[Wrf-users] "NetCDF error: NetCDF: Attribute not found" error during real.exe
mmkamal at uwaterloo.ca
mmkamal at uwaterloo.ca
Mon Sep 12 10:17:35 MDT 2011
Hi!
I have been trying to run WRF 3.3 in my machine (configuration is
given below) using IBM compiler but confused in some point. Although I
have successfully finish running WRF there but the following message
confused me. I am getting an error message called "NetCDF error:
NetCDF: Attribute not found" in the "rsl.error.0000" and
"rsl.out.0000" log file but not in the rest of the log files. But
fortunately I am getting the message "real_em: SUCCESS COMPLETE
REAL_EM INIT" at the end of each log files and running wrf.exe
generate history files. I have checked the output as well and looks
fine. Could anyone please tell me whether it is a problem or not? I
look forward to hearing from you.
Thanks
Kamal
PhD student
University of Waterloo, Canada
===================================================
Machine configuration
===================================================
3,328 cores of IBM Power 6 (4.7 GHz)
Operating System AIX 5.3
Interconnect Infiniband
Ram/Node 128 GB (256 on 2 nodes)
Cores/Node 32
Vendor Compilers xlc (C) xlf (fortran) xlC (C++)
----------------------------------------------------------
Libraries used
1) netcdf/4.0.1_nc3 2) parallel-netcdf/1.1.1
===================================================
I get the following message from LoadLeveler
==================================================
From: LoadLeveler
LoadLeveler Job Step: tcs-f11n06.33773.0
Executable: /scratch/mkamal/WRF_tcs/WRFV3/test/em_real/real.exe
Executable arguments:
State for machine: tcs-f08n10
LoadL_starter: The program, real.exe, exited normally and returned an
exit code of 0.
State for machine: tcs-f08n12
This job step was dispatched to run 1 time(s).
This job step was rejected by Starter 0 time(s).
Submitted at: Thu Sep 8 17:58:14 2011
Started at: Thu Sep 8 17:58:20 2011
Exited at: Thu Sep 8 18:00:56 2011
Real Time: 0 00:02:42
Job Step User Time: 0 02:24:16
Job Step System Time: 0 00:11:32
Total Job Step Time: 0 02:35:48
Starter User Time: 0 00:00:00
Starter System Time: 0 00:00:13
Total Starter Time: 0 00:00:13
---------------------------------------------------------------------
##############################################
gpc-f101n084-$ vi rsl.error.0000
##############################################
taskid: 0 hostname: tcs-f08n10
Namelist dfi_control not found in namelist.input. Using registry
defaults for variables in dfi_control
Namelist tc not found in namelist.input. Using registry defaults for
variables in tc
Namelist scm not found in namelist.input. Using registry defaults for
variables in scm
Namelist fire not found in namelist.input. Using registry defaults for
variables in fire
Ntasks in X 8 , ntasks in Y 16
--- NOTE: grid_fdda is 0 for domain 1, setting gfdda interval and
ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 1,
setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 1, setting obs nudging
interval and ending time to 0 for that domain.
--- NOTE: grid_fdda is 0 for domain 2, setting gfdda interval and
ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 2,
setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 2, setting obs nudging
interval and ending time to 0 for that domain.
--- NOTE: grid_fdda is 0 for domain 3, setting gfdda interval and
ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 3,
setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 3, setting obs nudging
interval and ending time to 0 for that domain.
--- NOTE: num_soil_layers has been set to 4
REAL_EM V3.3 PREPROCESSOR
real_em: calling alloc_and_configure_domain
*************************************
Parent domain
ids,ide,jds,jde 1 225 1 175
ims,ime,jms,jme -4 35 -4 18
ips,ipe,jps,jpe 1 28 1 11
*************************************
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 20923412 bytes allocated
setup_timekeeping: set xtime to 0.0000000000E+00
setup_timekeeping: set julian to 182.0000000
setup_timekeeping: returning...
d01 2002-07-02_00:00:00 real_em: calling set_scalar_indices_from_config
d01 2002-07-02_00:00:00 real_em: calling model_to_grid_config_rec
d01 2002-07-02_00:00:00 real_em: calling init_wrfio
d01 2002-07-02_00:00:00 Entering ext_gr1_ioinit
d01 2002-07-02_00:00:00 real_em: re-broadcast the configuration records
d01 2002-07-02_00:00:00 calling med_sidata_input
d01 2002-07-02_00:00:00 med_sidata_input: calling open_r_dataset for
met_em.d<domain>.<date>
d01 2002-07-02_00:00:00 med_sidata_input: calling input_auxinput1
metgrid input_wrf.F first_date_input = 2002-07-02_00:00:00
metgrid input_wrf.F first_date_nml = 2002-07-02_00:00:00
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code REAL,
line 83 Element P_TOP
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code REAL,
line 83 Element GMT
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code
INTEGER, line 83 Element JULYR
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code
INTEGER, line 83 Element JULDAY
d01 2002-07-02_00:00:00 mminlu = 'USGS'
######################################
gpc-f101n084-$ vi rsl.out.0000
######################################
taskid: 0 hostname: tcs-f08n10
Namelist dfi_control not found in namelist.input. Using registry
defaults for variables in dfi_control
Namelist tc not found in namelist.input. Using registry defaults for
variables in tc
Namelist scm not found in namelist.input. Using registry defaults for
variables in scm
Namelist fire not found in namelist.input. Using registry defaults for
variables in fire
Ntasks in X 8 , ntasks in Y 16
--- NOTE: grid_fdda is 0 for domain 1, setting gfdda interval and
ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 1,
setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 1, setting obs nudging
interval and ending time to 0 for that domain.
--- NOTE: grid_fdda is 0 for domain 2, setting gfdda interval and
ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 2,
setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 2, setting obs nudging
interval and ending time to 0 for that domain.
--- NOTE: grid_fdda is 0 for domain 3, setting gfdda interval and
ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain 3,
setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain 3, setting obs nudging
interval and ending time to 0 for that domain.
--- NOTE: num_soil_layers has been set to 4
REAL_EM V3.3 PREPROCESSOR
real_em: calling alloc_and_configure_domain
*************************************
Parent domain
ids,ide,jds,jde 1 225 1 175
ims,ime,jms,jme -4 35 -4 18
ips,ipe,jps,jpe 1 28 1 11
*************************************
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 20923412 bytes allocated
setup_timekeeping: set xtime to 0.0000000000E+00
setup_timekeeping: set julian to 182.0000000
setup_timekeeping: returning...
d01 2002-07-02_00:00:00 real_em: calling set_scalar_indices_from_config
d01 2002-07-02_00:00:00 real_em: calling model_to_grid_config_rec
d01 2002-07-02_00:00:00 real_em: calling init_wrfio
d01 2002-07-02_00:00:00 Entering ext_gr1_ioinit
d01 2002-07-02_00:00:00 real_em: re-broadcast the configuration records
d01 2002-07-02_00:00:00 calling med_sidata_input
Time period # 1 to process = 2002-07-02_00:00:00.
Time period # 2 to process = 2002-07-02_03:00:00.
Time period # 3 to process = 2002-07-02_06:00:00.
Time period # 4 to process = 2002-07-02_09:00:00.
Time period # 5 to process = 2002-07-02_12:00:00.
Time period # 6 to process = 2002-07-02_15:00:00.
Time period # 7 to process = 2002-07-02_18:00:00.
Time period # 8 to process = 2002-07-02_21:00:00.
Time period # 9 to process = 2002-07-03_00:00:00.
Total analysis times to input = 9.
-----------------------------------------------------------------------------
Domain 1: Current date being processed: 2002-07-02_00:00:00.0000,
which is loop # 1 out of 9
configflags%julyr, %julday, %gmt: 2002 183 0.0000000000E+00
d01 2002-07-02_00:00:00 med_sidata_input: calling open_r_dataset for
met_em.d<domain>.<date>
d01 2002-07-02_00:00:00 med_sidata_input: calling input_auxinput1
metgrid input_wrf.F first_date_input = 2002-07-02_00:00:00
metgrid input_wrf.F first_date_nml = 2002-07-02_00:00:00
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code REAL,
line 83 Element P_TOP
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code REAL,
line 83 Element GMT
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code
INTEGER, line 83 Element JULYR
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Attribute not found
d01 2002-07-02_00:00:00 NetCDF error in ext_ncd_get_dom_ti.code
INTEGER, line 83 Element JULDAY
d01 2002-07-02_00:00:00 mminlu = 'USGS'
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2002-07-02_00:00:00 NetCDF error in wrf_io.F90, line 2712 Varname PTHETA
d01 2002-07-02_00:00:00 NetCDF error: NetCDF: Variable not found
d01 2002-07-02_00:00:00 NetCDF error in wrf_io.F90, line 2712 Varname QV
==========================================================================
Configure.wrf
==========================================================================
#### Architecture specific settings ####
# Settings for AIX xlf compiler with xlc (dmpar)
#
DMPARALLEL = 1
OMPCPP = # -D_OPENMP
OMP = # -qsmp=noauto
OMPCC = # -qsmp=noauto
SFC = xlf90_r
SCC = cc_r
SC99 = c99_r
CCOMP = cc_r
DM_FC = mpxlf90_r
DM_CC = mpcc_r -DMPI2_SUPPORT
FC = timex $(DM_FC)
CC = $(DM_CC) -DFSEEKO64_OK
LD = $(FC)
RWORDSIZE = $(NATIVE_RWORDSIZE)
PROMOTION = -qrealsize=$(RWORDSIZE) -qintsize=4
ARCH_LOCAL = -DNONSTANDARD_SYSTEM_SUBR -DNATIVE_MASSV
CFLAGS_LOCAL = -DNOUNDERSCORE
LDFLAGS_LOCAL = -lmass -lmassv
CPLUSPLUSLIB = -lC
ESMF_LDFLAG = $(CPLUSPLUSLIB)
# -qhot commented out in 3.0.1.1 release because of reported problems with
# model results under certain configurations. Use at your own risk.
FCOPTIM = -O3 # -qhot
FCREDUCEDOPT = -O2
FCNOOPT = -qnoopt
FCDEBUG = # -g $(FCNOOPT) -qfullpath
FORMAT_FIXED = -qfixed
FORMAT_FREE = -qfree=f90
FCSUFFIX = -qsuffix=f=f90
BYTESWAPIO =
FCBASEOPTS_NO_G = -w -qspill=20000 -qmaxmem=32767 $(FORMAT_FREE)
$(BYTESWAPIO) #-qflttrap=zerodivide:invalid:enable -qsigtrap -C #
-qinitauto=7FF7FFFF
FCBASEOPTS = $(FCBASEOPTS_NO_G) $(FCDEBUG)
MODULE_SRCH_FLAG =
TRADFLAG =
CPP = /lib/cpp -C -P
AR = ar
ARFLAGS = ru
M4 = m4 -B 14000
RANLIB = ranlib
CC_TOOLS = cc
==========================================================================
LIB_EXTERNAL = \
-L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf
-L/scinet/tcs/Libraries/netcdf-4.0.1_nc3/lib -lnetcdf
-L$(WRF_SRC_ROOT_DIR)/external/io_pnetcdf -lwrfio_pnf
-L/scinet/tcs/Libraries/parallel-netcdf-1.1.1/lib -lpnetcdf
###########################################################
===========================================================
Configure.wps
===========================================================
#### Architecture specific settings ####
# Settings for AIX DM parallel, NO GRIB2
#
COMPRESSION_LIBS =
COMPRESSION_INC =
FDEFS =
NCARG_LIBS =
NCARG_LIBS2 = -L/usr/local/lib64/r4i4 -lncarg -lncarg_gks -lncarg_c \
-L/usr/X11R6/lib -lX11 -lpng_ncl -lz_ncl
FC = mpxlf90_r
SFC = xlf90_r
FFLAGS = -qfree=f90
F77FLAGS = -qfixed
FCSUFFIX = -qsuffix=f=f90
FNGFLAGS = $(FFLAGS)
LDFLAGS =
CC = mpcc_r
SCC = cc
CFLAGS =
CPP = /usr/lib/cpp -C -P
CPPFLAGS = -DAIX -DIBM4 -DIO_NETCDF -DIO_BINARY -DIO_GRIB1 -D_MPI -DBIT32
ARFLAGS =
============================================================================
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