Commit f8d895a6 authored by Chris Jewell's avatar Chris Jewell
Browse files

HMC model

parent e5645b64
......@@ -44,9 +44,6 @@ source /usr/shared_apps/admin/etc/sge/switch-gpu.sh
JOBNAME=c19_$arg_date_$arg_config
STDOUT=$arg_staging_dir/stdout.txt
# Final results dir
RESULTS_DEST_DIR=/mnt/covid/c19/covid_pipeline
mkdir -p ${arg_staging_dir}
qsub -N $JOBNAME -o $STDOUT \
pipeline.sge \
......
......@@ -60,8 +60,8 @@ done
. /etc/profile
. $HOME/.bash_profile
module add anaconda3/wmlce
module add cuda/11.0
export XLA_FLAGS="--xla_gpu_cuda_data_dir=$CUDA_HOME"
......@@ -72,7 +72,8 @@ echo Date range $DATELOW to $DATEHIGH
poetry run python -m covid.pipeline \
--config ${arg_config} \
--date-range $DATELOW $DATEHIGH \
--results-directory ${arg_staging_dir} ||
--results-directory ${arg_staging_dir} \
-v ||
error_exit "Pipeline job failed"
rsync -aP ${arg_staging_dir} ${arg_results_dir} ||
......
......@@ -7,8 +7,11 @@ license = "MIT"
[tool.poetry.dependencies]
python = "^3.7"
covid19uk = {git = "git@fhm-chicas-code.lancs.ac.uk:jewell/covid19uk.git", rev="65bd815"}
drmaa = "^0.7.9"
covid19uk = {path="/home/hpc/39/jewellcp/Projects/covid-hmc-impl", develop=true}
ipympl = "^0.6.3"
jupyter = "^1.0.0"
zarr = "^2.6.1"
jupyterlab = "^3.0.12"
[tool.poetry.dev-dependencies]
ipython = "^7.20.0"
......
......@@ -7,7 +7,8 @@ ProcessData:
mobility_matrix: data/mergedflows.csv
population_size: data/c2019modagepop.csv
commute_volume: # Can be replaced by DfT traffic flow data - contact authors <c.jewell@lancaster.ac.uk>
geopackage: data/UK2019mod_pop.gpkg
CasesData:
input: url
address: https://api.coronavirus.data.gov.uk/v2/data?areaType=ltla&metric=newCasesBySpecimenDate&format=json
......@@ -23,23 +24,29 @@ ProcessData:
- S # Scotland
- E # England
- W # Wales
- NI # Northern Ireland
- N # Northern Ireland
Mcmc:
dmax: 84 # Max distance to move events
nmax: 50 # Max num events per metapopulation/time to move
m: 1 # Number of metapopulations to move
occult_nmax: 15 # Max number of occults to add/delete per metapop/time
num_event_time_updates: 35 # Num event and occult updates per sweep of Gibbs MCMC sampler.
num_bursts: 200 # Number of MCMC bursts of `num_burst_samples`
num_event_time_updates: 200 # Num event and occult updates per sweep of Gibbs MCMC sampler.
num_bursts: 100 # Number of MCMC bursts of `num_burst_samples`
num_burst_samples: 50 # Number of MCMC samples per burst
thin: 20 # Thin MCMC samples every `thin` iterations
num_adaptation_iterations: 1000
ThinPosterior: # Post-process further chain thinning HDF5 -> .pkl.
start: 6000
end: 10000
start: -4000
end:
by: 10
Geopackage: # covid.tasks.summary_geopackage
base_geopackage: data/UK2019mod_pop.gpkg
base_layer: UK2019mod_pop_xgen
\ No newline at end of file
base_layer: UK2019mod_pop_xgen
AWSS3:
profile: covid-pipeline
bucket: lancaster-covid-devel
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