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use lb-run Proj/version instead of the obsolete lb-run Proj version
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pikacic committed Nov 28, 2016
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2 changes: 1 addition & 1 deletion davinci-grid.md
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Expand Up @@ -123,7 +123,7 @@ To look at the `root` file produced by the job start a new terminal, and
type:

```bash
$ lb-run DaVinci v41r2 $SHELL
$ lb-run DaVinci/v41r2 $SHELL
$ root -l path/to/the/job/output
```

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12 changes: 5 additions & 7 deletions davinci.md
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Expand Up @@ -58,7 +58,7 @@ One of the most important ones is *DaVinci*, which provides lots of *Algorithms*

You can run DaVinci using the following command:
```bash
lb-run DaVinci v41r2 gaudirun.py
lb-run DaVinci/v41r2 gaudirun.py
```

This will run the `gaudirun.py` command using version v41r2 of DaVinci.
Expand Down Expand Up @@ -89,15 +89,15 @@ During this run, DaVinci didn't do anything: We didn't specify any algorithms to
Usually, you will write an option file (e.g. `options.py`) and specify it as an argument to `gaudirun.py`:

```bash
lb-run DaVinci v41r2 gaudirun.py options.py
lb-run DaVinci/v41r2 gaudirun.py options.py
```

An `option.py` is just a regular Python script that specifies how to set things up in the software.
Many of the following lessons will teach you how to do something with DaVinci by showing you how to write or extend an `options.py`.
You can use the above command to test it.
You can also specify several option files like this:
```bash
lb-run DaVinci v41r2 gaudirun.py options1.py options2.py
lb-run DaVinci/v41r2 gaudirun.py options1.py options2.py
```
They will then both be used to set up DaVinci.

Expand All @@ -108,7 +108,7 @@ lb-run --list DaVinci
Do you want to start a shell that already contains the LHCb environment, so you don't have to use `lb-run`?
Execute
```bash
lb-run DaVinci v41r2 $SHELL
lb-run DaVinci/v41r2 $SHELL
```
A simple `gaudirun.py` should work as well now.
Typing `exit` will close the shell and leave the LHCb environment behind.
Expand All @@ -119,7 +119,5 @@ Typing `exit` will close the shell and leave the LHCb environment behind.
> `lb-run` is the new way of doing things and has some nice benefits over `SetupProject`.
> For most purposes, `SetupProject DaVinci v41r2` is equivalent to
> ```bash
> lb-run DaVinci v41r2 $SHELL
> lb-run DaVinci/v41r2 $SHELL
> ```
14 changes: 7 additions & 7 deletions interactive-dst.md
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Expand Up @@ -10,7 +10,7 @@ minutes: 10
> * Print all nodes in a DST
> * Explore the contents of the TES
> * Inspect a track
> * Inspect a stripping location
> * Inspect a stripping location
Data is stored in files called DSTs, which are processed
by DaVinci to make nTuples. However you can also explore
Expand Down Expand Up @@ -51,7 +51,7 @@ Place this into a file called `first.py` and run the following
command in a new terminal:

```bash
$ lb-run DaVinci v41r2 ipython -i first.py 00035742_00000002_1.allstreams.dst
$ lb-run DaVinci/v41r2 ipython -i first.py 00035742_00000002_1.allstreams.dst
```

This will open the DST and print out some of the TES locations
Expand Down Expand Up @@ -178,8 +178,8 @@ print_decay = appMgr.toolsvc().create(
print_decay.printTree(cands[0])
```

With our candidates in hand, it would be nice to be able to retrieve and
compute the variables we need for an analysis. On to [LoKi
With our candidates in hand, it would be nice to be able to retrieve and
compute the variables we need for an analysis. On to [LoKi
functors](loki-functors.html)!

> ## Fast DST browsing {.callout}
Expand All @@ -192,10 +192,10 @@ functors](loki-functors.html)!
> For example, to explore the `DST` we could have simply done:
>
> ```
> lb-run Bender bender 00035742_00000002_1.allstreams.dst
> lb-run Bender/latest bender 00035742_00000002_1.allstreams.dst
> ```
>
> This leaves us in a prompt in which we can proceed as discussed in this
> This leaves us in a prompt in which we can proceed as discussed in this
> lesson, with the advantage that some functions are already provided
> for us, such as `seekStripDecision` (which replaces our `advance`) or
> `ls` and `get`, which allow to list and get TES locations.
Expand All @@ -205,7 +205,7 @@ functors](loki-functors.html)!
> `Bender` also provides a useful command `dst-dump`, which is a quick way of
> figuring out what objects are present on a `DST` and where. Try out:
> ```
> lb-run Bender dst-dump -f -n 100 00035742_00000002_1.allstreams.dst
> lb-run Bender/latest dst-dump -f -n 100 00035742_00000002_1.allstreams.dst
> ```
> The `-f` option tells `Bender` to try and "unpack" the locations such as
> `/Event/AllStreams/pPhys/Particles` that we mentioned above, while `-n 100`
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112 changes: 56 additions & 56 deletions minimal-dv-job.md
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Expand Up @@ -5,15 +5,15 @@ subtitle: Running a minimal DaVinci job locally
minutes: 10
---

[Looping event-by-event](interactive-dst.html) over a file and [inspecting
interesting quantities with LoKi functors](loki-functors.html) is great for
exploration: to checking that the file contains the candidates you need, that
[Looping event-by-event](interactive-dst.html) over a file and [inspecting
interesting quantities with LoKi functors](loki-functors.html) is great for
exploration: to checking that the file contains the candidates you need, that
the topology makes sense, and so on.
It's impractical for most cases, though, where you want _all_ the candidates
your trigger/stripping line produced, which could be tens of millions of
It's impractical for most cases, though, where you want _all_ the candidates
your trigger/stripping line produced, which could be tens of millions of
decays.
In these cases we use DaVinci, the application for analysing high-level
information such as tracks and vertices, which we'll look at in this lesson to
In these cases we use DaVinci, the application for analysing high-level
information such as tracks and vertices, which we'll look at in this lesson to
produce a ROOT ntuple.

> ## Learning Objectives {.objectives}
Expand All @@ -22,23 +22,23 @@ produce a ROOT ntuple.
> * Inspect the ntuple output
> * Set up the job to run in Ganga
With some stripped data located, it's useful to store the information on the
With some stripped data located, it's useful to store the information on the
selected particles inside an ntuple.
This allows for quick, local analysis with [ROOT](https://root.cern.ch/),
rather than always searching through a DST that contains lots of things we're
This allows for quick, local analysis with [ROOT](https://root.cern.ch/),
rather than always searching through a DST that contains lots of things we're
not interested in.

As well as being the application that runs the stripping,
[DaVinci](http://lhcb-release-area.web.cern.ch/LHCb-release-area/DOC/davinci)
allows you to access events stored in DSTs and copy the information to ROOT
As well as being the application that runs the stripping,
[DaVinci](http://lhcb-release-area.web.cern.ch/LHCb-release-area/DOC/davinci)
allows you to access events stored in DSTs and copy the information to ROOT
ntuples.
You tell DaVinci what you want it to do through _options files_, written in
You tell DaVinci what you want it to do through _options files_, written in
Python.
There are lots of things you can do with DaVinci options files, as there's lots
of information available on the DST, but for now we'll just work on getting the
There are lots of things you can do with DaVinci options files, as there's lots
of information available on the DST, but for now we'll just work on getting the
bare essentials up and running.

Our main tool will be the `DecayTreeTuple` object, which we'll create inside a
Our main tool will be the `DecayTreeTuple` object, which we'll create inside a
file we will call `ntuple_options.py`:

```python
Expand All @@ -55,38 +55,38 @@ dtt.Inputs = ['/Event/{0}/Phys/{1}/Particles'.format(stream, line)]
dtt.Decay = '[D*(2010)+ -> (D0 -> K- pi+) pi+]CC'
```

This imports the `DecayTreeTuple` class, and then creates an object called
This imports the `DecayTreeTuple` class, and then creates an object called
`dtt` representing our ntuple.
Once DaVinci has run, the resulting ntuple will be saved in a folder within the
Once DaVinci has run, the resulting ntuple will be saved in a folder within the
output ROOT file called `TupleDstToD0pi_D0ToKpi`.

The `Inputs` attribute specifies where `DecayTreeTuple` should look for
particles, and here we want it to look at the output of the stripping line
The `Inputs` attribute specifies where `DecayTreeTuple` should look for
particles, and here we want it to look at the output of the stripping line
we're interested in.

As stripping lines can save many decays to a DST, the `Decay` attribute
As stripping lines can save many decays to a DST, the `Decay` attribute
specifies what decay we would like to have in our ntuple.
If there are no particles at the `Input` location, or the `Decay` string
If there are no particles at the `Input` location, or the `Decay` string
doesn't match any particles at that location, the ntuple will not be filled.

> ## Decay descriptors {.callout}
>
> There is a special syntax for the `Decay` attribute string, commonly called
> There is a special syntax for the `Decay` attribute string, commonly called
> 'decay descriptors', that allow a lot of flexibility with what you accept.
> For example, `D0 -> K- X+` will match any D0 decay that contains one
> For example, `D0 -> K- X+` will match any D0 decay that contains one
> negatively charged kaon and one positively charged track of any species.
> More information the decay descriptor syntax can be found on the [LoKi decay
> finders TWiki
> More information the decay descriptor syntax can be found on the [LoKi decay
> finders TWiki
> page](https://twiki.cern.ch/twiki/bin/view/LHCb/FAQ/LoKiNewDecayFinders).
Now we need to tell DaVinci how to behave.
The `DaVinci` class allows you to tell DaVinci how many events to run over,
what type of data is being used, what algorithms to run over the events, and so
The `DaVinci` class allows you to tell DaVinci how many events to run over,
what type of data is being used, what algorithms to run over the events, and so
on.

There are [many configuration
attributes](http://lhcb-release-area.web.cern.ch/LHCb-release-area/DOC/davinci/releases/v41r2/doxygen/py/dc/d2f/class_da_vinci_1_1_configuration_1_1_da_vinci.html#ac788f6a80f5f61d47056debe7b86ca71)
defined on the `DaVinci` object, but we will only set the ones that are
There are [many configuration
attributes](http://lhcb-release-area.web.cern.ch/LHCb-release-area/DOC/davinci/releases/v41r2/doxygen/py/dc/d2f/class_da_vinci_1_1_configuration_1_1_da_vinci.html#ac788f6a80f5f61d47056debe7b86ca71)
defined on the `DaVinci` object, but we will only set the ones that are
necessary for us.

```python
Expand All @@ -106,40 +106,40 @@ DaVinci().CondDBtag = 'sim-20130522-1-vc-md100'
DaVinci().DDDBtag = 'dddb-20130929-1'
```

Nicely, a lot of the attributes of the `DaVinci` object are self-explanatory:
`InputType` should be `'DST'` when giving DaVinci DST files; `PrintFreq`
defines how often DaVinci should print its status; `DataType` is the year of
data-taking the data corresponds to, which we get from looking at the
bookkeeping path used to get the input DST; `Simulation` should be `True` when
using Monte Carlo data, `Lumi` defines whether to store information on the
integrated luminosity the input data corresponds to; and `EvtMax` defines how
Nicely, a lot of the attributes of the `DaVinci` object are self-explanatory:
`InputType` should be `'DST'` when giving DaVinci DST files; `PrintFreq`
defines how often DaVinci should print its status; `DataType` is the year of
data-taking the data corresponds to, which we get from looking at the
bookkeeping path used to get the input DST; `Simulation` should be `True` when
using Monte Carlo data, `Lumi` defines whether to store information on the
integrated luminosity the input data corresponds to; and `EvtMax` defines how
many events to run over, where a value of `-1` means "all events".

The `CondDBtag` and `DDDBtag` attributes specify the exact detector conditions
The `CondDBtag` and `DDDBtag` attributes specify the exact detector conditions
that the Monte Carlo was generated with.
Specifying these tags is important, as without them you can end up with the
Specifying these tags is important, as without them you can end up with the
wrong magnet polarity value in your ntuple, amongst other Bad Things.
You can find the values for these tags in the [bookkeeping
file](data/MC_2012_27163003_Beam4000GeV2012MagDownNu2.5Pythia8_Sim08e_Digi13_Trig0x409f0045_Reco14a_Stripping20NoPrescalingFlagged_ALLSTREAMS.DST.py)
You can find the values for these tags in the [bookkeeping
file](data/MC_2012_27163003_Beam4000GeV2012MagDownNu2.5Pythia8_Sim08e_Digi13_Trig0x409f0045_Reco14a_Stripping20NoPrescalingFlagged_ALLSTREAMS.DST.py)
we downloaded earlier.

> ## Database tags {.callout}
>
> Generally, the `CondDB` and `DDDB` tags are different for each dataset you
> Generally, the `CondDB` and `DDDB` tags are different for each dataset you
> want to use, but will be the same for all DSTs within a given dataset.
> When using simulated data, *always* find out what the database tags are for
> When using simulated data, *always* find out what the database tags are for
> your dataset!
> For real collision data, you shouldn't specify these tags, as the default
> tags are the latest and greatest, so just remove those lines from the options
> For real collision data, you shouldn't specify these tags, as the default
> tags are the latest and greatest, so just remove those lines from the options
> file.
In order to run an algorithm that we have previously created, we need to add it
In order to run an algorithm that we have previously created, we need to add it
to the `UserAlgorithms` list.
The `TupleFile` attribute defines the name of the ROOT output file that DaVinci
The `TupleFile` attribute defines the name of the ROOT output file that DaVinci
will store any algorithm output in, which should be our ntuple.

All that's left to do is to say what data we would like to run over.
As we already have a data file [downloaded locally](files-from-grid.html), we
As we already have a data file [downloaded locally](files-from-grid.html), we
define that as our input data.

```python
Expand All @@ -151,19 +151,19 @@ IOHelper().inputFiles([
], clear=True)
```

This says to use the `.dst` file that is in the same directory as the options
This says to use the `.dst` file that is in the same directory as the options
file, and to clear any previous input files that might have been defined.

That's it! We're ready to run DaVinci.

In the same folder as your options file `ntuple_options.py` and your DST file
In the same folder as your options file `ntuple_options.py` and your DST file
ending in `.dst`, there's just a single command you need run on `lxplus`.

```shell
$ lb-run DaVinci v41r2 gaudirun.py ntuple_options.py
$ lb-run DaVinci/v41r2 gaudirun.py ntuple_options.py
```

The full options file we've created, `ntuple_options.py`, is [available
The full options file we've created, `ntuple_options.py`, is [available
here](./code/minimal-dv/ntuple_options.py).
A slightly modified version that uses remote files (using an XML catalog as
[described here](files-from-grid.html)) is [available
Expand All @@ -173,12 +173,12 @@ here](./code/minimal-dv/ntuple_options_xmlcatalog.py)
>
> A microDST (or µDST) is a smaller version of a DST.
> Some stripping lines go to µDSTs, and some go to DSTs.
> There are two things that need changing in our options file in order to have
> There are two things that need changing in our options file in order to have
> it work when it is used with a stripping line that goes to a µDST:
>
> 1. The `DecayTreeTuple.Inputs` attribute should start at the word
> `Phys`; and
> 2. The `RootInTES` attribute on the `DaVinci` object has to be set to
> 2. The `RootInTES` attribute on the `DaVinci` object has to be set to
> `/Event/$STREAM`
>
> In context, the changes look like
Expand Down

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