CESMInstall WIKI CESM - hydra
These are the CESM's installation notes in CIMA/IFAECI's HPC called hydra.
Notes and process carried out on 13-17th of May 2024, by Lluís Fita (UBA/CIMA/IFAECI, CABA, Argentina) with the assistance of Ass. Prof. Pedro DiNezio (U. Colorado, Boulder) and Dr Nicolás J. Cosentino (UBA/CIMA/IFAECI, CABA, Argentina), and the non-anonymous help of CESM forum and stackoverflow
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 activatedhydra: 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:
After succesfull compilation, verify the presence of all the required input data with:
$ tail run_case-build.log (...) siac built in 1.117004 seconds sesp built in 1.145180 seconds cam built in 1.169075 seconds Component glc build complete with 2 warnings cism built in 233.087502 seconds Building cesm from /home/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox/cime/src/drivers/mct/cime_config/buildexe with output to /home/lluis. fita/cesm/scratch/b.day1.0/bld/cesm.bldlog.240516-151609 Time spent not building: 6.916887 sec Time spent building: 260.266792 sec MODEL BUILD HAS FINISHED SUCCESSFULLY $ ./check_input_data --download >& run_check_input_data.log (...) Model cpl missing file wav2ocn_smapname = '/share/cesm/inputdata/cpl/gridmaps/ww3a/map_ww3a_TO_gx1v7_splice_170214.nc' Trying to download file: 'cpl/gridmaps/ww3a/map_ww3a_TO_gx1v7_splice_170214.nc' to path '/share/cesm/inputdata/cpl/gridmaps/ww3a/map_ww3a_T O_gx1v7_splice_170214.nc' using WGET protocol. SUCCESS
Errors
There are errors related to the use of python
$ 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
(...) 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
Editing various python scripts to make sure of the use of python3, in order to make this happen, from $ROOTCESM, I executed the following code:
$ head [place]/* | grep -B 2 'env python' | grep -v directory >& py.log $ cat py.log
being [place], incremental position within the folder structure of CESM: ./, *, */*, */*/*, */*/*/*, */*/*/*/*, */*/*/*/*/*, ...
For example
$ head ./* | grep -B 2 'env python' | grep -v directory >& py.log head: error reading './cime': Is a directory head: error reading './cime_config': Is a directory head: error reading './components': Is a directory head: error reading './components_orig': Is a directory head: error reading './doc': Is a directory head: error reading './manage_externals': Is a directory $ cat py.log ==> ./describe_version <== #!/usr/bin/env python3
Or even better:
$ grep -i python [place]/* | grep env | grep -v orig | grep -v python3 >& py.log
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/buildlib, 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/phys_cycle_postrun, components/pop/cime_config/phys_cycle_preruncomponents/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
Also: components/clm/python/ctsm/test/test_sys_lilac_build_ctsm.py, components/clm/python/ctsm/test/test_unit_lilac_build_ctsm.py, components/clm/python/ctsm/test/test_unit_lilac_make_runtime_inputs.py, components/clm/python/ctsm/test/test_unit_machine.py, components/clm/python/ctsm/test/test_unit_path_utils.py, components/clm/python/ctsm/test/test_unit_run_sys_tests.py, components/clm/python/ctsm/test/test_unit_utils.py, components/clm/src/fates/tools/FatesPFTIndexSwapper.py, components/clm/src/fates/tools/modify_fates_paramfile.py, components/clm/src/fates/tools/ncvarsort.py, components/pop/externals/CVMix/bld/cvmix_setup
Another set pf modified files: cime/config/cesm/machines/template.case.test, cime/config/cesm/machines/template.st_archive, cime/config/ufs/machines/template.case.run, vim cime/config/ufs/machines/template.case.test, cime/config/ufs/machines/template.st_archive, cime/scripts/lib/CIME/BuildTools/configure.py, cime/scripts/lib/CIME/case/case_submit.py
There is an error during the building of the CISM component. The output of case.build:
(...) - Building clm library Building lnd with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/lnd.bldlog.240515-155359 Component lnd build complete with 6 warnings clm built in 184.188484 seconds - Building atm Library Building atm with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/atm.bldlog.240515-155359 - Building ice Library Building ice with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/ice.bldlog.240515-155359 - Building ocn Library Building ocn with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/ocn.bldlog.240515-155359 - Building rof Library Building rof with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/rof.bldlog.240515-155359 - Building glc Library Building glc with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/glc.bldlog.240515-155359 - Building wav Library Building wav with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/wav.bldlog.240515-155359 - Building iac Library Building iac with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/iac.bldlog.240515-155359 - Building esp Library Building esp with output to /home/lluis.fita/cesm/scratch/b.day1.0/bld/esp.bldlog.240515-155359 sesp built in 1.537159 seconds siac built in 1.544745 seconds ifort: error #10236: File not found: '/home/lluis.fita/cesm/scratch/b.day1.0/bld/glc/fortran_autogen_srcs/glide_io.F90' ifort: error #10236: File not found: '/home/lluis.fita/cesm/scratch/b.day1.0/bld/glc/fortran_autogen_srcs/glint_io.F90' cism built in 35.435328 seconds mosart built in 42.410334 seconds ww built in 54.594975 seconds Component ice build complete with 1 warnings cice built in 81.223358 seconds Component ocn build complete with 13 warnings pop built in 145.569954 seconds Component atm build complete with 14 warnings cam built in 229.021996 seconds ERROR: BUILD FAIL: cism.buildlib failed, cat /home/lluis.fita/cesm/scratch/b.day1.0/bld/glc.bldlog.240515-155359
These files, that should be automatically created, are not being written:
bld/glc/fortran_autogen_srcs/glide_io.F90 bld/glc/fortran_autogen_srcs/glint_io.F90
In the case directory one has the file Buildconf/cismIOconf/cism.buildIO.csh, with the following content:
(...) # create new _io.F90 file using CISM's python script # --------------------------------------------------------------------------- $PYTHON generate_ncvars.py $file_varsdef ncdf_template.F90.in
It is looking for the environment variable that holds python. In the root directory of CESM the file components/cism/bld/cismIO/README.cismIO:
This directory and its scripts are intended to allow the user to change IO fields from the CISM code. The CISM IO files, *_io.F90, are auto-generated and typically difficult to modify. However, the corresponding variable definition files, *_vars.def, are easily modified and the IO files can be re-generated by running the cism.buildIO.csh script contained in this directory. Usage of this script requires that the user has defined an enviroment variable PYTHON pointing to a local version of python, After that, the user simply runs the enclosed cism.buildIO.csh script, which runs a python script on each (...)
Therefore I need to find where the PYTHON is defined within the cime/config/cesm/machines/config_*.xml files, or I defined it manually. It does not work it is defined previously the execution:
$ export PYTHON=/usr/bin/python3 $ echo $PYTHON /usr/bin/python3 $ ./case.build --clean $ ./case.build
Therefore, it is defined within Buildconf/cismIOconf/cism.buildIO.csh (must be defined in the template of this shell script!!). Looking in $ROOTCESM into components/cism/source_cism/utils/build/generate_ncvars.py, it is using python2! hydra does not support python2.
#!/usr/bin/env python2
Code is being modified by
#!/usr/bin/env python3
Then 2 other files need to be modified also: components/cism/source_cism/utils/build/autogenerate-in-build-dir, components/cism/source_cism/utils/build/autogen-for-glint-and-glad-in-build-dir, whenever they call python is replaced by python3
$ cat components/cism/source_cism/utils/build/autogenerate-in-build-dir | grep python # Call python script with source file arguments python3 -V python3 $CISM_SOURCE_DIR/utils/build/generate_ncvars.py $GLIDE_VARS_PATH $NCDF_TEMPL_PATH $ cat components/cism/source_cism/utils/build/autogen-for-glint-and-glad-in-build-dir | grep python # Call python script with source file arguments python3 -V python3 $CISM_SOURCE_DIR/utils/build/generate_ncvars.py $GLINT_VARS_PATH $NCDF_TEMPL_PATH python3 $CISM_SOURCE_DIR/utils/build/generate_ncvars.py $GLINT_MBAL_PATH $NCDF_TEMPL_PATH python3 $CISM_SOURCE_DIR/utils/build/generate_ncvars.py $GLAD_VARS_PATH $NCDF_TEMPL_PATH python3 $CISM_SOURCE_DIR/utils/build/generate_ncvars.py $GLAD_MBAL_PATH $NCDF_TEMPL_PATH
Case send
Submitting the case:
$ ./case.submit >& run_case-submit.log
Checking that it is running
$ qstat -u $USER
hydra:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
----------------------- ----------- -------- ---------------- ------ ----- ------ --------- --------- - ---------
43629.hydra lluis.fita larga run.b.day1.0 721 1 1 -- 168:00:00 R 00:00:51
43630.hydra lluis.fita larga st_archive.b.day -- 1 1 -- 00:20:00 H --
Errors
mpirun not found
Submission error as:
$ cat run.b.day1.0.o43627 (...) run command is mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >> cesm.log.$LID 2>&1 ERROR: RUN FAIL: Command 'mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >> cesm.log.$LID 2>&1 ' failed See log file for details: /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43627.hydra.240516-165514 $ cat /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43627.hydra.240516-165514 /bin/sh: 1: mpirun: not found
Redifined mpirun in cime/config/cesm/machines/config_machines.xml as:
<executable>/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun</executable>
If it is too late (prior to submit), it can be directly changed in the case directory in file env_mach_specific.xml
hydra's compilation environment
Simulation finished too early ...
$ qstat -u $USER
hydra:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
----------------------- ----------- -------- ---------------- ------ ----- ------ --------- --------- - ---------
43629.hydra lluis.fita larga run.b.day1.0 721 1 1 -- 168:00:00 C --
43630.hydra lluis.fita larga st_archive.b.day -- 1 1 -- 00:20:00 C --
Looking in the logs:
$ cat run.b.day1.0.o43629 Generating namelists for /share/cesm/expriments/b.day1.0 Creating component namelists (...) ------------------------------------------------------------------------- run command is /opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >> cesm.log.$LID 2>&1 tm_poll: got event 1 return 0 tm_poll: INIT nodes 1 tm_poll: INIT daddy jobid 43629.hydra tm_poll: INIT daddy node 0 tm_poll: INIT daddy tid 1 new_task: jobid=43629.hydra node=0 task=1 new_task: jobid=43629.hydra node=0 task=2 ERROR: RUN FAIL: Command '/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/ces m.exe >> cesm.log.$LID 2>&1 ' failed See log file for details: /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43629.hydra.240516-170533 $ cat /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43629.hydra.240516-170533 (...) Invalid character . in PBS_JOBID tm_poll: got event 1 return 0 tm_poll: INIT nodes 1 tm_poll: INIT daddy jobid 43629.hydra tm_poll: INIT daddy node -1 tm_poll: INIT daddy tid 0 new_task: jobid=43629.hydra node=-1 task=0 new_task: called with TM_ERROR_NODE new_task: jobid=43629.hydra node=0 task=1 =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 1006 RUNNING AT node43 = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== tm_poll: got event 2 return 0 new_task: jobid=43629.hydra node=0 task=2 tm_poll: got event 3 return 0 YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions
And also:
$ cat CaseStatus
2024-05-16 11:52:51: case.setup starting
---------------------------------------------------
2024-05-16 11:52:52: case.setup success
---------------------------------------------------
2024-05-16 11:55:32: case.build starting
---------------------------------------------------
2024-05-16 12:04:41: case.build error
ERROR: BUILD FAIL: cism.buildlib failed, cat /home/lluis.fita/cesm/scratch/b.day1.0/bld/glc.bldlog.240516-115532
---------------------------------------------------
2024-05-16 15:12:59: case.build starting
---------------------------------------------------
2024-05-16 15:13:16: case.build error
ERROR: BUILD FAIL: cism.buildlib failed, cat /home/lluis.fita/cesm/scratch/b.day1.0/bld/glc.bldlog.240516-151259
---------------------------------------------------
2024-05-16 15:16:09: case.build starting
---------------------------------------------------
CESM version is release-cesm2.2.2
Processing externals description file : Externals.cfg (/home/lluis.fita/CESM/v2.2.2/intel/my_cesm_sandbox)
(...)
Checking local status of required & optional components: cam, chem_proc, carma, cosp2, clubb, silhs, pumas, atmos_phys,
atmos_cubed_sphere, cice, cdeps, fox, cime, cmeps, cism, source_cism, clm, fates, fms, mom, mosart, pop, cvmix, marbl,
rtm, ww3,
M ./cime
modified sandbox, on cime5.8.32.9
e-o ./cime/src/drivers/nuopc/
-, not checked out -->
M ./components/cam
modified sandbox, on cam_cesm2_2_rel_09
./components/cam/chem_proc
clean sandbox, on tools/proc_atm/chem_proc/release_tags/chem_proc5_0_04
./components/cam/src/atmos_phys
clean sandbox, on version0_00_007
./components/cam/src/dynamics/fv3/atmos_cubed_sphere
clean sandbox, on fv3_cesm.04
./components/cam/src/physics/carma/base
clean sandbox, on carma/release_tags/carma3_49_rel
./components/cam/src/physics/clubb
clean sandbox, on clubb_release_b76a124_20200220_c20200320
./components/cam/src/physics/cosp2/src
clean sandbox, on v2.1.4cesm
./components/cam/src/physics/pumas
clean sandbox, on pumas_cam-release_v1.3
./components/cam/src/physics/silhs
clean sandbox, on silhs_clubb_release_b76a124_20200220_c20200320
M ./components/cdeps
modified sandbox, on d808b7c6f78a2d5dcfeb1da0d1a452a9b66e08c8
./components/cdeps/fox
clean sandbox, on 7b9488446b193192dd3f0378541e71099cb4e8a8
M ./components/cice
modified sandbox, on cice5-cesm2.2.2-20231220
M ./components/cism
modified sandbox, on cism2_1_69_b
M ./components/cism/source_cism
modified sandbox, on release-cesm2.2.2-f1a88d6derecho
M ./components/clm
modified sandbox, on release-cesm2.2.04
M ./components/clm/src/fates
modified sandbox, on sci.1.30.0_api.8.0.0
e-o ./components/mom
-, not checked out --> mi_20200908
M ./components/mosart
modified sandbox, on mosart1_0_37_1
M ./components/pop
modified sandbox, on pop2_cesm2_2_rel_n01
M ./components/pop/externals/CVMix
modified sandbox, on v0.98-beta
./components/pop/externals/MARBL
clean sandbox, on cesm2.2-n00
M ./components/rtm
modified sandbox, on rtm1_0_72
M ./components/ww3
modified sandbox, on ww3_200710
e-o ./libraries/FMS
-, not checked out --> fi_20200609_cesm2.2_231205
2024-05-16 15:20:36: case.build success
---------------------------------------------------
2024-05-16 16:55:05: case.submit starting
---------------------------------------------------
2024-05-16 16:55:12: case.submit error
ERROR: Command: 'qsub -q larga -l walltime=00:20:00 -A none -q larga -l walltime=00:20:00 -A none -W depend=afterok:43
627.hydra -v ARGS_FOR_SCRIPT='--resubmit' case.st_archive' failed with error 'qsub: submit error (Invalid request)' fro
m dir '/share/cesm/expriments/b.day1.0'
---------------------------------------------------
2024-05-16 16:55:14: case.run starting
---------------------------------------------------
2024-05-16 16:55:41: model execution starting
---------------------------------------------------
2024-05-16 16:55:41: model execution error
ERROR: Command: 'mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >> cesm.log.$LID 2>&1 ' failed
with error '' from dir '/home/lluis.fita/cesm/scratch/b.day1.0/run'
---------------------------------------------------
2024-05-16 16:55:41: case.run error
ERROR: RUN FAIL: Command 'mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe >> cesm.log.$LID 2>&1
' failed
See log file for details: /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43627.hydra.240516-165514
---------------------------------------------------
2024-05-16 17:05:25: case.submit starting
---------------------------------------------------
2024-05-16 17:05:33: case.submit error
ERROR: Command: 'qsub -q larga -l walltime=00:20:00 -A none -q larga -l walltime=00:20:00 -A none -W depend=afterok:43
629.hydra -v ARGS_FOR_SCRIPT='--resubmit' case.st_archive' failed with error 'qsub: submit error (Invalid request)' fro
m dir '/share/cesm/expriments/b.day1.0'
---------------------------------------------------
2024-05-16 17:05:33: case.run starting
---------------------------------------------------
2024-05-16 17:05:43: model execution starting
---------------------------------------------------
2024-05-16 17:06:34: model execution error
ERROR: Command: '/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.day1.0/bld/
cesm.exe >> cesm.log.$LID 2>&1 ' failed with error '' from dir '/home/lluis.fita/cesm/scratch/b.day1.0/run'
---------------------------------------------------
2024-05-16 17:06:34: case.run error
ERROR: RUN FAIL: Command '/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin/mpirun -np 768 /home/lluis.fita/cesm/scratch/b.da
y1.0/bld/cesm.exe >> cesm.log.$LID 2>&1 ' failed
See log file for details: /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43629.hydra.240516-170533
---------------------------------------------------
I suspect that it is related to the compilation environment. hydra does not have module. It set-ups compilation environment via shell scriupt /opt/load-libs.sh. There must be a way to systematically introduce it in the config_batch.xml in order to be executed in all the PBS jobs. A new post is created in the CESM forum #post-55530
From another attempt
$ cat /home/lluis.fita/cesm/scratch/b.day1.0/run/cesm.log.43633.hydra.240517-155125 | more /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading shared libraries: libnetcdf.so.19: cannot open shared object file: No suc h file or directory /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading shared libraries: libnetcdf.so.19: cannot open shared object file: No suc h file or directory /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading shared libraries: libnetcdf.so.19: cannot open shared object file: No suc h file or directory /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading shared libraries: libnetcdf.so.19: cannot open shared object file: No suc h file or directory /home/lluis.fita/cesm/scratch/b.day1.0/bld/cesm.exe: error while loading shared libraries: libnetcdf.so.19: cannot open shared object file: No suc h file or directory (...)
Is set to use the variable prerun_script into the file in the case directory env_run.xml, see more details (searching for it here)
Trying different options:
<entry id="PRERUN_SCRIPT">
<type>char</type>
<desc>External script to be run before model completion</desc>
<values>
<value>source /opt/load-libs.sh 1</value>
</values>
$ ./case.submit
$ cat run.b.day1.0.o43637
ERROR: External script source /opt/load-libs.sh 1 not found
Looking inside /opt/load-libs.sh
<entry id="PRERUN_SCRIPT">
<type>char</type>
<desc>External script to be run before model completion</desc>
<values>
<value>/opt/env_scripts/load_intel-2021.4.0_mpich-3.4.2.sh</value>
</values>
$ ./case.submit
$ cat run.b.day1.0.o43639
Running /opt/env_scripts/load_intel-2021.4.0_mpich-3.4.2.sh
/bin/sh: 1: Syntax error: Bad fd number
<entry id="PRERUN_SCRIPT">
<type>char</type>
<desc>External script to be run before model completion</desc>
<values>
<value>'source /opt/load-libs.sh 1'</value>
</values>
$ ./case.submit
$ cat run.b.day1.0.o43641
ERROR: External script 'source /opt/load-libs.sh 1' not found
Creation of a simple shell script with the required content in /home/lluis.fita/intel_env.csh
#!/bin/sh export PATH="/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin:$PATH" export PATH="/opt/netcdf/netcdf-4/intel/2021.4.0/bin:$PATH" export PATH="/opt/hdf5/hdf5-1.10.5/intel/2021.4.0/bin:$PATH" export PATH="/opt/jasper/jasper-version-2.0.33/intel/2021.4.0/bin:$PATH" export LD_LIBRARY_PATH=/opt/jasper/jasper-version-2.0.33/intel/2021.4.0/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/opt/zlib/zlib-1.2.11/intel/2021.4.0/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/opt/hdf5/hdf5-1.10.5/intel/2021.4.0/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/opt/netcdf/netcdf-4/intel/2021.4.0/lib:$LD_LIBRARY_PATH
And then
<entry id="PRERUN_SCRIPT">
<type>char</type>
<desc>External script to be run before model completion</desc>
<values>
<value>/home/lluis/intel_env.sh</value>
</values>
$ ./case.submit
$ cat run.b.day1.0.o43647
Running /home/lluis.fita/intel_env.csh
/bin/sh: 1: Syntax error: Bad fd number
whereas the execution of the shell from terminal does not give any error
$ /bin/sh /home/lluis.fita/intel_env.csh
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