What version of the code are you using?
CESM2.2.2
Describe every step you took leading up to the problem:
-
export PERL5LIB=/rhome/tzhu/.conda/envs/perl_env/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi
conda activate perl_env
source /etc/profile.d/hpcc_modules.sh
module unload openmpi
module load cmake
module load intel
source /opt/linux/centos/7.x/x86_64/pkgs/intel/2018/compilers_and_libraries_2018.0.128/linux/bin/compilervars.sh intel64
source /opt/linux/centos/7.x/x86_64/pkgs/intel/2018/compilers_and_libraries_2018.0.128/linux/mkl/bin/mklvars.sh intel64
source /opt/linux/centos/7.x/x86_64/pkgs/intel/2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64/bin/mpivars.sh intel64
# HDF5
export TACC_HDF5_LIB=/opt/linux/centos/7.x/x86_64/pkgs/hdf5/1.8.18_intel/lib
export LD_LIBRARY_PATH=$TACC_HDF5_LIB:$LD_LIBRARY_PATH
export LD_INCLUDE_PATH=/opt/linux/centos/7.x/x86_64/pkgs/netcdf/4.4.1.1_intel/include:/opt/linux/centos/7.x/x86_64/pkgs/netcdf-fortran/4.4.4_intel/include:$LD_INCLUDE_PATH
# Set NETCDF_PATH environment variable (optional, modify based on actual installation path)
module load netcdf/4.4.1.1_intel
module load netcdf-fortran/4.4.4_intel
export NETCDF_PATH=/opt/linux/centos/7.x/x86_64/pkgs/netcdf-fortran/4.4.4_intel/
cd ..../my_cesm2.2.2_sandbox/cime/scripts
./create_newcase --case .../cesm2_runs/case/CESM-F2000-ts --res f09_f09_mg17 --compset F2000climo --mach ucr-hpcc --compiler intel
./xmlchange --file env_run.xml --id STOP_OPTION --val nyear
./xmlchange --file env_run.xml --id STOP_N --val 1
./xmlchange --file env_run.xml --id REST_N --val 1
./xmlchange --file env_run.xml --id RESUBMIT --val 0
./xmlchange RUN_TYPE="startup"
./xmlchange --file env_run.xml --id RUN_STARTDATE --val 0000-01-01
./case.setup
./check_input_data --download
./case.build
If this is a port to a new machine: Please attach any files you added or changed for the machine port (e.g., config_compilers.xml, config_machines.xml, and config_batch.xml) and tell us the compiler version you are using on this machine.
Please attach any log files showing error messages or other useful information.
I change config files:
in config_compilers.xml added:
<compiler COMPILER="intel" MACH="ucr-hpcc">
<MPI_LIB_NAME>mpich</MPI_LIB_NAME>
<MPICC>mpiicc</MPICC>
<MPIFC>mpiifort</MPIFC>
<NETCDF_PATH>/opt/linux/centos/7.x/x86_64/pkgs/netcdf-fortran/4.4.4_intel</NETCDF_PATH>
</compiler>
in config_machines.xml added:
<machine MACH="ucr-hpcc">
<DESC>UCR HPCC cluster with appropriate modules</DESC>
<NODENAME_REGEX>r27</NODENAME_REGEX> <!-- Adjust to match the UCR HPCC hostname -->
<OS>LINUX</OS>
<COMPILERS>intel</COMPILERS> <!-- Modify based on the available compiler, e.g., intel or gnu -->
<MPILIBS>mpich</MPILIBS> <!-- Modify based on your MPI library -->
<PROJECT>none</PROJECT>
<CIME_OUTPUT_ROOT>/bigdata/wliulab/tzhu/cesm2_runs/output</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>/bigdata/wliulab/tzhu/cesm2_runs/input/$CASE</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/bigdata/wliulab/tzhu/cesm2_runs/input/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>
<GMAKE>gmake</GMAKE>
<GMAKE_J>8</GMAKE_J>
<BATCH_SYSTEM>slurm</BATCH_SYSTEM> <!-- Modify this if the cluster uses a specific batch system -->
<SUPPORTED_BY>user@ucr.edu</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>32</MAX_TASKS_PER_NODE> <!-- Modify based on your system's configuration -->
<MAX_MPITASKS_PER_NODE>32</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="ntasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<module_system type="module">
<!-- Load necessary modules for UCR HPCC -->
</module_system>
</machine>
in config_batch.xml added:
<batch_system MACH="ucr-hpcc" type="slurm">
<directives>
<directive>-l nodes={{ num_nodes }}:ppn={{ tasks_per_node }}</directive>
<directive default="/bin/bash" > -S {{ shell }} </directive>
</directives>
<queues>
<queue walltimemax="36:00:00" default="true">batch</queue>
</queues>
</batch_system>
when I run ./case.build, there are some errors. I attached the build log with errors info.
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
cmake: error while loading shared libraries: librhash.so.0: cannot open shared object file: No such file or directory
gmake: *** [/bigdata/*/cesm2_runs/output/CESM-F2000-ts/bld/intel/mpich/nodebug/nothreads/mct/pio/pio2/Makefile] Error 127
ERROR: cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
cmake: error while loading shared libraries: librhash.so.0: cannot open shared object file: No such file or directory
gmake: *** [/bigdata/*/cesm2_runs/output/CESM-F2000-ts/bld/intel/mpich/nodebug/nothreads/mct/pio/pio2/Makefile] Error 127
CESM2.2.2
Describe every step you took leading up to the problem:
-
export PERL5LIB=/rhome/tzhu/.conda/envs/perl_env/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi
conda activate perl_env
source /etc/profile.d/hpcc_modules.sh
module unload openmpi
module load cmake
module load intel
source /opt/linux/centos/7.x/x86_64/pkgs/intel/2018/compilers_and_libraries_2018.0.128/linux/bin/compilervars.sh intel64
source /opt/linux/centos/7.x/x86_64/pkgs/intel/2018/compilers_and_libraries_2018.0.128/linux/mkl/bin/mklvars.sh intel64
source /opt/linux/centos/7.x/x86_64/pkgs/intel/2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64/bin/mpivars.sh intel64
# HDF5
export TACC_HDF5_LIB=/opt/linux/centos/7.x/x86_64/pkgs/hdf5/1.8.18_intel/lib
export LD_LIBRARY_PATH=$TACC_HDF5_LIB:$LD_LIBRARY_PATH
export LD_INCLUDE_PATH=/opt/linux/centos/7.x/x86_64/pkgs/netcdf/4.4.1.1_intel/include:/opt/linux/centos/7.x/x86_64/pkgs/netcdf-fortran/4.4.4_intel/include:$LD_INCLUDE_PATH
# Set NETCDF_PATH environment variable (optional, modify based on actual installation path)
module load netcdf/4.4.1.1_intel
module load netcdf-fortran/4.4.4_intel
export NETCDF_PATH=/opt/linux/centos/7.x/x86_64/pkgs/netcdf-fortran/4.4.4_intel/
cd ..../my_cesm2.2.2_sandbox/cime/scripts
./create_newcase --case .../cesm2_runs/case/CESM-F2000-ts --res f09_f09_mg17 --compset F2000climo --mach ucr-hpcc --compiler intel
./xmlchange --file env_run.xml --id STOP_OPTION --val nyear
./xmlchange --file env_run.xml --id STOP_N --val 1
./xmlchange --file env_run.xml --id REST_N --val 1
./xmlchange --file env_run.xml --id RESUBMIT --val 0
./xmlchange RUN_TYPE="startup"
./xmlchange --file env_run.xml --id RUN_STARTDATE --val 0000-01-01
./case.setup
./check_input_data --download
./case.build
If this is a port to a new machine: Please attach any files you added or changed for the machine port (e.g., config_compilers.xml, config_machines.xml, and config_batch.xml) and tell us the compiler version you are using on this machine.
Please attach any log files showing error messages or other useful information.
I change config files:
in config_compilers.xml added:
<compiler COMPILER="intel" MACH="ucr-hpcc">
<MPI_LIB_NAME>mpich</MPI_LIB_NAME>
<MPICC>mpiicc</MPICC>
<MPIFC>mpiifort</MPIFC>
<NETCDF_PATH>/opt/linux/centos/7.x/x86_64/pkgs/netcdf-fortran/4.4.4_intel</NETCDF_PATH>
</compiler>
in config_machines.xml added:
<machine MACH="ucr-hpcc">
<DESC>UCR HPCC cluster with appropriate modules</DESC>
<NODENAME_REGEX>r27</NODENAME_REGEX> <!-- Adjust to match the UCR HPCC hostname -->
<OS>LINUX</OS>
<COMPILERS>intel</COMPILERS> <!-- Modify based on the available compiler, e.g., intel or gnu -->
<MPILIBS>mpich</MPILIBS> <!-- Modify based on your MPI library -->
<PROJECT>none</PROJECT>
<CIME_OUTPUT_ROOT>/bigdata/wliulab/tzhu/cesm2_runs/output</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>/bigdata/wliulab/tzhu/cesm2_runs/input/$CASE</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/bigdata/wliulab/tzhu/cesm2_runs/input/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>
<GMAKE>gmake</GMAKE>
<GMAKE_J>8</GMAKE_J>
<BATCH_SYSTEM>slurm</BATCH_SYSTEM> <!-- Modify this if the cluster uses a specific batch system -->
<SUPPORTED_BY>user@ucr.edu</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>32</MAX_TASKS_PER_NODE> <!-- Modify based on your system's configuration -->
<MAX_MPITASKS_PER_NODE>32</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="ntasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<module_system type="module">
<!-- Load necessary modules for UCR HPCC -->
</module_system>
</machine>
in config_batch.xml added:
<batch_system MACH="ucr-hpcc" type="slurm">
<directives>
<directive>-l nodes={{ num_nodes }}:ppn={{ tasks_per_node }}</directive>
<directive default="/bin/bash" > -S {{ shell }} </directive>
</directives>
<queues>
<queue walltimemax="36:00:00" default="true">batch</queue>
</queues>
</batch_system>
when I run ./case.build, there are some errors. I attached the build log with errors info.
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
cmake: error while loading shared libraries: librhash.so.0: cannot open shared object file: No such file or directory
gmake: *** [/bigdata/*/cesm2_runs/output/CESM-F2000-ts/bld/intel/mpich/nodebug/nothreads/mct/pio/pio2/Makefile] Error 127
ERROR: cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
cmake: error while loading shared libraries: librhash.so.0: cannot open shared object file: No such file or directory
gmake: *** [/bigdata/*/cesm2_runs/output/CESM-F2000-ts/bld/intel/mpich/nodebug/nothreads/mct/pio/pio2/Makefile] Error 127