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ERROR in mksurfdata_map when building single point model in CLM45

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Z

zichongchen22@gmail_com

New Member
Hi All,

I am running single-point model of CLM4.5 and using mksurfdata.pl to create surface dataset. When I run the command "./mksurfdata.pl -r usrspec -usr_gname 1x1_Marcell -usr_gdate 150925", I could create several files successfully,but also got a error message as follow:

Code: 
CSMDATA is /panfs/roc/groups/8/grifbake/public/inputdata/CESM resolution:
1x1_Marcell rcp=-999.9 sim_year = 1850
namelist: namelist.............................
Attempting to make PFTs .....
Creating surface datasets with the standard # of PFTs =          16
domain_read_dims_2d read lon and lat dims from lon/lat
domain_read initialized domain domain_read
read LANDMASK
Open PFT file:  /panfs/roc/groups/8/grifbake/public/inputdata/CESM/lnd/clm2/rawdata/pftlandused yn.0.5x0.5.simyr1850-2005.c090630/mksrf_landuse_rc1850_c090630.nc
(gridmap_map_read) reading mapping matrix data...
(gridmap_map_read) * file name                  : ../../shared/mkmapdata/map_0.5x0.5_MODIS_to_1x1_Marcell_nomask_aave_da_c150925.nc
* matrix dimensions rows x cols :      259200  x           1
* number of non-zero elements:            4
domain_clean: cleaning       259200
Successfully made PFTs........................................
urface data output file = surfdata_1x1_Marcell_simyr1850_c150930.nc
This file contains the land model surface data
Diagnostic log file      = surfdata_1x1_Marcell_simyr1850_c150930.log
See this file for a summary of the dataset
Successfully created surface dataset..................................
Attempting to make PFTs .....
Creating surface datasets with the standard # of PFTs =          16
netcdf error from domain_read rcode =            2
error =  No such file or directory
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
mksurfdata_map     0000000000537FD1  Unknown               Unknown  Unknown
mksurfdata_map     0000000000536727  Unknown               Unknown  Unknown
mksurfdata_map     00000000004EE394  Unknown               Unknown  Unknown
mksurfdata_map     00000000004EE1A6  Unknown               Unknown  Unknown
mksurfdata_map     0000000000491364  Unknown               Unknown  Unknown
mksurfdata_map     00000000004960DD  Unknown               Unknown  Unknown
libpthread.so.0    00002AAFF5F89710  Unknown               Unknown  Unknown
mksurfdata_map     000000000053EE62  Unknown               Unknown  Unknown
mksurfdata_map     0000000000485320  Unknown               Unknown  Unknown
mksurfdata_map     000000000040D73D  mkdomainmod_mp_ch         788  mkdomainMod.F90
mksurfdata_map     000000000040D8DE  mkdomainmod_mp_do         396  mkdomainMod.F90
mksurfdata_map     000000000043921D  mkpftmod_mp_mkpft         233  mkpftMod.F90
mksurfdata_map     000000000045217B  MAIN__                    501  mksurfdat.F90
mksurfdata_map     000000000040A25E  Unknown               Unknown  Unknown
libc.so.6          00002AAFF61B5D5D  Unknown               Unknown  Unknown
mksurfdata_map     000000000040A0F9  Unknown               Unknown  Unknown
ERROR in mksurfdata_map: 44544

I checked the namelist and ensure the files fine. At the first time, The PFTs can be successfully created but the follow process showed that " netcdf error from domain_read rcode =2 error =No such file or directory". I don't know why the information said netcdf error from domain_read at the second making PFTs. I think it might be my netcdf version incorrect, but I got the same output by using different netcdf versions such as fortran-4.4-intel-sp1-update3-parallel,fortran-4.2.intel,4.3.2-intel-sp1-update3-parallel, and so on. I attach the whole message and will appreciate any help you give me.
 
Last edited by a moderator:
X

Xax

Member
Hi,I am receiving the same error creating surfdatasets for a global grid. Did you ever solve this issue?
 
A

abdulla_sakalli@iste_edu_tr

New Member
Dear All,
I've got the same error during creating the surface data. My command is:

./mksurfdata.pl -res usrspec -usr_gname alaro_0p22 -usr_gdate 200406 -y 2000
Click to expand...

and the error is:
mksrf_gridtype = global
Output ALL data in file as 64-bit
Set wetland to 0% over land
In mkpftMod::mkpftInit()...
calling domain_read
finished domain_read
fsurdat is 2d lat/lon grid
nlon= 333 nlat= 223
(OPNFIL): Successfully opened file surfdata_alaro_0p22_hist_78pfts_CMIP6_simyr2000_c200407.log on unit= 99
mksrf_gridtype = global

In mkpftMod::mkpft()...
Attempting to make PFTs .....
Creating surface datasets with extra types for crops; total pfts = 78
netcdf error from domain_read rcode = 2 error = No such file or directory

Program aborted. Backtrace:
#0 0x7FCF23588E08
#1 0x7FCF23589CE2
#2 0x7FCF23664488
#3 0x403B54 in __mkdomainmod_MOD_check_ret at mkdomainMod.F90:?
#4 0x404800 in __mkdomainmod_MOD_domain_read
#5 0x4374CE in __mkpftmod_MOD_mkpft
#6 0x455E7E in MAIN__ at mksurfdat.F90:?
Aborted (core dumped)
ERROR in mksurfdata_map: 34304
Click to expand...

The mksurfdata_map was compiled successfully. Could you solve the error? I'd like to thank you all in advance for your replies.
 
M

majun

Member
zichongchen22@gmail_com said:
Hi All,

I am running single-point model of CLM4.5 and using mksurfdata.pl to create surface dataset. When I run the command "./mksurfdata.pl -r usrspec -usr_gname 1x1_Marcell -usr_gdate 150925", I could create several files successfully,but also got a error message as follow:

Code: 
CSMDATA is /panfs/roc/groups/8/grifbake/public/inputdata/CESM resolution:
1x1_Marcell rcp=-999.9 sim_year = 1850
namelist: namelist.............................
Attempting to make PFTs .....
Creating surface datasets with the standard # of PFTs =          16
domain_read_dims_2d read lon and lat dims from lon/lat
domain_read initialized domain domain_read
read LANDMASK
Open PFT file:  /panfs/roc/groups/8/grifbake/public/inputdata/CESM/lnd/clm2/rawdata/pftlandused yn.0.5x0.5.simyr1850-2005.c090630/mksrf_landuse_rc1850_c090630.nc
(gridmap_map_read) reading mapping matrix data...
(gridmap_map_read) * file name                  : ../../shared/mkmapdata/map_0.5x0.5_MODIS_to_1x1_Marcell_nomask_aave_da_c150925.nc
* matrix dimensions rows x cols :      259200  x           1
* number of non-zero elements:            4
domain_clean: cleaning       259200
Successfully made PFTs........................................
urface data output file = surfdata_1x1_Marcell_simyr1850_c150930.nc
This file contains the land model surface data
Diagnostic log file      = surfdata_1x1_Marcell_simyr1850_c150930.log
See this file for a summary of the dataset
Successfully created surface dataset..................................
Attempting to make PFTs .....
Creating surface datasets with the standard # of PFTs =          16
netcdf error from domain_read rcode =            2
error =  No such file or directory
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
mksurfdata_map     0000000000537FD1  Unknown               Unknown  Unknown
mksurfdata_map     0000000000536727  Unknown               Unknown  Unknown
mksurfdata_map     00000000004EE394  Unknown               Unknown  Unknown
mksurfdata_map     00000000004EE1A6  Unknown               Unknown  Unknown
mksurfdata_map     0000000000491364  Unknown               Unknown  Unknown
mksurfdata_map     00000000004960DD  Unknown               Unknown  Unknown
libpthread.so.0    00002AAFF5F89710  Unknown               Unknown  Unknown
mksurfdata_map     000000000053EE62  Unknown               Unknown  Unknown
mksurfdata_map     0000000000485320  Unknown               Unknown  Unknown
mksurfdata_map     000000000040D73D  mkdomainmod_mp_ch         788  mkdomainMod.F90
mksurfdata_map     000000000040D8DE  mkdomainmod_mp_do         396  mkdomainMod.F90
mksurfdata_map     000000000043921D  mkpftmod_mp_mkpft         233  mkpftMod.F90
mksurfdata_map     000000000045217B  MAIN__                    501  mksurfdat.F90
mksurfdata_map     000000000040A25E  Unknown               Unknown  Unknown
libc.so.6          00002AAFF61B5D5D  Unknown               Unknown  Unknown
mksurfdata_map     000000000040A0F9  Unknown               Unknown  Unknown
ERROR in mksurfdata_map: 44544

I checked the namelist and ensure the files fine. At the first time, The PFTs can be successfully created but the follow process showed that " netcdf error from domain_read rcode =2 error =No such file or directory". I don't know why the information said netcdf error from domain_read at the second making PFTs. I think it might be my netcdf version incorrect, but I got the same output by using different netcdf versions such as fortran-4.4-intel-sp1-update3-parallel,fortran-4.2.intel,4.3.2-intel-sp1-update3-parallel, and so on. I attach the whole message and will appreciate any help you give me.
Click to expand...
have you fixed it out? what's the problem? I'm facing the same problem. thank you
 
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