CESMInstall WIKI CESM - hydra
(→Errors) |
(→Errors) |
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| Línea 559: | Línea 559: | ||
Modifying more python scripts in <CODE>cime/src/build_scripts</CODE>: <CODE>cime/src/build_scripts/buildlib.cprnc, cime/src/build_scripts/buildlib.csm_share, cime/src/build_scripts/buildlib.gptl, cime/src/build_scripts/buildlib.kokkos, cime/src/build_scripts/buildlib.mct, cime/src/build_scripts/buildlib.mpi-serial, cime/src/build_scripts/buildlib.pio</CODE> |
Modifying more python scripts in <CODE>cime/src/build_scripts</CODE>: <CODE>cime/src/build_scripts/buildlib.cprnc, cime/src/build_scripts/buildlib.csm_share, cime/src/build_scripts/buildlib.gptl, cime/src/build_scripts/buildlib.kokkos, cime/src/build_scripts/buildlib.mct, cime/src/build_scripts/buildlib.mpi-serial, cime/src/build_scripts/buildlib.pio</CODE> |
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| − | Modifying more python scripts: <CODE>components/clm/bld/namelist_files/createMkSrfEntry.py, components/clm/run_sys_tests, </CODE> |
+ | Modifying more python scripts: <CODE>components/clm/bld/namelist_files/createMkSrfEntry.py, components/clm/run_sys_tests, components/cam/cime_config/buildcpp, components/cam/cime_config/buildnml, components/cam/manage_externals/checkout_externals, components/cdeps/cime_config/buildlib, components/cice/cime_config/buildcpp, components/cice/cime_config/buildlib, components/cice/cime_config/buildlib, components/cice/cime_config/buildnml, components/cism/manage_externals/checkout_externals, components/clm/cime_config/buildlib, components/clm/cime_config/buildnml, components/clm/manage_externals/checkout_externals, components/clm/python/run_ctsm_py_tests, components/mosart/cime_config/buildlib, components/mosart/cime_config/buildnml, components/pop/cime_config/buildcpp, components/pop/cime_config/buildlib, components/pop/cime_config/buildnml, components/rtm/cime_config/buildlibm components/rtm/cime_config/buildnml, components/ww3/cime_config/buildlib, components/ww3/cime_config/buildnml</CODE> |
== Case send == |
== Case send == |
||
Revisión de 15:06 15 mayo 2024
Contenido |
intel compilation
CIMA's hydra intel configuration is done via the following instruction:
$ source /opt/load-libs.sh 1 The following libraries, compiled with Intel 2021.4.0 compilers, were loaded: * MPICH 3.4.2 * NetCDF 4 * HDF5 1.10.5 * JASPER 2.0.33
Which creates the following environment:
declare -x ACL_BOARD_VENDOR_PATH="/opt/Intel/OpenCLFPGA/oneAPI/Boards" declare -x ADVISOR_2021_DIR="/opt/intel/oneapi/advisor/2021.4.0" declare -x APM="/opt/intel/oneapi/advisor/2021.4.0/perfmodels" declare -x CCL_CONFIGURATION="cpu_gpu_dpcpp" declare -x CCL_ROOT="/opt/intel/oneapi/ccl/2021.4.0" declare -x CLASSPATH="/opt/intel/oneapi/mpi/2021.4.0//lib/mpi.jar:/opt/intel/oneapi/dal/2021.4.0/lib/onedal.jar" declare -x CLCK_ROOT="/opt/intel/oneapi/clck/2021.4.0" declare -x CMAKE_PREFIX_PATH="/opt/intel/oneapi/vpl/2021.6.0:/opt/intel/oneapi/tbb/2021.4.0/env/..:/opt/intel/oneapi/dal/2021.4.0" declare -x CMPLR_ROOT="/opt/intel/oneapi/compiler/2021.4.0" declare -x CPATH="/opt/intel/oneapi/vpl/2021.6.0/include:/opt/intel/oneapi/tbb/2021.4.0/env/../include:/opt/intel/oneapi/mpi/2021.4.0//include:/opt/intel/oneapi/mkl/2021.4.0/include:/opt/intel/oneapi/ipp/2021.4.0/include:/opt/intel/oneapi/ippcp/2021.4.0/include:/opt/intel/oneapi/ipp/2021.4.0/include:/opt/intel/oneapi/dpl/2021.5.0/linux/include:/opt/intel/oneapi/dpcpp-ct/2021.4.0/include:/opt/intel/oneapi/dnnl/2021.4.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/intel/oneapi/dev-utilities/2021.4.0/include:/opt/intel/oneapi/dal/2021.4.0/include:/opt/intel/oneapi/compiler/2021.4.0/linux/include:/opt/intel/oneapi/ccl/2021.4.0/include/cpu_gpu_dpcpp" declare -x CPLUS_INCLUDE_PATH="/opt/intel/oneapi/clck/2021.4.0/include" declare -x DAALROOT="/opt/intel/oneapi/dal/2021.4.0" declare -x DALROOT="/opt/intel/oneapi/dal/2021.4.0" declare -x DAL_MAJOR_BINARY="1" declare -x DAL_MINOR_BINARY="1" declare -x DBUS_SESSION_BUS_ADDRESS="unix:path=/run/user/1624/bus" declare -x DNNLROOT="/opt/intel/oneapi/dnnl/2021.4.0/cpu_dpcpp_gpu_dpcpp" declare -x DPCT_BUNDLE_ROOT="/opt/intel/oneapi/dpcpp-ct/2021.4.0" declare -x DPL_ROOT="/opt/intel/oneapi/dpl/2021.5.0" declare -x FI_PROVIDER_PATH="/opt/intel/oneapi/mpi/2021.4.0//libfabric/lib/prov:/usr/lib64/libfabric" declare -x FPGA_VARS_ARGS="1" declare -x FPGA_VARS_DIR="/opt/intel/oneapi/compiler/2021.4.0/linux/lib/oclfpga" declare -x GDB_INFO="/opt/intel/oneapi/debugger/10.2.4/documentation/info/" declare -x HOME="/home/lluis.fita" declare -x INFOPATH="/opt/intel/oneapi/debugger/10.2.4/gdb/intel64/lib" declare -x INSPECTOR_2021_DIR="/opt/intel/oneapi/inspector/2021.4.0" declare -x INTELFPGAOCLSDKROOT="/opt/intel/oneapi/compiler/2021.4.0/linux/lib/oclfpga" declare -x INTEL_LICENSE_FILE="/opt/intel/licenses:/home/lluis.fita/intel/licenses:/opt/intel/oneapi/clck/2021.4.0/licensing:/opt/intel/licenses:/home/lluis.fita/intel/licenses:/Users/Shared/Library/Application Support/Intel/Licenses" declare -x INTEL_PYTHONHOME="/opt/intel/oneapi/debugger/10.2.4/dep" declare -x IPPCP_TARGET_ARCH="intel64" declare -x IPPCRYPTOROOT="/opt/intel/oneapi/ippcp/2021.4.0" declare -x IPPROOT="/opt/intel/oneapi/ipp/2021.4.0" declare -x IPP_TARGET_ARCH="intel64" declare -x I_MPI_ROOT="/opt/intel/oneapi/mpi/2021.4.0" declare -x LANG="en_US.UTF-8" declare -x LANGUAGE="en_US:en" declare -x LD_LIBRARY_PATH="/opt/netcdf/netcdf-4/intel/2021.4.0/lib:/opt/hdf5/hdf5-1.10.5/intel/2021.4.0/lib:/opt/zlib/zlib-1.2.11/intel/2021.4.0/lib:/opt/jasper/jasper-version-2.0.33/intel/2021.4.0/lib:/opt/intel/oneapi/vpl/2021.6.0/lib:/opt/intel/oneapi/tbb/2021.4.0/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.4.0//libfabric/lib:/opt/intel/oneapi/mpi/2021.4.0//lib/release:/opt/intel/oneapi/mpi/2021.4.0//lib:/opt/intel/oneapi/mkl/2021.4.0/lib/intel64:/opt/intel/oneapi/itac/2021.4.0/slib:/opt/intel/oneapi/ipp/2021.4.0/lib/intel64:/opt/intel/oneapi/ippcp/2021.4.0/lib/intel64:/opt/intel/oneapi/ipp/2021.4.0/lib/intel64:/opt/intel/oneapi/dnnl/2021.4.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/intel/oneapi/debugger/10.2.4/gdb/intel64/lib:/opt/intel/oneapi/debugger/10.2.4/libipt/intel64/lib:/opt/intel/oneapi/debugger/10.2.4/dep/lib:/opt/intel/oneapi/dal/2021.4.0/lib/intel64:/opt/intel/oneapi/compiler/2021.4.0/linux/lib:/opt/intel/oneapi/compiler/2021.4.0/linux/lib/x64:/opt/intel/oneapi/compiler/2021.4.0/linux/lib/emu:/opt/intel/oneapi/compiler/2021.4.0/linux/lib/oclfpga/host/linux64/lib:/opt/intel/oneapi/compiler/2021.4.0/linux/lib/oclfpga/linux64/lib:/opt/intel/oneapi/compiler/2021.4.0/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/ccl/2021.4.0/lib/cpu_gpu_dpcpp" declare -x LIBRARY_PATH="/opt/intel/oneapi/vpl/2021.6.0/lib:/opt/intel/oneapi/tbb/2021.4.0/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.4.0//libfabric/lib:/opt/intel/oneapi/mpi/2021.4.0//lib/release:/opt/intel/oneapi/mpi/2021.4.0//lib:/opt/intel/oneapi/mkl/2021.4.0/lib/intel64:/opt/intel/oneapi/ipp/2021.4.0/lib/intel64:/opt/intel/oneapi/ippcp/2021.4.0/lib/intel64:/opt/intel/oneapi/ipp/2021.4.0/lib/intel64:/opt/intel/oneapi/dnnl/2021.4.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/intel/oneapi/dal/2021.4.0/lib/intel64:/opt/intel/oneapi/compiler/2021.4.0/linux/compiler/lib/intel64_lin:/opt/intel/oneapi/compiler/2021.4.0/linux/lib:/opt/intel/oneapi/clck/2021.4.0/lib/intel64:/opt/intel/oneapi/ccl/2021.4.0/lib/cpu_gpu_dpcpp" declare -x LOGNAME="lluis.fita" declare -x LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:" declare -x MANPATH="/opt/intel/oneapi/mpi/2021.4.0/man:/opt/intel/oneapi/itac/2021.4.0/man:/opt/intel/oneapi/debugger/10.2.4/documentation/man:/opt/intel/oneapi/compiler/2021.4.0/documentation/en/man/common:/opt/intel/oneapi/clck/2021.4.0/man::" declare -x MKLROOT="/opt/intel/oneapi/mkl/2021.4.0" declare -x MOTD_SHOWN="pam" declare -x NLSPATH="/opt/intel/oneapi/mkl/2021.4.0/lib/intel64/locale/%l_%t/%N" declare -x OCL_ICD_FILENAMES="libintelocl_emu.so:libalteracl.so:/opt/intel/oneapi/compiler/2021.4.0/linux/lib/x64/libintelocl.so" declare -x OLDPWD declare -x ONEAPI_ROOT="/opt/intel/oneapi" declare -x PATH="/opt/jasper/jasper-version-2.0.33/intel/2021.4.0/bin:/opt/hdf5/hdf5-1.10.5/intel/2021.4.0/bin:/opt/netcdf/netcdf-4/intel/2021.4.0/bin:/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin:/opt/intel/oneapi/vtune/2021.7.1/bin64:/opt/intel/oneapi/vpl/2021.6.0/bin:/opt/intel/oneapi/mpi/2021.4.0//libfabric/bin:/opt/intel/oneapi/mpi/2021.4.0//bin:/opt/intel/oneapi/mkl/2021.4.0/bin/intel64:/opt/intel/oneapi/itac/2021.4.0/bin:/opt/intel/oneapi/inspector/2021.4.0/bin64:/opt/intel/oneapi/dpcpp-ct/2021.4.0/bin:/opt/intel/oneapi/dev-utilities/2021.4.0/bin:/opt/intel/oneapi/debugger/10.2.4/gdb/intel64/bin:/opt/intel/oneapi/compiler/2021.4.0/linux/lib/oclfpga/llvm/aocl-bin:/opt/intel/oneapi/compiler/2021.4.0/linux/lib/oclfpga/bin:/opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64:/opt/intel/oneapi/compiler/2021.4.0/linux/bin:/opt/intel/oneapi/clck/2021.4.0/bin/intel64:/opt/intel/oneapi/advisor/2021.4.0/bin64:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin" declare -x PKG_CONFIG_PATH="/opt/intel/oneapi/vtune/2021.7.1/include/pkgconfig/lib64:/opt/intel/oneapi/vpl/2021.6.0/lib/pkgconfig:/opt/intel/oneapi/tbb/2021.4.0/env/../lib/pkgconfig:/opt/intel/oneapi/mpi/2021.4.0/lib/pkgconfig:/opt/intel/oneapi/mkl/2021.4.0/lib/pkgconfig:/opt/intel/oneapi/ippcp/2021.4.0/lib/pkgconfig:/opt/intel/oneapi/inspector/2021.4.0/include/pkgconfig/lib64:/opt/intel/oneapi/dpl/2021.5.0/lib/pkgconfig:/opt/intel/oneapi/dal/2021.4.0/lib/pkgconfig:/opt/intel/oneapi/compiler/2021.4.0/lib/pkgconfig:/opt/intel/oneapi/ccl/2021.4.0/lib/pkgconfig:/opt/intel/oneapi/advisor/2021.4.0/include/pkgconfig/lib64:" declare -x PWD="/home/lluis.fita" declare -x PYTHONPATH="/opt/intel/oneapi/advisor/2021.4.0/pythonapi" declare -x SETVARS_COMPLETED="1" declare -x SETVARS_VARS_PATH="/opt/intel/oneapi/vtune/latest/env/vars.sh" declare -x SHELL="/bin/bash" declare -x SHLVL="1" declare -x SSH_CLIENT="157.92.36.32 41330 22" declare -x SSH_CONNECTION="157.92.36.32 41330 157.92.28.248 22" declare -x SSH_TTY="/dev/pts/0" declare -x TBBROOT="/opt/intel/oneapi/tbb/2021.4.0/env/.." declare -x TERM="xterm-256color" declare -x USER="lluis.fita" declare -x VTUNE_PROFILER_2021_DIR="/opt/intel/oneapi/vtune/2021.7.1" declare -x VT_ADD_LIBS="-ldwarf -lelf -lvtunwind -lm -lpthread" declare -x VT_LIB_DIR="/opt/intel/oneapi/itac/2021.4.0/lib" declare -x VT_MPI="impi4" declare -x VT_ROOT="/opt/intel/oneapi/itac/2021.4.0" declare -x VT_SLIB_DIR="/opt/intel/oneapi/itac/2021.4.0/slib" declare -x XDG_DATA_DIRS="/usr/local/share:/usr/share:/var/lib/snapd/desktop" declare -x XDG_RUNTIME_DIR="/run/user/1624" declare -x XDG_SESSION_CLASS="user" declare -x XDG_SESSION_ID="1848" declare -x XDG_SESSION_TYPE="tty" declare -x http_proxy="http://proxy1.cima.fcen.uba.ar:3128/"
Downloading CESM2
Following CESM2 Quick Start Guide and CESM2 github instructions and this tutorial
Cloning the code for version 2.2.2:
$ mkdir -p CESM/v2.2.2/intel $ git clone -b release-cesm2.2.2 git@github.com:ESCOMP/CESM.git my_cesm_sandbox
This will create a directory my_cesm_sandbox/ in your current working directory.
We got the following
$ cd my_cesm_sandbox/ $ ls ChangeLog CODE_OF_CONDUCT.md Externals.cfg manage_externals ChangeLog_template describe_version Externals_cime.cfg README.rst cime_config doc LICENSE.txt
Verifying that installation was fine:
$ ./manage_externals/checkout_externals $ ls ChangeLog CODE_OF_CONDUCT.md Externals.cfg README.rst ChangeLog_template components Externals_cime.cfg cime describe_version LICENSE.txt cime_config doc manage_externals
Defining the compilation / installation
Machine
We need to create the configuration for hydra. For that purpose we are going to use the exampled configuration for"centos7-linux" from file cime/config/cesm/machines/config_machines.xml. This is its content:
<machine MACH="hydra">
<DESC>
Example port to CIMA's hydra
</DESC>
<NODENAME_REGEX>node</NODENAME_REGEX>
<OS>LINUX Debian</OS>
<PROXY> https://howto.get.out </PROXY>
<COMPILERS>gnu</COMPILERS>
<MPILIBS>mpich</MPILIBS>
<PROJECT>none</PROJECT>
<SAVE_TIMING_DIR> </SAVE_TIMING_DIR>
<CIME_OUTPUT_ROOT>$ENV{HOME}/cesm/scratch</CIME_OUTPUT_ROOT>
<DIN_LOC_ROOT>/share/cesm/inputdata</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/share/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>/share/cesm/expriments/$CASE</DOUT_S_ROOT>
<BASELINE_ROOT>$ENV{HOME}/cesm/cesm_baselines</BASELINE_ROOT>
<CCSM_CPRNC>$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc</CCSM_CPRNC>
<GMAKE>make</GMAKE>
<GMAKE_J>8</GMAKE_J>
<BATCH_SYSTEM>pbs</BATCH_SYSTEM>
<SUPPORTED_BY>soporte@cima.fcen.uba.ar</SUPPORTED_BY>
<MAX_TASKS_PER_NODE>128</MAX_TASKS_PER_NODE>
<MAX_MPITASKS_PER_NODE>128</MAX_MPITASKS_PER_NODE>
<PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
<mpirun mpilib="impi">
<executable>mpiexec</executable>
<arguments>
<arg name="ntasks"> -np {{ total_tasks }} </arg>
</arguments>
</mpirun>
<environment_variables>
<env name="OMP_STACKSIZE">256M</env>
</environment_variables>
<resource_limits>
<resource name="RLIMIT_STACK">-1</resource>
</resource_limits>
</machine>
Creation of the hydra's CESM main folders
$ mkdir /share/cesm/expriments/ $ mkdir /share/cesm/inputdata
Compilers
Configuration of the compilers is done via the file cime/config/cesm/machines/config_cmopilers.xml.
Some modifications are introduced in order to make sure that compilation is done throughtout hydra's intel configration (after this post)
$ cp cime/config/cesm/machines/config_compilers.xml cime/config/cesm/machines/config_compilers_orig.xml
$ diff cime/config/cesm/machines/config_compilers.xml cime/config/cesm/machines/config_compilers_orig.xml
1636,1690d1635
< <compiler MACH="hydra" COMPILER="intel">
< <CFLAGS>
< <base> -qno-opt-dynamic-align -fp-model precise -std=gnu99 </base>
< <append compile_threaded="TRUE"> -qopenmp </append>
< <append DEBUG="FALSE"> -O2 -debug minimal </append>
< <append DEBUG="TRUE"> -O0 -g </append>
< </CFLAGS>
< <CPPDEFS>
< <!-- http://software.intel.com/en-us/articles/intel-composer-xe/ -->
< <append> -DFORTRANUNDERSCORE -DCPRINTEL</append>
< </CPPDEFS>
< <CXX_LINKER>FORTRAN</CXX_LINKER>
< <FC_AUTO_R8>
< <base> -r8 </base>
< </FC_AUTO_R8>
< <FFLAGS>
< <base> -qno-opt-dynamic-align -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -fp-model source </base>
< <append compile_threaded="TRUE"> -qopenmp </append>
< <append DEBUG="TRUE"> -O0 -g -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created </append>
< <append DEBUG="FALSE"> -O2 -debug minimal </append>
< </FFLAGS>
< <FFLAGS_NOOPT>
< <base> -O0 </base>
< </FFLAGS_NOOPT>
< <NETCDF_C_PATH>/opt/netcdf/netcdf-4/intel/2021.4.0</NETCDF_C_PATH>
< <NETCDF_FORTRAN_PATH>/opt/netcdf/netcdf-4/intel/2021.4.0/lib</NETCDF_FORTRAN_PATH>
< <FIXEDFLAGS>
< <base> -fixed </base>
< </FIXEDFLAGS>
< <FREEFLAGS>
< <base> -free </base>
< </FREEFLAGS>
< <LDFLAGS>
< <append compile_threaded="TRUE"> -qopenmp </append>
< </LDFLAGS>
< <MPICC> /opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpicc </MPICC>
< <MPICXX> /opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpicxx </MPICXX>
< <MPIFC> /opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpif90 </MPIFC>
< <SCC> /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/icc </SCC>
< <SCXX> /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/icpc </SCXX>
< <SFC> /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/ifort </SFC>
< <SLIBS>
< <append MPILIB="mpich"> -mkl=cluster </append>
< <append MPILIB="mpich2"> -mkl=cluster </append>
< <append MPILIB="mvapich"> -mkl=cluster </append>
< <append MPILIB="mvapich2"> -mkl=cluster </append>
< <append MPILIB="mpt"> -mkl=cluster </append>
< <append MPILIB="openmpi"> -mkl=cluster </append>
< <append MPILIB="impi"> -mkl=cluster </append>
< <append MPILIB="mpi-serial"> -mkl </append>
< <append>-L$(NETCDF_C_PATH)/lib -L$(NETCDF_FORTRAN_PATH)/lib -lnetcdff -lnetcdf -L$ENV{MKLROOT} -lmkl_rt </append>
< </SLIBS>
< <SUPPORTS_CXX>TRUE</SUPPORTS_CXX>
< </compiler>
<
PIO
Configuration of the Parallel I/O Library (PIO) used for the input/output of the model is done with the file cime/config/cesm/machines/config_pio.xml.
By now it is left as it is provided.
Batch
Configuration of the batch system is done with the file cime/config/cesm/machines/config_batch.xml
A new configuration has been added for hydra pbs queue system
$ cp cime/config/cesm/machines/config_batch.xml cime/config/cesm/machines/config_batch_orig.xml
$ diff cime/config/cesm/machines/config_batch.xml cime/config/cesm/machines/config_batch_orig.xml
698,728d697
< <batch_system MACH="hydra" type="pbs" >
< <batch_query args="-f" >qstat</batch_query>
< <batch_submit>qsub </batch_submit>
< <batch_cancel>qdel</batch_cancel>
< <batch_env>-v</batch_env>
< <batch_directive>#PBS</batch_directive>
< <jobid_pattern>^(\S+)$</jobid_pattern>
< <depend_string> -W depend=afterok:jobid</depend_string>
< <depend_allow_string> -W depend=afterany:jobid</depend_allow_string>
< <depend_separator>:</depend_separator>
< <walltime_format>%H:%M:%S</walltime_format>
< <batch_mail_flag>-M</batch_mail_flag>
< <batch_mail_type_flag>-m</batch_mail_type_flag>
< <batch_mail_type>, bea, b, e, a</batch_mail_type>
< <submit_args>
< <arg flag="-q" name="$JOB_QUEUE"/>
< <arg flag="-l walltime=" name="$JOB_WALLCLOCK_TIME"/>
< <arg flag="-A" name="$PROJECT"/>
< </submit_args>
< <directives>
< <directive>-N {{ job_id }}</directive>
< <directive default="n"> -r {{ rerunnable }} </directive>
< <!-- <directive> -j oe {{ job_id }} </directive> -->
< <directive> -j oe </directive>
< <directive> -V </directive>
< </directives>
< <queues>
< <queue walltimemin="" walltimemax="168:00:00" nodemin="0" nodemax="5" default="true">larga</queue>
< </queues>
< </batch_system>
<
Work-flow
configuration of the work-flow is done via the file cime/config/cesm/machines/config_batch.xml
By now is it left as it is.
Case creation
Prior to the compilation, we need to make sure that all the optional additional components have already been compiled (see next section). After that we are going to use cime/scripts/create_newcase to compile and use the model. The model is compiled for each new experiment, since user might activate different components each time and compiling only the required components makes the simulation more efficient.
./create_newcase --case [CaseName] --res [Resolution] --compset [Compset] --mach hydra
Where:
-
[CaseName]: Convention for the name of the experiment is done following this CESM Naming conventions web-page -
[Resolution]: Available resolutions to use from CESM grids (not working). (We can use either:python3 cime/scripts/query_config --grids --full) -
[Compset]: Componets activated -
hydra: HPC to use
$ source /opt/load-libs.sh 1 $ cd cime/scripts/ $ ./create_newcase --case /share/cesm/expriments/b.day1.0 --res f19_g17 --compset B1850 --mach hydra >& run_create_newcase.log
Errors found
One must be aware, that it seems that error messages are not quite informative (by now)
Python error
/usr/bin/env: ‘python’: No such file or directory
Fixed by imposing python3
$ cp create_newcase create_newcase_orig $ diff create_newcase create_newcase_orig 1c1 < #!/usr/bin/env python3 --- > #!/usr/bin/env python
Checking for the correct execution in file run_create_newcase.log and an error message is detected:
xmllint not found,...
Which seems to be related to the absence of the package libxml2-utils
New error:
Compset specific settings: name is RUN_STARTDATE and value is 0001-01-01 ERROR: Command: '/usr/bin/xmllint --xinclude --noout --schema /home/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox/cime/config/xml_schemas/co nfig_machines.xsd /home/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml' failed with error '/hom e/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml:2776: element machine: Schemas validity error : Element 'machine': Missing child element(s). Expected is one of ( mpirun, module_system ). /home/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml fails to validate' from dir '/home/lluis.f ita/CESM/v2.2.2/intel/my_cesm_sandbox/cime/scripts'
machine configuration for hydra was lacking, that it does not have modules, so it was included:
(...)
</mpirun>
<module_system type="none"/>
(...)
Queue-system related error:
Batch_system_type is pbs job is case.run USER_REQUESTED_WALLTIME None USER_REQUESTED_QUEUE None WALLTIME_FORMAT %H:%M:%S WARNING: No queue on this system met the requirements for this job. Falling back to defaults ERROR: No queues found
No queue system was created for hydra. Now it has been added into cime/config/cesm/machines/config_batch.xml
Case setup
Now we are ready to set-up the case.
Going to the folder with the case ($ROOTCASE folder as it is understood)
$ cd /share/cesm/expriments/b.day1.0 $ ./case.setup >& run_case-setup.log
Looking for errors:
$ tail run_case-setup.log You can now run './preview_run' to get more info on how your case will be run
Which provides the following configuration:
$ ./preview_run >& run_preview_run.log
$ cat run_preview_run.log
CASE INFO:
nodes: 6
total tasks: 768
tasks per node: 128
thread count: 1
BATCH INFO:
FOR JOB: case.run
ENV:
Setting Environment OMP_NUM_THREADS=1
SUBMIT CMD:
qsub -q larga -l walltime=168:00:00 -A none -q larga -l walltime=168:00:00 -A none -v ARGS_FOR_SCRIPT='--resubmit' .case.run
MPIRUN (job=case.run):
mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >> cesm.log.$LID 2>&1
FOR JOB: case.st_archive
ENV:
Setting Environment OMP_NUM_THREADS=1
SUBMIT CMD:
qsub -q larga -l walltime=00:20:00 -A none -q larga -l walltime=00:20:00 -A none -W depend=afterok:0 -v ARGS_FOR_SCRIPT='--resubmit' case.st_archive
errors
First error related to python...
$ ./case.setup /usr/bin/env: ‘python’: No such file or directory
Modifying it to use python3
$ cp case.setup case.setup_orig $ diff case.setup case.setup_orig 1c1 < #!/usr/bin/env python3 --- > #!/usr/bin/env python
It happens everywhere, so, either I ask my IT team (as root) to fix it by creating a symlink to python, but based in python3 (see here)
# ln -s /usr/bin/python3 /usr/bin/python
Or I go back to the cime/scripts folder and change it everywhere: create_clone, create_newcase, create_test, query_config, query_testlists
Modify all the python scripts within cime/scripts/Tools
$ cp -R Tools Tools_orig
Scripts being modified: Tools/archive_metadata, Tools/bld_diff, Tools/bless_test_results, Tools/case.build, Tools/case.cmpgen_namelists, Tools/case_diff, Tools/case.qstatus, Tools/case.setup, Tools/case.submit, Tools/check_case, Tools/check_input_data, Tools/check_lockedfiles, Tools/cime_bisect, Tools/code_checker, Tools/compare_namelists, Tools/compare_test_results, Tools/component_compare_baseline, Tools/component_compare_copy, Tools/component_compare_test, Tools/component_generate_baseline, Tools/cs.status, Tools/e3sm_check_env, Tools/generate_cylc_workflow.py, Tools/get_case_env, Tools/get_standard_makefile_args, Tools/getTiming, Tools/jenkins_generic_job, Tools/list_e3sm_tests, Tools/list_e3sm_tests, Tools/mvsource, Tools/normalize_cases, Tools/pelayout, Tools/preview_namelists, Tools/preview_run, Tools/save_provenance, Tools/simple_compare, Tools/testreporter.py, Tools/wait_for_tests, Tools/xmlchange, Tools/xmlquery
Also inside folder Tools/xmlconvertors: Tools/xmlconvertors/config_pes_converter.py, Tools/xmlconvertors/grid_xml_converter.py, Tools/xmlconvertors/convert-grid-v1-to-v2
Case Build
Compiling the code for the case, before we are going to clean it, just in case...
$ ./case.build --clean $ ./case.build >& run_case-build.log
Looking for errors:
$ tail run_case-build.log (...) Building lnd with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/lnd.bldlog.240515-143236 clm built in 0.009455 seconds ERROR: BUILD FAIL: clm.buildlib failed, cat /home/lluis.fita/cesm/scratch/b.day1.0/bld/lnd.bldlog.240515-143236
Looking into:
cat /home/lluis.fita/cesm/scratch/b.day1.0/bld/lnd.bldlog.240515-143236 /usr/bin/env: ‘python’: No such file or directory
Errors
There are errors related to the use of python
(...) ERROR: Command /home/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox/components/pop/bld/build-namelist failed rc=2 out=ERROR in MARBL_diags_to_tavg.py err=/usr/bin/env: ‘python’: No such file or directory ERROR: env CASEROOT=/share/cesm/expriments/b.day1.0 CASEBUILD=/share/cesm/expriments/b.day1.0/Buildconf OCN_GRID=gx1v7OCN_TAVG_TRAC ER_BUDGET=FALSE POPROOT=/home/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox/components/pop /home/lluis.fita/CESM/v2.2.2/intel/my_ces m_sandbox/components/pop/input_templates/ocn.ecosys.tavg.csh 4 .false. .true. failed: 256
Editting various python scripts to make sure of the use of python3: components/pop/MARBL_scripts/add_cocco_to_init.py, components/pop/MARBL_scripts/MARBL_diags_to_tavg.py, cime/src/components/stub_comps_mct/siac/cime_config/buildlib, cime/src/components/stub_comps_mct/siac/cime_config/buildlib_cmake, cime/src/components/stub_comps_mct/siac/cime_config/buildnml
Modifying more python scripts in cime/src/build_scripts: cime/src/build_scripts/buildlib.cprnc, cime/src/build_scripts/buildlib.csm_share, cime/src/build_scripts/buildlib.gptl, cime/src/build_scripts/buildlib.kokkos, cime/src/build_scripts/buildlib.mct, cime/src/build_scripts/buildlib.mpi-serial, cime/src/build_scripts/buildlib.pio
Modifying more python scripts: components/clm/bld/namelist_files/createMkSrfEntry.py, components/clm/run_sys_tests, components/cam/cime_config/buildcpp, components/cam/cime_config/buildnml, components/cam/manage_externals/checkout_externals, components/cdeps/cime_config/buildlib, components/cice/cime_config/buildcpp, components/cice/cime_config/buildlib, components/cice/cime_config/buildlib, components/cice/cime_config/buildnml, components/cism/manage_externals/checkout_externals, components/clm/cime_config/buildlib, components/clm/cime_config/buildnml, components/clm/manage_externals/checkout_externals, components/clm/python/run_ctsm_py_tests, components/mosart/cime_config/buildlib, components/mosart/cime_config/buildnml, components/pop/cime_config/buildcpp, components/pop/cime_config/buildlib, components/pop/cime_config/buildnml, components/rtm/cime_config/buildlibm components/rtm/cime_config/buildnml, components/ww3/cime_config/buildlib, components/ww3/cime_config/buildnml
Case send
Optional additional components
ESM
It is necessary the High Performance Modeling Infrastructure (ESM) in May 2024, the latest version was the 8.6.0 and is the one being installed.
Getting the code in hydra in folder ESM
$ wget https://github.com/esmf-org/esmf/archive/refs/tags/v8.6.0.tar.gz
Compilation is done following these documentation, which the right detailed procedure specific-compilation-instructions.
GNU compilation
Installation location
$ mkdir -p v860/gnu $ cd v860/gnu $ tar xvfz ../v8.6.0.tar.gz $ cd esmf-8.6.0/ $ ls build build_config cmake LICENSE makefile README.md scripts src
Starting by defining the location of the code
$ export ESMF_DIR=$PWD
Running to get local information
$ make info >& run_make_info.log
Launching the makefile in parallel:
$ make -j8 lib >& run_make.log $ tail run_make.log (...) ESMF library built successfully on Mon 13 May 2024 12:58:46 PM -03 To verify, build and run the unit and system tests with: make check or the more extensive: make all_tests
Verifying that installation worked fine
$ make all_tests >& run_make_tests.log $ $ cat run_make_tests.log | grep failed The following unit test files failed to build, failed to execute or crashed during execution: Found 7800 non-exhaustive single processor unit tests, 7744 passed and 56 failed. Found 8 single processor system tests, 8 passed and 0 failed. Found 44 single processor examples, 44 passed and 0 failed. Found 8 single processor system tests, 8 passed and 0 failed. Found 44 single processor examples, 44 passed and 0 failed. Found 7800 non-exhaustive single processor unit tests, 7744 passed and 56 failed.
Installing
$ make install >& run_make_install.log $ tail run_make_install.log (...) ESMF installation complete.
intel compilation
Loading hydra's intel compilation environment
$ source /opt/load-libs.sh 1
Installation location
$ mkdir v860/intel $ cd v860/intel $ tar xvfz ../v8.6.0.tar.gz $ cd esmf-8.6.0/ $ ls build build_config cmake LICENSE makefile README.md scripts src
Porting and validating CIME on a new platform
http://esmci.github.io/cime/versions/master/html/users_guide/porting-cime.html
Downloading the Input data
All input data will be downloaded in
/share/cesm
Input datasets are needed to run the model. CESM input data are available through a separate Subversion input data repository.
- Change check_input_data header so it runs with Python 2.7.x version:
sed -i -e 's!/usr/bin/env python!/share/anaconda2/bin/python!' ./cime/scripts/Tools/check_input_data
