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branch run examples
- Thread starter TCNasa
- Start date
Hi Tom,
I'm not sure exactly what you mean by example here, but the way to set up a branch run is:
./create_newcase [all of your case info here]
cd /directory/to/case
./case.setup
./xmlchange RUN_TYPE='branch'
You will probably need to set RUN_REFCASE and RUN_REFDATE to the case you are branching from and the date for the restart files. Then copy the restart files into the run directory for your branch run.
There's a lot of specific help in this year's tutorial materials here: Hybrid, Branch and Startup — CESM Tutorial
I'm not sure exactly what you mean by example here, but the way to set up a branch run is:
./create_newcase [all of your case info here]
cd /directory/to/case
./case.setup
./xmlchange RUN_TYPE='branch'
You will probably need to set RUN_REFCASE and RUN_REFDATE to the case you are branching from and the date for the restart files. Then copy the restart files into the run directory for your branch run.
There's a lot of specific help in this year's tutorial materials here: Hybrid, Branch and Startup — CESM Tutorial
Thanks. I have a related question. When running preview_namelists to set up the branch run, I get an error when prestaging the start data. Any idea what I should do for this?:
ERROR: Command /CERES/sarb/caldwell/CESM2.2/components/clm/bld/build-namelist failed rc=2
out=
err=Can't locate XML/LibXML.pm in @INC (@INC contains: /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/lib/Perl_Lib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
ERROR: Command /CERES/sarb/caldwell/CESM2.2/components/clm/bld/build-namelist failed rc=2
out=
err=Can't locate XML/LibXML.pm in @INC (@INC contains: /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/lib/Perl_Lib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
I'm reposting to include more lines:
Thanks. I have a related question. When running preview_namelists to set up the branch run, I get an error when prestaging the start data. Any idea what I should do for this?:
Creating component namelists
2023-07-13 14:06:41 atm
Calling /CERES/sarb/caldwell/CESM2.2/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /CERES/sarb/caldwell/CESM2.2/cime/scripts/July13-branch/Buildconf/camconf/atm_in file2 /CERES/sarb/caldwell/CESM2.2/cime/output/July13-branch/run/atm_in
2023-07-13 14:06:41 lnd
Calling /CERES/sarb/caldwell/CESM2.2/components/clm//cime_config/buildnml
WARNING: the start file being used for a multi-instance case is a single instance: July13-base.clm2.r.20100101-00000.nc
ERROR: Command /CERES/sarb/caldwell/CESM2.2/components/clm/bld/build-namelist failed rc=2
out=
err=Can't locate XML/LibXML.pm in @INC (@INC contains: /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/lib/Perl_Lib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
Compilation failed in require at /CERES/sarb/caldwell/CESM2.2/components/clm/bld/CLMBuildNamelist.pm line 410.
Thanks. I have a related question. When running preview_namelists to set up the branch run, I get an error when prestaging the start data. Any idea what I should do for this?:
Creating component namelists
2023-07-13 14:06:41 atm
Calling /CERES/sarb/caldwell/CESM2.2/components/cam//cime_config/buildnml
...calling cam buildcpp to set build time options
CAM namelist copy: file1 /CERES/sarb/caldwell/CESM2.2/cime/scripts/July13-branch/Buildconf/camconf/atm_in file2 /CERES/sarb/caldwell/CESM2.2/cime/output/July13-branch/run/atm_in
2023-07-13 14:06:41 lnd
Calling /CERES/sarb/caldwell/CESM2.2/components/clm//cime_config/buildnml
WARNING: the start file being used for a multi-instance case is a single instance: July13-base.clm2.r.20100101-00000.nc
ERROR: Command /CERES/sarb/caldwell/CESM2.2/components/clm/bld/build-namelist failed rc=2
out=
err=Can't locate XML/LibXML.pm in @INC (@INC contains: /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib /CERES/sarb/caldwell/CESM2.2/components/clm/bld /CERES/lib/Perl_Lib /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
BEGIN failed--compilation aborted at /CERES/sarb/caldwell/CESM2.2/cime/scripts/Tools/../../utils/perl5lib/Config/SetupTools.pm line 5.
Compilation failed in require at /CERES/sarb/caldwell/CESM2.2/components/clm/bld/CLMBuildNamelist.pm line 410.
Hello, I am encountering the same error. Could you please tell me how you solved with the env?I got past this. An issue with setting up my env correctly.
I think it was an issue with setting paths correctly so that CESM could find what it needed. I don't know what hardware or operating system you are using but I have to set a lot of paths manually (which I just put into a csh run script). My statements look like these:
source /SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64/environment.csh
setenv PATH "/homedir/tecaldwe/openmpi/bin:${PATH}"
setenv CFLAGS "-I/homedir/tecaldwe/openmpi/include ${CFLAGS}"
setenv LDFLAGS "-L/homedir/tecaldwe/openmpi/lib ${LDFLAGS}"
setenv LD_LIBRARY_PATH "/homedir/tecaldwe/openmpi/lib:${LD_LIBRARY_PATH}"
rehash
setenv NETCDF_PATH /SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64
setenv LDFLAGS "-L/SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64/lib -lhdf5_hl -lhdf5 -lhdf5hl_fortran -lhdf5_fortran -lz -lsz -ldl -L/homedir/tecaldwe/lapack/src/lapack-3.10.0 -llapack -lrefblas"
setenv TMPDIR /CERES/sarb/caldwell/CESM2.2/cime/scripts/tmp
I'm not sure exactly which paths are your problem but it seems like your CESM can't find what it needs for the build. Hence, the "Can't locate" errors. You might need to ask your sys admins for the correct paths to Perl libraries and such also to use for building your case.
source /SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64/environment.csh
setenv PATH "/homedir/tecaldwe/openmpi/bin:${PATH}"
setenv CFLAGS "-I/homedir/tecaldwe/openmpi/include ${CFLAGS}"
setenv LDFLAGS "-L/homedir/tecaldwe/openmpi/lib ${LDFLAGS}"
setenv LD_LIBRARY_PATH "/homedir/tecaldwe/openmpi/lib:${LD_LIBRARY_PATH}"
rehash
setenv NETCDF_PATH /SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64
setenv LDFLAGS "-L/SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64/lib -lhdf5_hl -lhdf5 -lhdf5hl_fortran -lhdf5_fortran -lz -lsz -ldl -L/homedir/tecaldwe/lapack/src/lapack-3.10.0 -llapack -lrefblas"
setenv TMPDIR /CERES/sarb/caldwell/CESM2.2/cime/scripts/tmp
I'm not sure exactly which paths are your problem but it seems like your CESM can't find what it needs for the build. Hence, the "Can't locate" errors. You might need to ask your sys admins for the correct paths to Perl libraries and such also to use for building your case.
I think it was an issue with setting paths correctly so that CESM could find what it needed. I don't know what hardware or operating system you are using but I have to set a lot of paths manually (which I just put into a csh run script). My statements look like these:
source /SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64/environment.csh
setenv PATH "/homedir/tecaldwe/openmpi/bin:${PATH}"
setenv CFLAGS "-I/homedir/tecaldwe/openmpi/include ${CFLAGS}"
setenv LDFLAGS "-L/homedir/tecaldwe/openmpi/lib ${LDFLAGS}"
setenv LD_LIBRARY_PATH "/homedir/tecaldwe/openmpi/lib:${LD_LIBRARY_PATH}"
rehash
setenv NETCDF_PATH /SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64
setenv LDFLAGS "-L/SPG_ops/utils/CERES/TOOLKIT/scf_toolkit5.2.20v1-x86_64/lib -lhdf5_hl -lhdf5 -lhdf5hl_fortran -lhdf5_fortran -lz -lsz -ldl -L/homedir/tecaldwe/lapack/src/lapack-3.10.0 -llapack -lrefblas"
setenv TMPDIR /CERES/sarb/caldwell/CESM2.2/cime/scripts/tmp
I'm not sure exactly which paths are your problem but it seems like your CESM can't find what it needs for the build. Hence, the "Can't locate" errors. You might need to ask your sys admins for the correct paths to Perl libraries and such also to use for building your case.
Thank you very much for your prompt response. I am attempting to modify the env. Best wishes.