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2023-08-22 11:50:18 +02:00
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@ -25,8 +25,20 @@ Automatic Processing tool checks for the new files/runs produced by sf-daq and r
### Pre-installed software (recommended)
Automatic Processing tool is installed in /sf/jungrau/applications/ap place and it's recommended to use if from that place (all examples below will be using that tool place).
Installed conda environment can be activated with
> $ source /sf/jungfrau/applications/miniconda3/etc/profile.d/conda.sh
>
> $ conda activate ap
### Installation from source
git, conda (for gspread)
Automatic Processing tool can also be installed from scratch with:
> $ git clone https://gitlab.psi.ch/sf-daq/ap.git # or via ssh with "git clone git@gitlab.psi.ch:sf-daq/ap.git"
>
> $ conda create -n ap gspread
>
> $ conda activate ap
In case of installation from source, so different location of the code and conda environment - change correspondingly line in scripts/env_setup.sh
## Configuration files<a name="config"></a>
Here description of configuration files will be, together with format and hints of usage
@ -71,7 +83,7 @@ Here description of configuration files will be, together with format and hints
* create (an empty) google spreadsheet
* create (several distinct) credentials files (see section [google authentication] how to create service accounts if not done before) and store them with the names in the config directory (it's important to have file with name credentials.json and have few(3 is enough) with names credentials-1.json, credentials-2.json...):
* create (several distinct) credentials files (see section [google authentication](#google-api) how to create service accounts and keys if not done before) and store them with the names in the config directory (it's important to have file with name credentials.json and have few(3 is enough) with names credentials-1.json, credentials-2.json...):
> $ ls res/ap/credentials*json
>
>credentials.json credentials-1.json credentials-2.json credentials-3.json
@ -81,14 +93,13 @@ Here description of configuration files will be, together with format and hints
* give write access to the google spreadsheet to the service-accounts (recommended) or give full editor access to all who know url of the logbook(quicker, but not recommended action). To find e-mails of the service accounts:
> $ grep client_email credentials*json
* edit env_setup.sh file to fill URL_TO_GOOGLE_SPREADSHEET(https://...) to the LOGBOOK variable
* setup/prepare spreadsheet for automatic filling:
> $ source /sf/jungfrau/applications/miniconda3/etc/profile.d/conda.sh
> $ . ./env_setup.sh
>
> $ conda activate sf-dap
>
> $ python /sf/jungrau/applications/ap/ap/update-spreadsheet.py --setup --log URL_TO_GOOGLE_SPEADSHEET(https://...)
> $ python /sf/jungrau/applications/ap/ap/update-spreadsheet.py --setup --log ${LOGBOOK}
* edit env_setup.sh file to fill URL_TO_GOOGLE_SPREADSHEET to the LOGBOOK variable
### During Beamtime<a name="usage2"></a>
@ -97,7 +108,7 @@ Here description of configuration files will be, together with format and hints
* login to swissfel online computing infrastructure with your personal PSI account:
> $ ssh psi_account@sf-l-001
* go to the directory with configuration files:
* go to the directory with configuration files (prepared in the [Before Beamtime](#usage1) step):
> $ cd /sf/alvra/data/p12345/res/ap
* start automatic processing tool execution
@ -126,7 +137,7 @@ in case of need to re-run indexing (new config parameters, new geometry file etc
>
> check that there are no jobs with such numbers/name running, looking at CURRENT_JOBS.txt file or *squeue*
>
> remove ap/output/run*4048-4071*.index* files to re-run indexing for that scan
> remove res/ap/output/run*4048-4071*.index* files to re-run indexing for that scan
#### pausing indexing<a name="usage2_pause"></a>
in case of unknown processing parameters (detector distance, geometry file(beam center), not yet known cell file...), it's possible to pause (not start indexing jobs) putting semaphore file NO_INDEXING in config directory