commit d1f5c5656c7595c7784fe293e3a099e557a7f823
Author: baol <j2eer@163.com>
Date:   Tue Jun 4 14:20:20 2024 +0800

    first commit

diff --git a/.gitignore b/.gitignore
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index 0000000..e69de29
diff --git a/Dockerfile b/Dockerfile
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+++ b/Dockerfile
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+FROM ubuntu:22.04
+
+## CLM5.0
+MAINTAINER "SHUD"
+
+WORKDIR /model
+ENV DEBIAN_FRONTEND=noninteractive
+
+ENV VERSION_CODENAME=jammy
+
+
+RUN rm /etc/apt/sources.list \
+ && echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME} main restricted universe multiverse" >> /etc/apt/sources.list \
+ && echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME}-updates main restricted universe multiverse" >> /etc/apt/sources.list \
+ && echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME}-backports main restricted universe multiverse" >> /etc/apt/sources.list \
+ && echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME}-security main restricted universe multiverse" >> /etc/apt/sources.list \
+ && echo 'Acquire::https { Verify-Peer "false"; Verify-Host "false"; }' >> /etc/apt/apt.conf.d/tuna.conf
+
+# && echo "deb https://cloud.r-project.org/bin/linux/ubuntu cosmic-cran35/" >> /etc/apt/sources.list
+
+RUN apt-get update \
+ && apt install -y --no-install-recommends --assume-yes \
+    ca-certificates \
+    dejagnu \
+    sudo libtool \
+    vim git subversion gfortran cmake \
+    libxml2-utils libxml-libxml-perl \
+    python \
+    make m4 \
+    libcurl4-openssl-dev liblapack-dev libblas-dev mpich libmpich-dev \
+    gnupg wget curl \
+ && apt-get clean
+
+ADD pkgs/*.gz /usr/local/src/
+
+ARG ZDIR=/usr/local/zlib
+RUN cd /usr/local/src/zlib-1.2.11 \
+ && CC=mpicc ./configure --prefix=${ZDIR} \
+ && make \
+ # && make check \
+ && make install \
+ && rm -rf /usr/local/src/zlib-1.2.11
+
+ENV CC=mpicc \
+    CXX=mpicxx \
+    FC=mpif90 \
+    F77=mpif90
+
+ARG PNDIR=/usr/local/pnetcdf
+RUN cd /usr/local/src/pnetcdf-1.11.0 \
+ && FC=mpif90 MPICC=mpicc CFLAGS="-fPIC -g -O2" \
+    ./configure --prefix=${PNDIR} --enable-shared --enable-profiling\
+ && make \
+ # && make tests \
+ # && make check \
+ # && make ptests \
+ && make install \
+ && rm -rf /usr/local/src/pnetcdf-1.11.0
+
+# Parallel OpenMPI-HDF5-NetCDF stack
+# https://gist.github.com/milancurcic/3a6c1a97a99d291f88cc61dae6621bdf
+ARG H5DIR=/usr/local/hdf5
+RUN cd /usr/local/src/hdf5-1.10.4 \
+ && CC=mpicc FC=mpif90 CFLAGS="-fPIC -w" ./configure --prefix=${H5DIR} \
+ --with-zlib=${ZDIR} --enable-parallel --enable-hl \
+ && make \
+ # && make check \
+ && make install \
+ && rm -rf /usr/local/src/hdf5-1.10.4
+#--enable-shared --enable-fortran
+
+ARG NCDIR=/usr/local/netcdf4
+RUN cd /usr/local/src/netcdf-c-4.6.2 \
+ && CC=mpicc CPPFLAGS="-I${PNDIR}/include -I${H5DIR}/include -I${ZDIR}/include" \
+    LDFLAGS="-L${PNDIR}/lib -L${H5DIR}/lib -L${ZDIR}/lib" \
+    ./configure --prefix=${NCDIR} --enable-parallel-tests \
+ && make \
+ # && make check \
+ && make install \
+ && rm -rf /usr/local/src/netcdf-c-4.6.2
+
+ARG NFDIR=/usr/local/netcdff4
+RUN cd /usr/local/src/netcdf-fortran-4.4.5 \
+ && CPPFLAGS=-I${NCDIR}/include LDFLAGS=-L${NCDIR}/lib \
+    ./configure --prefix=${NFDIR} \
+ && make \
+ # && make check \
+ && make install \
+ && rm -rf /usr/local/src/netcdf-fortran-4.4.5
+
+RUN echo ${NCDIR}/lib > /etc/ld.so.conf.d/netcdf.conf \
+ && echo ${NFDIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
+ && echo ${ZDIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
+ && echo ${H5DIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
+ && echo ${PNDIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
+ && ldconfig
+
+ENV USER=clm
+RUN useradd -m -G adm,sudo -s /bin/bash $USER \
+ && echo "root:root" | chpasswd \
+ && echo "clm:clm" | chpasswd \
+ && apt-get remove wget -y
+
+RUN git clone -b release-clm5.0 https://github.com/ESCOMP/ctsm \
+ && cd ctsm && ./manage_externals/checkout_externals \
+ && chown -R clm:clm /model/ctsm \
+ && cd ..
+
+VOLUME ["/inputdata"]
+ENV PATH="/model/ctsm/cime/scripts:${NCDIR}/bin:${PATH}" \
+    LANG=C.UTF-8
+
+COPY config/*.xml /home/${USER}/.cime/
+COPY config /home/${USER}/cesm/config
+COPY run_CLM50_example01.sh /home/${USER}/cesm/
+
+WORKDIR /home/${USER}/cesm
+
+RUN chown -R clm:clm /home /home/${USER} /home/${USER}/.cime /inputdata
+ # && chmod 755 -R /inputdata /home/${USER}/.cime /home/${USER} \
+
+USER ${USER}
+CMD bash
diff --git a/README.md b/README.md
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+++ b/README.md
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+## container for CLM5.0(Community Land Surface Model)
+
+### Usage
+
+```bash
+docker run -it --rm -v /data/cesm/inputdata:/inputdata -v ${PWD}:/home/clm/cesm -e USERID=$UID . bash
+```
+
+* Document of CLM5.0:
+https://escomp.github.io/ctsm-docs/
+https://github.com/ESCOMP/ctsm.
diff --git a/bin/findpkg b/bin/findpkg
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+++ b/bin/findpkg
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+#!/bin/bash
+# Dongdong Kong
+# Find install related packages
+
+for pkg in "$@"
+do
+    echo "====================================================================="
+    echo $pkg
+    echo "====================================================================="
+    # dpkg --listfiles $pkg
+    dpkg --list | grep $pkg
+done
diff --git a/bin/pkginfo b/bin/pkginfo
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--- /dev/null
+++ b/bin/pkginfo
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+#!/bin/bash
+# Dongdong Kong
+# Show package detailed info
+
+for pkg in "$@"
+do
+    echo "====================================================================="
+    echo $pkg
+    echo "====================================================================="
+    dpkg --listfiles $pkg
+done
diff --git a/config/config_compilers.xml b/config/config_compilers.xml
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+++ b/config/config_compilers.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<config_compilers version="2.0">
+    <!--
+========================================================================
+This file defines compiler flags for building CESM.  General flags are listed first
+followed by flags specific to particular operating systems, followed by particular machines.
+
+More general flags are replaced by more specific flags.
+
+Attributes indicate that an if clause should be added to the Macros so that these flags are added
+only under the conditions described by the attribute(s).
+
+The env_mach_specific file may set environment variables or load modules which set environment variables
+which are then  used in the Makefile.   For example the NETCDF_PATH on many machines is set by a module.
+
+========================================================================
+Serial/MPI compiler specification
+========================================================================
+
+SCC   and  SFC specifies the serial compiler
+MPICC and  MPICC specifies the mpi compiler
+
+if $MPILIB is set to mpi-serial then
+CC = $SCC
+FC = $SFC
+MPICC = $SCC
+MPIFC = $SFC
+INC_MPI = $(CIMEROOT)/src/externals/mct/mpi-serial
+
+========================================================================
+Options for including C++ code in the build
+========================================================================
+
+SUPPORTS_CXX (TRUE/FALSE): Whether we have defined all the necessary
+settings for including C++ code in the build for this compiler (or
+this compiler/machine combination). See below for a description of the
+necessary settings.
+
+The following are required for a compiler to support the inclusion of
+C++ code:
+
+SCXX: serial C++ compiler
+
+MPICXX: mpi C++ compiler
+
+CXX_LINKER (CXX/FORTRAN): When C++ code is included in the build, do
+we use a C++ or Fortran linker?
+
+In addition, some compilers require additional libraries or link-time
+flags, specified via CXX_LIBS or CXX_LDFLAGS, as in the following
+examples:
+
+<CXX_LIBS> -L/path/to/directory -lfoo </CXX_LIBS>
+
+or
+
+<CXX_LDFLAGS> -cxxlib </CXX_LDFLAGS>
+
+Note that these libraries or LDFLAGS will be added on the link line,
+regardless of whether we are using a C++ or Fortran linker. For
+example, if CXX_LINKER=CXX, then the above CXX_LIBS line should
+specify extra libraries needed when linking C++ and fortran code using
+a C++ linker. If CXX_LINKER=FORTRAN, then the above CXX_LDFLAGS line
+should specify extra LDFLAGS needed when linking C++ and fortran code
+using a fortran linker.
+-->
+    <!-- Define default values that can be overridden by specific
+     compilers -->
+    <compiler COMPILER="gnu" MACH="shudmach">
+        <CFLAGS>
+            <base> -std=gnu99 </base>
+            <append compile_threaded="true"> -fopenmp </append>
+            <append DEBUG="TRUE"> -g -Wall -Og -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds </append>
+            <append DEBUG="FALSE"> -O </append>
+        </CFLAGS>
+        <CPPDEFS>
+            <!-- http://gcc.gnu.org/onlinedocs/gfortran/ -->
+            <append> -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU</append>
+        </CPPDEFS>
+        <CXX_LINKER>FORTRAN</CXX_LINKER>
+        <FC_AUTO_R8>
+            <base> -fdefault-real-8 </base>
+        </FC_AUTO_R8>
+        <FFLAGS>
+            <!-- -ffree-line-length-none and -ffixed-line-length-none need to be in FFLAGS rather than in FIXEDFLAGS/FREEFLAGS
+       so that these are passed to cmake builds (cmake builds don't use FIXEDFLAGS and FREEFLAGS). -->
+            <base> -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none </base>
+            <append compile_threaded="true"> -fopenmp </append>
+            <!-- Ideally, we would also have 'invalid' in the ffpe-trap list. But at
+         least with some versions of gfortran (confirmed with 5.4.0, 6.3.0 and
+         7.1.0), gfortran's isnan (which is called in cime via the
+         CPRGNU-specific shr_infnan_isnan) causes a floating point exception
+         when called on a signaling NaN. -->
+            <append DEBUG="TRUE"> -g -Wall -Og -fbacktrace -ffpe-trap=zero,overflow -fcheck=bounds </append>
+            <append DEBUG="FALSE"> -O </append>
+        </FFLAGS>
+        <FFLAGS_NOOPT>
+            <base> -O0 </base>
+        </FFLAGS_NOOPT>
+        <FIXEDFLAGS>
+            <base> -ffixed-form </base>
+        </FIXEDFLAGS>
+        <FREEFLAGS>
+            <base> -ffree-form </base>
+        </FREEFLAGS>
+        <HAS_F2008_CONTIGUOUS>FALSE</HAS_F2008_CONTIGUOUS>
+        <!-- <LDFLAGS>
+    <append compile_threaded="true"> -fopenmp </append>
+  </LDFLAGS> -->
+        <MPICC> mpicc </MPICC>
+        <MPICXX> mpicxx </MPICXX>
+        <MPIFC> mpif90 </MPIFC>
+        <SCC> gcc </SCC>
+        <SCXX> g++ </SCXX>
+        <SFC> gfortran </SFC>
+        <!-- <NETCDF_PATH>/opt/netcdf</NETCDF_PATH> -->
+        <!-- <PNETCDF_PATH>/opt/pnetcdf</PNETCDF_PATH> -->
+        <SLIBS>
+            <append>-L/usr/local/netcdf4/lib -L/usr/local/netcdff4/lib -lnetcdff -lnetcdf</append>
+            <append>-llapack -lblas</append>
+        </SLIBS>
+        <!-- <SLIBS>
+    <append> -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="mpich">     -mkl=cluster -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="mpich2">    -mkl=cluster -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="mvapich">   -mkl=cluster -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="mvapich2">  -mkl=cluster -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="mpt">       -mkl=cluster -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="openmpi">   -mkl=cluster -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="impi">      -mkl=cluster -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+    <append MPILIB="mpi-serial">-mkl -L/usr/lib/x86_64-linux-gnu -lnetcdff -lnetcdf </append>
+  </SLIBS> -->
+        <SUPPORTS_CXX>TRUE</SUPPORTS_CXX>
+    </compiler>
+</config_compilers>
diff --git a/config/config_machines.xml b/config/config_machines.xml
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+++ b/config/config_machines.xml
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+<?xml version="1.0"?>
+<config_machines version="2.0">
+    <machine MACH="shudmach">
+        <DESC>
+            Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
+            using modules from http://www.admin-magazine.com/HPC/Articles/Environment-
+            Modules
+        </DESC>
+        <NODENAME_REGEX>.*</NODENAME_REGEX>
+        <OS>LINUX</OS>
+        <!--<PROXY> http://172.17.0.1:1081 </PROXY>-->
+        <COMPILERS>gnu</COMPILERS>
+        <MPILIBS>mpich</MPILIBS>
+        <PROJECT>none</PROJECT>
+        <SAVE_TIMING_DIR>$ENV{HOME}/cesm</SAVE_TIMING_DIR>
+        <CIME_OUTPUT_ROOT>$ENV{HOME}/cesm</CIME_OUTPUT_ROOT>
+        <DIN_LOC_ROOT>/inputdata</DIN_LOC_ROOT>
+        <DIN_LOC_ROOT_CLMFORC>/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
+        <DOUT_S_ROOT>$ENV{HOME}/cesm/$CASE/archive</DOUT_S_ROOT>
+        <BASELINE_ROOT>$ENV{HOME}/cesm/cesm_baselines</BASELINE_ROOT>
+        <CCSM_CPRNC>$ENV{HOME}/cesm/cprnc</CCSM_CPRNC>
+        <GMAKE>make</GMAKE>
+        <GMAKE_J>2</GMAKE_J>
+        <BATCH_SYSTEM>none</BATCH_SYSTEM>
+        <SUPPORTED_BY>admin@shud.xyz</SUPPORTED_BY>
+        <MAX_TASKS_PER_NODE>2</MAX_TASKS_PER_NODE>
+        <MAX_MPITASKS_PER_NODE>2</MAX_MPITASKS_PER_NODE>
+        <PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
+        <mpirun mpilib="mpich">
+            <executable>mpirun</executable>
+            <arguments>
+                <arg name="ntasks"> -np {{ total_tasks }} </arg>
+            </arguments>
+        </mpirun>
+        <module_system type="none" />
+        <environment_variables>
+            <!-- <env name="HOME">/mnt/d/Github/model</env> -->
+            <!-- <env name="OMP_STACKSIZE">256M</env> -->
+            <env name="NETCDF_C_PATH">/usr/local/netcdf4</env>
+            <env name="NETCDF_FORTRAN_PATH">/usr/local/netcdff4</env>
+            <!-- <env name="NetCDF_Fortran_LIBRARY">$ENV{NETCDF_PATH}/lib</env> -->
+            <env name="PNETCDF_PATH">/usr/local/pnetcdf</env>
+            <!-- <env name="PnetCDF_Fortran_LIBRARY">/usr/local/pnetcdf/lib</env> -->
+            <!-- <env name="NetCDF_C_LIBRARY">$ENV{NETCDF_PATH}/lib</env>
+            <env name="NetCDF_C_INCLUDE_DIR">$ENV{NETCDF_PATH}/include</env>
+            <env name="NetCDF_Fortran_INCLUDE_DIR">$ENV{NETCDF_PATH}/include</env> -->
+        </environment_variables>
+        <resource_limits>
+            <resource name="RLIMIT_STACK">-1</resource>
+        </resource_limits>
+    </machine>
+    <!-- <default_run_suffix>
+        <default_run_exe>${EXEROOT}/cesm.exe </default_run_exe>
+        <default_run_misc_suffix> >> cesm.log.$LID 2>&amp;1
+        </default_run_misc_suffix>
+    </default_run_suffix> -->
+</config_machines>
diff --git a/pkgs/hdf5-1.10.4.tar.gz b/pkgs/hdf5-1.10.4.tar.gz
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diff --git a/pkgs/pio2_3_1.tar.gz b/pkgs/pio2_3_1.tar.gz
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diff --git a/pkgs/zlib-1.2.11.tar.gz b/pkgs/zlib-1.2.11.tar.gz
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diff --git a/run_CLM50_example01.sh b/run_CLM50_example01.sh
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+++ b/run_CLM50_example01.sh
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+# /bin/bash
+
+## initial project
+# git clone https://github.com/ESCOMP/cesm
+# git clone https://github.com/ESCOMP/ctsm
+casename=year2019 # test
+
+dir_cime=/model/ctsm/cime
+
+
+## 1. create_newcase
+${dir_cime}/scripts/create_newcase --case $casename --res f19_g16 --compset I1850Clm50Bgc --run-unsupported  \
+    --compiler gnu --mach shudmach
+
+cd $casename # year2019
+
+# # setup YR_START and YR_END
+# ./xmlchange DATM_CLMNCEP_YR_START=2000,DATM_CLMNCEP_YR_END=2000
+# ./xmlchange NTASKS=2
+
+## CLM5 configure
+# ROOT_INPUT=/inputdata # ${HOME}/cesm
+# ROOT_CLMFORC=${ROOT_INPUT}/atm/datm7 # lmwg #
+
+./xmlquery DATM_CLMNCEP_YR_START,DATM_CLMNCEP_YR_END
+./xmlchange DATM_CLMNCEP_YR_START=2010,DATM_CLMNCEP_YR_END=2010
+./xmlquery NTASKS
+./xmlchange NTASKS=2 #[核心数]
+./xmlquery DIN_LOC_ROOT,DIN_LOC_ROOT_CLMFORC
+./xmlchange DIN_LOC_ROOT=${ROOT_INPUT},DIN_LOC_ROOT_CLMFORC=${ROOT_CLMFORC}
+
+./xmlquery STOP_N
+./xmlquery STOP_OPTION
+
+./xmlchange STOP_N=14,STOP_OPTION=ndays
+
+## build and submit task
+./case.setup
+./case.build
+./case.submit