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cesm1.2.1 esmf error with mkmapdata.sh

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matthias_demuzere@ees_kuleuven_be

New Member
Dear, At the moment I am trying to create the surface datasets for my own single point site. This I do according to this script, based on the Boulder example from the User Guide:#!/usr/bin/tcsh# set the GRIDNAME and creation date that will be used later
setenv CSMDATA /home/matthiasd/data/inputdata
setenv GRIDNAME 1x1_torniHEL
setenv CDATE `date +%y%m%d`
setenv LAT 60.1678027778
setenv LON 24.9386888889
setenv CCSMROOT /home/rcs/software/cesm1_2_1# Create the SCRIP grid file for the location and create a unity mapping file for it.
cd /home/rcs/software/cesm1_2_1/models/lnd/clm/tools/shared/mkmapdata
./mknoocnmap.pl -p ${LAT},${LON} -n $GRIDNAME# Set pointer to MAPFILE just created that will be used later
setenv MAPFILE `pwd`/map_${GRIDNAME}_noocean_to_${GRIDNAME}_nomask_aave_da_${CDATE}.nc# create the mapping files needed by mksurfdata_map.
cd /home/rcs/software/cesm1_2_1/models/lnd/clm/tools/shared/mkmapdata
setenv GRIDFILE /home/rcs/software/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_${GRIDNAME}_nomask_${CDATE}.nc
./mkmapdata.sh -r $GRIDNAME -f $GRIDFILE -t regional
# create the domain file
cd /home/rcs/software/cesm1_2_1/tools/mapping/gen_domain_files/src
/home/rcs/software/cesm1_2_1/scripts/ccsm_utils/Machines/configure -mach RCS -compiler intel
gmakecd ..
setenv OCNDOM domain.ocn_noocean.nc
setenv ATMDOM domain.lnd.{$GRIDNAME}_noocean.nc
./gen_domain -m $MAPFILE -o $OCNDOM -l $ATMDOM# Save the location where the domain file was created
setenv GENDOM_PATH `pwd`# Finally create the surface dataset
cd /home/rcs/software/cesm1_2_1/models/lnd/clm/tools/clm4_5/mksurfdata_map
./mksurfdata.pl -r usrspec -usr_gname $GRIDNAME -usr_gdate $CDATEUntil ./mkmapdata.sh all goes well.But when I execute the ./mkmapdata.sh command, I get the following error:ERROR: Unable to get dimension information from:
/home/matthiasd/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVH
RR_c110228.nc


Please check the PET*.RegridWeightGen.Log files for the NetCDF error message.The PET*. file provides the following info:20140107 182838.955 INFO PET0 Running with ESMF Version 5.2.0rp3
20140107 182838.955 ERROR PET0 ESMF_IOScrip.F90:200 ESMF_ScripInq Library needed by ESMF not present - - ESMF_NETCDF not defined when lib was compiled
20140107 183336.232 INFO PET0 Running with ESMF Version 5.2.0rp3
20140107 183336.232 ERROR PET0 ESMF_IOScrip.F90:200 ESMF_ScripInq Library needed by ESMF not present - - ESMF_NETCDF not defined when lib was compiled
20140107 220640.533 INFO PET0 Running with ESMF Version 5.2.0rp3
20140107 220640.534 ERROR PET0 ESMF_IOScrip.F90:200 ESMF_ScripInq Library needed by ESMF not present - - ESMF_NETCDF not defined when lib was compiled
20140107 221619.054 INFO PET0 Running with ESMF Version 5.2.0rp3
20140107 221619.055 ERROR PET0 ESMF_IOScrip.F90:200 ESMF_ScripInq Library needed by ESMF not present - - ESMF_NETCDF not defined when lib was compiled
20140107 223031.809 INFO PET0 Running with ESMF Version 5.2.0rp3
20140107 223031.810 ERROR PET0 ESMF_IOScrip.F90:200 ESMF_ScripInq Library needed by ESMF not present - - ESMF_NETCDF not defined when lib was compiled So apparently something is going wrong with esmf. Nevertheless, I just compiled esmf myself using the intel compilar and having the NETCDF directories set:make distcleanexport ESMF_NETCDF=/home/rcs/software/intel/netcdf/4.1.3
export ESMF_NETCDF_INCLUDE=/home/rcs/software/intel/netcdf/4.1.3/include
export ESMF_NETCDF_LIBPATH=/home/rcs/software/intel/netcdf/4.1.3/lib
export ESMF_NETCDF_LIBS="-lnetcdff -lnetcdf"export ESMF_INSTALL_PREFIX=/home/rcs/software/intel/esmf/5.2.0
export ESMF_COMPILER=intel
export ESMF_DIR=/home/rcs/software/intel/esmf
export ESMF_COMM=mpiunigmake info &> info.log
gmake check &> check.log
gmake install &> install.logThis compilation succeeded without a problem.The link to the ESMFBIN_PATH is provided in the mkmapdata.sh file:ESMFBIN_PATH=/home/rcs/software/intel/esmf/5.2.0/bin/binO/Linux.intel.64.mpiuni.defaultSo I am not sure what I can change more at this step? Is there a way for me to test whether esmf really compiled well with netcdf linked?Or is there any other workaround? I read somewhere on this forum that I could also link to ncl. Would this work as well?Thanks in advance,Matthias 
 
M

matthias_demuzere@ees_kuleuven_be

New Member
Dear, Following up on the post above, I recompiled ESMF, providing more detailed link to the NETCDF_LIBS in EMSF: export ESMF_NETCDF_LIBS="-L/home/rcs/software/intel/netcdf/4.1.3/lib -lnetcdff -lnetcdf_c++ -lnetcdf"Doing so, I got another error when running ./mkmapdata, related to libimf.so. So I located this file and added the lib to my library path in my environment.This seems to do the trick, but now I get another error when executing ./mkmapdata:./mkmapdata.sh: line 106: 27814 Segmentation fault      (core dumped) ${cmd}ERROR: mapping file for this resolution does NOT exist (../../shared/mkmapdata/map_3x3min_MODIS_to_1x1_torniHEL_nomask_aave_da_c140108.nc).  The full log file is inluded in attach. Any ideas on these errors?Regards, Matthias
 
M

matthias_demuzere@ees_kuleuven_be

New Member
Dear, Following up on the post above, I recompiled ESMF, providing more detailed link to the NETCDF_LIBS in EMSF: export ESMF_NETCDF_LIBS="-L/home/rcs/software/intel/netcdf/4.1.3/lib -lnetcdff -lnetcdf_c++ -lnetcdf"Doing so, I got another error when running ./mkmapdata, related to libimf.so. So I located this file and added the lib to my library path in my environment.This seems to do the trick, but now I get another error when executing ./mkmapdata:./mkmapdata.sh: line 106: 27814 Segmentation fault      (core dumped) ${cmd}ERROR: mapping file for this resolution does NOT exist (../../shared/mkmapdata/map_3x3min_MODIS_to_1x1_torniHEL_nomask_aave_da_c140108.nc).  The full log file is inluded in attach. Any ideas on these errors?Regards, Matthias
 
erik

erik

Erik Kluzek
CSEG and Liaisons
Staff member

Code: 
It looks like it's failing on one of these two files...<br /><br />ingrid = /home/matthiasd/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_LandScan2004_c120517.nc
ingrid = /home/matthiasd/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODIS_c110915.nc<br /><br />Figure out which one, add the "--verbose" option to mkmapdata.sh to see if you get more information and to see if you can run the call <br />to the ESMF regrid program by hand, so you can see exactly what's happening.<br /><br /><br /><br /><br />
 
erik

erik

Erik Kluzek
CSEG and Liaisons
Staff member

Code: 
It looks like it's failing on one of these two files...<br /><br />ingrid = /home/matthiasd/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_LandScan2004_c120517.nc
ingrid = /home/matthiasd/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_MODIS_c110915.nc<br /><br />Figure out which one, add the "--verbose" option to mkmapdata.sh to see if you get more information and to see if you can run the call <br />to the ESMF regrid program by hand, so you can see exactly what's happening.<br /><br /><br /><br /><br />
 
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