大气化学模块
[sysu_syli_3@ln42%tianhe2-H FWHIST-BGC]$ ./xmlquery CAM_CONFIG_OPTS CAM_CONFIG_OPTS: -phys cam6 -age_of_air_trcs -chem waccm_tsmlt_mam4 ./xmlchange --append "CAM_CONFIG_OPTS=-phys cam6 -chem none" [sysu_syli_3@ln42%tianhe2-H FWHIST-BGC]$ ./xmlquery CAM_CONFIG_OPTS CAM_CONFIG_OPTS: -phys cam6 -age_of_air_trcs -chem waccm_tsmlt_mam4 -phys cam6 -chem none查询变量在哪个文件中grep
grep CAM_CONFIG_OPTS*.xml查询并修改PE配置:
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlquery DIN_LOC_ROOT DIN_LOC_ROOT: /BIGDATA1/sysu_syli_3/CESM2/inputdata [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlquery NTASKS,NTHRDS,ROOTPE Results in group mach_pes NTASKS: ['CPL:24', 'ATM:24', 'LND:24', 'ICE:24', 'OCN:24', 'ROF:24', 'GLC:24', 'WAV:24', 'ESP:1'] NTHRDS: ['CPL:1', 'ATM:1', 'LND:1', 'ICE:1', 'OCN:1', 'ROF:1', 'GLC:1', 'WAV:1', 'ESP:1'] ROOTPE: ['CPL:0', 'ATM:0', 'LND:0', 'ICE:0', 'OCN:0', 'ROF:0', 'GLC:0', 'WAV:0', 'ESP:0'] [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlchange NTASKS=120 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlchange NTASKS_ESP=5 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlquery NTASKS,NTHRDS,ROOTPE Results in group mach_pes NTASKS: ['CPL:120', 'ATM:120', 'LND:120', 'ICE:120', 'OCN:120', 'ROF:120', 'GLC:120', 'WAV:120', 'ESP:5'] NTHRDS: ['CPL:1', 'ATM:1', 'LND:1', 'ICE:1', 'OCN:1', 'ROF:1', 'GLC:1', 'WAV:1', 'ESP:1'] ROOTPE: ['CPL:0', 'ATM:0', 'LND:0', 'ICE:0', 'OCN:0', 'ROF:0', 'GLC:0', 'WAV:0', 'ESP:0']修改user_nl_clm
vim user_nl_clm hist_empty_htapes = .true hist_avgflag_pertape = 'A' hist_nhtfrq = 0 hist_mfilt = 1 hist_fincl1="QOVER","QH2OSFC","H2OSOI","GPP","NPP","NEP","TLAI","FLDS","FSDS","Rnet","QVEGT","QSOIL","QINTR","FSH","TSA","Q2M"setup成功之后,CASEROOT/run 目录和CASEROOT/bld/ 目录:
查询大气化学模块
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlquery CAM_CONFIG_OPTS CAM_CONFIG_OPTS: -phys cam6 -age_of_air_trcs -chem waccm_tsmlt_mam4 # 查询 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlquery STOP_OPTION,STOP_N,RUN_TYPE,CONTINUE_RUN,RUN_REFCASE,RUN_REFDATE,RUN_STARTDATE,RUN_REFDIR,DOUT_S,DOUT_S_ROOT,JOB_WALLCLOCK_TIME,RESUBMIT Results in group case.run JOB_WALLCLOCK_TIME: 00:20:00 Results in group case.st_archive JOB_WALLCLOCK_TIME: 0:20:00 Results in group run_begin_stop_restart STOP_OPTION: ndays STOP_N: 5 RUN_TYPE: hybrid CONTINUE_RUN: FALSE RUN_REFCASE: b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2 RUN_REFDATE: 1950-01-01 RUN_STARTDATE: 1950-01-01 RUN_REFDIR: cesm2_init RESUBMIT: 0 Results in group run_data_archive DOUT_S: FALSE Results in group run_dout DOUT_S_ROOT: /BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCtest/archive # 更改一些设置 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlchange DOUT_S=TRUE [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlchange JOB_WALLCLOCK_TIME=12:00:00 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./xmlchange STOP_N=3,STOP_OPTION=nmonths通过build来获取输入数据链接,重新下载数据
./preview_namelists ./check_input_data --download &> FWHISTtest.inputdata尝试重新下载数据后拷贝:
chmod -R 755 /BIGDATA1/sysu_syli_3/CESM2/inputdata ./case.build --skip-provenance-check &> FWHIST_BGCtest.build.log没有输入数据并不影响build是否成功? input file list文件是通过./preview_namelist命令产生,有了input file list文件才可以./check_input_data ./preview_namelist命令内置在./case.build中了
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCtest]$ ./preview_namelists - Prestaging REFCASE (/BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01) to /BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCtest/run Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.lnd Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.ocn.ovf Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.ice Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.ocn.restart Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.rof Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.atm Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.drv Copy rpointer /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/rpointer.glc Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.pop.r.1950-01-01-00000.nc Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/README Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.ww3.r.1950-01-01-00000 Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.pop.ro.1950-01-01-00000 Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.cpl.r.1950-01-01-00000.nc Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.cism.r.1950-01-01-00000.nc Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.cice.r.1950-01-01-00000.nc Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/list Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.clm2.r.1950-01-01-00000.nc Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.mosart.r.1950-01-01-00000.nc Staging file /BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2.cam.i.1950-01-01-00000.nc Creating component namelists Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/cam//cime_config/buildnml ...calling cam buildcpp to set build time options CAM namelist copy: file1 /BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCtest/Buildconf/camconf/atm_in file2 /BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCtest/run/atm_in Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/clm//cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/cice//cime_config/buildnml ...buildnml calling cice buildcpp to set build time options Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/components/data_comps/docn/cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/mosart//cime_config/buildnml Running /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/cism//cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/components/stub_comps/swav/cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/components/stub_comps/sesp/cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/drivers/mct/cime_config/buildnml NOTE: ignoring setting of rof2ocn_ice_rmapname=idmap in seq_maps.rc NOTE: ignoring setting of rof2ocn_liq_rmapname=idmap in seq_maps.rc Finished creating component namelists报错: /BIGDATA1/sysu_syli_3/CESM2/inputdata/atm/cam/chem/stratvolc/VolcanEESMv3.11_SO 001: 2_850-2016_Mscale_Zreduc_1deg_c180812.nc 6356992 001: NetCDF: HDF error 001: pio_support::pio_die:: myrank= -1 : ERROR: pionfget_mod.F90:
https://bb.cgd.ucar.edu/cesm/threads/transient-volcano-forcing-in-waccm.3360/
查询并修改PE配置:
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery NTASKS,NTHRDS,ROOTPE Results in group mach_pes NTASKS: ['CPL:24', 'ATM:24', 'LND:24', 'ICE:24', 'OCN:24', 'ROF:24', 'GLC:24', 'WAV:24', 'ESP:1'] NTHRDS: ['CPL:1', 'ATM:1', 'LND:1', 'ICE:1', 'OCN:1', 'ROF:1', 'GLC:1', 'WAV:1', 'ESP:1'] ROOTPE: ['CPL:0', 'ATM:0', 'LND:0', 'ICE:0', 'OCN:0', 'ROF:0', 'GLC:0', 'WAV:0', 'ESP:0'] [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlchange NTASKS=120 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlchange NTASKS_ESP=5 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery NTASKS,NTHRDS,ROOTPE Results in group mach_pes NTASKS: ['CPL:120', 'ATM:120', 'LND:120', 'ICE:120', 'OCN:120', 'ROF:120', 'GLC:120', 'WAV:120', 'ESP:5'] NTHRDS: ['CPL:1', 'ATM:1', 'LND:1', 'ICE:1', 'OCN:1', 'ROF:1', 'GLC:1', 'WAV:1', 'ESP:1'] ROOTPE: ['CPL:0', 'ATM:0', 'LND:0', 'ICE:0', 'OCN:0', 'ROF:0', 'GLC:0', 'WAV:0', 'ESP:0']默认设置:
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery STOP_OPTION,STOP_N,RUN_TYPE,CONTINUE_RUN,RUN_REFCASE,RUN_REFDATE,RUN_STARTDATE,RUN_REFDIR,DOUT_S,DOUT_S_ROOT,JOB_WALLCLOCK_TIME,RESUBMIT Results in group case.run JOB_WALLCLOCK_TIME: 00:20:00 Results in group case.st_archive JOB_WALLCLOCK_TIME: 0:20:00 Results in group run_begin_stop_restart STOP_OPTION: ndays STOP_N: 5 RUN_TYPE: hybrid CONTINUE_RUN: FALSE RUN_REFCASE: b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2 RUN_REFDATE: 1950-01-01 RESUBMIT: 0 RUN_STARTDATE: 1950-01-01 RUN_REFDIR: cesm2_init Results in group run_data_archive DOUT_S: FALSE Results in group run_dout DOUT_S_ROOT: /BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCstartup/archive修改RUN_TYPE=startup
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery RUN_TYPE,CONTINUE_RUN,RUN_REFCASE,RUN_REFDATE,RUN_STARTDATE,RUN_REFDIR,GET_REFCASE,GET_REFCASE Results in group run_begin_stop_restart RUN_TYPE: hybrid CONTINUE_RUN: FALSE RUN_REFCASE: b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001_v2 RUN_REFDATE: 1950-01-01 RUN_STARTDATE: 1950-01-01 RUN_REFDIR: cesm2_init GET_REFCASE: TRUE [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlchange RUN_TYPE=startup,RUN_REFCASE=case.std,RUN_REFDATE=0001-01-01,RUN_STARTDATE=1850-01-01,GET_REFCASE=FALSE [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery RUN_TYPE,CONTINUE_RUN,RUN_REFCASE,RUN_REFDATE,RUN_STARTDATE,RUN_REFDIR,GET_REFCASE Results in group run_begin_stop_restart RUN_TYPE: startup CONTINUE_RUN: FALSE RUN_REFCASE: case.std RUN_REFDATE: 0001-01-01 RUN_STARTDATE: 1850-01-01 RUN_REFDIR: cesm2_init GET_REFCASE: FALSE修改user_nl_clm
vim user_nl_clm hist_empty_htapes = .true hist_avgflag_pertape = 'A' hist_nhtfrq = 0 hist_mfilt = 1 hist_fincl1="QOVER","QH2OSFC","H2OSOI","GPP","NPP","NEP","TLAI","FLDS","FSDS","Rnet","QVEGT","QSOIL","QINTR","FSH","TSA","Q2M"修改大气化学模块
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery CAM_CONFIG_OPTS CAM_CONFIG_OPTS: -phys cam6 -age_of_air_trcs -chem waccm_tsmlt_mam4 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlchange "CAM_CONFIG_OPTS=-phys cam6 -chem none" [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery CAM_CONFIG_OPTS CAM_CONFIG_OPTS: -phys cam6 -chem none事先通过./preview_namelists 生成所需的输入文件链接列表,随后利用./check_input_data 检查缺失的输入数据,利用wget下载准备好。
注意: NOTE: ignoring setting of rof2ocn_ice_rmapname=idmap in seq_maps.rc NOTE: ignoring setting of rof2ocn_liq_rmapname=idmap in seq_maps.rc
[sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./preview_namelists Creating component namelists Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/cam//cime_config/buildnml ...calling cam buildcpp to set build time options CAM namelist copy: file1 /BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCstartup/Buildconf/camconf/atm_in file2 /BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCstartup/run/atm_in Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/clm//cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/cice//cime_config/buildnml ...buildnml calling cice buildcpp to set build time options Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/components/data_comps/docn/cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/mosart//cime_config/buildnml Running /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/components/cism//cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/components/stub_comps/swav/cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/components/stub_comps/sesp/cime_config/buildnml Calling /BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/src/drivers/mct/cime_config/buildnml NOTE: ignoring setting of rof2ocn_ice_rmapname=idmap in seq_maps.rc NOTE: ignoring setting of rof2ocn_liq_rmapname=idmap in seq_maps.rc Finished creating component namelists ./check_input_data --download &> FWHIST_BGCstartup.input.log Loading input file list: 'Buildconf/cpl.input_data_list' Loading input file list: 'Buildconf/mosart.input_data_list' Loading input file list: 'Buildconf/cism.input_data_list' Loading input file list: 'Buildconf/clm.input_data_list' Model clm missing file finidat = '/BIGDATA1/sysu_syli_3/CESM2/inputdata/lnd/clm2/initdata_map/clmi.B1850.1171-01-01.0.9x1.25_gx1v7_simyr1850_c181029.nc' Loading input file list: 'Buildconf/cice.input_data_list' Loading input file list: 'Buildconf/docn.input_data_list' Loading input file list: 'Buildconf/cam.input_data_list' Model cam missing file ncdata = '/BIGDATA1/sysu_syli_3/CESM2/inputdata/cesm2_init/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001/1950-01-01/b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.001.cam.i.1950-01-01-00000.nc' Client protocol gftp not enabled Using protocol wget with user anonymous and passwd user@example.edu Could not connect to repo 'ftp://ftp.cgd.ucar.edu/cesm/inputdata' This is most likely either a proxy, or network issue . Trying to download file: '../inputdata_checksum.dat' to path '/BIGDATA1/sysu_syli_3/CESM2/scratch/FWHIST_BGCstartup/run/inputdata_checksum.dat.raw' using NoneType protocol. Traceback (most recent call last): File "./check_input_data", line 76, in <module> _main_func(__doc__) File "./check_input_data", line 71, in _main_func chksum=chksum) else 1) File "/BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 163, in check_all_input_data _download_checksum_file(self.get_value("RUNDIR")) File "/BIGDATA1/sysu_syli_3/CESM2/my_cesm_sandbox/cime/scripts/Tools/../../scripts/lib/CIME/case/check_input_data.py", line 54, in _download_checksum_file success = server.getfile(rel_path, new_file) AttributeError: 'NoneType' object has no attribute 'getfile' ./case.build --skip-provenance-check &> FWHIST_BGCstartup_build.log # 更改一些设置 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlchange DOUT_S=TRUE [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlchange JOB_WALLCLOCK_TIME=12:00:00 [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlchange STOP_N=3,STOP_OPTION=nmonths [sysu_syli_3@ln42%tianhe2-H FWHIST_BGCstartup]$ ./xmlquery STOP_OPTION,STOP_N,RUN_TYPE,CONTINUE_RUN,RUN_REFCASE,RUN_REFDATE,RESUBMIT,RUN_STARTDATE,RUN_REFDIR,DOUT_S,DOUT_S_ROOT,JOB_WALLCLOCK_TIME错误是一致的。
