Scheduled Downtime
On Tuesday 24 October 2023 @ 5pm MT the forums will be in read only mode in preparation for the downtime. On Wednesday 25 October 2023 @ 5am MT, this website will be down for maintenance and expected to return online later in the morning.
Normal Operations
The forums are back online with normal operations. If you notice any issues or errors related to the forums, please reach out to help@ucar.edu

./mkmapdata.sh

P

pengxq13@lzu_edu_cn

New Member
Dear all, I prepared to creat the single-point surface data, when I come to this step,there are several errors:[PengXiaoqing@localhost mkmapdata]$ export ESMFBIN_PATH=/home/public/software/esmf-6.3.0/bin/binO/Linux.intel.64.mpiuni.default[PengXiaoqing@localhost mkmapdata]$ export MY_ESMF_REGRID=/home/public/software/esmf-6.3.0/bin/binO/Linux.intel.64.mpiuni.default/ESMF_RegridWeightGen[PengXiaoqing@localhost mkmapdata]$ ./mkmapdata.sh -r 1x1_arou -f /home/PengXiaoqing/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_arou_nomask_c150105.nc -t regional./mkmapdata.shScript to create mapping files required by mksurfdata_mapquery command is ./../../../bld/queryDefaultNamelist.pl -silent -namelist clmexp -phys clm4_5  -justvalue -options sim_year=2000 -csmdata /home/PengXiaoqing/model/cesm1_2_1/inputdata Using user specified scrip grid file: /home/PengXiaoqing/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_arou_nomask_c150105.ncOutput grid resolution is 1x1_arouMachine localhost.localdomain NOT recognizedCreating mapping file: map_0.5x0.5_AVHRR_to_1x1_arou_nomask_aave_da_c150106.ncFrom input grid: /home/PengXiaoqing/model/cesm1_2_1/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.ncFor output grid: /home/PengXiaoqing/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_arou_nomask_c150105.nc   ERROR: Unable to get dimension information from: /home/PengXiaoqing/model/cesm1_2_1/inputdata/lnd/clm2/mappingdata/grids/SCRIPgr id_0.5x0.5_AVHRR_c110228.nc                                                                                                                                       ERROR: Problem on processor            0  . Please see the PET*.RegridWeightGen.Log files for a traceback.Error status returned from mkmapdata script[PengXiaoqing@localhost mkmapdata]$ vi PET0.RegridWeightGen.Log  20150106 113708.650 INFO             PET0 Running with ESMF Version 6.3.0rp120150106 113708.650 ERROR            PET0 ESMF_IOScrip.F90:204 ESMF_ScripInq Library needed by ESMF not present - - ESMF_NETCDF not defined when lib was compiled20150106 113708.650 ERROR            PET0 ESMF_RegridWeightGen.F90:585 ESMF_RegridWeightGenFile Library needed by ESMF not present - Internal subroutine call returned Error  But I have install the ESMF6.3.0，and installed sucessful.
 
J

jedwards

CSEG and Liaisons
Staff member
You need to build ESMF with netcdf IO configured:    ESMF_NETCDF not defined when lib was compiled 
 
P

pengxq13@lzu_edu_cn

New Member
When I install the ESMF, I have defined the ESMF_NETCDF [root@localhost esmf]#  export ESMF_OS=Linux[root@localhost esmf]# export ESMF_DIR=/home/public/source/esmf[root@localhost esmf]# export ESMF_TESTWITHREADS=OFF[root@localhost esmf]# export ESMF_COMM=mpiuni[root@localhost esmf]# export ESMF_COMPILER=intel[root@localhost esmf]# export ESMF_ABI=64[root@localhost esmf]# export ESMF_INSTALL_PREFIX=/home/public/software/esmf-6.3.0[root@localhost esmf]# export ESMF_SITE=default[root@localhost esmf]# export ESMF_TESTEXHAUSTIVE=ON[root@localhost esmf]# export ESMF_NETCDF=/home/public/software/netcdf-4.3[root@localhostesmf]#export ESMF_NETCDF_INCLUDE=/home/public/software/netcdf-4.3/include[root@localhost esmf]# export ESMF_NETCDF_LIBPATH=/home/public/software/netcdf-4.3/lib [root@localhost esmf]# export ESMF_NETCDF_LIBS='-lnetcdf -lnetcdff'
 
P

pengxq13@lzu_edu_cn

New Member
Thank you! this problem have been solved like you said that the problem is the ESMF. But I have also another problem:  [guser002@login mkmapdata]$ export GRIDNAME=1x1_boulderCO
[guser002@login mkmapdata]$ export CDATE='date +150108'
[guser002@login mkmapdata]$ ./mknoocnmap.pl -p 40,255 -n $GRIDNAME

Create SCRIP grid and mapping files for a single-point
Create land SCRIP gridfile
Execute: env S_LAT=39.95 W_LON=254.95 N_LAT=40.05 E_LON=255.05 NX=1 NY=1 PTNAME=1x1_boulderCO   GRIDFILE=/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc ncl mkscripgrid.ncl
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
Create ocean SCRIP gridfile
Execute: env S_LAT=39.95 W_LON=254.95 N_LAT=40.05 E_LON=255.05 NX=1 NY=1 PTNAME=1x1_boulderCO   GRIDFILE=/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_noocean_c150108.nc IMASK=0 ncl mkscripgrid.ncl
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
Create unity mapping file between the two gridfile
Execute: env GRIDFILE1=/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_noocean_c150108.nc GRIDFILE2=/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc MAPFILE=map_1x1_boulderCO_noocean_to_1x1_boulderCO_nomask_aave_da_150108.nc  ncl /public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapdata/mkunitymap.ncl
Copyright (C) 1995-2014 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.2.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.

Successfully created grid/mapping files for single-point

[guser002@login mkmapdata]$ ls
createXMLEntries.pl                                                  mkunitymap.ncl            regridbatch.sh
map_1x1_boulderCO_noocean_to_1x1_boulderCO_nomask_aave_da_150108.nc  mvNimport.sh              rmdups.ncl
mkmapdata.sh                                                         PET0.RegridWeightGen.Log
mknoocnmap.pl                                                        README

[guser002@login mkmapdata]$ export CSMDATA=/public3/home/external/gansu/guser002/model/cesm1_2_1/inputdata
[guser002@login mkmapdata]$ export ESMFBIN_PATH=/public3/home/external/gansu/guser002/software/esmf-6.3.0/bin/binO/Linux.intel.64.mpiuni.default
[guser002@login mkmapdata]$ export MY_ESMF_REGRID=/public3/home/external/gansu/guser002/software/esmf-6.3.0/bin/binO/Linux.intel.64.mpiuni.default/ESMF_RegridWeightGen
[guser002@login mkmapdata]$ export GRIDFILE=/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc
[guser002@login mkmapdata]$ ./mkmapdata.sh -r $GRIDNAME -f $GRIDFILE -t regional

./mkmapdata.sh
Script to create mapping files required by mksurfdata_map
query command is ./../../../bld/queryDefaultNamelist.pl -silent -namelist clmexp -phys clm4_5  -justvalue -options sim_year=2000 -csmdata /public3/home/external/gansu/guser002/model/cesm1_2_1/inputdata
Using user specified scrip grid file: /public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc
Output grid resolution is 1x1_boulderCO
Machine login NOT recognized
Creating mapping file: map_0.5x0.5_AVHRR_to_1x1_boulderCO_nomask_aave_da_c150108.nc
From input grid: /public3/home/external/gansu/guser002/model/cesm1_2_1/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.nc
For output grid: /public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc

Skipping creation of map_0.5x0.5_AVHRR_to_1x1_boulderCO_nomask_aave_da_c150108.nc as already exists
Creating mapping file: map_0.5x0.5_MODIS_to_1x1_boulderCO_nomask_aave_da_c150108.nc
From input grid: /public3/home/external/gansu/guser002/model/cesm1_2_1/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_MODIS_c110228.nc
For output grid: /public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc

Skipping creation of map_0.5x0.5_MODIS_to_1x1_boulderCO_nomask_aave_da_c150108.nc as already exists
Creating mapping file: map_3x3min_LandScan2004_to_1x1_boulderCO_nomask_aave_da_c150108.nc
From input grid: /public3/home/external/gansu/guser002/model/cesm1_2_1/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_3minx3min_LandScan2004_c120517.nc
For output grid: /public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shared/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc

Starting weight generation with these inputs:
   Source File:
/public3/home/external/gansu/guser002/model/cesm1_2_1/inputdata/lnd/clm2/mappin
gdata/grids/SCRIPgrid_3minx3min_LandScan2004_c120517.nc
   Destination File:
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc
   Weight File:
map_3x3min_LandScan2004_to_1x1_boulderCO_nomask_aave_da_c150108.nc
   Source File is in SCRIP format
   Source Grid is a global grid
   Source Grid is a logically rectangular grid
   Destination File is in SCRIP format
   Destination Grid is a regional grid
   Destination Grid is a logically rectangular grid
   Regrid Method: conserve
   Pole option: NONE
   Ignore unmapped destination points
   Output weight file in 64bit offset NetCDF file format
   Norm Type: dstarea

./mkmapdata.sh: line 106: 13372 Segmentation fault      (core dumped) ${cmd}
Error status returned from mkmapdata script


[guser002@login gen_domain_files]$ export OCNDOM=domain.ocn_noocean.nc
[guser002@login gen_domain_files]$ export ATMDOM domain.lnd.1x1_boulderCO_noocean.nc
[guser002@login gen_domain_files]$ export ATMDOM=domain.lnd.1x1_boulderCO_noocean.nc
[guser002@login gen_domain_files]$ ./gen_domain -m $MAPFILE -o $OCNDOM -l $ATMDOM

fmap   =
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapdata/map_1x1_boulderCO_noocean_to_1x1_boulderCO_nomask_aave_da_150108.n
c
fn1_out_ocn= domain.ocn.domain.ocn_noocean.nc.150108.nc
fn2_out_lnd=
domain.lnd.domain.lnd.1x1_boulderCO_noocean.nc_domain.ocn_noocean.nc.150108.nc
fn2_out_ocn=
domain.ocn.domain.lnd.1x1_boulderCO_noocean.nc_domain.ocn_noocean.nc.150108.nc
usercomment= null
eps    =   9.999999960041972E-013
fminval=   1.000000047497451E-003
fmaxval=    1.00000000000000     
set_fv_pole_yc =            0
  
input SCRIP data...
pole_fix =  F
  
input file  =
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapdata/map_1x1_boulderCO_noocean_to_1x1_boulderCO_nomask_aave_da_150108.n
c
open
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapdata/map_1x1_boulderCO_noocean_to_1x1_boulderCO_nomask_aave_da_150108.n
c
domain_a     =
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapgrids/SCRIPgrid_1x1_boulderCO_noocean_c150108.nc
domain_b     =
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc
grid_file_ocn=
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapgrids/SCRIPgrid_1x1_boulderCO_noocean_c150108.nc
grid_file_atm=
/public3/home/external/gansu/guser002/model/cesm1_2_1/models/lnd/clm/tools/shar
ed/mkmapgrids/SCRIPgrid_1x1_boulderCO_nomask_c150108.nc
n,nv,ni,nj,na,ns=            1           4           1           1           1
           1
  
output domain data...
nf =            1
create domain.ocn.domain.ocn_noocean.nc.150108.nc
write domain.ocn.domain.ocn_noocean.nc.150108.nc
(shr_sys_getenv) ERROR: no implementation of getenv for this architecture
(shr_sys_getenv) no implementation of getenv for this machine
 
C

Christophe D

Christophe Durand
New Member
umair@skku_edu said:
Hy,

I have the same issue. Please share if you solved this problem.
Click to expand...
Hello,
I have had the same error for gen_domain:
(shr_sys_getenv) ERROR: no implementation of getenv for this architecture
(shr_sys_getenv) no implementation of getenv for this machine
Click to expand...
My fix has been to add OS=LINUX in the Makefile, as the environment variable is not set automatically by the system. Then I compiled the code again and it disappeared.
For the segmentation fault, I just used :
ulimit -s unlimited
Click to expand...
Please tell me if it solves it on your side.
 
You must log in or register to reply here.
Top