Set up python-fabm

インストール

Linux上において，python-fabmのセットアップを行った備忘録です．ホームディレクトリ[cci]~/[/cci]直下にインストールすることを想定します．また，Python 2.7が必要です．[cci]miniconda[/cci]でPython 2.7の仮想環境[cci]pyfabm[/cci]を作成し，activateしておきます．さらに，jupyter notebookをはじめ，一通りのパッケージが[cci]pyfabm[/cci]環境でインストールされている必要があります．

ソースコードの入手

Githubから最新のソースコードを入手します．展開すると，[cci]~/fabm/[/cci]が作成されます．
[cc lang='bash']
~/$ git clone https://github.com/fabm-model/fabm.git
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インストールスクリプトの準備

ビルド用のディレクトリ[cci]~/fabm/build/[/cci]を作成しておきます．
[cci]~/fabm/scripts/linux/[/cci]に存在するconfigureとbuild用のスクリプト，[cci]fabm_configure_python.sh[/cci]と[cci]fabm_build_python.sh[/cci]を[cci]~/fabm/build/[cci]にコピーします．[cci]fabm_configure_python.sh[/cci]を適切に編集します．ifortでコンパイルする場合の例を以下に示します．
[cc lang='bash']
#!/bin/sh

# if not set use the suggested source code installation directories
FABM_BASE=${FABM_BASE:=~/fabm}

# default Fortran compiler is gfortran - overide by setting compuiler like:
export compiler=ifort
compiler=${compiler:=gfortran}

host=python
# ready to configure
mkdir -p $host/$compiler
cd $host/$compiler
cmake $FABM_BASE/src/drivers/python \
-DFABM_EMBED_VERSION=on \
-DCMAKE_Fortran_COMPILER=$compiler
cd ../..
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次に，[cci]fabm_build_python.sh[/cci]を以下のように編集します．
[cc lang='bash']
#!/bin/bash

if [ "$1" != "" ]; then
action=$1
echo "doing a "$action
else
action=install
fi

# default Fortran compiler is gfortran - overide by setting compuiler like:
export compiler=ifort
compiler=${compiler:=gfortran}

host=python

np=-j8
cd $host/$compiler
make $np $action
cd ../..
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ビルド

用意したスクリプトを用いてconfigureおよびbuildしインストールします．[cci]~/fabm/build/[/cci]に移動します．
[cc lang='bash']
~/fabm/build$ ./fabm_configure_python.sh
-- The Fortran compiler identification is Intel 18.0.3.20180410
-- Check for working Fortran compiler: /opt/intel/compilers_and_libraries_2018.3.222/linux/bin/intel64/ifort
-- Check for working Fortran compiler: /opt/intel/compilers_and_libraries_2018.3.222/linux/bin/intel64/ifort -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /opt/intel/compilers_and_libraries_2018.3.222/linux/bin/intel64/ifort supports Fortran 90
-- Checking whether /opt/intel/compilers_and_libraries_2018.3.222/linux/bin/intel64/ifort supports Fortran 90 -- yes
-- Found PythonInterp: /home/username/miniconda3/envs/pyfabm/bin/python (found version "2.7.15")
-- Installation prefix: /home/username/.local/lib/python2.7/site-packages
-- Configuring done
-- Generating done
-- Build files have been written to: /home/username/fabm/build/python/ifort
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[cc lang='bash']
~/fabm/build$ ./fabm_build_python.sh
Scanning dependencies of target fabm_version
Scanning dependencies of target yaml
Scanning dependencies of target fabm_base
[ 1%] Retrieving description of last FABM commit...
[ 2%] Building Fortran object fabm/yaml/CMakeFiles/yaml.dir/yaml_types.F90.o
[ 3%] Building Fortran object fabm/CMakeFiles/fabm_base.dir/fabm_driver.F90.o
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[ 5%] Built target fabm_version
[ 6%] Building Fortran object fabm/yaml/CMakeFiles/yaml.dir/yaml.F90.o
[ 7%] Building Fortran object fabm/CMakeFiles/fabm_base.dir/fabm_types.F90.o
[ 7%] Built target yaml
[ 8%] Building Fortran object fabm/CMakeFiles/fabm_base.dir/fabm_builtin_models.F90.o
[ 11%] Building Fortran object fabm/CMakeFiles/fabm_base.dir/fabm_particle.F90.o
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[ 11%] Built target fabm_base
Scanning dependencies of target fabm_models_aed
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Scanning dependencies of target fabm_models_hzg
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[ 12%] Building Fortran object fabm/models/metu/CMakeFiles/fabm_models_metu.dir/mnemiopsis/mnemiopsis.F90.o
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[ 23%] Building Fortran object fabm/models/aed/CMakeFiles/fabm_models_aed.dir/aed_util.F90.o
[ 23%] Built target fabm_models_klimacampus
[ 24%] Building Fortran object fabm/models/bb/CMakeFiles/fabm_models_bb.dir/lorenz63/lorenz63.F90.o
Scanning dependencies of target fabm_models_examples
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[ 24%] Built target fabm_models_msi
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Scanning dependencies of target fabm_models_pml
[ 28%] Building Fortran object fabm/models/pml/CMakeFiles/fabm_models_pml.dir/carbonate/carbonate.F90.o
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[ 36%] Building Fortran object fabm/models/jrc/CMakeFiles/fabm_models_jrc.dir/med_ergom/med_ergom.F90.o
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[ 41%] Building Fortran object fabm/models/aed/CMakeFiles/fabm_models_aed.dir/aed_iron.F90.o
[ 42%] Building Fortran object fabm/models/iow/CMakeFiles/fabm_models_iow.dir/iow_model_library.F90.o
[ 43%] Building Fortran object fabm/models/pml/CMakeFiles/fabm_models_pml.dir/carbonate/co2_dyn.F90.o
[ 44%] Building Fortran object fabm/models/examples/CMakeFiles/fabm_models_examples.dir/light_cycle.F90.o
[ 45%] Building Fortran object fabm/models/gotm/CMakeFiles/fabm_models_gotm.dir/light/light.F90.o
[ 46%] Building Fortran object fabm/models/jrc/CMakeFiles/fabm_models_jrc.dir/jrc_model_library.F90.o
[ 46%] Built target fabm_models_au
[ 46%] Built target fabm_models_bb
Scanning dependencies of target fabm_models_niva
[ 47%] Building Fortran object fabm/models/aed/CMakeFiles/fabm_models_aed.dir/aed_nitrogen.F90.o
Scanning dependencies of target fabm_models_akvaplan
[ 48%] Building Fortran object fabm/models/niva/CMakeFiles/fabm_models_niva.dir/brom/brom_bio.F90.o
[ 50%] Building Fortran object fabm/models/akvaplan/CMakeFiles/fabm_models_akvaplan.dir/plume_injection.F90.o
[ 50%] Built target fabm_models_iow
[ 50%] Built target fabm_models_pml
[ 51%] Building Fortran object fabm/models/akvaplan/CMakeFiles/fabm_models_akvaplan.dir/tracer.F90.o
[ 52%] Building Fortran object fabm/models/examples/CMakeFiles/fabm_models_examples.dir/mean.F90.o
[ 53%] Building Fortran object fabm/models/examples/CMakeFiles/fabm_models_examples.dir/npzd/det.F90.o
[ 54%] Building Fortran object fabm/models/gotm/CMakeFiles/fabm_models_gotm.dir/npzd/npzd.F90.o
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[ 55%] Building Fortran object fabm/models/examples/CMakeFiles/fabm_models_examples.dir/npzd/nut.F90.o
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[ 63%] Building Fortran object fabm/models/examples/CMakeFiles/fabm_models_examples.dir/npzd/zoo.F90.o
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[ 67%] Building Fortran object fabm/models/niva/CMakeFiles/fabm_models_niva.dir/brom/brom_eqconst.F90.o
[ 67%] Built target fabm_models_akvaplan
[ 68%] Building Fortran object fabm/models/aed/CMakeFiles/fabm_models_aed.dir/aed_sulfur.F90.o
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[ 84%] Built target fabm_models_examples
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[ 85%] Built target fabm_models_niva
[ 86%] Building Fortran object fabm/models/aed/CMakeFiles/fabm_models_aed.dir/aed_models.F90.o
[ 86%] Built target fabm_models_aed
Scanning dependencies of target fabm
[ 87%] Building Fortran object fabm/CMakeFiles/fabm.dir/fabm_coupling.F90.o
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[ 93%] Linking Fortran static library libfabm.a
[ 93%] Built target fabm
Scanning dependencies of target python_fabm
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[100%] Linking Fortran shared library libpython_fabm.so
[100%] Built target python_fabm
Install the project...
-- Install configuration: "Release"
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/libpython_fabm.so
-- Up-to-date: /home/username/.local/lib/python2.7/site-packages/pyfabm
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/complete_yaml.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/gui_qt.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/utils
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/utils/fabm_complete_yaml.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/utils/fabm_configuration_gui.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/utils/fabm_describe_model.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/utils/fabm_evaluate.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/utils/fabm_stress_test.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/utils/__init__.py
-- Installing: /home/username/.local/lib/python2.7/site-packages/pyfabm/__init__.py
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