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how to change the SST forcing in a branch run?

1

1062628489@qq_com

New Member
Hello,everyoneFirstly,I ran a startup of F_2000_CAM5 by using climatological SSTs(Path and File:  .../inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc) ,and it succeeded,the case name was case01 . Then, I changed the SSTs in the tropical pacific(plus 1.0°by NCL),and got a new file named CP_SST.nc (Path and File:  .../inputdata/forcing/CP_SST.nc). And now, I want to run a branch ,the reference case is case01,by this method, I can compare their difference. My question is how do  I replace the two SSTs files? where i need to modify in the case ,such as env_conf.xml, env_build.xml,env_run.xml and so on ? by the way ,I check the variables in the sst_HadOIBl_bc_64x128_clim_c050526.nc, there are two sst variables named SST_cpl and SST_cpl_prediddle, I want to know their difference.Can anybody help me in this question? I would really appreciate your help, Thanks.
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
## To Change the SST dataset, use SSTICE* variables in env)run.xml     ## For the difference between SST_cpl and SST_cpl_prediddle, see:https://bb.cgd.ucar.edu/source-sst-dataset-cam5-f-compset-simulations
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
## To Change the SST dataset, use SSTICE* variables in env)run.xml     ## For the difference between SST_cpl and SST_cpl_prediddle, see:https://bb.cgd.ucar.edu/source-sst-dataset-cam5-f-compset-simulations
 
1

1062628489@qq_com

New Member
hannay, thanks for your help and i am so sorry to post this problem at the other place,i delete it right now.according  to  your guide,i checked my env_run.xml, but i didn't find the  id="SSTICE_DATA_FILENAME"it's the problem about my cesm version? I use cesm1_0_4 to do my work.what should i do?  thanks again for your enthusiastic help。
 
1

1062628489@qq_com

New Member
hannay, thanks for your help and i am so sorry to post this problem at the other place,i delete it right now.according  to  your guide,i checked my env_run.xml, but i didn't find the  id="SSTICE_DATA_FILENAME"it's the problem about my cesm version? I use cesm1_0_4 to do my work.what should i do?  thanks again for your enthusiastic help。
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
Yes the name was different in  cesm1_0_4.It was:DOCN_SSTDATA_FILENAME
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
Yes the name was different in  cesm1_0_4.It was:DOCN_SSTDATA_FILENAME
 
1

1062628489@qq_com

New Member
hello hannay， thank you so much for everything.follow your guide, I  modify my env_conf.xml. But I don't know whether the entry id="DOCN_SSTDATA_YEAR_START"   and  entry id="DOCN_SSTDATA_YEAR_END"  need to be changed  .So I try it respectivelyfirstly ,i don't modify it ,it can run successfully,but when i check the the docn.stream.txt, i find that the SST file is sst_HadOIBl_bc_64x128_clim_c050526.nc , and in the file of docn.input_data_list, file1 = /nuist/p/work/vikicam/inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc. so I think my forcing file is not used in this case.then, I modify the start and end year, I change them to 0001(start) and 0001(end) , I chcek the  docn.stream.txt and [/b]docn.input_data_list [/i]again, [/i] it change to  /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc. it is reasonable But there are new errors in the ocn.log......the error :(docn_comp_init)  ocn_in = docn_ocn_in(docn_comp_init)  decomp = 1d(docn_comp_init)  restfilm = undefined(docn_comp_init)  restfils = undefined(shr_strdata_readnml) reading input namelist file: docn_ocn_in(shr_stream_init) Reading file docn.stream.txt(shr_sys_abort) ERROR: (shr_stream_getCalendar)  ERROR: nf90_open file /nuist/scratch/vikicam/inputdata/forcing/CP_I.nc(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping what should  I do ?   thanks again
 
1

1062628489@qq_com

New Member
hello hannay， thank you so much for everything.follow your guide, I  modify my env_conf.xml. But I don't know whether the entry id="DOCN_SSTDATA_YEAR_START"   and  entry id="DOCN_SSTDATA_YEAR_END"  need to be changed  .So I try it respectivelyfirstly ,i don't modify it ,it can run successfully,but when i check the the docn.stream.txt, i find that the SST file is sst_HadOIBl_bc_64x128_clim_c050526.nc , and in the file of docn.input_data_list, file1 = /nuist/p/work/vikicam/inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc. so I think my forcing file is not used in this case.then, I modify the start and end year, I change them to 0001(start) and 0001(end) , I chcek the  docn.stream.txt and [/b]docn.input_data_list [/i]again, [/i] it change to  /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc. it is reasonable But there are new errors in the ocn.log......the error :(docn_comp_init)  ocn_in = docn_ocn_in(docn_comp_init)  decomp = 1d(docn_comp_init)  restfilm = undefined(docn_comp_init)  restfils = undefined(shr_strdata_readnml) reading input namelist file: docn_ocn_in(shr_stream_init) Reading file docn.stream.txt(shr_sys_abort) ERROR: (shr_stream_getCalendar)  ERROR: nf90_open file /nuist/scratch/vikicam/inputdata/forcing/CP_I.nc(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping what should  I do ?   thanks again
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
You should look for the units for the variable "time" into your file  /nuist/p/work/vikicam/inputdata/forcing/CP_I.ncFor instance, if it is  double time(time) ;                time:units = "days since 0000-01-01 00:00:00" ;it means that the year for climatology is the year 0000DOCN_SSTDATA_YEAR_START = 0DOCN_SSTDATA_YEAR_END = 0  Make sure that the format file (variable, units, ..) /nuist/scratch/vikicam/inputdata/forcing/CP_I.nclooks like:/nuist/p/work/vikicam/inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc
 
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
You should look for the units for the variable "time" into your file  /nuist/p/work/vikicam/inputdata/forcing/CP_I.ncFor instance, if it is  double time(time) ;                time:units = "days since 0000-01-01 00:00:00" ;it means that the year for climatology is the year 0000DOCN_SSTDATA_YEAR_START = 0DOCN_SSTDATA_YEAR_END = 0  Make sure that the format file (variable, units, ..) /nuist/scratch/vikicam/inputdata/forcing/CP_I.nclooks like:/nuist/p/work/vikicam/inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc
 
 
1

1062628489@qq_com

New Member
hello hannayI check my  variable "time"  and it shows  double time(time) ;time:units = "days since 0000-01-01 00:00:00" ;time:calendar = "365_day" ;so  I change it to DOCN_SSTDATA_YEAR_START = 0                          DOCN_SSTDATA_YEAR_END = 0but there are new errors in ocn.log.....(shr_stream_restRead) ERROR in stream filenames        1       1 sst_HadOIBl_bc_64x128_clim_c050526.nc CP_I.nc(shr_stream_restRead) * stream     1 first file name = CP_I.nc(shr_stream_restRead) * stream     1 first have data =   T(shr_stream_restRead) * stream     1 first nt        =       12(shr_stream_restRead) * stream     1 first date secs =      116   43200(shr_stream_restRead) * stream     1 last  date secs =     1216   43200(shr_stream_restRead)  ERROR: yearAlign disagrees        1       0       1(shr_stream_restRead) ERRORS Detected ABORTING NOW(shr_sys_abort) ERROR: (shr_stream_restRead) : ERRORS Detected ABORTING NOW(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping
it puzzle  me so I creat a new case and run a startup by using my file of CP_I.nc i change something in the docn.buildnml.csh（old）set dat_datpath = $DIN_LOC_ROOT/ocn/docn7/SSTDATA           set dat_datfile = sst_HadOIBl_bc_64x128_clim_c050526.nc（new）set dat_datpath = $DIN_LOC_ROOT/forcing             set dat_datfile = CP_I.ncand the case ran successfully there are some information in the ocn.log...(docn_comp_init) copy domains(docn_comp_init) allocate AVs(docn_comp_init)  restart filenames from rpointer(docn_comp_init)  reading expcpi.docn.rs1.0008-07-01-00000.bin(shr_stream_restRead) case name        : expcpi(shr_stream_restRead) case description : SDOCN strdata(shr_stream_restRead) File created     : 2015-04-21 20:27:17(shr_stream_restRead) Number of streams     1(shr_stream_restRead) * stream     1 first file name = CP_I.nc(shr_stream_restRead) * stream     1 first have data =   T(shr_stream_restRead) * stream     1 first nt        =       12(shr_stream_restRead) * stream     1 first date secs =      116   43200(shr_stream_restRead) * stream     1 last  date secs =     1216   43200(shr_dmodel_readLBUB) reading file: /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc       6(shr_dmodel_readLBUB) reading file: /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc       7(docn_comp_run) ocn: model date    80701       0s(docn_comp_init) docn_comp_init done(docn_comp_run) ocn: model date    80701    1200s(docn_comp_run) ocn: model date    80701    2400s(docn_comp_run) ocn: model date    80701    3600s(docn_comp_run) ocn: model date    80701    4800s(docn_comp_run) ocn: model date    80701    6000s(docn_comp_run) ocn: model date    80701    7200s(docn_comp_run) ocn: model date    80701    8400swhat should i do ? thank youby the way ,my CP_I.nc is created by NCLthis is codes:load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"   load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"beginf1    = addfile("/nuist/p/work/vikicam/data/sst_HadOIBl_bc_64x128_clim_c050526.nc","r") ice  = f1->ice_cov(:,:,:)icep  = f1->ice_cov_prediddle(:,:,:)sst  = f1->SST_cpl(:,:,:)sstp  = f1->SST_cpl_prediddle(:,:,:) print(sst(time|11,{lat|-5:5},{lon|180:220}))  sst(time|0,{lat|-10:10},{lon|160:250}) =sst(time|0,{lat|-10:10},{lon|160:250})+0.5  sst(time|1,{lat|-10:10},{lon|160:250}) =sst(time|1,{lat|-10:10},{lon|160:250})+0.5  sst(time|10,{lat|-10:10},{lon|160:250}) =sst(time|10,{lat|-10:10},{lon|160:250})+0.5  sst(time|11,{lat|-10:10},{lon|160:250}) =sst(time|11,{lat|-10:10},{lon|160:250})+0.5    sst(time|0,{lat|-5:5},{lon|180:220}) =sst(time|0,{lat|-5:5},{lon|180:220})+0.5 sst(time|1,{lat|-5:5},{lon|180:220}) =sst(time|1,{lat|-5:5},{lon|180:220})+0.5 sst(time|10,{lat|-5:5},{lon|180:220}) =sst(time|10,{lat|-5:5},{lon|180:220})+0.5 sst(time|11,{lat|-5:5},{lon|180:220}) =sst(time|11,{lat|-5:5},{lon|180:220})+0.5print(sst(time|11,{lat|-5:5},{lon|180:220})) f2   = addfile ("/nuist/p/work/vikicam/data/CP_I.nc","c")f2->ice_cov=icef2->ice_cov_prediddle=icepf2->SST_cpl=sstf2->SST_cpl_prediddle=sstp printVarSummary(f2) end  
 
1

1062628489@qq_com

New Member
hello hannayI check my  variable "time"  and it shows  double time(time) ;time:units = "days since 0000-01-01 00:00:00" ;time:calendar = "365_day" ;so  I change it to DOCN_SSTDATA_YEAR_START = 0                          DOCN_SSTDATA_YEAR_END = 0but there are new errors in ocn.log.....(shr_stream_restRead) ERROR in stream filenames        1       1 sst_HadOIBl_bc_64x128_clim_c050526.nc CP_I.nc(shr_stream_restRead) * stream     1 first file name = CP_I.nc(shr_stream_restRead) * stream     1 first have data =   T(shr_stream_restRead) * stream     1 first nt        =       12(shr_stream_restRead) * stream     1 first date secs =      116   43200(shr_stream_restRead) * stream     1 last  date secs =     1216   43200(shr_stream_restRead)  ERROR: yearAlign disagrees        1       0       1(shr_stream_restRead) ERRORS Detected ABORTING NOW(shr_sys_abort) ERROR: (shr_stream_restRead) : ERRORS Detected ABORTING NOW(shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping
it puzzle  me so I creat a new case and run a startup by using my file of CP_I.nc i change something in the docn.buildnml.csh（old）set dat_datpath = $DIN_LOC_ROOT/ocn/docn7/SSTDATA           set dat_datfile = sst_HadOIBl_bc_64x128_clim_c050526.nc（new）set dat_datpath = $DIN_LOC_ROOT/forcing             set dat_datfile = CP_I.ncand the case ran successfully there are some information in the ocn.log...(docn_comp_init) copy domains(docn_comp_init) allocate AVs(docn_comp_init)  restart filenames from rpointer(docn_comp_init)  reading expcpi.docn.rs1.0008-07-01-00000.bin(shr_stream_restRead) case name        : expcpi(shr_stream_restRead) case description : SDOCN strdata(shr_stream_restRead) File created     : 2015-04-21 20:27:17(shr_stream_restRead) Number of streams     1(shr_stream_restRead) * stream     1 first file name = CP_I.nc(shr_stream_restRead) * stream     1 first have data =   T(shr_stream_restRead) * stream     1 first nt        =       12(shr_stream_restRead) * stream     1 first date secs =      116   43200(shr_stream_restRead) * stream     1 last  date secs =     1216   43200(shr_dmodel_readLBUB) reading file: /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc       6(shr_dmodel_readLBUB) reading file: /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc       7(docn_comp_run) ocn: model date    80701       0s(docn_comp_init) docn_comp_init done(docn_comp_run) ocn: model date    80701    1200s(docn_comp_run) ocn: model date    80701    2400s(docn_comp_run) ocn: model date    80701    3600s(docn_comp_run) ocn: model date    80701    4800s(docn_comp_run) ocn: model date    80701    6000s(docn_comp_run) ocn: model date    80701    7200s(docn_comp_run) ocn: model date    80701    8400swhat should i do ? thank youby the way ,my CP_I.nc is created by NCLthis is codes:load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"   load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"beginf1    = addfile("/nuist/p/work/vikicam/data/sst_HadOIBl_bc_64x128_clim_c050526.nc","r") ice  = f1->ice_cov(:,:,:)icep  = f1->ice_cov_prediddle(:,:,:)sst  = f1->SST_cpl(:,:,:)sstp  = f1->SST_cpl_prediddle(:,:,:) print(sst(time|11,{lat|-5:5},{lon|180:220}))  sst(time|0,{lat|-10:10},{lon|160:250}) =sst(time|0,{lat|-10:10},{lon|160:250})+0.5  sst(time|1,{lat|-10:10},{lon|160:250}) =sst(time|1,{lat|-10:10},{lon|160:250})+0.5  sst(time|10,{lat|-10:10},{lon|160:250}) =sst(time|10,{lat|-10:10},{lon|160:250})+0.5  sst(time|11,{lat|-10:10},{lon|160:250}) =sst(time|11,{lat|-10:10},{lon|160:250})+0.5    sst(time|0,{lat|-5:5},{lon|180:220}) =sst(time|0,{lat|-5:5},{lon|180:220})+0.5 sst(time|1,{lat|-5:5},{lon|180:220}) =sst(time|1,{lat|-5:5},{lon|180:220})+0.5 sst(time|10,{lat|-5:5},{lon|180:220}) =sst(time|10,{lat|-5:5},{lon|180:220})+0.5 sst(time|11,{lat|-5:5},{lon|180:220}) =sst(time|11,{lat|-5:5},{lon|180:220})+0.5print(sst(time|11,{lat|-5:5},{lon|180:220})) f2   = addfile ("/nuist/p/work/vikicam/data/CP_I.nc","c")f2->ice_cov=icef2->ice_cov_prediddle=icepf2->SST_cpl=sstf2->SST_cpl_prediddle=sstp printVarSummary(f2) end  
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
I am not sure if you can only change the SST in docn.buildnml.csh. If you do this, I think it will only change in the data ocean model and not in the sea-ice. Then the two datasets are not consistent anymore. Can you check which SST dataset is used in the ocean and the sea-ice namelists ? I am puzzled when the error you get. Please could you attach the files env_run.xml, and the namelists for the 2 cases:1) when you change  DOCN_SSTDATA_YEAR_START and  DOCN_SSTDATA_YEAR_END 2) when you change docn.buildnml.csh
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
I am not sure if you can only change the SST in docn.buildnml.csh. If you do this, I think it will only change in the data ocean model and not in the sea-ice. Then the two datasets are not consistent anymore. Can you check which SST dataset is used in the ocean and the sea-ice namelists ? I am puzzled when the error you get. Please could you attach the files env_run.xml, and the namelists for the 2 cases:1) when you change  DOCN_SSTDATA_YEAR_START and  DOCN_SSTDATA_YEAR_END 2) when you change docn.buildnml.csh
 
1

1062628489@qq_com

New Member
hannay, thanks for your patient guide.on the one hand, to my new startup case,firstly,I create it by "./create_newcase -case sst_sym -res T42_T42 -compset FC5 -mach viki". then, I configure it without setting DOCN_SSTDATA_FILENAME .by this step,it will create a file named Buildconf . and then ,I enter into this file and vi docn.buildnml.csh , the original setting is set dat_datpath = $DIN_LOC_ROOT/ocn/docn7/SSTDATAset dat_datfile = sst_HadOIBl_bc_64x128_clim_c050526.nc  .but now ,I change it to dat_datpath = $DIN_LOC_ROOT/forcing set dat_datfile = CP_I.nc (the sst_HadOIBl_bc_64x128_clim_c050526.nc and CP_I.nc is exactly alike except for winter sst values, so I consider that the CP_I.nc can force atmosphere and get anomalies ,and this anomalies will help me to analyse relationship between sst and atm) finally I build it and run it successfully ,in the file of Buildconf, there are new file named docn.input_data_list and the content is DOMAINFILE=/nuist/p/work/vikicam/inputdata/atm/cam/ocnfrac/domain.camocn.64x128_USGS_070807.ncdomain1=/nuist/p/work/vikicam/inputdata/atm/cam/ocnfrac/domain.camocn.64x128_USGS_070807.ncfile1 = /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc  (if i don't change the docn.buildnml.csh file1=/nuist/p/work/vikicam/inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc)the total process run normally, but there are many “BalanceCheck: soil balance error nstep =    297343 point =  2559 imbalance =    0.000000 W/m2”I don’t know whether it’s serious.On the oher hand ,in my branch case runFirstly ,i create a new case and set the branch run and reference case and date
 
1

1062628489@qq_com

New Member
hannay, thanks for your patient guide.on the one hand, to my new startup case,firstly,I create it by "./create_newcase -case sst_sym -res T42_T42 -compset FC5 -mach viki". then, I configure it without setting DOCN_SSTDATA_FILENAME .by this step,it will create a file named Buildconf . and then ,I enter into this file and vi docn.buildnml.csh , the original setting is set dat_datpath = $DIN_LOC_ROOT/ocn/docn7/SSTDATAset dat_datfile = sst_HadOIBl_bc_64x128_clim_c050526.nc  .but now ,I change it to dat_datpath = $DIN_LOC_ROOT/forcing set dat_datfile = CP_I.nc (the sst_HadOIBl_bc_64x128_clim_c050526.nc and CP_I.nc is exactly alike except for winter sst values, so I consider that the CP_I.nc can force atmosphere and get anomalies ,and this anomalies will help me to analyse relationship between sst and atm) finally I build it and run it successfully ,in the file of Buildconf, there are new file named docn.input_data_list and the content is DOMAINFILE=/nuist/p/work/vikicam/inputdata/atm/cam/ocnfrac/domain.camocn.64x128_USGS_070807.ncdomain1=/nuist/p/work/vikicam/inputdata/atm/cam/ocnfrac/domain.camocn.64x128_USGS_070807.ncfile1 = /nuist/p/work/vikicam/inputdata/forcing/CP_I.nc  (if i don't change the docn.buildnml.csh file1=/nuist/p/work/vikicam/inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc)the total process run normally, but there are many “BalanceCheck: soil balance error nstep =    297343 point =  2559 imbalance =    0.000000 W/m2”I don’t know whether it’s serious.On the oher hand ,in my branch case runFirstly ,i create a new case and set the branch run and reference case and date
 
hannay

hannay

Cecile Hannay
AMWG Liaison
Staff member
I have done 2 runs with the default SST and with the modified SSTs. I was able to run both cases without any troubles. Here the commands I used: 1) with the default SSTcd /glade/p/cesm/releases/cesm1_0_6/scripts./create_newcase -case /glade/scratch/hannay/test_sst2 -compset FC5 -res T42_T42 -mach yellowstonecd /glade/scratch/hannay/test_sst2./xmlchange -file env_conf.xml -id DOCN_SSTDATA_FILENAME -val /glade/p/cesm/cseg/inputdata/ocn/docn7/SSTDATA/sst_HadOIBl_bc_64x128_clim_c050526.nc./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_START -val 0./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_END -val 0./configure -case./test_sst2.yellowstone.build  ./test_sst2.yellowstone.submit 2) with the modified SSt cd /glade/p/cesm/releases/cesm1_0_6/scripts./create_newcase -case /glade/scratch/hannay/test_sst3 -compset FC5 -res T42_T42 -mach yellowstonecd /glade/scratch/hannay/test_sst3./xmlchange -file env_conf.xml -id DOCN_SSTDATA_FILENAME -val /glade/p/cesmdata/cseg/inputdata/atm/cam/sst/CP_I.nc./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_START -val 0./xmlchange -file env_conf.xml -id DOCN_SSTDATA_YEAR_END -val 0./configure -case./configure -case./test_sst3.yellowstone.build  ./test_sst3.yellowstone.submit
 
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