseg/gsize        =      256  221184
(seq_rearr_gsmapCreate)   mpisize/active_pes =      256     256
(seq_rearr_gsmapCreate)   avg seg per pe/ape =        1       1
(seq_rearr_gsmapCreate)   nlseg/maxnlsegs    =        1       1
(map_atm2atm_init_mct)  gsmaps ARE IDENTICAL, copyoption =  T
(seq_rearr_gsmapCreate) created new gsmap decomp_type =       2
(seq_rearr_gsmapCreate)   ngseg/gsize        =     2324    3300
(seq_rearr_gsmapCreate)   mpisize/active_pes =      256     256
(seq_rearr_gsmapCreate)   avg seg per pe/ape =        9       9
(seq_rearr_gsmapCreate)   nlseg/maxnlsegs    =       10      10
(map_lnd2lnd_init_mct)  gsmaps are not identical
(seq_rearr_gsmapCreate) created new gsmap decomp_type =       2
(seq_rearr_gsmapCreate)   ngseg/gsize        =     2382  259200
(seq_rearr_gsmapCreate)   mpisize/active_pes =      256     256
(seq_rearr_gsmapCreate)   avg seg per pe/ape =        9       9
(seq_rearr_gsmapCreate)   nlseg/maxnlsegs    =       10      10
(map_rof2rof_init_mct)  gsmaps are not identical
(seq_mct_drv) : Initializing merge components
(seq_mct_drv) : Initializing atm/lnd mapping
(seq_mct_drv) : Performing domain checking
 (domain_check_mct)  error: global atmsize =       221184  global lndsize=
        3300
***********ccsm log is attached and it says "(domain_check_mct) :  atm and lnd grid must have the same global size
000.MCT(MPEU)::die.: from (domain_check_mct)()
 (domain_check_mct)  error: global atmsize =       221184  global lndsize=
        3300 "
Any Idea where  I went wrong? Thanks a lot for your time.
 
slevis

slevis

Moderator
Staff member
This error suggests an inconsisitency in the domain files that you use for the atmosphere vs. the land model. In env_conf set these four variables to be the same for ATM and LND, similar to my example below:










Sam
 
D

devarajun@gmail_com

Dev
Member
Dear Sam, Thanks a lot. I am able tu run now.  I have one more error agian while building I_1850_CN with cndv option. Below is the error:ifort -c -I.  -I/home/devaraju/netcdf-4.1.1/include -I/home/devaraju/netcdf-4.1.1/include -I/home/devaraju/mpich2-install/include -I. -I/home/devaraju/CLM4/india/cases/cndv_ctl/SourceMods/src.clm -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/cpl_share -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/main -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeophys -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/cpl_mct -I/home/devaraju/CLM4/india/scratch//cndv_ctl/lib/include  -DMAXPATCH_PFT=17 -DCNDV -DCN -D_USEBOX -D_NETCDF -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH  -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR  /home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem/CNDVEstablishmentMod.F90
ifort -c -I.  -I/home/devaraju/netcdf-4.1.1/include -I/home/devaraju/netcdf-4.1.1/include -I/home/devaraju/mpich2-install/include -I. -I/home/devaraju/CLM4/india/cases/cndv_ctl/SourceMods/src.clm -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/cpl_share -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/main -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeophys -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/cpl_mct -I/home/devaraju/CLM4/india/scratch//cndv_ctl/lib/include  -DMAXPATCH_PFT=17 -DCNDV -DCN -D_USEBOX -D_NETCDF -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH  -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR  /home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem/CNDVLightMod.F90
ifort -c -I.  -I/home/devaraju/netcdf-4.1.1/include -I/home/devaraju/netcdf-4.1.1/include -I/home/devaraju/mpich2-install/include -I. -I/home/devaraju/CLM4/india/cases/cndv_ctl/SourceMods/src.clm -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/cpl_share -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/main -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeophys -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem -I/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/cpl_mct -I/home/devaraju/CLM4/india/scratch//cndv_ctl/lib/include  -DMAXPATCH_PFT=17 -DCNDV -DCN -D_USEBOX -D_NETCDF -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH  -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR  /home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem/CNDVMod.F90
/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem/CNDVMod.F90(160): error #6580: Name in only-list does not exist.   [FRIVINP_RTM]
                                 frivinp_rtm, iulog
---------------------------------^
/home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem/CNDVMod.F90(295): error #6404: This name does not have a type, and must have an explicit type.   [FRIVINP_RTM]
    if (frivinp_rtm /= ' ') then
--------^
compilation aborted for /home/devaraju/CLM4/india/cesm1_0_4/models/lnd/clm/src/biogeochem/CNDVMod.F90 (code 1)
gmake: *** [CNDVMod.o] Error 1

Please suggest whats going on here? Thanks again for your time.
 
slevis

slevis

Moderator
Staff member
Looks to me like a bug. Add the following two lines around all instances of the variable frivinp_rtm, as done in clm_varctl.F90.#ifdef RTM
#endifSam
 
D

devarajun@gmail_com

Dev
Member
Dear Dr Sam,Yes thats a bug. It worked for me. As you suggested, Added the two lines around all instances of the variable frivinp_rtm in CNDVMod.F90.Thanks a lot for your quick respone. I am able to run now.
 
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