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Dockerfile
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FROM ubuntu:22.04
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## CLM5.0
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MAINTAINER "SHUD"
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WORKDIR /model
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ENV DEBIAN_FRONTEND=noninteractive
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ENV VERSION_CODENAME=jammy
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RUN rm /etc/apt/sources.list \
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&& echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME} main restricted universe multiverse" >> /etc/apt/sources.list \
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&& echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME}-updates main restricted universe multiverse" >> /etc/apt/sources.list \
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&& echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME}-backports main restricted universe multiverse" >> /etc/apt/sources.list \
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&& echo "deb [trusted=yes] https://mirrors.tuna.tsinghua.edu.cn/ubuntu/ ${VERSION_CODENAME}-security main restricted universe multiverse" >> /etc/apt/sources.list \
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&& echo 'Acquire::https { Verify-Peer "false"; Verify-Host "false"; }' >> /etc/apt/apt.conf.d/tuna.conf
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# && echo "deb https://cloud.r-project.org/bin/linux/ubuntu cosmic-cran35/" >> /etc/apt/sources.list
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RUN apt-get update \
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&& apt install -y --no-install-recommends --assume-yes \
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ca-certificates \
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dejagnu \
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sudo libtool \
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vim git subversion gfortran cmake \
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libxml2-utils libxml-libxml-perl \
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python \
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make m4 \
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libcurl4-openssl-dev liblapack-dev libblas-dev mpich libmpich-dev \
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gnupg wget curl \
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&& apt-get clean
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ADD pkgs/*.gz /usr/local/src/
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ARG ZDIR=/usr/local/zlib
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RUN cd /usr/local/src/zlib-1.2.11 \
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&& CC=mpicc ./configure --prefix=${ZDIR} \
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&& make \
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# && make check \
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&& make install \
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&& rm -rf /usr/local/src/zlib-1.2.11
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ENV CC=mpicc \
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CXX=mpicxx \
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FC=mpif90 \
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F77=mpif90
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ARG PNDIR=/usr/local/pnetcdf
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RUN cd /usr/local/src/pnetcdf-1.11.0 \
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&& FC=mpif90 MPICC=mpicc CFLAGS="-fPIC -g -O2" \
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./configure --prefix=${PNDIR} --enable-shared --enable-profiling\
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&& make \
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# && make tests \
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# && make check \
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# && make ptests \
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&& make install \
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&& rm -rf /usr/local/src/pnetcdf-1.11.0
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# Parallel OpenMPI-HDF5-NetCDF stack
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# https://gist.github.com/milancurcic/3a6c1a97a99d291f88cc61dae6621bdf
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ARG H5DIR=/usr/local/hdf5
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RUN cd /usr/local/src/hdf5-1.10.4 \
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&& CC=mpicc FC=mpif90 CFLAGS="-fPIC -w" ./configure --prefix=${H5DIR} \
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--with-zlib=${ZDIR} --enable-parallel --enable-hl \
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&& make \
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# && make check \
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&& make install \
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&& rm -rf /usr/local/src/hdf5-1.10.4
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#--enable-shared --enable-fortran
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ARG NCDIR=/usr/local/netcdf4
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RUN cd /usr/local/src/netcdf-c-4.6.2 \
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&& CC=mpicc CPPFLAGS="-I${PNDIR}/include -I${H5DIR}/include -I${ZDIR}/include" \
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LDFLAGS="-L${PNDIR}/lib -L${H5DIR}/lib -L${ZDIR}/lib" \
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./configure --prefix=${NCDIR} --enable-parallel-tests \
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&& make \
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# && make check \
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&& make install \
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&& rm -rf /usr/local/src/netcdf-c-4.6.2
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ARG NFDIR=/usr/local/netcdff4
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RUN cd /usr/local/src/netcdf-fortran-4.4.5 \
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&& CPPFLAGS=-I${NCDIR}/include LDFLAGS=-L${NCDIR}/lib \
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./configure --prefix=${NFDIR} \
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&& make \
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# && make check \
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&& make install \
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&& rm -rf /usr/local/src/netcdf-fortran-4.4.5
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RUN echo ${NCDIR}/lib > /etc/ld.so.conf.d/netcdf.conf \
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&& echo ${NFDIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
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&& echo ${ZDIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
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&& echo ${H5DIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
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&& echo ${PNDIR}/lib >> /etc/ld.so.conf.d/netcdf.conf \
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&& ldconfig
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ENV USER=clm
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RUN useradd -m -G adm,sudo -s /bin/bash $USER \
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&& echo "root:root" | chpasswd \
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&& echo "clm:clm" | chpasswd \
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&& apt-get remove wget -y
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RUN git clone -b release-clm5.0 https://github.com/ESCOMP/ctsm \
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&& cd ctsm && ./manage_externals/checkout_externals \
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&& chown -R clm:clm /model/ctsm \
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&& cd ..
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VOLUME ["/inputdata"]
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ENV PATH="/model/ctsm/cime/scripts:${NCDIR}/bin:${PATH}" \
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LANG=C.UTF-8
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COPY config/*.xml /home/${USER}/.cime/
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COPY config /home/${USER}/cesm/config
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COPY run_CLM50_example01.sh /home/${USER}/cesm/
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WORKDIR /home/${USER}/cesm
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RUN chown -R clm:clm /home /home/${USER} /home/${USER}/.cime /inputdata
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# && chmod 755 -R /inputdata /home/${USER}/.cime /home/${USER} \
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USER ${USER}
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CMD bash
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11
README.md
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README.md
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## container for CLM5.0(Community Land Surface Model)
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### Usage
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```bash
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docker run -it --rm -v /data/cesm/inputdata:/inputdata -v ${PWD}:/home/clm/cesm -e USERID=$UID . bash
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```
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* Document of CLM5.0:
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https://escomp.github.io/ctsm-docs/
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https://github.com/ESCOMP/ctsm.
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12
bin/findpkg
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bin/findpkg
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#!/bin/bash
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# Dongdong Kong
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# Find install related packages
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||||||
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for pkg in "$@"
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do
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echo "====================================================================="
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echo $pkg
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echo "====================================================================="
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||||||
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# dpkg --listfiles $pkg
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|
dpkg --list | grep $pkg
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|
done
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11
bin/pkginfo
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bin/pkginfo
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#!/bin/bash
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# Dongdong Kong
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# Show package detailed info
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||||||
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||||||
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for pkg in "$@"
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|
do
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echo "====================================================================="
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||||||
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echo $pkg
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echo "====================================================================="
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||||||
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dpkg --listfiles $pkg
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|
done
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135
config/config_compilers.xml
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config/config_compilers.xml
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<?xml version="1.0" encoding="UTF-8"?>
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<config_compilers version="2.0">
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<!--
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|
========================================================================
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|
This file defines compiler flags for building CESM. General flags are listed first
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followed by flags specific to particular operating systems, followed by particular machines.
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|
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|
More general flags are replaced by more specific flags.
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|
Attributes indicate that an if clause should be added to the Macros so that these flags are added
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|
only under the conditions described by the attribute(s).
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|
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||||||
|
The env_mach_specific file may set environment variables or load modules which set environment variables
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|
which are then used in the Makefile. For example the NETCDF_PATH on many machines is set by a module.
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|
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||||||
|
========================================================================
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|
Serial/MPI compiler specification
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|
========================================================================
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||||||
|
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||||||
|
SCC and SFC specifies the serial compiler
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||||||
|
MPICC and MPICC specifies the mpi compiler
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|
|
||||||
|
if $MPILIB is set to mpi-serial then
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|
CC = $SCC
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|
FC = $SFC
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|
MPICC = $SCC
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|
MPIFC = $SFC
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|
INC_MPI = $(CIMEROOT)/src/externals/mct/mpi-serial
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||||||
|
|
||||||
|
========================================================================
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||||||
|
Options for including C++ code in the build
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||||||
|
========================================================================
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||||||
|
|
||||||
|
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:
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||||||
|
|
||||||
|
SCXX: serial C++ compiler
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||||||
|
|
||||||
|
MPICXX: mpi C++ compiler
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||||||
|
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||||||
|
CXX_LINKER (CXX/FORTRAN): When C++ code is included in the build, do
|
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|
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:
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||||||
|
|
||||||
|
<CXX_LIBS> -L/path/to/directory -lfoo </CXX_LIBS>
|
||||||
|
|
||||||
|
or
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||||||
|
|
||||||
|
<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 -->
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||||||
|
<compiler COMPILER="gnu" MACH="shudmach">
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||||||
|
<CFLAGS>
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||||||
|
<base> -std=gnu99 </base>
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||||||
|
<append compile_threaded="true"> -fopenmp </append>
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||||||
|
<append DEBUG="TRUE"> -g -Wall -Og -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds </append>
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||||||
|
<append DEBUG="FALSE"> -O </append>
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||||||
|
</CFLAGS>
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||||||
|
<CPPDEFS>
|
||||||
|
<!-- http://gcc.gnu.org/onlinedocs/gfortran/ -->
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||||||
|
<append> -DFORTRANUNDERSCORE -DNO_R16 -DCPRGNU</append>
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||||||
|
</CPPDEFS>
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||||||
|
<CXX_LINKER>FORTRAN</CXX_LINKER>
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||||||
|
<FC_AUTO_R8>
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||||||
|
<base> -fdefault-real-8 </base>
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||||||
|
</FC_AUTO_R8>
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||||||
|
<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>
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||||||
|
<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>
|
||||||
57
config/config_machines.xml
Normal file
57
config/config_machines.xml
Normal file
@ -0,0 +1,57 @@
|
|||||||
|
<?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>&1
|
||||||
|
</default_run_misc_suffix>
|
||||||
|
</default_run_suffix> -->
|
||||||
|
</config_machines>
|
||||||
BIN
pkgs/hdf5-1.10.4.tar.gz
Normal file
BIN
pkgs/hdf5-1.10.4.tar.gz
Normal file
Binary file not shown.
BIN
pkgs/netcdf-c-4.6.2.tar.gz
Normal file
BIN
pkgs/netcdf-c-4.6.2.tar.gz
Normal file
Binary file not shown.
BIN
pkgs/netcdf-fortran-4.4.5.tar.gz
Normal file
BIN
pkgs/netcdf-fortran-4.4.5.tar.gz
Normal file
Binary file not shown.
BIN
pkgs/pio2_3_1.tar.gz
Normal file
BIN
pkgs/pio2_3_1.tar.gz
Normal file
Binary file not shown.
BIN
pkgs/pnetcdf-1.11.0.tar.gz
Normal file
BIN
pkgs/pnetcdf-1.11.0.tar.gz
Normal file
Binary file not shown.
BIN
pkgs/zlib-1.2.11.tar.gz
Normal file
BIN
pkgs/zlib-1.2.11.tar.gz
Normal file
Binary file not shown.
40
run_CLM50_example01.sh
Normal file
40
run_CLM50_example01.sh
Normal file
@ -0,0 +1,40 @@
|
|||||||
|
# /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
|
||||||
Loading…
x
Reference in New Issue
Block a user