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2023-09-06 15:56:29 +02:00
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README.md
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@ -54,10 +54,9 @@ In case of installation from source, so different location of the code and conda
### Before beamtime<a name="usage1"></a>
* make directory in res/ space of corresponding pgroup and populate it with configuration files (name **ap** is used as directory name in examples below, but any name can be choosen) using **prepare.sh** script:
* make directory in res/ space of corresponding pgroup and populate it with configuration files using **prepare.sh** script:
```
$ mkdir p12345/res/ap
$ cd p12345/res/ap
$ cd p12345/res
$ /sf/jungfrau/applications/ap/scripts/prepare.sh
```
* make corresponding changes in the configuration files (see section [Configuration files](#config)):
@ -74,12 +73,12 @@ In case of installation from source, so different location of the code and conda
* put in ap/CELL directory cell files of the protein which will be exposed during beamtime (format of the files should be readable by crystfel). Name of the cell files needs to be <cell_name>.cell.
```
$ ls res/ap/CELL
$ ls res/ap_config/CELL
lyso.cell hewl.cell
```
**HINT** - in case there are several space group at which protein can be indexed, it's possible to run automatically indexing in the *alternative* space group. To do this - provide an alternative space group settings in the file <cell_name>.cell_alternative. Example:
```
> $ ls res/ap/CELL
> $ ls res/ap_config/CELL
lyso.cell chim.cell chim.cell_alternative
```
runs with the <cell_name>=lyso will be indexed using lyso.cell file, while for the <cell_name>=chim - indexing will be done twice, using chim.cell and chim.cell_alternative files (and results of both indexing will be filled in logbook)
@ -89,7 +88,7 @@ In case of installation from source, so different location of the code and conda
* 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
$ ls res/ap_config/credentials*json
credentials.json credentials-1.json credentials-2.json credentials-3.json
```
***RECOMMENDATION*** - use/generate new credentials files for each beamtime to not expose experiment information
@ -130,7 +129,7 @@ $ ssh psi_account@sf-l-001
```
* go to the directory with configuration files (prepared in the [Before Beamtime](#usage1) step):
```
$ cd /sf/alvra/data/p12345/res/ap
$ cd /sf/alvra/data/p12345/res/ap_config
```
* start automatic processing tool execution:
```
@ -142,7 +141,7 @@ $ /sf/jungfrau/applications/ap/scripts/ap.sh
* if running from your account : Ctrl-C in corresponding session
* if running by other account - put file STOP inside configuration directory
```
$ touch /sf/alvra/data/p12345/res/ap/STOP
$ touch /sf/alvra/data/p12345/res/ap_config/STOP
```
(if such file is present inside directory - new automatic processing tool will not start, so remove file before re-starting the tool)
@ -159,12 +158,12 @@ $ grep unique_acquisition_run_number raw/run0206*/meta/acq*.json
or look at logbook, **unique_acquisition_run_number** is the first column of spreadsheet
check that there are no jobs with such numbers/name running, looking at CURRENT_JOBS.txt file or *squeue*
remove res/ap/output/run*4048-4071*.index* files to re-run indexing for that scan
remove res/ap_config/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
```
$ touch res/ap/NO_INDEXING
$ touch res/ap_config/NO_INDEXING
```
once this file is removed - all not indexed runs will be processed by the tool