Some useful oq commands

The oq command-line script is the entry point for several commands, the most important one being oq engine, which is documented in the manual.

The commands documented here are not in the manual because they have not reached the same level of maturity and stability. Still, some of them are quite stable and quite useful for the final users, so feel free to use them.

You can see the full list of commands by running oq help:

$ oq help
usage: oq [--version]
{upgrade_nrml,checksum,run_server,webui,export,compare,plot_memory,to_shapefile,restore,show_attrs,dbserver,plot,shell,prepare_site_model,importcalc,show,reduce_sm,plot_pyro,reduce,extract,plot_losses,dump,purge,celery,abort,engine,reset,info,plot_ac,plot_sites,workers,tidy,to_hdf5,db,download_shakemap,run,from_shapefile,zip,plot_assets,check_input,help}
         ...

positional arguments:
{upgrade_nrml,checksum,run_server,webui,export,compare,plot_memory,to_shapefile,restore,show_attrs,dbserver,plot,shell,prepare_site_model,importcalc,show,reduce_sm,plot_pyro,reduce,extract,plot_losses,dump,purge,celery,abort,engine,reset,info,plot_ac,plot_sites,workers,tidy,to_hdf5,db,download_shakemap,run,from_shapefile,zip,plot_assets,check_input,help}
                      available subcommands; use oq help <subcmd>

optional arguments:
--version, -v         show program's version number and exit

This is the output that you get at the present time (engine 3.6); depending on your version of the engine you may get a different output. As you see, there are several commands, like purge, show_attrs, export, restore, … You can get information about each command with oq help <command>; for instance, here is the help for purge:

$ oq help purge
usage: oq purge [-h] calc_id

Remove the given calculation. If you want to remove all calculations, use oq
reset.

positional arguments:
  calc_id     calculation ID

optional arguments:
  -h, --help  show this help message and exit

Some of these commands are highly experimental and may disappear; others are meant for debugging and are not meant to be used by end-users. Here I will document only the commands that are useful for the general public and have reached some level of stability.

Probably the most important command is oq info. It has several features.

1. It can be invoked with a job.ini file to extract information about the logic tree of the calculation.

2. When invoked with the –report option, it produces a .rst report with several important informations about the computation. It is ESSENTIAL in the case of large calculations, since it will give you an idea of the feasibility of the computation without running it. Here is an example of usage:

$ oq info --report job.ini
Generated /tmp/report_1644.rst
<Monitor info, duration=10.910529613494873s, memory=60.16 MB>

You can open /tmp/report_1644.rst and read the informations listed there (1644 is the calculation ID, the number will be different each time).

3. It can be invoked without a job.ini file, and it that case it provides global information about the engine and its libraries. Try, for instance:

$ oq info calculators # list available calculators
$ oq info gsims       # list available GSIMs
$ oq info views       # list available views
$ oq info exports     # list available exports
$ oq info parameters  # list all job.ini parameters

The second most important command is oq export. It allows customization of the exports from the datastore with additional flexibility compared to the oq engine export commands. In the future the oq engine exports commands might be deprecated and oq export might become the official export command, but we are not there yet.

Here is the usage message:

$ oq help export
usage: oq export [-h] [-e csv] [-d .] datastore_key [calc_id]

Export an output from the datastore.

positional arguments:
  datastore_key         datastore key
  calc_id               number of the calculation [default: -1]

optional arguments:
  -h, --help            show this help message and exit
  -e csv, --exports csv
                      export formats (comma separated)
  -d ., --export-dir .  export directory

The list of available exports (i.e. the datastore keys and the available export formats) can be extracted with the oq info exports command; at the moment there are 52 exporters defined, but this number changes at each version:

$ oq info exports
agg_curves-rlzs ['csv']
agg_curves-stats ['csv']
agg_losses-rlzs ['csv']
agg_losses-stats ['csv']
agg_risk ['csv']
agglosses ['csv']
aggregate_by ['csv']
asset_risk ['csv']
avg_losses-rlzs ['csv']
avg_losses-stats ['csv']
bcr-rlzs ['csv']
bcr-stats ['csv']
damages-rlzs ['csv']
damages-stats ['csv']
disagg ['xml', 'csv']
disagg_by_src ['csv']
dmg_by_asset ['npz', 'csv']
dmg_by_event ['csv']
events ['csv']
fullreport ['rst']
gmf_data ['npz', 'csv']
hcurves ['csv', 'xml', 'npz']
hmaps ['csv', 'xml', 'npz']
input ['zip']
loss_curves ['csv']
loss_curves-rlzs ['csv']
loss_curves-stats ['csv']
loss_maps-rlzs ['csv', 'npz']
loss_maps-stats ['csv', 'npz']
losses_by_asset ['npz', 'csv']
losses_by_event ['csv']
realizations ['csv']
ruptures ['xml', 'csv']
tot_curves-rlzs ['csv']
tot_curves-stats ['csv']
tot_losses-rlzs ['csv']
tot_losses-stats ['csv']
uhs ['csv', 'xml', 'npz']
There are 51 exporters defined.

At the present the supported export types are xml, csv, rst, npz and hdf5. xml has been deprecated for some outputs and is not the recommended format for large exports. For large exports, the recommended formats are npz (which is a binary format for numpy arrays) and hdf5. If you want the data for a specific realization (say the first one), you can use:

$ oq export hcurves/rlz-0 --exports csv
$ oq export hmaps/rlz-0 --exports csv
$ oq export uhs/rlz-0 --exports csv

but currently this only works for csv and xml. The exporters are one of the most time-consuming parts on the engine, mostly because of the sheer number of them; the are more than fifty exporters and they are always increasing. If you need new exports, please [add an issue on GitHub](https://github.com/gem/oq-engine/issues).

oq zip

An extremely useful command if you need to copy the files associated to a computation from a machine to another is oq zip:

$ oq help zip
usage: oq zip [-h] [-r] what [archive_zip]

positional arguments:
  what               path to a job.ini, a ssmLT.xml file, or an exposure.xml
  archive_zip        path to a non-existing .zip file [default: '']

optional arguments:
  -h, --help         show this help message and exit
  -r , --risk-file   optional file for risk

For instance, if you have two configuration files job_hazard.ini and job_risk.ini, you can zip all the files they refer to with the command:

$ oq zip job_hazard.ini -r job_risk.ini

oq zip is actually more powerful than that; other than job.ini files, it can also zip source models:

$ oq zip ssmLT.xml

and exposures:

$ oq zip my_exposure.xml

Importing a remote calculation

Here is the command:

$ oq importcalc --help
usage: oq importcalc [-h] calc_id

Import a remote calculation into the local database. server, username and
password must be specified in an openquake.cfg file.
NB: calc_id can be a local pathname to a datastore not already present in
the database: in that case it is imported in the db.

positional arguments:
  calc_id     calculation ID or pathname

optional arguments:
  -h, --help  show this help message and exit

plotting commands

The engine provides several plotting commands. They are all experimental and subject to change. They will always be. The official way to plot the engine results is by using the QGIS plugin. Still, the oq plotting commands are useful for debugging purposes. Here I will describe only the plot_assets command, which allows to plot the exposure used in a calculation together with the hazard sites:

$ oq help plot_assets
usage: oq plot_assets [-h] [calc_id]

Plot the sites and the assets

positional arguments:
  calc_id     a computation id [default: -1]

optional arguments:
  -h, --help  show this help message and exit

This is particularly interesting when the hazard sites do not coincide with the asset locations, which is normal when gridding the exposure.

prepare_site_model

The command oq prepare_site_model, introduced in engine 3.3, is quite useful if you have a vs30 file with fields lon, lat, vs30 and you want to generate a site model from it. Normally this feature is used for risk calculations: given an exposure, one wants to generate a collection of hazard sites covering the exposure and with vs30 values extracted from the vs30 file with a nearest neighbour algorithm:

$ oq prepare_site_model -h
usage: oq prepare_site_model [-h] [-e [EXPOSURE_XML [EXPOSURE_XML ...]]]
                             [-s [SITES_CSV [SITES_CSV ...]]] [-1] [-2] [-3]
                             [-g 0] [-a 5] [-o site_model.csv]
                             vs30_csv [vs30_csv ...]

Prepare a site_model.csv file from exposure xml files/site csv files, vs30 csv
files and a grid spacing which can be 0 (meaning no grid). For each site the
closest vs30 parameter is used. The command can also generate (on demand) the
additional fields z1pt0, z2pt5 and vs30measured which may be needed by your
hazard model, depending on the required GSIMs.

positional arguments:
  vs30_csv              files with lon,lat,vs30 and no header

optional arguments:
  -h, --help            show this help message and exit
  -e [EXPOSURE_XML [EXPOSURE_XML ...]], --exposure-xml [EXPOSURE_XML [EXPOSURE  _XML ...]]
                        exposure(s) in XML format
  -s [SITES_CSV [SITES_CSV ...]], --sites-csv [SITES_CSV [SITES_CSV ...]]
                        sites in CSV format
  -1, --z1pt0           build the z1pt0
  -2, --z2pt5           build the z2pt5
  -3, --vs30measured    build the vs30measured
  -g 0, --grid-spacing 0
                        grid spacing in km (the default 0 means no grid)
  -a 5, --assoc-distance 5
                        sites over this distance are discarded
  -o site_model.csv, --output site_model.csv
                        output file

The command works in two modes: with non-gridded exposures (the default) and with gridded exposures. In the first case the assets are aggregated in unique locations and for each location the vs30 coming from the closest vs30 record is taken. In the second case, when a grid_spacing parameter is passed, a grid containing all of the exposure is built and the points with assets are associated to the vs30 records. In both cases if the closest vs30 record is over the site_param_distance - which by default is 5 km - a warning is printed.

In large risk calculations, it is quite preferable to use the gridded mode because with a well spaced grid,

  1. the results are the nearly the same than without the grid and
  2. the calculation is a lot faster and uses a lot less memory.

Gridding of the exposure makes large calculations more manageable. The command is able to manage multiple Vs30 files at once. Here is an example of usage:

$ oq prepare_site_model Vs30/Ecuador.csv Vs30/Bolivia.csv -e Exposure/Exposure_Res_Ecuador.csv Exposure/Exposure_Res_Bolivia.csv --grid-spacing=10

Reducing the source model

Source models are usually large, at the continental scale. If you are interested in a city or in a small region, it makes sense to reduce the model to only the sources that would affect the region, within the integration distance. To fulfil this purpose there is the oq reduce_sm command. The suggestion is run a preclassical calculation (i.e. set calculation_mode=preclassical in the job.ini) with the full model in the region of interest, keep track of the calculation ID and then run:

$ oq reduce_sm <calc_id>

The command will reduce the source model files and add an extension .bak to the original ones.

$ oq reduce_sm -h
usage: oq reduce_sm [-h] calc_id

Reduce the source model of the given (pre)calculation by discarding all
sources that do not contribute to the hazard.

positional arguments:
  calc_id     calculation ID

optional arguments:
  -h, --help  show this help message and exit

Comparing hazard results

If you are interested in sensitivity analysis, i.e. in how much the results of the engine change by tuning a parameter, the oq compare command is useful. For the moment it is able to compare hazard curves and hazard maps. Here is the help message:

$ oq compare --help
usage: oq compare [-h] [-f] [-s 100] [-r 0] [-a 0.001] [-t 0.01]
                  {hcurves,hmaps} imt calc_ids [calc_ids ...]

Compare the hazard curves or maps of two or more calculations

positional arguments:
  {hcurves,hmaps}       hmaps or hcurves
  imt                   intensity measure type to compare
  calc_ids              calculation IDs

optional arguments:
  -h, --help            show this help message and exit
  -f, --files           write the results in multiple files
  -s 100, --samplesites 100
                        sites to sample (or fname with site IDs)
  -r 0, --rtol 0        relative tolerance
  -a 0.001, --atol 0.001
                        absolute tolerance
  -t 0.01, --threshold 0.01
                        ignore the hazard curves below it