HMC model

enqueue_pipeline.sh

@@ -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 \

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}  ||

pyproject.toml

@@ -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"

uk_config.yaml

@@ -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