CESM: Difference between revisions
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(Updated machine files and new batch file) |
(add descriptive introduction) |
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{{draft}} | {{draft}} | ||
"The [https://www.cesm.ucar.edu/ Community Earth System Model] is a fully coupled global climate model developed in collaboration with colleagues in the research community. CESM provides state of the art computer simulations of Earth's past, present, and future climate states." | |||
=Porting and Validating= | =Porting and Validating= | ||
The below configuration files and commands are designed for a local installation of CESM 2.1.5: | |||
Before making the adaptations as described below, please [https://www.cesm.ucar.edu/models/cesm2/download download CESM 2.1.5 from the CESM developers] in your local directory. | |||
==Local machine file== | ==Local machine file== | ||
| Line 23: | Line 29: | ||
<OS>LINUX</OS> | <OS>LINUX</OS> | ||
<COMPILERS>intel,gnu</COMPILERS> | <COMPILERS>intel,gnu</COMPILERS> | ||
<MPILIBS>openmpi | <MPILIBS>openmpi</MPILIBS> | ||
<PROJECT>def-EDIT_THIS</PROJECT> | <PROJECT>def-EDIT_THIS</PROJECT> | ||
<CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | ||
<CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT> | <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> | ||
<DIN_LOC_ROOT>$ | <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/ | <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> | |||
<GMAKE>make</GMAKE> | |||
<GMAKE_J>8</GMAKE_J> | |||
<BATCH_SYSTEM>slurm</BATCH_SYSTEM> | <BATCH_SYSTEM>slurm</BATCH_SYSTEM> | ||
<SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | ||
| Line 38: | Line 46: | ||
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | ||
<mpirun mpilib=" | <mpirun mpilib="openmpi"> | ||
<executable> | <executable>mpirun</executable> | ||
<arguments> | |||
<arg name="anum_tasks"> -np {{ total_tasks }}</arg> | |||
<!--arg name="labelstdout">-prepend-rank</arg> --> | |||
</arguments> | |||
</mpirun> | </mpirun> | ||
<module_system type="module" allow_error="true"> | |||
<init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> | |||
<init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> | |||
<init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> | |||
<init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> | |||
<cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> | |||
<cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> | |||
<cmd_path lang="csh">module</cmd_path> | |||
<cmd_path lang="sh">module</cmd_path> | |||
<modules> | |||
<command name="purge"/> | |||
<command name="load">StdEnv/2023</command> | |||
</modules> | |||
<modules compiler="intel"> | |||
<command name="load">intel/2023.2.1</command> | |||
<command name="load">git-annex/10.20231129</command> | |||
<command name="load">cmake/3.27.7</command> | |||
</modules> | |||
<modules mpilib="openmpi"> | |||
<command name="load">openmpi/4.1.5</command> | |||
<command name="load">hdf5-mpi/1.14.2</command> | |||
<command name="load">netcdf-c++4-mpi/4.3.1</command> | |||
<command name="load">netcdf-fortran-mpi/4.6.1</command> | |||
<command name="load">netcdf-mpi/4.9.2</command> | |||
<command name="load">xml-libxml/2.0208</command> | |||
<command name="load">flexiblas/3.3.1</command> | |||
</modules> | |||
</module_system> | |||
<environment_variables> | |||
<env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> | |||
<env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> | |||
<env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> | |||
<env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> | |||
<env name="OMP_STACKSIZE">256M</env> | |||
<env name="I_MPI_CC">icc</env> | |||
<env name="I_MPI_FC">ifort</env> | |||
<env name="I_MPI_F77">ifort</env> | |||
<env name="I_MPI_F90">ifort</env> | |||
<env name="I_MPI_CXX">icpc</env> | |||
</environment_variables> | |||
<resource_limits> | |||
<resource name="RLIMIT_STACK">300000000</resource> | |||
</resource_limits> | |||
</machine> | </machine> | ||
</config_machines> | </config_machines> | ||
}} | }} | ||
| Line 65: | Line 115: | ||
<OS>LINUX</OS> | <OS>LINUX</OS> | ||
<COMPILERS>intel,gnu</COMPILERS> | <COMPILERS>intel,gnu</COMPILERS> | ||
<MPILIBS>openmpi | <MPILIBS>openmpi</MPILIBS> | ||
<PROJECT>def-EDIT_THIS</PROJECT> | <PROJECT>def-EDIT_THIS</PROJECT> | ||
<CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | ||
<CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT> | <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> | ||
<DIN_LOC_ROOT>$ | <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/ | <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> | |||
<GMAKE>make</GMAKE> | |||
<GMAKE_J>8</GMAKE_J> | |||
<BATCH_SYSTEM>slurm</BATCH_SYSTEM> | <BATCH_SYSTEM>slurm</BATCH_SYSTEM> | ||
<SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | ||
| Line 80: | Line 132: | ||
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | ||
<mpirun mpilib=" | <mpirun mpilib="openmpi"> | ||
<executable> | <executable>mpirun</executable> | ||
<arguments> | |||
<arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> | |||
</arguments> | |||
</mpirun> | </mpirun> | ||
<module_system type="module" allow_error="true"> | |||
<init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> | |||
<init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> | |||
<init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> | |||
<init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> | |||
<cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> | |||
<cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> | |||
<cmd_path lang="csh">module</cmd_path> | |||
<cmd_path lang="sh">module</cmd_path> | |||
<modules> | |||
<command name="purge"/> | |||
<command name="load">StdEnv/2023</command> | |||
</modules> | |||
<modules compiler="intel"> | |||
<command name="load">intel/2023.2.1</command> | |||
<command name="load">git-annex/10.20231129</command> | |||
<command name="load">cmake/3.27.7</command> | |||
</modules> | |||
<modules mpilib="openmpi"> | |||
<command name="load">openmpi/4.1.5</command> | |||
<command name="load">hdf5-mpi/1.14.2</command> | |||
<command name="load">netcdf-c++4-mpi/4.3.1</command> | |||
<command name="load">netcdf-fortran-mpi/4.6.1</command> | |||
<command name="load">netcdf-mpi/4.9.2</command> | |||
<command name="load">xml-libxml/2.0208</command> | |||
<command name="load">flexiblas/3.3.1</command> | |||
</modules> | |||
</module_system> | |||
<environment_variables> | |||
<env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> | |||
<env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> | |||
<env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> | |||
<env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> | |||
<env name="OMP_STACKSIZE">256M</env> | |||
<env name="I_MPI_CC">icc</env> | |||
<env name="I_MPI_FC">ifort</env> | |||
<env name="I_MPI_F77">ifort</env> | |||
<env name="I_MPI_F90">ifort</env> | |||
<env name="I_MPI_CXX">icpc</env> | |||
</environment_variables> | |||
<resource_limits> | |||
<resource name="RLIMIT_STACK">300000000</resource> | |||
</resource_limits> | |||
</machine> | </machine> | ||
</config_machines> | </config_machines> | ||
}} | }} | ||
| Line 107: | Line 200: | ||
<OS>LINUX</OS> | <OS>LINUX</OS> | ||
<COMPILERS>intel,gnu</COMPILERS> | <COMPILERS>intel,gnu</COMPILERS> | ||
<MPILIBS>openmpi | <MPILIBS>openmpi</MPILIBS> | ||
<PROJECT>def-EDIT_THIS</PROJECT> | <PROJECT>def-EDIT_THIS</PROJECT> | ||
<CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | ||
<CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT> | <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> | ||
<DIN_LOC_ROOT>$ | <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/ | <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> | |||
<GMAKE>make</GMAKE> | |||
<GMAKE_J>8</GMAKE_J> | |||
<BATCH_SYSTEM>slurm</BATCH_SYSTEM> | <BATCH_SYSTEM>slurm</BATCH_SYSTEM> | ||
<SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | ||
| Line 122: | Line 217: | ||
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | ||
<mpirun mpilib=" | <mpirun mpilib="openmpi"> | ||
<executable> | <executable>mpirun</executable> | ||
<arguments> | |||
<arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> | |||
</arguments> | |||
</mpirun> | </mpirun> | ||
<module_system type="module" allow_error="true"> | |||
<init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> | |||
<init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> | |||
<init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> | |||
<init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> | |||
<cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> | |||
<cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> | |||
<cmd_path lang="csh">module</cmd_path> | |||
<cmd_path lang="sh">module</cmd_path> | |||
<modules> | |||
<command name="purge"/> | |||
<command name="load">StdEnv/2023</command> | |||
</modules> | |||
<modules compiler="intel"> | |||
<command name="load">intel/2023.2.1</command> | |||
<command name="load">git-annex/10.20231129</command> | |||
<command name="load">cmake/3.27.7</command> | |||
</modules> | |||
<modules mpilib="openmpi"> | |||
<command name="load">openmpi/4.1.5</command> | |||
<command name="load">hdf5-mpi/1.14.2</command> | |||
<command name="load">netcdf-c++4-mpi/4.3.1</command> | |||
<command name="load">netcdf-fortran-mpi/4.6.1</command> | |||
<command name="load">netcdf-mpi/4.9.2</command> | |||
<command name="load">xml-libxml/2.0208</command> | |||
<command name="load">flexiblas/3.3.1</command> | |||
</modules> | |||
</module_system> | |||
<environment_variables> | |||
<env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> | |||
<env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> | |||
<env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> | |||
<env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> | |||
<env name="OMP_STACKSIZE">256M</env> | |||
<env name="I_MPI_CC">icc</env> | |||
<env name="I_MPI_FC">ifort</env> | |||
<env name="I_MPI_F77">ifort</env> | |||
<env name="I_MPI_F90">ifort</env> | |||
<env name="I_MPI_CXX">icpc</env> | |||
</environment_variables> | |||
<resource_limits> | |||
<resource name="RLIMIT_STACK">300000000</resource> | |||
</resource_limits> | |||
</machine> | </machine> | ||
</config_machines> | </config_machines> | ||
}} | }} | ||
| Line 149: | Line 285: | ||
<OS>LINUX</OS> | <OS>LINUX</OS> | ||
<COMPILERS>intel,gnu</COMPILERS> | <COMPILERS>intel,gnu</COMPILERS> | ||
<MPILIBS>openmpi | <MPILIBS>openmpi</MPILIBS> | ||
<PROJECT>def-EDIT_THIS</PROJECT> | <PROJECT>def-EDIT_THIS</PROJECT> | ||
<CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | ||
<CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT> | <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> | ||
<DIN_LOC_ROOT>$ | <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/ | <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> | |||
<GMAKE>make</GMAKE> | |||
<GMAKE_J>8</GMAKE_J> | |||
<BATCH_SYSTEM>slurm</BATCH_SYSTEM> | <BATCH_SYSTEM>slurm</BATCH_SYSTEM> | ||
<SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | ||
| Line 164: | Line 302: | ||
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | ||
<mpirun mpilib=" | <mpirun mpilib="openmpi"> | ||
<executable> | <executable>mpirun</executable> | ||
<arguments> | |||
<arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> | |||
</arguments> | |||
</mpirun> | </mpirun> | ||
<module_system type="module" allow_error="true"> | |||
<init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> | |||
<init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> | |||
<init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> | |||
<init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> | |||
<cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> | |||
<cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> | |||
<cmd_path lang="csh">module</cmd_path> | |||
<cmd_path lang="sh">module</cmd_path> | |||
<modules> | |||
<command name="purge"/> | |||
<command name="load">StdEnv/2023</command> | |||
</modules> | |||
<modules compiler="intel"> | |||
<command name="load">intel/2023.2.1</command> | |||
<command name="load">git-annex/10.20231129</command> | |||
<command name="load">cmake/3.27.7</command> | |||
</modules> | |||
<modules mpilib="openmpi"> | |||
<command name="load">openmpi/4.1.5</command> | |||
<command name="load">hdf5-mpi/1.14.2</command> | |||
<command name="load">netcdf-c++4-mpi/4.3.1</command> | |||
<command name="load">netcdf-fortran-mpi/4.6.1</command> | |||
<command name="load">netcdf-mpi/4.9.2</command> | |||
<command name="load">xml-libxml/2.0208</command> | |||
<command name="load">flexiblas/3.3.1</command> | |||
</modules> | |||
</module_system> | |||
<environment_variables> | |||
<env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> | |||
<env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> | |||
<env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> | |||
<env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> | |||
<env name="OMP_STACKSIZE">256M</env> | |||
<env name="I_MPI_CC">icc</env> | |||
<env name="I_MPI_FC">ifort</env> | |||
<env name="I_MPI_F77">ifort</env> | |||
<env name="I_MPI_F90">ifort</env> | |||
<env name="I_MPI_CXX">icpc</env> | |||
</environment_variables> | |||
<resource_limits> | |||
<resource name="RLIMIT_STACK">300000000</resource> | |||
</resource_limits> | |||
</machine> | </machine> | ||
</config_machines> | </config_machines> | ||
}} | }} | ||
| Line 191: | Line 370: | ||
<OS>LINUX</OS> | <OS>LINUX</OS> | ||
<COMPILERS>intel,gnu</COMPILERS> | <COMPILERS>intel,gnu</COMPILERS> | ||
<MPILIBS>openmpi | <MPILIBS>openmpi</MPILIBS> | ||
<PROJECT>def-EDIT_THIS</PROJECT> | <PROJECT>def-EDIT_THIS</PROJECT> | ||
<CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> | ||
<CIME_OUTPUT_ROOT>/scratch/$USER</CIME_OUTPUT_ROOT> | <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> | ||
<DIN_LOC_ROOT>$ | <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/ | <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> | ||
<DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> | |||
<GMAKE>make</GMAKE> | |||
<GMAKE_J>8</GMAKE_J> | |||
<BATCH_SYSTEM>slurm</BATCH_SYSTEM> | <BATCH_SYSTEM>slurm</BATCH_SYSTEM> | ||
<SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> | ||
| Line 206: | Line 387: | ||
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> | ||
<mpirun mpilib=" | <mpirun mpilib="openmpi"> | ||
<executable> | <executable>mpirun</executable> | ||
<arguments> | |||
<arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> | |||
</arguments> | |||
</mpirun> | </mpirun> | ||
<module_system type="module" allow_error="true"> | |||
<init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> | |||
<init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> | |||
<init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> | |||
<init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> | |||
<cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> | |||
<cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> | |||
<cmd_path lang="csh">module</cmd_path> | |||
<cmd_path lang="sh">module</cmd_path> | |||
<modules> | |||
<command name="purge"/> | |||
<command name="load">StdEnv/2023</command> | |||
</modules> | |||
<modules compiler="intel"> | |||
<command name="load">intel/2023.2.1</command> | |||
<command name="load">git-annex/10.20231129</command> | |||
<command name="load">cmake/3.27.7</command> | |||
</modules> | |||
<modules mpilib="openmpi"> | |||
<command name="load">openmpi/4.1.5</command> | |||
<command name="load">hdf5-mpi/1.14.2</command> | |||
<command name="load">netcdf-c++4-mpi/4.3.1</command> | |||
<command name="load">netcdf-fortran-mpi/4.6.1</command> | |||
<command name="load">netcdf-mpi/4.9.2</command> | |||
<command name="load">xml-libxml/2.0208</command> | |||
<command name="load">flexiblas/3.3.1</command> | |||
</modules> | |||
</module_system> | |||
<environment_variables> | |||
<env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> | |||
<env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> | |||
<env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> | |||
<env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> | |||
<env name="OMP_STACKSIZE">256M</env> | |||
<env name="I_MPI_CC">icc</env> | |||
<env name="I_MPI_FC">ifort</env> | |||
<env name="I_MPI_F77">ifort</env> | |||
<env name="I_MPI_F90">ifort</env> | |||
<env name="I_MPI_CXX">icpc</env> | |||
</environment_variables> | |||
<resource_limits> | |||
<resource name="RLIMIT_STACK">300000000</resource> | |||
</resource_limits> | |||
</machine> | </machine> | ||
</config_machines> | </config_machines> | ||
}} | }} | ||
| Line 224: | Line 446: | ||
{{Command2 | {{Command2 | ||
|prompt=[name@server ~]$| | |prompt=[name@server ~]$ | ||
|xmllint --noout --schema /path/to/CESM/cime/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml | |||
|result= | |result= | ||
/home/ | /home/name/.cime/config_machines.xml validates | ||
}} | |||
{{Command2 | |||
|prompt=[name@beluga ~]$ | |||
|query_config --machines current | |||
|result= | |||
beluga (current) : https://docs.alliancecan.ca/wiki/Béluga/en | |||
os LINUX | |||
compilers intel,gnu | |||
pes/node 40 | |||
max_tasks/node 40 | |||
}} | }} | ||
</li> | </li> | ||
| Line 234: | Line 467: | ||
{{Command2 | {{Command2 | ||
|prompt=[name@server ~]$ | |prompt=[name@server ~]$ | ||
|less | |less /path/to/CESM/cime/config/xml_schemas/config_machines_template.xml | ||
}} | }} | ||
</li> | </li> | ||
| Line 271: | Line 504: | ||
{{Command2 | {{Command2 | ||
|prompt=[name@server ~]$| | |prompt=[name@server ~]$ | ||
|xmllint --noout --schema /path/to/CESM/cime/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml | |||
|result= | |result= | ||
/home/ | /home/name/.cime/config_batch.xml validates | ||
}} | }} | ||
</li> | </li> | ||
| Line 279: | Line 513: | ||
<li>Check the documentation for additional <b>[https://esmci.github.io/cime/versions/maint-5.6/html/xml_files/cesm.html#cimeroot-config-cesm-machines configuration parameters and examples]</b>.</li> | <li>Check the documentation for additional <b>[https://esmci.github.io/cime/versions/maint-5.6/html/xml_files/cesm.html#cimeroot-config-cesm-machines configuration parameters and examples]</b>.</li> | ||
</ul> | </ul> | ||
==Local compilers file== | |||
<ul> | |||
<li>Create and edit the file <code>~/.cime/config_compilers.xml</code> from the following minimal content per cluster: | |||
<tabs> | |||
<tab name="Beluga"> | |||
{{File | |||
|name=~/.cime/config_compilers.xml | |||
|lang="xml" | |||
|contents= | |||
<?xml version="1.0"?> | |||
<compiler MACH="beluga"> | |||
<CPPDEFS> | |||
<!-- these flags enable nano timers --> | |||
<append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> | |||
</CPPDEFS> | |||
<NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> | |||
<PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> | |||
<PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> | |||
<SLIBS> | |||
<append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> | |||
</SLIBS> | |||
</compiler> | |||
}} | |||
</tab> | |||
<tab name="Cedar"> | |||
{{File | |||
|name=~/.cime/config_compilers.xml | |||
|lang="xml" | |||
|contents= | |||
<?xml version="1.0"?> | |||
<compiler MACH="cedar"> | |||
<CPPDEFS> | |||
<!-- these flags enable nano timers --> | |||
<append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> | |||
</CPPDEFS> | |||
<NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> | |||
<PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> | |||
<PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> | |||
<SLIBS> | |||
<append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> | |||
</SLIBS> | |||
</compiler> | |||
}} | |||
</tab> | |||
<tab name="Graham"> | |||
{{File | |||
|name=~/.cime/config_compilers.xml | |||
|lang="xml" | |||
|contents= | |||
<?xml version="1.0"?> | |||
<compiler MACH="graham"> | |||
<CPPDEFS> | |||
<!-- these flags enable nano timers --> | |||
<append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> | |||
</CPPDEFS> | |||
<NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> | |||
<PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> | |||
<PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> | |||
<SLIBS> | |||
<append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> | |||
</SLIBS> | |||
</compiler> | |||
}} | |||
</tab> | |||
<tab name="Narval"> | |||
{{File | |||
|name=~/.cime/config_compilers.xml | |||
|lang="xml" | |||
|contents= | |||
<?xml version="1.0"?> | |||
<compiler MACH="narval"> | |||
<CPPDEFS> | |||
<!-- these flags enable nano timers --> | |||
<append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> | |||
</CPPDEFS> | |||
<NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> | |||
<PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> | |||
<PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> | |||
<SLIBS> | |||
<append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> | |||
</SLIBS> | |||
</compiler> | |||
}} | |||
</tab> | |||
<tab name="Niagara"> | |||
{{File | |||
|name=~/.cime/config_compilers.xml | |||
|lang="xml" | |||
|contents= | |||
<?xml version="1.0"?> | |||
<compiler MACH="niagara"> | |||
<CPPDEFS> | |||
<!-- these flags enable nano timers --> | |||
<append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> | |||
</CPPDEFS> | |||
<NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> | |||
<PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> | |||
<PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> | |||
<SLIBS> | |||
<append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> | |||
</SLIBS> | |||
</compiler> | |||
}} | |||
</tab> | |||
</tabs> | |||
==Checkout externals== | |||
Before your first use of CESM, you may checkout the individual model components by running the checkout_externals script. | |||
{{Command2 | |||
|prompt=[name@server ~]$ | |||
|/path/to/CESM/manage_externals/checkout_externals | |||
}} | |||
You may need to accept a certificate from the CESM repository to download input files. | |||
==Creating a test case== | |||
The following command assumes the default model <code>cesm</code> and the <code>current</code> machine: | |||
{{Command2 | |||
|prompt=[name@server ~]$ | |||
|/path/to/CESM/cime/scripts/create_newcase --case test_case --compset IHistClm50Bgc --res f19_g17 | |||
}} | |||
=Reference= | =Reference= | ||
Latest revision as of 14:14, 10 October 2024
This article is a draft
This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.
"The Community Earth System Model is a fully coupled global climate model developed in collaboration with colleagues in the research community. CESM provides state of the art computer simulations of Earth's past, present, and future climate states."
Porting and Validating[edit]
The below configuration files and commands are designed for a local installation of CESM 2.1.5:
Before making the adaptations as described below, please download CESM 2.1.5 from the CESM developers in your local directory.
Local machine file[edit]
- Create and edit the file
~/.cime/config_machines.xmlfrom the following minimal content per cluster:File : ~/.cime/config_machines.xml<?xml version="1.0"?> <config_machines version="2.0"> <machine MACH="beluga"> <DESC>https://docs.alliancecan.ca/wiki/Béluga/en</DESC> <NODENAME_REGEX>b[cegl].*.int.ets1.calculquebec.ca</NODENAME_REGEX> <OS>LINUX</OS> <COMPILERS>intel,gnu</COMPILERS> <MPILIBS>openmpi</MPILIBS> <PROJECT>def-EDIT_THIS</PROJECT> <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> <GMAKE>make</GMAKE> <GMAKE_J>8</GMAKE_J> <BATCH_SYSTEM>slurm</BATCH_SYSTEM> <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> <MAX_TASKS_PER_NODE>40</MAX_TASKS_PER_NODE> <MAX_MPITASKS_PER_NODE>40</MAX_MPITASKS_PER_NODE> <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> <mpirun mpilib="openmpi"> <executable>mpirun</executable> <arguments> <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> </arguments> </mpirun> <module_system type="module" allow_error="true"> <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> <cmd_path lang="csh">module</cmd_path> <cmd_path lang="sh">module</cmd_path> <modules> <command name="purge"/> <command name="load">StdEnv/2023</command> </modules> <modules compiler="intel"> <command name="load">intel/2023.2.1</command> <command name="load">git-annex/10.20231129</command> <command name="load">cmake/3.27.7</command> </modules> <modules mpilib="openmpi"> <command name="load">openmpi/4.1.5</command> <command name="load">hdf5-mpi/1.14.2</command> <command name="load">netcdf-c++4-mpi/4.3.1</command> <command name="load">netcdf-fortran-mpi/4.6.1</command> <command name="load">netcdf-mpi/4.9.2</command> <command name="load">xml-libxml/2.0208</command> <command name="load">flexiblas/3.3.1</command> </modules> </module_system> <environment_variables> <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> <env name="OMP_STACKSIZE">256M</env> <env name="I_MPI_CC">icc</env> <env name="I_MPI_FC">ifort</env> <env name="I_MPI_F77">ifort</env> <env name="I_MPI_F90">ifort</env> <env name="I_MPI_CXX">icpc</env> </environment_variables> <resource_limits> <resource name="RLIMIT_STACK">300000000</resource> </resource_limits> </machine> </config_machines>
File : ~/.cime/config_machines.xml<?xml version="1.0"?> <config_machines version="2.0"> <machine MACH="cedar"> <DESC>https://docs.alliancecan.ca/wiki/Cedar</DESC> <NODENAME_REGEX>c[de].*.computecanada.ca</NODENAME_REGEX> <OS>LINUX</OS> <COMPILERS>intel,gnu</COMPILERS> <MPILIBS>openmpi</MPILIBS> <PROJECT>def-EDIT_THIS</PROJECT> <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> <GMAKE>make</GMAKE> <GMAKE_J>8</GMAKE_J> <BATCH_SYSTEM>slurm</BATCH_SYSTEM> <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> <MAX_TASKS_PER_NODE>48</MAX_TASKS_PER_NODE> <MAX_MPITASKS_PER_NODE>48</MAX_MPITASKS_PER_NODE> <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> <mpirun mpilib="openmpi"> <executable>mpirun</executable> <arguments> <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> </arguments> </mpirun> <module_system type="module" allow_error="true"> <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> <cmd_path lang="csh">module</cmd_path> <cmd_path lang="sh">module</cmd_path> <modules> <command name="purge"/> <command name="load">StdEnv/2023</command> </modules> <modules compiler="intel"> <command name="load">intel/2023.2.1</command> <command name="load">git-annex/10.20231129</command> <command name="load">cmake/3.27.7</command> </modules> <modules mpilib="openmpi"> <command name="load">openmpi/4.1.5</command> <command name="load">hdf5-mpi/1.14.2</command> <command name="load">netcdf-c++4-mpi/4.3.1</command> <command name="load">netcdf-fortran-mpi/4.6.1</command> <command name="load">netcdf-mpi/4.9.2</command> <command name="load">xml-libxml/2.0208</command> <command name="load">flexiblas/3.3.1</command> </modules> </module_system> <environment_variables> <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> <env name="OMP_STACKSIZE">256M</env> <env name="I_MPI_CC">icc</env> <env name="I_MPI_FC">ifort</env> <env name="I_MPI_F77">ifort</env> <env name="I_MPI_F90">ifort</env> <env name="I_MPI_CXX">icpc</env> </environment_variables> <resource_limits> <resource name="RLIMIT_STACK">300000000</resource> </resource_limits> </machine> </config_machines>
File : ~/.cime/config_machines.xml<?xml version="1.0"?> <config_machines version="2.0"> <machine MACH="graham"> <DESC>https://docs.alliancecan.ca/wiki/Graham</DESC> <NODENAME_REGEX>gra.*</NODENAME_REGEX> <OS>LINUX</OS> <COMPILERS>intel,gnu</COMPILERS> <MPILIBS>openmpi</MPILIBS> <PROJECT>def-EDIT_THIS</PROJECT> <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> <GMAKE>make</GMAKE> <GMAKE_J>8</GMAKE_J> <BATCH_SYSTEM>slurm</BATCH_SYSTEM> <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> <MAX_TASKS_PER_NODE>44</MAX_TASKS_PER_NODE> <MAX_MPITASKS_PER_NODE>44</MAX_MPITASKS_PER_NODE> <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> <mpirun mpilib="openmpi"> <executable>mpirun</executable> <arguments> <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> </arguments> </mpirun> <module_system type="module" allow_error="true"> <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> <cmd_path lang="csh">module</cmd_path> <cmd_path lang="sh">module</cmd_path> <modules> <command name="purge"/> <command name="load">StdEnv/2023</command> </modules> <modules compiler="intel"> <command name="load">intel/2023.2.1</command> <command name="load">git-annex/10.20231129</command> <command name="load">cmake/3.27.7</command> </modules> <modules mpilib="openmpi"> <command name="load">openmpi/4.1.5</command> <command name="load">hdf5-mpi/1.14.2</command> <command name="load">netcdf-c++4-mpi/4.3.1</command> <command name="load">netcdf-fortran-mpi/4.6.1</command> <command name="load">netcdf-mpi/4.9.2</command> <command name="load">xml-libxml/2.0208</command> <command name="load">flexiblas/3.3.1</command> </modules> </module_system> <environment_variables> <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> <env name="OMP_STACKSIZE">256M</env> <env name="I_MPI_CC">icc</env> <env name="I_MPI_FC">ifort</env> <env name="I_MPI_F77">ifort</env> <env name="I_MPI_F90">ifort</env> <env name="I_MPI_CXX">icpc</env> </environment_variables> <resource_limits> <resource name="RLIMIT_STACK">300000000</resource> </resource_limits> </machine> </config_machines>
File : ~/.cime/config_machines.xml<?xml version="1.0"?> <config_machines version="2.0"> <machine MACH="narval"> <DESC>https://docs.alliancecan.ca/wiki/Narval/en</DESC> <NODENAME_REGEX>n[acgl].*.narval.calcul.quebec</NODENAME_REGEX> <OS>LINUX</OS> <COMPILERS>intel,gnu</COMPILERS> <MPILIBS>openmpi</MPILIBS> <PROJECT>def-EDIT_THIS</PROJECT> <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> <GMAKE>make</GMAKE> <GMAKE_J>8</GMAKE_J> <BATCH_SYSTEM>slurm</BATCH_SYSTEM> <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> <MAX_TASKS_PER_NODE>64</MAX_TASKS_PER_NODE> <MAX_MPITASKS_PER_NODE>64</MAX_MPITASKS_PER_NODE> <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> <mpirun mpilib="openmpi"> <executable>mpirun</executable> <arguments> <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> </arguments> </mpirun> <module_system type="module" allow_error="true"> <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> <cmd_path lang="csh">module</cmd_path> <cmd_path lang="sh">module</cmd_path> <modules> <command name="purge"/> <command name="load">StdEnv/2023</command> </modules> <modules compiler="intel"> <command name="load">intel/2023.2.1</command> <command name="load">git-annex/10.20231129</command> <command name="load">cmake/3.27.7</command> </modules> <modules mpilib="openmpi"> <command name="load">openmpi/4.1.5</command> <command name="load">hdf5-mpi/1.14.2</command> <command name="load">netcdf-c++4-mpi/4.3.1</command> <command name="load">netcdf-fortran-mpi/4.6.1</command> <command name="load">netcdf-mpi/4.9.2</command> <command name="load">xml-libxml/2.0208</command> <command name="load">flexiblas/3.3.1</command> </modules> </module_system> <environment_variables> <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> <env name="OMP_STACKSIZE">256M</env> <env name="I_MPI_CC">icc</env> <env name="I_MPI_FC">ifort</env> <env name="I_MPI_F77">ifort</env> <env name="I_MPI_F90">ifort</env> <env name="I_MPI_CXX">icpc</env> </environment_variables> <resource_limits> <resource name="RLIMIT_STACK">300000000</resource> </resource_limits> </machine> </config_machines>
File : ~/.cime/config_machines.xml<?xml version="1.0"?> <config_machines version="2.0"> <machine MACH="niagara"> <DESC>https://docs.alliancecan.ca/wiki/Niagara</DESC> <NODENAME_REGEX>nia.*.scinet.local</NODENAME_REGEX> <OS>LINUX</OS> <COMPILERS>intel,gnu</COMPILERS> <MPILIBS>openmpi</MPILIBS> <PROJECT>def-EDIT_THIS</PROJECT> <CHARGE_ACCOUNT>def-EDIT_THIS</CHARGE_ACCOUNT> <CIME_OUTPUT_ROOT>/scratch/$USER/cesm/output</CIME_OUTPUT_ROOT> <DIN_LOC_ROOT>/scratch/$USER/cesm/inputdata</DIN_LOC_ROOT> <DIN_LOC_ROOT_CLMFORC>${DIN_LOC_ROOT}/atm/datm7</DIN_LOC_ROOT_CLMFORC> <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/case</DOUT_S_ROOT> <GMAKE>make</GMAKE> <GMAKE_J>8</GMAKE_J> <BATCH_SYSTEM>slurm</BATCH_SYSTEM> <SUPPORTED_BY>support@tech.alliancecan.ca</SUPPORTED_BY> <MAX_TASKS_PER_NODE>40</MAX_TASKS_PER_NODE> <MAX_MPITASKS_PER_NODE>40</MAX_MPITASKS_PER_NODE> <PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED> <mpirun mpilib="openmpi"> <executable>mpirun</executable> <arguments> <arg name="anum_tasks"> -np [[:Template:Total tasks]]</arg> </arguments> </mpirun> <module_system type="module" allow_error="true"> <init_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/perl</init_path> <init_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/env_modules_python.py</init_path> <init_path lang="csh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/csh</init_path> <init_path lang="sh">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/init/sh</init_path> <cmd_path lang="perl">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod perl</cmd_path> <cmd_path lang="python">/cvmfs/soft.computecanada.ca/custom/software/lmod/lmod/libexec/lmod python</cmd_path> <cmd_path lang="csh">module</cmd_path> <cmd_path lang="sh">module</cmd_path> <modules> <command name="purge"/> <command name="load">StdEnv/2023</command> </modules> <modules compiler="intel"> <command name="load">intel/2023.2.1</command> <command name="load">git-annex/10.20231129</command> <command name="load">cmake/3.27.7</command> </modules> <modules mpilib="openmpi"> <command name="load">openmpi/4.1.5</command> <command name="load">hdf5-mpi/1.14.2</command> <command name="load">netcdf-c++4-mpi/4.3.1</command> <command name="load">netcdf-fortran-mpi/4.6.1</command> <command name="load">netcdf-mpi/4.9.2</command> <command name="load">xml-libxml/2.0208</command> <command name="load">flexiblas/3.3.1</command> </modules> </module_system> <environment_variables> <env name="NETCDF_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/pnetcdf/1.12.3</env> <env name="NETCDF_FORTRAN_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-fortran-mpi/4.6.1/</env> <env name="NETCDF_C_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/MPI/intel2023/openmpi4/netcdf-c++4-mpi/4.3.1/</env> <env name="NETLIB_LAPACK_PATH">/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0/</env> <env name="OMP_STACKSIZE">256M</env> <env name="I_MPI_CC">icc</env> <env name="I_MPI_FC">ifort</env> <env name="I_MPI_F77">ifort</env> <env name="I_MPI_F90">ifort</env> <env name="I_MPI_CXX">icpc</env> </environment_variables> <resource_limits> <resource name="RLIMIT_STACK">300000000</resource> </resource_limits> </machine> </config_machines>
- Validate your XML machine file with the following commands:
[name@server ~]$ xmllint --noout --schema /path/to/CESM/cime/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml /home/name/.cime/config_machines.xml validates
[name@beluga ~]$ query_config --machines current beluga (current) : https://docs.alliancecan.ca/wiki/Béluga/en os LINUX compilers intel,gnu pes/node 40 max_tasks/node 40
- Check the official template for additional parameters:
[name@server ~]$ less /path/to/CESM/cime/config/xml_schemas/config_machines_template.xml
Local batch file[edit]
- Create and edit the file
~/.cime/config_batch.xmlfrom the following minimal content:File : ~/.cime/config_batch.xml<?xml version="1.0"?> <config_batch version="2.1"> <batch_system type="slurm"> <batch_submit>sbatch</batch_submit> <submit_args> <arg flag="--time" name="$JOB_WALLCLOCK_TIME"/> <arg flag="--account" name="$PROJECT"/> </submit_args> <directives> <directive>--mem=0</directive> </directives> <queues> <queue default="true">default</queue> </queues> </batch_system> </config_batch>
- Validate your XML machine file with the following commands:
[name@server ~]$ xmllint --noout --schema /path/to/CESM/cime/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml /home/name/.cime/config_batch.xml validates
- Check the documentation for additional configuration parameters and examples.
Local compilers file[edit]
- Create and edit the file
~/.cime/config_compilers.xmlfrom the following minimal content per cluster:File : ~/.cime/config_compilers.xml<?xml version="1.0"?> <compiler MACH="beluga"> <CPPDEFS> <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> </CPPDEFS> <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> <SLIBS> <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> </SLIBS> </compiler>
File : ~/.cime/config_compilers.xml<?xml version="1.0"?> <compiler MACH="cedar"> <CPPDEFS> <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> </CPPDEFS> <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> <SLIBS> <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> </SLIBS> </compiler>
File : ~/.cime/config_compilers.xml<?xml version="1.0"?> <compiler MACH="graham"> <CPPDEFS> <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> </CPPDEFS> <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> <SLIBS> <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> </SLIBS> </compiler>
File : ~/.cime/config_compilers.xml<?xml version="1.0"?> <compiler MACH="narval"> <CPPDEFS> <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> </CPPDEFS> <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> <SLIBS> <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> </SLIBS> </compiler>
File : ~/.cime/config_compilers.xml<?xml version="1.0"?> <compiler MACH="niagara"> <CPPDEFS> <append MODEL="gptl"> -DHAVE_NANOTIME -DBIT64 -DHAVE_VPRINTF -DHAVE_BACKTRACE -DHAVE_SLASHPROC -DHAVE_COMM_F2C -DHAVE_TIMES -DHAVE_GETTIMEOFDAY </append> </CPPDEFS> <NETCDF_PATH>$ENV{NETCDF_FORTRAN_ROOT}</NETCDF_PATH> <PIO_FILESYSTEM_HINTS>lustre</PIO_FILESYSTEM_HINTS> <PNETCDF_PATH>$ENV{PARALLEL_NETCDF_ROOT}</PNETCDF_PATH> <SLIBS> <append>-L$(NETCDF_PATH)/lib -lnetcdff -L$(NETCDF_C_ROOT)/lib -lnetcdf -L$(NETLIB_LAPACK_PATH)/lib/intel64 -lmkl -ldl </append> </SLIBS> </compiler>
Checkout externals[edit]
Before your first use of CESM, you may checkout the individual model components by running the checkout_externals script.
[name@server ~]$ /path/to/CESM/manage_externals/checkout_externalsYou may need to accept a certificate from the CESM repository to download input files.
Creating a test case[edit]
The following command assumes the default model
cesmand thecurrentmachine:[name@server ~]$ /path/to/CESM/cime/scripts/create_newcase --case test_case --compset IHistClm50Bgc --res f19_g17
Reference[edit]