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Chris Jewell
covid-pipeline
Commits
f8d895a6
Commit
f8d895a6
authored
Apr 20, 2021
by
Chris Jewell
Browse files
HMC model
parent
e5645b64
Changes
4
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enqueue_pipeline.sh
View file @
f8d895a6
...
...
@@ -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
View file @
f8d895a6
...
...
@@ -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
View file @
f8d895a6
...
...
@@ -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
View file @
f8d895a6
...
...
@@ -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
-
N
I
# 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
:
2
00
# 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
:
1
00
# 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
:
6
000
end
:
10000
start
:
-4
000
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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