CLM single-point stimulation error ./mkmapdata.sh

[baofangling21@mails.ucas.]

I want to use CLM5.0 for single-point simulation and need to make own single-point surface data. However, now I encountered this problem above when making mapping files by using "./mkmapdata.sh -r $GRIDNAME -f $GRIDFILE -t regional" code.
The following is my error message：
Script to create mapping files required by mksurfdata_map
query command is ./../../bld/queryDefaultNamelist.pl -silent -namelist clmexp -justvalue -options sim_year=2000 -csmdata /home/fangling/clm5.0/tools/mkmapgrids/

Using user specified scrip grid file: ../mkmapgrids/SCRIPgrid_0.25x0.25_nomask_230301.nc
Output grid resolution is 0.25x0.25
Hostname = ubuntu
Machine ubuntu NOT recognized
rm: cannot remove 'PET*.Log': No such file or directory
Creating mapping file: map_0.5x0.5_AVHRR_to_0.25x0.25_nomask_aave_da_c230301.nc
From input grid: /home/fangling/clm5.0/tools/mkmapgrids//lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.nc
For output grid: ../mkmapgrids/SCRIPgrid_0.25x0.25_nomask_230301.nc

Input grid file does NOT exist: /home/fangling/clm5.0/tools/mkmapgrids//lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.nc

 

[oleson]

I think the option "-csmdata" should be pointing to where your "inputdata" directory is. For example, on our system, it is:

/glade/p/cesm/cseg/inputdata

and then the full path for the file that is not found is:

/glade/p/cesm/cseg/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.nc

 

[baofangling21@mails.ucas.]

I think the option "-csmdata" should be pointing to where your "inputdata" directory is. For example, on our system, it is:

/glade/p/cesm/cseg/inputdata

and then the full path for the file that is not found is:

/glade/p/cesm/cseg/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.nc

I just tried that,but it didn't work.Do I need to download all the grids data first?

 

[oleson]

Yes.

 

[baofangling21@mails.ucas.]

I've downloaded all the data and rerun it, but there was another error:
./mkmapdata.sh: line 101: 7428 Killed ${cmd}
Error status returned from mkmapdata script
I want to know why?

 

[baofangling21@mails.ucas.]

I've downloaded all the data and rerun it, but there was another error:
./mkmapdata.sh: line 101: 7428 Killed ${cmd}
Error status returned from mkmapdata script
I want to know why?

And I found another error when I went on to the next step:
(shr_sys_getenv) ERROR: no implementation of getenv for this architecture
(shr_sys_getenv) no implementation of getenv for this machine

 

[oleson]

Regarding your first error "Killed", it's hard to know the cause without seeing all of the output, you can attach it here. It could simply be that you are running out of memory on your machine.
Regarding your second error, what next step are you referring to? Maybe this post will be helpful regarding getenv:

Problems with mkmapdata.sh while trying to set up a point scale run on CLM4.5 on cheyenne machine.

Dear All,I am trying to create a surface data-set for single point run taking example 'Example 5-5. Example of creating a surface dataset for a single point' from the user guide.I am doing it on NCAR cheyenne machine. When I try to run the following step it fails:./mkmapdata.sh -r $GRIDNAME -f...

bb.cgd.ucar.edu

A new alternative to creating single-point surface datasets is to use the subset_data script. It can be found in this directory of a CTSM clone: tools/site_and_regional. There is a README in that directory and some additional information can be found here:

How do I create a single-point run with the NUOPC (default) coupler? · ESCOMP CTSM · Discussion #1833

We get this question a lot: I am trying to set up a case for a specific latitude and longitude. I want to use GSWP3 climate data, how do I set this up?

github.com

 

[baofangling21@mails.ucas.]

Regarding your first error "Killed", it's hard to know the cause without seeing all of the output, you can attach it here. It could simply be that you are running out of memory on your machine.
Regarding your second error, what next step are you referring to? Maybe this post will be helpful regarding getenv:

Problems with mkmapdata.sh while trying to set up a point scale run on CLM4.5 on cheyenne machine.

Dear All,I am trying to create a surface data-set for single point run taking example 'Example 5-5. Example of creating a surface dataset for a single point' from the user guide.I am doing it on NCAR cheyenne machine. When I try to run the following step it fails:./mkmapdata.sh -r $GRIDNAME -f...

bb.cgd.ucar.edu

A new alternative to creating single-point surface datasets is to use the subset_data script. It can be found in this directory of a CTSM clone: tools/site_and_regional. There is a README in that directory and some additional information can be found here:

How do I create a single-point run with the NUOPC (default) coupler? · ESCOMP CTSM · Discussion #1833

We get this question a lot: I am trying to set up a case for a specific latitude and longitude. I want to use GSWP3 climate data, how do I set this up?

github.com

Thanks for your advice,I will try again.

 

[baofangling21@mails.ucas.]

Thanks for your advice,I will try again.

Dear Keith,I have tried many times,but also have the same problem.I've listed all the outputs here.Can you tell me how to solve this problem?
export NCARG_ROOT=/home/fangling/app
export PATH=$NCARG_ROOT/bin/:$PATH
export ESMFBIN_PATH=/home/fangling/app/bin
export CDATE=230308
export CSMDATA=/home/fangling/cesm/inputdata
cd ~/clm5.0/tools/mkmapdata
./mknoocnmap.pl -p 24.80,113.58 -n $GRIDNAME

Create SCRIP grid and mapping files for a single-point
Create land SCRIP gridfile
Execute: env S_LAT=24.75 W_LON=113.53 N_LAT=24.85 E_LON=113.63 NX=1 NY=1 PTNAME=0.25x0.25_shaoguan GRIDFILE=/home/fangling/clm5.0/tools/mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc ncl mkscripgrid.ncl
Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
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=24.75 W_LON=113.53 N_LAT=24.85 E_LON=113.63 NX=1 NY=1 PTNAME=0.25x0.25_shaoguan GRIDFILE=/home/fangling/clm5.0/tools/mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_noocean_c230308.nc IMASK=0 ncl mkscripgrid.ncl
Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
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=/home/fangling/clm5.0/tools/mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_noocean_c230308.nc GRIDFILE2=/home/fangling/clm5.0/tools/mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc MAPFILE=map_0.25x0.25_shaoguan_noocean_to_0.25x0.25_shaoguan_nomask_aave_da_230308.nc ncl /home/fangling/clm5.0/tools/mkmapdata/mkunitymap.ncl
Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
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

export GRIDFILE=../mkmapgrids/SCRIPgrid_${GRIDNAME}_nomask_${CDATE}.nc
./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 -justvalue -options sim_year=2000 -csmdata /home/fangling/cesm/inputdata

Using user specified scrip grid file: ../mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc
Output grid resolution is 0.25x0.25_shaoguan
Hostname = ubuntu
Machine ubuntu NOT recognized
Creating mapping file: map_0.5x0.5_AVHRR_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
From input grid: /home/fangling/cesm/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.nc
For output grid: ../mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc


WARNING: deprecated switch -src_type will be ignored. The file type will be detected automatically

WARNING: deprecated switch -dst_type will be ignored. The file type will be detected automatically
Starting weight generation with these inputs:
Source File: /home/fangling/cesm/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_AVHRR_c110228.nc
Destination File: ../mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc
Weight File: map_0.5x0.5_AVHRR_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
Source File is in SCRIP format
Source Grid is a global grid
Source Grid is a logically rectangular grid
Use the center coordinates of the source grid to do the regrid
Destination File is in SCRIP format
Destination Grid is a regional grid
Destination Grid is a logically rectangular grid
Use the center coordinates of the destination grid to do the regrid
Regrid Method: conserve
Pole option: NONE
Ignore unmapped destination points
Line Type: greatcircle
Norm Type: dstarea
Extrap. Method: none

Completed weight generation successfully.

Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) map file: map_0.5x0.5_AVHRR_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
(0) n_s = 1 max(row)=1 max(col)=165468
(0) checking for dups, sorting...
(0) zeroing out any dups...
(0) No duplicate weights to remove from mapping file
Creating mapping file: map_0.25x0.25_MODIS_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
From input grid: /home/fangling/cesm/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.25x0.25_MODIS_c170321.nc
For output grid: ../mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc


WARNING: deprecated switch -src_type will be ignored. The file type will be detected automatically

WARNING: deprecated switch -dst_type will be ignored. The file type will be detected automatically
Starting weight generation with these inputs:
Source File: /home/fangling/cesm/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.25x0.25_MODIS_c170321.nc
Destination File: ../mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc
Weight File: map_0.25x0.25_MODIS_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
Source File is in SCRIP format
Source Grid is a global grid
Source Grid is a logically rectangular grid
Use the center coordinates of the source grid to do the regrid
Destination File is in SCRIP format
Destination Grid is a regional grid
Destination Grid is a logically rectangular grid
Use the center coordinates of the destination grid to do the regrid
Regrid Method: conserve
Pole option: NONE
Ignore unmapped destination points
Line Type: greatcircle
Norm Type: dstarea
Extrap. Method: none

Completed weight generation successfully.

Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
(0) map file: map_0.25x0.25_MODIS_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
(0) n_s = 2 max(row)=1 max(col)=662135
(0) checking for dups, sorting...
(0) zeroing out any dups...
(0) No duplicate weights to remove from mapping file
Creating mapping file: map_0.5x0.5_MODIS_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
From input grid: /home/fangling/cesm/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_MODIS_c110228.nc
For output grid: ../mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc


WARNING: deprecated switch -src_type will be ignored. The file type will be detected automatically

WARNING: deprecated switch -dst_type will be ignored. The file type will be detected automatically
Starting weight generation with these inputs:
Source File: /home/fangling/cesm/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.5x0.5_MODIS_c110228.nc
Destination File: ../mkmapgrids/SCRIPgrid_0.25x0.25_shaoguan_nomask_c230308.nc
Weight File: map_0.5x0.5_MODIS_to_0.25x0.25_shaoguan_nomask_aave_da_c230308.nc
Source File is in SCRIP format
Source Grid is a global grid
Source Grid is a logically rectangular grid
Use the center coordinates of the source grid to do the regrid
Destination File is in SCRIP format
Destination Grid is a regional grid
Destination Grid is a logically rectangular grid
Use the center coordinates of the destination grid to do the regrid
Regrid Method: conserve
Pole option: NONE
Ignore unmapped destination points
Line Type: greatcircle
Norm Type: dstarea
Extrap. Method: none

./mkmapdata.sh: line 101: 3495 Killed ${cmd}
Error status returned from mkmapdata script

 

[oleson]

I tried this in release-cesm2.1.3 and it worked fine.
I had previously made a couple of changes to mkmapdata.sh:

esmfvers=8.0.0
intelvers=19.0.5

You could try that. But it may simply be that your machine doesn't have enough memory.
I've put the mapping files that were created on our ftp site if that helps you:

ftp://ftp.cgd.ucar.edu/pub/oleson/baofangling21

Again, if you still have problems you could try the subset_data script.

 

[baofangling21@mails.ucas.]

I tried this in release-cesm2.1.3 and it worked fine.
I had previously made a couple of changes to mkmapdata.sh:

esmfvers=8.0.0
intelvers=19.0.5

You could try that. But it may simply be that your machine doesn't have enough memory.
I've put the mapping files that were created on our ftp site if that helps you:

ftp://ftp.cgd.ucar.edu/pub/oleson/baofangling21

Again, if you still have problems you could try the subset_data script.

Thank you very much!

 

[wjp1997]

I have face the same question with you,if you have solve this problem,could you please tell me some suggestion?

this is my ERROR:

$ ./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 ustvalue -options sim_year=2000 -csmdata /home/wangjp/data/inputdata

Using user specified scrip grid file: ../mkmapgrids/SCRIPgrid_1x1_new_nomask_c411.nc
Output grid resolution is 1x1_new
Hostname = dell-PowerEdge-T440
Machine dell-PowerEdge-T440 NOT recognized
Creating mapping file: map_0.5x0.5_AVHRR_to_1x1_new_nomask_aave_da_c230411.nc
From input grid: /home/wangjp/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPg_0.5x0.5_AVHRR_c110228.nc
For output grid: ../mkmapgrids/SCRIPgrid_1x1_new_nomask_c230411.nc

Skipping creation of map_0.5x0.5_AVHRR_to_1x1_new_nomask_aave_da_c230411.nc asready exists
Creating mapping file: map_0.25x0.25_MODIS_to_1x1_new_nomask_aave_da_c230411.n
From input grid: /home/wangjp/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPg_0.25x0.25_MODIS_c170321.nc
For output grid: ../mkmapgrids/SCRIPgrid_1x1_new_nomask_c230411.nc


WARNING: deprecated switch -src_type will be ignored. The file type will be
tected automatically

WARNING: deprecated switch -dst_type will be ignored. The file type will be
tected automatically
Starting weight generation with these inputs:
Source File:
/home/wangjp/data/inputdata/lnd/clm2/mappingdata/grids/SCRIPgrid_0.25x0.25_MO
S_c170321.nc
Destination File: ../mkmapgrids/SCRIPgrid_1x1_new_nomask_c230411.nc
Weight File: map_0.25x0.25_MODIS_to_1x1_new_nomask_aave_da_c230411.nc
Source File is in SCRIP format
Source Grid is a global grid
Source Grid is a logically rectangular grid
Use the center coordinates of the source grid to do the regrid
Destination File is in SCRIP format
Destination Grid is a regional grid
Destination Grid is a logically rectangular grid
Use the center coordinates of the destination grid to do the regrid
Regrid Method: conserve
Pole option: NONE
Ignore unmapped destination points
Line Type: greatcircle
Norm Type: dstarea
Extrap. Method: none

./mkmapdata.sh：line 101: 3730067 error
Error status returned from mkmapdata script

 

[oleson]

@baofangling21@mails.ucas. did you solve this?

 

[Yuan Sun]

same error: ./mkmapdata.sh: 1944784 Killed ${cmd}