PermafrostExecutorSiwenna
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. Further, as of 2018-03-20, wind back the `netcdf-fortran` package so that HDF5 1.8.18 is used. There are problems with HDF5 1.10.1 and ESMF, used in PyMT. To ensure all the packages meet the same dependencies (looking at you, numpy), simultaneously install `cca-tools`, `netcdf-fortran`, `pymt=0.2` and `csdms-ilamb` using the csdms-stack conda channel (the Bakery),
conda install cca-tools netcdf-fortran=4.4.4=5 pymt==0.2 csdms-ilamb -c csdms-stack -c defaults -c conda-forge
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
Note that when running IPython remotely on siwenna, it's helpful to set
export MPLBACKEND=Agg
Install executor software
Install the `wmt-exe` package from source.
mkdir -p $install_dir/opt && cd $install_dir/opt git clone https://github.com/csdms/wmt-exe cd wmt-exe python setup.py develop
Create a site configuration file that describes the executor and symlink it to the executor's etc/ diectory.
python setup.py configure --wmt-prefix=$install_dir --launch-dir='/scratch/$USER/wmt/permafrost' --exec-dir='/scratch/$USER/wmt/permafrost' ln -s "$(realpath wmt.cfg)" $install_dir/conda/etc
Here I've configured the executor to do stuff in the /scratch directory instead of the default ~/.wmt.
Install and test CSDMS components
Each section below describes how to install and test a particular CSDMS component.
Currently installed components:
- BenchmarkIngestTool
- CMIP
- CRUAKTemp
- FrostNumberGeoModel
- FrostNumberModel
- ILAMB
- KuGeoModel
- KuModel
- ModelIngestTool
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 https://github.com/permamodel/pbs-executor 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
This metapackage contains
- csdms-permamodel-ku
- csdms-permamodel-frostnumber
- csdms-permamodel-kugeo
- csdms-permamodel-frostnumbergeo
- csdms-cruaktemp
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')
CMIP
Download and install the `cmip` software from source.
cd $install_dir/opt git clone https://github.com/permamodel/cmip cd cmip python setup.py develop
Babelize the CMIP tool.
cd $install_dir mkdir -p build && cd build bmi-babelize $install_dir/opt/cmip --prefix=$install_dir/conda
Download the sample config file and test the babelized CMIP component by starting a Python session in $install_dir/test and executing the setup and IRF methods.
from pymt.components import CMIP
comp = CMIP()
comp.get_component_name()
comp.initialize('sample_cmip-siwenna.cfg')
comp.get_start_time()
comp.get_end_time()
comp.get_current_time()
comp.update()
comp.get_current_time()
comp.update_until(comp.get_end_time())
comp.get_current_time()
comp.finalize()
