update dockerfile

dockerfile/cime_config/config_compilers.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<config_compilers version="2.0">
+    <compiler MACH="clmu-app" COMPILER="gnu">
+        <NETCDF_PATH>/usr</NETCDF_PATH>
+        <NETCDF_C_PATH>/usr</NETCDF_C_PATH>
+        <NETCDF_FORTRAN_PATH>/usr</NETCDF_FORTRAN_PATH>
+        <FFLAGS>
+            <append> -I/usr/lib64/gfortran/modules </append>
+        </FFLAGS>
+        <SLIBS>
+            <append> -llapack -lblas </append>
+            <append> -lnetcdf -lnetcdff </append>
+        </SLIBS>
+    </compiler>
+</config_compilers>

dockerfile/cime_config/config_machines.xml

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+<?xml version="1.0"?>
+
+<config_machines version="2.0">
+    <machine MACH="clmu-app">
+        <DESC>clmu container</DESC>
+        <NODENAME_REGEX>clmu-app.*</NODENAME_REGEX>
+        <OS>LINUX</OS>
+        <COMPILERS>gnu</COMPILERS>
+        <MPILIBS>mpi-serial</MPILIBS>
+        <CIME_OUTPUT_ROOT>$ENV{CESMDATAROOT}/CaseOutputs</CIME_OUTPUT_ROOT>
+        <DIN_LOC_ROOT>$ENV{CESMDATAROOT}/inputdata</DIN_LOC_ROOT>
+        <DIN_LOC_ROOT_CLMFORC>$ENV{CESMDATAROOT}/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
+        <DOUT_S_ROOT>$ENV{CESMDATAROOT}/Archive</DOUT_S_ROOT>
+        <BASELINE_ROOT>$ENV{CESMDATAROOT}/BaselineTests</BASELINE_ROOT>
+        <CCSM_CPRNC>$CCSMROOT/tools/cprnc/build/cprnc</CCSM_CPRNC>
+        <GMAKE>make</GMAKE>
+        <GMAKE_J>32</GMAKE_J>
+        <BATCH_SYSTEM>none</BATCH_SYSTEM>
+        <SUPPORTED_BY>The_Uinversity_of_Manchester</SUPPORTED_BY>
+        <MAX_TASKS_PER_NODE>32</MAX_TASKS_PER_NODE>
+        <MAX_MPITASKS_PER_NODE>32</MAX_MPITASKS_PER_NODE>
+        <module_system type="none"/>
+    </machine>
+</config_machines>

dockerfile/dockerfile

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+# escape=`
+FROM fedora:31
+
+# This dockerfile is partly reference from https://github.com/HPSCTerrSys/dockerfiles/blob/master/clm5/Dockerfile
+
+# note: svn <=1.1 is not installed in this image, but is required for CESM installation
+LABEL `
+    org.label-schema.schema-version="1.0" `
+    org.label-schema.name="clmu-app" `
+    org.label-schema.version="1" `
+    org.label-schema.build-date="20240202" `
+    clm.version.major="5.0" `
+    clm.env.compiler="GCC" `
+    clm.env.compiler.version="9.3.1" `
+    clm.env.cmake.version="3.18" `
+    clm.env.netcdf-c.version="4.7.0-2" `
+    clm.env.netcdf-fortran.version="4.5.2-3" `
+    clm.env.python.version="3.7.9" `
+    clm.env.svn.version="1.12" ` 
+    clm.os.version="Fedora 31" 
+
+# Import cime config
+COPY cime_config/* /root/.cime/
+
+# Install required packages from base repo
+
+RUN dnf update -y `
+    && yum install dnf-plugins-core -y `
+    && dnf group install -y "Development Tools" `
+    && dnf install -y glibc-langpack-en libcurl-devel git wget autoconf perl-App-cpanminus `
+    && dnf install -y hdf5-devel lapack-devel ncl nco netcdf-devel netcdf-fortran netcdf-fortran-devel openssl-devel`
+    && dnf clean all `
+    && cpanm bigint && cpanm XML::LibXML
+
+# Install CMake
+RUN mkdir -vp /tmp/download `
+    && cd /tmp/download `
+    && wget -c https://github.com/Kitware/CMake/releases/download/v3.18.4/cmake-3.18.4.tar.gz `
+    && tar zxf cmake-3.18.4.tar.gz && cd cmake-3.18.4 `
+    && ./bootstrap && make && make install `
+    `
+# Clean files
+    && cd /tmp && rm -rf /tmp/download
+
+# Add user account
+WORKDIR /home
+
+RUN groupadd -g 1555 clmu-app `
+    && sudo usermod -aG clmu-app root `
+    `
+# Set compiler and library paths for CLM5
+    && echo "" >> /root/.bashrc `
+    && echo "# Set compiler and library paths for CLM5" >> /root/.bashrc `
+    && echo "source /etc/profile.d/ncarg.sh" >> /root/.bashrc `
+    `
+# Set CLM5 environment variables
+    && echo "" >> /root/.bashrc `
+    && echo "# CLM5 environment variables" >> /root/.bashrc `
+    && echo "" >> /root/.bashrc `
+    && echo "export PROJECT=/p/project" >> /root/.bashrc `
+    && echo "export SCRATCH=/p/scratch" >> /root/.bashrc `
+    && echo "export CESMDATAROOT=/p/scratch/CESMDATAROOT" >> /root/.bashrc `
+    && echo "export CSMDATA=$CESMDATAROOT/inputdata" >> /root/.bashrc `
+    && echo "export CASESCRIPT=/p/project/clm5.0/cime/scripts" >> /root/.bashrc `
+# Set usr account
+    && echo "export USER=root" >> /root/.bashrc
+
+# case and inputdata dir
+RUN mkdir -vp /p/project /p/scratch/CESMDATAROOT/inputdata/ForcingData p/pyscripts `
+    && cd /p/project `
+    && git clone -b release-clm5.0 https://github.com/ESCOMP/CTSM.git clm5.0 `
+    && cd clm5.0 `
+    && ./manage_externals/checkout_externals
+
+USER root
+WORKDIR /root
+CMD ["/bin/bash","-l"]

dockerfile/readme.md

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+# 1 installation CTSM-ENV-IMGANE
+Junjie Yu, 2023-11-28, Manchester, UK
+
+```
+# into the work dir
+cd to current dir with a dockerfile and cime_config
+docker build -t clmu-app:1 .
+```
+
+```
+# case and inputdata dir
+mkdir -vp p/project p/scratch/CESMDATAROOT/inputdata/ForcingData p/pyscripts
+```
+
+# 2 biuld container
+
+```
+docker run --hostname clmu-app --name clmu -it clmu-app:1.0
+```
+
+# 3 install CTSM or CLM5.0
+```
+# in docker containls
+cd /p/project
+git clone -b release-clm5.0 https://github.com/ESCOMP/CTSM.git myclm
+cd myclm
+./manage_externals/checkout_externals
+```
+
+# [key notes for seting config_manchine.xml](https://bb.cgd.ucar.edu/cesm/threads/issue-installing-on-centos-8-with-slurm-and-lmod.5884/#post-39110)
+The reference set it wrong.
+
+***This is the corret version***
+You have defined it here...
+
+<DIN_LOC_ROOT_CLMFORC>common/contrib/cesm/inputdata/lmwg</DIN_LOC_ROOT_CLMFORC>
+
+Change it so that it points to this...
+
+<DIN_LOC_ROOT_CLMFORC>$DIN_LOC_ROOT/atm/datm7</DIN_LOC_ROOT_CLMFORC>
+
+that should then get the paths to line up so it can download the data. As we talk about in the first link I share above I recommend that you only download the forcing data a few years at a time. It's likely going to take days to download and as such you don't want to do it all once.
+
+
+# 4 Singularity
+
+Singularity provides a mechanism to run containers where containers can be used to package entire scientific workflows, software and libraries, and even data.
+Ref: https://ri.itservices.manchester.ac.uk/csf3/software/applications/singularity/
+
+Using Singularity from docker image
+
+```
+# save image as tar file
+docker save -o ~/docker/clm5docker.tar clm5docker:1
+# transport tar file
+scp ~/docker/clm5docker.tar ...
+# biuld image form tar
+singularity build clm5docker.sif docker-archive://clm5docker.tar
+scp /Users/user/Documents/GitHub/DRL_urban_climate_adaptation/2_CTSM_container/dockerfile/cime_config/config_machines.xml [email protected]:~/.cime
+scp /Users/user/Documents/GitHub/DRL_urban_climate_adaptation/2_CTSM_container/dockerfile/cime_config/config_compilers.xml [email protected]:~/.cime
+mkdir -vp p/project p/scratch/CESMDATAROOT/inputdata
+
+singularity run --hostname clm5-docker -B "$(pwd)"/p:/p clm5docker.sif # do not change hostname, either need to change cime.config file 
+
+singularity run --net --network=none --hostname clm5-docker -B "$(pwd)"/p:/p clm5docker.sif
+
+# then in singularity, as singularity are not same as 
+# CLM5 environment variables
+
+export PROJECT=/p/project
+export SCRATCH=/p/scratch
+export BUDGET_ACCOUNTS=slts
+export CESMDATAROOT=/p/scratch/CESMDATAROOT
+export CSMDATA=/p/scratch/CESMDATAROOT/inputdata
+export CASESCRIPT=/p/project/myclm/cime/scripts
+export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+export OMPI_ALLOW_RUN_AS_ROOT=1
+```