PermafrostExecutorSiwenna

wmt-permafrost executor on siwenna

Instructions for installing and configuring a WMT executor on siwenna.

--Mpiper (talk) 14:52, 22 February 2018 (MST)

Set install directory

The install directory for this executor is /home/csdms/wmt/permafrost.

install_dir=/home/csdms/wmt/permafrost
mkdir -p $install_dir

Install Python

Install a Python distribution to be used locally by WMT. We like to use Miniconda.

cd $install_dir
curl https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -o miniconda.sh
bash ./miniconda.sh -f -b -p $(pwd)/conda
export PATH=$(pwd)/conda/bin:$PATH

If working with an existing Miniconda install, be sure to update everything before continuing:

conda update conda
conda update --all

Install the CSDMS software stack

A limiting factor in setting up this executor is the componentized version of ILAMB can only be run with `pymt=0.2`; in particular, the BMI I wrote for ILAMB is incompatible with the `model_metadata` package in newer versions of PyMT. To ensure all the packages meet the same dependencies (looking at you, numpy), simultaneously install `cca-tools`, `pymt=0.2` and `csdms-ilamb` using the csdms-stack conda channel (the Bakery),

conda install cca-tools pymt=0.2 csdms-ilamb -c csdms-stack -c defaults -c conda-forge

Next, install `wmt-exe` from source.

mkdir -p $install_dir/opt && cd $install_dir/opt
git clone https://github.com/csdms/wmt-exe
cd wmt-exe
python setup.py develop

Install the `babelizer` for components that need to be built from source.

conda install -c csdms-stack babelizer

Optionally install IPython for testing.

conda install ipython

When running IPython remotely on siwenna, it's helpful to set

export MPLBACKEND=Agg

Install and test CSDMS components

Each section below describes how to install and test a particular CSDMS component.

ILAMB

We installed ILAMB above. Test it by starting a Python session in $install_dir/test and executing the setup and IRF methods.

from pymt.components import ILAMB

comp = ILAMB()
comp.get_component_name()
comp.setup('.')

At this point, stop and edit bmi_ilamb.yaml, updating the `ilamb_root` attribute with the appropriate location on siwenna, /home/csdms/ilamb. All other attributes can be left unchanged with their default values.

comp.initialize('bmi_ilamb.yaml')
comp.get_start_time()
comp.get_end_time()
comp.get_current_time()
comp.update()
comp.finalize()

ILAMB is run at the call to `update`. The default run takes about 75 min.

PBS

Download and install the `pbs-executor` software from source.

cd $install_dir/opt
git clone git@github.com:permamodel/pbs-executor.git
cd pbs-executor
python setup.py develop

Babelize the PBS components.

cd $install_dir
mkdir -p build && cd build
bmi-babelize $install_dir/opt/pbs-executor --prefix=$install_dir/conda

Test a component (here, ModelIngestTool) by starting a Python session in $install_dir/test and executing the setup and IRF methods.

from pymt.components import ModelIngestTool

comp = ModelIngestTool()
comp.get_component_name()
comp.setup('.')

At this point, suspend the IPython session and copy a sample config file and data from the `pbs-executor` repo. (This could be improved.)

cd $install_dir/opt/pbs-executor/pbs-executor/data
cp ingest.yaml sftlf_fx_PBS-test_historical_r9i0p0.nc $install_dir/test
cd -

Restore the IPython session and continue.

comp.initialize('ingest.yaml')
comp.update()
comp.finalize()

View the index.html file that results.

Permamodel

Install the permamodel components from the Bakery using the `csdms-permamodel` metapackage.

conda install csdms-permamodel -c csdms-stack

Test a component (here, FnM) by starting a Python session in $install_dir/test and executing the setup and IRF methods.

from pymt.components import FrostNumberModel

comp = FrostNumberModel()
comp.get_component_name()
# args = comp.setup('.')
# comp.initialize(*args)
comp.setup('.')
comp.initialize('frostnumber_model.cfg')
comp.get_start_time()
comp.get_end_time()
comp.get_current_time()
comp.update()
comp.finalize()

Check the ouput of the run

$ cat frostnumber_output.dat
Year: 2000  output=('0.396', '-1.000', '-1.000')