Hello. I'm a novice in CESM2.1.3 and I learned a lot after reading the user's guide.Recently, I have some problems in running model. I want to run the coupling test of CMIP6, and then modify the parameters for sensitivity test. So, I did the following.
At first, ./create_newcase --case ~/cases/test/BHISTcmip6 --compset BHISTcmip6 --res f09_g17 --run-unsupported --compiler intel ;
./case.setup
./case.build
I downloaded the files in this directory(ftp://ftp.cgd.ucar.edu/cesm/inputdata/cesm2_init/b.e21.B1850.f09_g17.CMIP6-piControl.001_v3hist/ and other required files) and put them in the inputdata directory.
./case.submit
I have not made any changes such as the run time, run type and so on. They are all default settings. I calculated nearly 5 and a half hours with 576 cores, but output with very little storage. The output is as follows：
12M Sep 22 10:39 BHISTcmip6_5day.cism.initial_hist.1850-01-01-00000.nc
82M Sep 22 10:41 BHISTcmip6_5day.clm2.h3.1850-01-01-00000.nc
86M Sep 22 10:41 BHISTcmip6_5day.clm2.h4.1850-01-01-00000.nc
3 Sep 22 10:39 BHISTcmip6_5day.pop.dd.1850-01-01-03600
3 Sep 22 10:39 BHISTcmip6_5day.pop.do.1850-01-01-03600
3 Sep 22 10:39 BHISTcmip6_5day.pop.dt.1850-01-01-03600
3 Sep 22 10:39 BHISTcmip6_5day.pop.dv.1850-01-01-03600
114M Sep 22 10:39 BHISTcmip6_5day.pop.hv.nc
I thought there was something wrong with the calculation, so I canceled the work. After a week of troubleshooting, I still don't know what happened. The cpl.log.825669.200922-093117 shows that the model initialization is complete, but the calculation has not started. The cesm.log.825669.200922-093117 shows that it is stuck in the program shown below and will not continue to output the history file. I didn't find any obvious errors in the log file, so it bothered me a lot. The attachment is the relevant mode status and log file. Due to the size limit of the upload file, thecesm.log.825669.200922-093117 is divided into two parts.
I hope you can give me some help and let me know where the error occurs and how to modify it. I'm sorry for this confusion in my part. Any answer will be of great help to me and I will be very grateful.
./preview_run output as follow:
CASE INFO:
nodes: 9
total tasks: 576
tasks per node: 64
thread count: 1
BATCH INFO:
FOR JOB: case.run
ENV:
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python purge
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python load anaconda/2-Python2.7.16-new-wxl-public3 cmake/3.9.0-zyq-public3 mpi/intel/18.0.2-thc-public3 pnetcdf/intel18/1.11.1-icc18-ls-public3
Setting Environment OMP_STACKSIZE=256M
Setting Environment MPI_TYPE_DEPTH=16
Setting Environment I_MPI_HYDRA_BOOTSTRAP=squeue
Setting Environment I_MPI_HYDRA_BRANCH_COUNT=-1
Setting Environment I_MPI_LSF_USE_COLLECTIVE_LAUNCH=1
Setting Environment NETCDF_PATH=/public3/soft/netcdf/4.4.1-parallel-icc18
Setting Environment PNETCDF_PATH=/public3/soft/pnetcdf/1.11.1/intel18-ls
Setting Environment OMP_NUM_THREADS=1
SUBMIT CMD:
None
MPIRUN (job=case.run):
srun -n 576 /public3/home/sc52515/my_cesm_sandbox/output/BHISTcmip6_5day/bld/cesm.exe >> cesm.log.$LID 2>&1
FOR JOB: case.st_archive
ENV:
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python purge
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python load anaconda/2-Python2.7.16-new-wxl-public3 cmake/3.9.0-zyq-public3 mpi/intel/18.0.2-thc-public3 pnetcdf/intel18/1.11.1-icc18-ls-public3
Setting Environment OMP_STACKSIZE=256M
Setting Environment MPI_TYPE_DEPTH=16
Setting Environment I_MPI_HYDRA_BOOTSTRAP=squeue
Setting Environment I_MPI_HYDRA_BRANCH_COUNT=-1
Setting Environment I_MPI_LSF_USE_COLLECTIVE_LAUNCH=1
Setting Environment NETCDF_PATH=/public3/soft/netcdf/4.4.1-parallel-icc18
Setting Environment PNETCDF_PATH=/public3/soft/pnetcdf/1.11.1/intel18-ls
Setting Environment OMP_NUM_THREADS=1
SUBMIT CMD:
None
At first, ./create_newcase --case ~/cases/test/BHISTcmip6 --compset BHISTcmip6 --res f09_g17 --run-unsupported --compiler intel ;
./case.setup
./case.build
I downloaded the files in this directory(ftp://ftp.cgd.ucar.edu/cesm/inputdata/cesm2_init/b.e21.B1850.f09_g17.CMIP6-piControl.001_v3hist/ and other required files) and put them in the inputdata directory.
./case.submit
I have not made any changes such as the run time, run type and so on. They are all default settings. I calculated nearly 5 and a half hours with 576 cores, but output with very little storage. The output is as follows：
12M Sep 22 10:39 BHISTcmip6_5day.cism.initial_hist.1850-01-01-00000.nc
82M Sep 22 10:41 BHISTcmip6_5day.clm2.h3.1850-01-01-00000.nc
86M Sep 22 10:41 BHISTcmip6_5day.clm2.h4.1850-01-01-00000.nc
3 Sep 22 10:39 BHISTcmip6_5day.pop.dd.1850-01-01-03600
3 Sep 22 10:39 BHISTcmip6_5day.pop.do.1850-01-01-03600
3 Sep 22 10:39 BHISTcmip6_5day.pop.dt.1850-01-01-03600
3 Sep 22 10:39 BHISTcmip6_5day.pop.dv.1850-01-01-03600
114M Sep 22 10:39 BHISTcmip6_5day.pop.hv.nc
I thought there was something wrong with the calculation, so I canceled the work. After a week of troubleshooting, I still don't know what happened. The cpl.log.825669.200922-093117 shows that the model initialization is complete, but the calculation has not started. The cesm.log.825669.200922-093117 shows that it is stuck in the program shown below and will not continue to output the history file. I didn't find any obvious errors in the log file, so it bothered me a lot. The attachment is the relevant mode status and log file. Due to the size limit of the upload file, thecesm.log.825669.200922-093117 is divided into two parts.
I hope you can give me some help and let me know where the error occurs and how to modify it. I'm sorry for this confusion in my part. Any answer will be of great help to me and I will be very grateful.
./preview_run output as follow:
CASE INFO:
nodes: 9
total tasks: 576
tasks per node: 64
thread count: 1
BATCH INFO:
FOR JOB: case.run
ENV:
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python purge
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python load anaconda/2-Python2.7.16-new-wxl-public3 cmake/3.9.0-zyq-public3 mpi/intel/18.0.2-thc-public3 pnetcdf/intel18/1.11.1-icc18-ls-public3
Setting Environment OMP_STACKSIZE=256M
Setting Environment MPI_TYPE_DEPTH=16
Setting Environment I_MPI_HYDRA_BOOTSTRAP=squeue
Setting Environment I_MPI_HYDRA_BRANCH_COUNT=-1
Setting Environment I_MPI_LSF_USE_COLLECTIVE_LAUNCH=1
Setting Environment NETCDF_PATH=/public3/soft/netcdf/4.4.1-parallel-icc18
Setting Environment PNETCDF_PATH=/public3/soft/pnetcdf/1.11.1/intel18-ls
Setting Environment OMP_NUM_THREADS=1
SUBMIT CMD:
None
MPIRUN (job=case.run):
srun -n 576 /public3/home/sc52515/my_cesm_sandbox/output/BHISTcmip6_5day/bld/cesm.exe >> cesm.log.$LID 2>&1
FOR JOB: case.st_archive
ENV:
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python purge
module command is /public3/soft/lmod/8.4/lmod/8.4/libexec/lmod python load anaconda/2-Python2.7.16-new-wxl-public3 cmake/3.9.0-zyq-public3 mpi/intel/18.0.2-thc-public3 pnetcdf/intel18/1.11.1-icc18-ls-public3
Setting Environment OMP_STACKSIZE=256M
Setting Environment MPI_TYPE_DEPTH=16
Setting Environment I_MPI_HYDRA_BOOTSTRAP=squeue
Setting Environment I_MPI_HYDRA_BRANCH_COUNT=-1
Setting Environment I_MPI_LSF_USE_COLLECTIVE_LAUNCH=1
Setting Environment NETCDF_PATH=/public3/soft/netcdf/4.4.1-parallel-icc18
Setting Environment PNETCDF_PATH=/public3/soft/pnetcdf/1.11.1/intel18-ls
Setting Environment OMP_NUM_THREADS=1
SUBMIT CMD:
None