CESMInstall WIKI CESM - hydra

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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 

$ 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
320,325c320,325
<   <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>
---
>   <MPICC> mpicc  </MPICC>
>   <MPICXX> mpicxx </MPICXX>
>   <MPIFC> mpif90 </MPIFC>
>   <SCC> icc </SCC>
>   <SCXX> icpc </SCXX>
>   <SFC> ifort </SFC>

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

By now, is it left as it is.

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.


Compilation

Prior to the compilation, we need to make sure that all the optional additional components have already been compiled (see next section). After that


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
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