# Welcome to Detector Support Guidelines’s documentation!

Contents:

## Logging onto exflgateway

Most detector control and online calibration will require you to work from a host within the control network. This procedure describes how to log into exflgateway. From there you can access control network hosts if you have the correct privileges.

Note

Your account has to be registered to access the control network. You can do this by filling out this form, and obtaining the relevant signatures

1. if not using a DESY VPN connection, log on to bastion.desy.de if you need X forwarding:

       ssh -X username@bastion.desy.de

   For using port forwarding with a Jupyter notebook

       ssh -L XXXX:localhost:XXXX username@bastion.desy.de

   where you replace XXXX with a port number, e.g. 7999.

Note

Use ssh -Y on MacOs computers.

2. log on to exflgateway; you can do this directly when using a VPN connection:

       ssh -X exflgateway

   or for port forwarding

       ssh -L XXXX:localhost:XXXX exflgateway

   be sure to use the same port as before.

## Initializing a Karabo Environment for an Instrument

To initialize a Karabo environment for a specific instrument please use the instructions for one of the following scenarios:

### In the Hutch/Control Room

The control network client PCs should already point to the correct Karabo environment, so usually

    karabo-gui

should suffice. If the karabo-gui command is not found, try

    source ~/karabo/activate.

If this does not work either, please ask an instrument scientist or call CAS OCD.

### On exflgateway - GUI only

Log onto exflgateway (Logging onto exflgateway). Then activate the most up-to-date Karabo environment and start the GUI:

    source /opt/karabo/karabo/activate
    karabo-gui

In the login dialog,

The Karabo logon dialog.

connect to the GUI server corresponding to your instrument:

Instrument | Hostname
--- | ---
SPB | spb-rr-sys-con-gui1
FXE | fxe-rr-sys-con-gui1
SQS | sqs-rr-sys-con-gui1
SCS | scs-rr-sys-con-gui1
MID | mid-rr-sys-con-gui1
HED | hed-rr-sys-con-gui1

### On exflgateway - iKarabo

Log onto exflgateway (Logging onto exflgateway). Then activate the most up-to-date Karabo environment and start the GUI:

    source /opt/karabo/karabo/activate

You will now need to set-up the broker information for the respective instrument:

    export KARABO_BROKER_TOPIC=<INSTRUMENT>
    export export KARABO_BROKER=tcp://<SASE>-br-sys-broker-1:7777

where you should fill in <INSTRUMENT> and <SASE>:

Instrument | <INSTRUMENT> | <SASE>
--- | --- | ---
SPB | SPB | sa1
FXE | FXE | sa1
MID | MID | sa2
HED | HED | sa2
SCS | SCS | sa3
SQS | SQS | sa3

Now you can run iKarabo:

    ikarabo

Verify correct settings, but obtaining a list of devices for the instrument

    getDevices()

## Restarting Online Calibration

### Preface

Restarting the online calibration devices should happen as part of normal shift start-up and during trouble shooting. Please read the following sections first, in case you are not sure if a restart is actually needed:

General Detector DAQ Troubleshooting

### Before Restart

Since the restart process involves many device which act on input in an event driven (push) fashion, it is best to assure that no new data is input into the pipeline during the restart process. Either:

- stop the detector from sending data. DAQ can stay in monitoring mode
- if you do not want to stop the detector, switch the DAQ to ignore mode

### Restart via GUI

Follow this procedure in case you are on-site or otherwise have stable and fast access to a Karabo-GUI of the respective instrument.

1. Follow the instructions in Initializing a Karabo Environment for an Instrument to open a Karabo-GUI, then load the master project of the respective detector. The will be a sub-project for calibration, which contains a MANAGER scene.
2. In this scene click on the Restart servers button, as shown in the screenshot. This will restart all servers involved in online calibration. It will take about 1 minute and will output the message “All servers restarted!” in the log window right above the button.
3. After restarting all servers, click Start pipeline to actually start the pipeline again. This might take a few minutes, especially until all constants have been loaded. The state color field will turn to green and the general state will turn to active when it is done, as shown in the screenshot.

Restarting servers and re-initializing calibration pipeline for MHz detectors.

### Remote restart via command line

Follow this procedure in case you are giving remote support and do not have stable and fast access to a Karabo-GUI.

1. The restart needs to happen with the control network, please follow the instructions given at Logging onto exflgateway

2. You will also need to set-up a Karabo environment for the respective interface: Initializing a Karabo Environment for an Instrument

3. Open an iKarabo console:

       ikarabo

4. Get the restart device and restart the device servers:

       d = getDevice("<DEVICE_ID>")
       d.restart()
       waitUntil(lambda: d.state == State.ACTIVE)

   where <DEVICE_ID> is the following for the different instruments:

   Instrument | <DEVICE_ID>
   --- | ---
   SPB | SPB_DET_AGIPD1M-1/CAL/RESTART
   MID | MID_DET_AGIPD1M-1/CAL/RESTART
   FXE | FXE_DET_LPD1M-1/CAL/RESTART
   SCS | SCS_DET_DSSC1M-1/CAL/RESTART

   Note

   The SQS and HED instrument currently do not use MHz detectors and thus all calibration devices are started from the Karabo project.

   The last command will only return after the pipeline is initialized again.

5. Now re-init the calibration pipeline

       d = getDevice("<DEVICE_ID>")
       d.start_pipeline()
       waitUntil(lambda: d.state == State.ACTIVE)

   where <DEVICE_ID> is the following for the different instruments:

   Instrument | <DEVICE_ID>
   --- | ---
   SPB | SPB_DET_AGIPD1M-1/CAL/INIT
   MID | MID_DET_AGIPD1M-1/CAL/INIT
   FXE | FXE_DET_LPD1M-1/CAL/INIT
   SCS | SCS_DET_DSSC1M-1/CAL/INIT

   The last command will only return after the pipeline is initialized again.

Note

If for any reasons one or the other of the above needed devices are not running, ask the instrument to instantiate them via the Karabo-GUI. They are in the online calibration subproject. You can also call CAS OCD.

### After restart - push initial data

Regardless of how you restarted the pipeline, after the restart you should first leave, or instruct the instrument operator to leave the filter pulse expression and the output every nth trains at the default value. They should then have the detector push data.

The pipeline is fully initialized if all components show green state colors on the MANAGER scene. This may take up to about 30 seconds - the detector can continuously produce data during this time.

After all indicators are green, the filter expressions may be set to lower values.

### Restarting only parts of the pipeline

If only individual components of the pipeline have crashed or are otherwise disfunctional, you can attempt to restart only these, instead of restarting everything. This might be considerably faster than a full restart.

0. Stop the detector from producing data

1. Shutdown those devices which need a restart in case they are still alive

2. Make sure the pipeline is in an idle state: either click Reset in the MANAGER scene, or on the command line, find the calibration manager device and then use its reset method:

       d = getDevice("<DEVICE_ID>")
       d.resedt()
       waitUntil(lambda: d.state == State.PASSIVE)

   where <DEVICE_ID> is the following for the different instruments:

   Instrument | <DEVICE_ID>
   --- | ---
   SPB | SPB_DET_AGIPD1M-1/CAL/CAL_MANAGER
   MID | MID_DET_AGIPD1M-1/CAL/CAL_MANAGER
   FXE | FXE_DET_LPD1M-1/CAL/CAL_MANAGER
   SCS | SCS_DET_DSSC1M-1/CAL/CAL_MANAGER

3. Now start the pipeline using either the Start pipeline button on the MANAGER scene, or via the command line

       d = getDevice("<DEVICE_ID>")
       d.start_pipeline()
       waitUntil(lambda: d.state == State.ACTIVE)

   As with a full restart the overall state should turn to ACTIVE once the restart is done.

## Restart Offline Calibration

In the following the procedures for verifying operation and restarting of offline calibration are described

### Preface

The offline calibration runs on max-exfl016 under the xcal user account. You need to be able to kinit yourself into that account in case you want to perform any of the below procedures. Please ask ITDM for access.

You can login direcly from within the DESY network.

    kinit <username>
    ssh xcal@max-exfl016

Remotely, when not on a VPN you need to go via Bastion:

    ssh <username>@bastion.desy.de
    ssh xcal@max-exfl016

Warning

You are working on the production offline calibration service. Please proceed with care

### Checking Status

The following status checks should be performed to verify if the service is working correctly:

#### Is the Service Running

The service is run as a Python webservice. To check if it is running type:

    ps aux | grep webservice

This should result in output similar to

    xcal     15440  0.0  0.0 401188 36464 ?        Sl   Jun10   0:20 /home/xcal/calibration_webservice_venv/bin/python /home/xcal/calibration_webservice/webservice/webservice.py --mode prod --logging INFO --config-file /home/xcal/calibration_webservice/webservice/webservice.yaml
    xcal     17569  0.0  0.0 112812  1020 pts/1    S+   13:49   0:00 grep --color=auto webservice
    xcal     21500  0.0  0.0 222752 87788 ?        S    Jun02   2:23 /home/xcal/calibration_webservice_venv/bin/python /home/xcal/calibration_webservice/webservice/serve_overview.py --config /home/xcal/calibration_webservice/webservice/serve_overview.yaml

It is important that the first line is present.

As the offline calibration webservice is running using a virtual environment, you will need to activate this environment before you go further.

The path for the bin folder for the python environment should be shown as the above output. to activate this python environment write:

source /home/xcal/calibration_webservice_venv/bin/activate

#### Checking the Logs

The logs are located the max-exfl016:8008 web page:

or they can be accessed in the webservice run subdirectory:

    tail -500f calibration_webservice_run/web.log

You should see entries similar to:

    2019-07-04 12:20:48,988 - root - INFO - Copying /gpfs/exfel/exp/SQS...
    2019-07-04 12:20:48,996 - root - INFO - Copying /gpfs/exfel/exp/SQS...
    2019-07-04 12:20:49,004 - root - INFO - Copying /gpfs/exfel/exp/SQS...
    2019-07-04 12:20:49,013 - root - INFO - Copying /gpfs/exfel/exp/SQS...
    2019-07-09 16:11:29,966 - root - INFO - python -m xfel_calibrate.calibrate JUNGFRAU CORRECT ...
    2019-07-09 16:11:36,987 - root - INFO - SUCCESS: Started correction: proposal 900063, run 1051

These will tell you the last processes that were started. Especially useful are the lines which start with python -m xfel_calibrate.calibrate … as these tell you which calibration jobs were launched and with which parameters.

#### Checking for running Jobs

The following command will display a list of currently running jobs on Maxwell:

    squeue  -u xcal -o "%.18i %60j %.3t %.10M %R"

You should check that jobs are not piling up, e.g. have been queued for a long time. If this is the case, the instrument should be contacted.

### Restarting the Service

Restarting the calibration webservice should rarely be necessary, and if so, should only be done with great care as it can affect the entire facility. If you are unsure, first consult with other colleagues.

1. Check if the service process is still running and kill it:

       ps aux | grep webservice.py

   Note down the PID and kill that process if it is running:

       kill -9 <PID>

2. Restart the service:

       cd calibration_webservice_run
       nohup /home/xcal/calibration_webservice_venv/bin/python /home/xcal/calibration_webservice/webservice/webservice.py --mode prod --logging INFO --config-file /home/xcal/calibration_webservice/webservice/webservice.yaml > nohup_webservice.out&

3. Verify it is running by checking for the process:

       ps aux | grep webservice.py

   and the logs:

       tail -500f /home/xcal/calibration_webservice_run/web.log

4. Notify the instruments that the service was down:

       send-to: <all instrument emails>
       subject: Restart of Calibration Webservice

       The calibration webservice required a restart due to....

       The restart was performed in the time from XXX to YYY. During this time some jobs submitted through the
       MDC or calibrate_dark script may not have been handled. If you submitted jobs during this time, please consider
       resubmitting them. If you have questions, please contact det-support@xfel.eu. Please also forward this information
       to your users.

### Restarting the overview webpage

Previous first step for restarting the calibration webservice should be performed then

2. Restart the overview page:

       cd calibration_webservice_run
       nohup /home/xcal/calibration_webservice_venv/bin/python /home/xcal/calibration_webservice/webservice/serve_overview.py --config /home/xcal/calibration_webservice/webservice/serve_overview.yaml > nohup_serve_overview.out &

3. Verify it is running by checking for the process:

       ps aux | grep webservice.py

   and the webpage through max-exfl16:8008 from a browser accessing the maxwell network.

## Requesting Dark Characterization

Dark characterization is currently done via max-exfl016:8008:

1. Record the dark images as appropriate for the detector in use. This will result in either one or three relevant runs.
2. Migrate these runs to Maxwell using the metadata catalogue.
3. Open a firefox browser from xfel network and access max-exfl016:8008
4. Go to Request dark section and enter the CYCLE and PROPOSAL numbers, then select the INSTRUMENT. Select the needed detector from the choices appearing and enter the dark runs numbers.

## Connecting a Single Module’s Raw Data to the Bridge

Follow the procedure below to connect a ZMQ bridge directly to a single modules data stream in extraordinary case and in the only supported way.

0. Talk to the users and instrument. Question if they really needs this option. Then question again if they really really need it and if they know how to handle raw data from the detector. Tell them that for any calibration they will be on their own, and that it impacts online views of the instrument.
1. Stop the detector from producing data
2. Remove the module for the mandatory modules list, found at the bottom left corners of the CORRECTED and RAW overview scenes, in case it is configured there.
3. Find the corresponding SPLITTER device by searching the topology for the module location, e.g. FEM_SPLITTER_Q1M1.
4. On this device, set Output to GPU to false and select set Output to to B. This will make sure no data is forwarded to the online pipeline anymore.
5. On the same device you can now reconfigure Filter pulses to individual ranges other than the global setting in the manager scene.
6. In a differnt Karabo-GUI, open the ZMQ Bridge project corresponding to the instrument and detector. Navigate to the ZEROMQ/RAW device and shut it down. Now reconfigure the bridge device to …output_1 instead of …output_0. Make sure it also connects to the correct splitter device id. Then reinstantiate the device.
7. Finally, you can now decrease the train module number on the corresponding data aggregator. You will find them in the corresponding subproject. They are named by channel, where for AGIPD e.g. Q1M1 is channel 0 and Q4M4 is channel 15. You will find the field as DataDispatcher.trainStride. Note that 1, and thus every train, will likely fail. A train stride of 2 has worked in the past.

To revert, step through the sequence in reversed order.

## Disabling Calibration Constants

Sometimes it turns out that faulty calibration parameters have been injected. In this case disabling the relevant constant versions will assure that future correction tasks (both online and offline) will not use these parameters anymore.

Warning

This procedure can have severe impact on detector calibration. Only proceed if you know what you are doing!

### Screencast of Procedure

How to disable calibration constants in the database backend.

### Step by Step Instructions

Disabling is done via the calibration database backend.

1. Navigate to the database backend and log in using your normal LDAP credentials. For the following steps you will need elevated access rights, which can be requested at det-support@xfel.eu.

   Logging into the calibration database backend

2. After logging in, navigate to the Admin area, and here to Calibration constant versions. This will list you the latest calibration parameters injected into the database.

   The calibration database version overview. Setting a filter is highlighted.

3. You should now apply filters to find the faulty constants. It is usually most appropriate to filter by Physical device and Start date. The Physical device filter is fuzzy; hence entering e.g. AGIPD will list all AGIPD modules.

   The Start date filter will usually match when the data used for characterization was taken.

   Setting filter options on the calibration constant version page and selecting versions to disable

4. After having located the faulty parameters you need to disable them. For Dark image derived constants usually come in triplets: Noise, Offset, and Bad Pixels, or for AGIPD additionally with Thresholds. You should disable each one, by clicking on the pen symbol at the far right and editing the constant version in a new tab.

   The edit calibration constant version dialog.

5. On the edit page, scroll to the bottom and uncheck the two boxes labelled deployed and good quality`. Then click save.

   > Disabling deployed and good quality markers for a constant version.

6. Refreshing the filtered calibration constant version view should now list these calibration parameters as disabled.

   Disabled versions in the overview.

## Offline Characterization Reports

All offline characterization tasks run via xfel_calibrate should produce a report in the report folder given upon task execution. This report is generated from the Jupyter notebooks which are run as part of the processing job.

For dark characterization tasks launched using the Requesting Dark Characterization in the max-exfl016:8008 web page, the output reports can be access through:

> 1. Accessing last report characterization reports from max-exfl016:8008 as shown

> 2. Accessing all dark reports requested for all Instruments from the link at the end of Last characterization runs.

> 3. In a standardized location, identified as:

>        /gpfs/exfel/d/cal/caldb_store/xfel/reports/{instrument}/{det_instance}/dark/dark_{proposal}_{runs}_{time_stamp}

For all other task the location will vary according to the input.

Reports are in PDF format and may be opened using any standard PDF viewer.

### No Report is Generated

If you have launched a characterization job and after a reasonable time (~ 30 minutes) no report has appeared in the anticipated location, the following points should be checked:

- has the job been executed and finished? Check on Maxwell if it is very busy and if jobs on the xcal account are still queued:

      ssh user@max-exfl
      squeue  -u xcal -o "%.18i %60j %.3t %.10M %R"

- has the job been launched at all? Check the logs of the calibration webservice, if your job has launched without an error:

  > 1. Check written logs in Webservice log section in max-exfl016:8008 web page.

  > 2. With permission for xcal, check log file directly:

  >        ssh xcal@max-exfl016
  >        grep "{DETECTOR} {TYPE}" calibration_webservice_run/webservice/web.log

  Here {DETECTOR}` should be e.g. AGIPD and {TYPE} frequently will be DARK.

- were there failures in the report rendering? Checking this is a bit more tedious and a solution will require intervention by an expert as the notebook generating the code will likely have to be updated.

  First check if there is a an entry for your characterizaton task in the temp directory of the webservice. It should not have been deleted after job completion if rendering errors were present:

      ssh xcal@max-exfl016
      ll -tr calibration_webservice_run/webservice/temp

  will list you a time sorted list of entries in the directory, with each folder named slurm_out_<detector>_<task>_t<time_stamp>. Investigate those closest to the time when you launched the characterization job. In the slurm sub-folders you will find the notebooks executed and an inputParameters.rst. Inspecting this file should allow you to confirm the corrected given input parameters.

  Now check the output of the slurmXXX.out file with the latest file modification date. This is the output from the slurm job responsible for running the PDF rendering process and finally copying the final report to the output directory. Hence it will contain any errors that prevented correct execution and led to the missing report. Inform det-support@xfel.eu about your observations.

### Report is Generated with many errors.

- has the constants been created and injected to the database? If constants were injected to the database, the notebook should have printed messages similar to:

      Inject Offset constants from 2020-07-23 09:06:39+02:00
      Inject Noise constants from 2020-07-23 09:06:39+02:00

  1. If they are injected to the database, then the errors might be related to the plotting in the report. This should not prevent the online calibration from retrieving the constants as long as it was injected with the right parameter conditions.
  2. If they were not injected to the database, then check if all Input parameters in the first report pages are correct and inform det-support@xfel.eu about your observations to correct the input configurations from the offline calibration webservice.

## Webservice Overview

At max-exfl016:8008 an overview of the current calibration webservice status is available.

Note

This is currently still considered an experimental service, so there might be unexpected down times.

### Maxwell Status

The Maxwell overview status panel. It indicates the current number of busy and free nodes, as well as nodes available on the xcal reservation.

It will also give you a recommendation on whether it makes sense to submit to a user proposal reservation, if available, or if there are enough free nodes on the general cluster partition.

Note

This is only a momentary snap shot and may change any second.

### Running Calibration Jobs

An overview of the jobs currently being run through the webservice. Jobs currently being executed are shown in green, pending jobs are indicated yellow.

### Last Characterization Runs

Last characterizations for each instrument and detector. This will indicate the total file size of files in the run(s), link to the calibration database entries for this detector, and provide a download link for the PDF report, if one was generated.

### Webservice Log

This outputs the last lines of the log files of the webservice.

## General Detector DAQ Troubleshooting

The following general points should be verified in case a detector is reported to have DAQ problems:

### No data written to disk

- Verify that indeed no data is written to disk. You need to be on the control-network to see, Logging onto exflgateway in case you are not in the hutch. Go to one of the online cluster servers:

  SASE | suggested server
  --- | ---
  1 | exflonc10
  2 | exflonc17
  3 | exflonc14

  Then check file sizes for the last run:

      ssh <username>@<server>
      ll -alh /gpfs/exfel/exp/<instrument>/<cycle>/<proposal>/raw/<run>

  For the MHz detector you expect file sizes in the gigabyte range.

- Is the DAQ in the RECORD state? If not put the DAQ into the RECORD state.

- Is the detector sending data? Check that the detector is powered, configured and sending data. You can further verify this via the RunDeck tool, which is linked in the browser bookmarks of each instrument.

- Are the data aggregators in an error state? The DAQ projects are subprojects of the MHz detector top-level project; check the 16 XTDF data aggregators therein in the project panel. If they are in error state, call ITDM OCD.

### No data on Online Views

- Is the DAQ in the MONITOR or RECORD state? If not put the DAQ into into the MONITOR.
- Is the detector sending data? Check that the detector is powered, configured and sending data. You can further verify this via the RunDeck tool, which is linked in the browser bookmarks of each instrument.
- Is the online calbration pipeline started, and are constants loaded? You can check this on the MANAGER scene, all devices should be active, and indicator lights should be green for any device connected to a data output. Date and times should be shown for all constants.
- Is the pipeline output data to the GUI? This can be checked in the MANAGER scene. The APPENDER devices show time of flight and update rates. Are these updating? If not, check if the minimum number of modules configured matches the number of modules in the detector actually producing data. If updates are happening, the GUI is not displaying them: call CAS OCD.

## General Online Calibration Troubleshooting

### Restart Servers Script does not run through

Restarting the calibration pipeline servers is the initial step of re-initializing the larger calibration pipelines. For AGIPD, DSSC and LPD, this is done using the restart server script (see Restarting Online Calibration). In case of misconfiguration or addition of new servers this script has stalled in the past. You will see this if updates in the restart server status field stop before “Restarted all servers” is displayed. Failures have previously occurred for the following reasons:

- a new device server had been added on one of the hosts the restart works on:

  Instrument | Hosts | Account
  --- | --- | ---
  SPB | spb-br-sys-cal-[0-7] | spbonc
  FXE | sa1-br-sys-cal-[0-7] | fxeonc
  SCS | scs-br-sys-cal-[0-7] | scsonc
  SQS | sqs-br-sys-cal-1 | sqsonc
  MID | mid-br-sys-cal-[0-7] | midonc
  HED | hed-br-sys-cal-1 | hedonc

  Such new device servers, which should usually not be restarted, need to be added to the Omit from restart field of the RESTART device which an expression that matches (parts of) the server naming (see Fig. 14).

- a webserver on one of the hosts is not running. The restart works by calling karabo webservers. Hence, if they are not running, it will fail. SSH onto the respective hosts (see table above) and check that the servers are running:

      source /scratch/[account]/karabo/activate
      karabo-check

  Should include a line

      webserver: up (pid 1249) 2475094 seconds, normally down, running

  If not one needs to investigate why it is not running (CAS OCD will help).

- a webserver used to restart calibration is misconfigured in its filter settings:

      [spbonc@exflong01 ~]$ cat /scratch/spbonc/karabo/var/service/webserver/run
      #!/bin/bash
      # this file has been generated by ansible
      exec 2>&1
      exec envdir ../../environment env \
      karabo-webserver serverId=webserver \
      --port 8080 --filter cppspb_spb_cal_1 pyspb_spb_cal_1 mlspb_spb_cal_

  Note how it will only act on the servers specified. If a server runs on that host that does not match this criterion and is not exempt by the omit from restart settings, the restart will stall.

- the template used to address the webservers is misconfigured in the RESTART device.

The RESTART device configuration

### Start Pipeline Times Out on Initializing Devices

If the restart ran successfully and reinitializing devices has failed when clicking on Start Pipeline. This has happened for the following reasons in the past:

- the Detector is actively pushing data during a restart. This might result in a device not correctly initializing. In general: the DAQ can stay in Monitoring mode during restart, but the detector must not send data! If this happened restart the servers, and then try again.

- a Karabo installation on one of the hosts was not started at all. Check on each of an instruments hosts

  Instrument | Hosts | Account
  --- | --- | ---
  SPB | spb-br-sys-cal-[0-7] | spbonc
  FXE | sa1-br-sys-cal-[0-7] | fxeonc
  SCS | scs-br-sys-cal-[0-7] | scsonc
  SQS | sqs-br-sys-cal-1 | sqsonc
  MID | mid-br-sys-cal-[0-7] | midonc
  HED | hed-br-sys-cal-1 | hedonc

  that Karabo is running:

      source /scratch/[account]/karabo/activate
      karabo-check

  If not start it:

      karabo-start

  and try again.

- the execution environment of a GPU enabled server is not configured properly:

      cat /scratch/spbonc/karabo/var/service/pyspb_spb_cal_1/run
      #!/bin/bash
      # this file has been generated by ansible
      exec 2>&1
      exec envdir ../../environment env \
      PATH=/usr/local/cuda-10.1/bin/:$PATH \
      karabo-pythonserver serverId=pySPB/spb_cal_1 \
      Logger.priority=INFO

  Note how CUDA is added to the path. In general the code should not fail if no GPU is present, but rather it will lead to much slower processing (see …) for details)

  Also, cross check that the used CUDA version is installed and available.

      ll /usr/local/cuda-10.1

- an older installation has been started and device ids are already in use. This has happened a few times. Before we had GPUs available the online calibration was installed on other (CPU) only hosts. From time to time, something or someone seems to start these again, conflicting with the current installation. No calibration devices or servers should be running on exflonc hosts for the large detectors. You can check e.g. via iKarabo.

### Calibration Parameters are not loaded

After initializing devices the calibration manager device instructs all processing devices to load their respective calibration parameters. This will usually show itself by having the calibration devices stuck in CHANGING state and the calibration parameter dates empty. This has in the past failed for the following reasons:

- the detector is producing data when constants are loaded. This might lead to failures. Stop the detector, restart the pipeline and try again.

- the calibration DB remote devices are not running. These devices are under ITDM responsiblity, but may sometimes have note been initialized yet after a reboot or power failure. In general they run on the same hosts as the calibration pipeline under the xcal account:

  Instrument | Hosts | Account
  --- | --- | ---
  SPB | spb-br-sys-cal-[0-8] | xcal
  FXE | fxe-br-sys-cal-[0-8] | xcal
  SCS | scs-br-sys-cal-[0-8] | xcal
  SQS | scs-br-sys-cal-[0-8] | xcal
  MID | mid-br-sys-cal-[0-8] | xcal
  HED | mid-br-sys-cal-[0-8] | xcal

  Note how the instruments without MHz detectors also use these devices.

  You can identify this problem by grepping the calibration device logs for Resource temporarly not available:

      grep "Resource temporarily" /scratch/scsonc/karabo/var/log/pythonserver_scs_cal_1/current
      WARN  SCS_CDIDET_DSSC/CAL/OFFSET_CORR_Q1M2  : Could not find constant Offset: Resource temporarily unavailable
      WARN  SCS_CDIDET_DSSC/CAL/OFFSET_CORR_Q3M2  : Could not find constant Offset: Resource temporarily unavailable

  In such a case check the respective devices responsible for the SASE:

      ssh xcal@spb-br-sys-cal-0
      [xcal@exflong08 ~]$ source /scratch/xcal/karabo/activate
      [xcal@exflong08 ~]$ karabo-check
      pythonserver_sa1_daq_rcal_0: up (pid 32532) 59542 seconds, normally down, running

  If the server is not running, restart it or resolve the problem. The devices are configured to auto-start. Then restart the pipeline.

- detector operating settings do not match anything in the database. To investigate this, first check the the common operating conditions set on the CAL_MANAGER device if they are what you expect (if you know what to expect that is). An example is shown in Fig. 15. Note that beam_energy should usually be empty. Also you do not want any fields to display “None”. If this is the case, delete “None” such that the field is empty, or set it to a value.

  Example of common operating conditions for the SPB AGIPD.

  If you do not know what to expect, chances are that the last offsets were injected with reasonable settings to the calibration database. To check to the following:

  Navigate to the database backend and log in. Click Admin->Calibration constant versions and filter for the detector you are investigating by adding a physical device filter:

  Example of constants injected into the calibration database.

  Note that for AGIPD you will need to differentiate MID and SPB instances. If you know approximately when the last dark run was taken you can usually do this via the Start date column. If not, you will find the current module mapping here. The SPB AGIPD is the AGIPD1M1 instance, the MID the AGIPD1M2 instance.

  Click on a constant which contains the work Offset in its name. The click on the link under Condition. Here you will now find a list of Parameter conditions which you can inspect to see if their values match the expectations in the common operating conditions field.

  Note that the field will likely contain additional parameters not applicable to calibration parameters produced from dark images. These change much less frequently though, so setting the appropriate parameters for dark image derived parameters will suffice in most cases.

  Once you are done, click apply all on the calibration manager device, then click reset and finally init.

Note

The AGIPD pipeline will run if no flat field constants (FF) are found.

### “Wrong” Calibration parameters are loaded

Sometime other parameters than expected seem to be loaded. Most frequently, offsets are of older date than the users expect. Verify the following:

- have new offsets been characterized?, e.g. has the procedure for dark characterization been followed (see Requesting Dark Characterization). Has data been been migrated, before running the script? Is Maxwell particularly busy, such that jobs are queued? In this case it is advisable to wait till the jobs are finished and try to click reset, then click init in the CAL MANAGER to retrieve and use the correct constants. If you are unsure, you can check the database backend for the latest injected constants and verify these are the ones you expect.
- do the detector operating conditions match what is set in the CAL MANAGER device. This can quite frequently occur if operators have changed AGIPD operation scenarios from 1.1 MHz to e.g. 4.5 MHz or change the number of memory cells. click verify config on the karabo scene if available, which will check the table with the detector middle layer and generate the verification result on the CAL MANAGER status. If this button is not presence then ask if detector operations has recently been changed, and then adjust the settings as described in Calibration Parameters are not loaded.

### Pipeline Initialized but no Image Updates on the GUI

If all (expected) constants loaded, but pushing data through the pipeline does not result in corrected data being displayed, check the following:

- on the CAL MANAGER scene (see Fig. 18) is the RAW appender updating, are all splitter input rates updating according to the Output every nth train setting? If so, data is entering the pipeline and something went wrong on initialization. Perform the check mentioned above. If there are no updates, check that the DAQ is in monitoring/acquiring state and that the proper data sources are selected, try again. Follow general DAQ trouble shooting instruction (General Detector DAQ Troubleshooting).

- If you see updates on the splitters but no updated images, in the RAW appender, go to the RAW OVERVIEW scene and reduce the minimum number of modules required for forwarding data.

  APPENDER setting for online previews.

  If some modules are updating, but others are not pushing data into the pipeline. Check if the respective DAQ aggregators are in an error state and call ITDM OCD in case this is the issue. If the DAQ looks fine, use the run-deck tool to verify these modules are sending data. Troubleshoot the detector if not.

  In case you want to continue with a reduced number of modules, make sure the CORRECTED appender is also set to reflect this through setting parameter “min-modules=available number of modules”.

- the RAW appender is updating but the CORRECTED appender is not updating for an AGIPD detector, right after a pipeline restart. The MEDIUM GAIN ADJUST are not in the ACTIVE (green) state.

  This is normal. These devices need to first calculate some parameters, which can take up to a minute after first pushing data. It is important that all devices left of them have switched to ACTIVE. If this is the case, simply wait. If not, troubleshoot as above.

- the APPENDER rates are updating, but the images are not. This is likely then a GUI connection problem. Try a different GUI server and call CAS OCD.

Calibration pipeline overview scene of AGIPD. Other detectors look similar.

### Pipeline is slow

In general the pipeline has been shown to handle up to 256 images/s in various settings with about 2000ms latency for corrected data. A conservative always safe setting are train rate and pulse filter numbers which multiply to 128 images/s. This should give about 1500ms latency for corrected data. If this is not achieved check the following:

- the the output “every nth train” setting correct. It defaults to 50 on a restart and once the pipeline is initialized should be set to 10.

- Is the pulse filter setting correct. It accepts range expressions, but also lists. To increase useful data, e.g. in an alternating pulse pattern, add those data indices you would like forwarded to it, e.g. “0,2,4,5,6”, or use an range with stride, e.g. “range(0,250,2)”.

- If too aggressive settings have been chose, the pipeline updates will decouple and train matching rarely occurs at the final APPENDER. This can be identified by the following:

  - the latency of the APPENDER devices starts piling up or varying greatly
  - the update rates of pipeline components do not match the rate at the SPLITTER anymore, or have large variations.

  In either case, the pipeline should recover after a few seconds of streaming data with known safe settings, e.g. outputting every 10th train, and a filter of range(128).

Performance relevant settings on the manager scene.

- If a user wants single module data with low latency, you can connect to a singular modules data stream directly. There is a procedure here: Connecting a Single Module’s Raw Data to the Bridge.

### GPU related

- The GPU memory fields shows 0 MB free and are red. This is fine after a restart. They will update once the detector pushes data.
- The GPU memory still is not at zero but very low. This usually indicates that parts of the pipeline are not fully functional. Check the logs on the respective servers for any errors and check that it is connected to the correct DAQ output.

## Debugging the CalibrationDbRemote Devices

The so-called calibrationDbRemote devices are the access points to the calibration database, both for the online and the offline services. Retrieving and injecting constants through them are performed using ZMQ requests. The devices themselves run in a Karabo environment.

For online calibration one should check the procedures at General Online Calibration Troubleshooting for how to identify and debug problems with these devices.

The offline devices run under the xcal account on max-exfl016 in a Karabo environment installed in the /scratch/xcal/karabo folder. This installation is maintained by ITDM. Note the the folder is only accessible from max-exfl016; it is not shared across Maxwell hosts.

### Inspecting Logs

To inspect logs, log onto xcal@max-exfl016 and tail the log file of the device server:

    ssh xcal@max-exfl016
    tail -500f /scratch/xcal/karabo/var/log/pythonserver_max_web_rcal_0/current

This should result in an output similar to:

    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_5  : Waiting on data
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_5  : Saved file cal.1567178413.0473201.h5 at xfel/cal/agipd-type/agipd_siv1_agipdv11_m400/
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_5  : Start writing to Calibration Catalogue...
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_5  : Finnish writing to Calibration Catalogue...
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_5  : Registered cal.1567178413.0473201.h5 successfully

for when parameters are being written to the database, or:

    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_0  : Waiting on data
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_0  : Start searching in Calibration Catalogue...
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_0  : Got calibration: Offset (AGIPD1M1), meta_only: True
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_0  : Waiting on data
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_0  : Start searching in Calibration Catalogue...
    INFO  MAX_WEB_DATA/DM/CAL_REMOTE_0  : Got calibration: BadPixelsDarkCCD (FastCCD1), meta_only: False

when retrieving parameters from the database.

There are a total of 30 devices acting as access points, and most calibration routines will randomly pick one of these and retry contacting another one if it is not available.

### Error Scenarios

The following error scenarios have been known to occur:

- Calibration database devices do not respond to queries. This can be due to a temporary overload of the server, such that the processes running the access points were not able to allocate sufficient memory. This should not happen anymore if meta_data only retrieval mode is used for larger parameters, like those of AGIPD and LPD. It can be diagnosed by the log outputs not updating even though querying jobs have been launched.

  It can be solved by restarting the calibrationDbRemote server:

      source /scratch/xcal/karabo/activate
      karabo-kill -k pythonserver_max_web_rcal_0

  Note that this might lead to errors on calibration jobs currently in flight, when the restart occurs. All devices will autostart after the server restart. The procedure takes about 30 seconds until the system will be running again.

  To diagnose if the problems occured through requesting large constants, while not using meta_only mode, check memory consumption via htop:

  > htop

  and assure that no swapping had occurred.

  Example output of htop command. The swap bar should be near zero.

- Unusually high number of request, of the same parameters can occur if ZMQ requests with improper timeout error handling are being made. This will lead to recurring log entries requesting the same parameters. Current production code has long enough timeouts set, but legacy code is known to run into this scenario. To fix it, first check if you can find processes that might be responsible for the requests:

      squeue -u xcal

  and stop these, e.g. by using scancel. The restart the calibration database devices as mentioned above. Make sure to increase timeouts on calling code before initiating new requests.

- Reports show `Version already taken` error. This is not really a failure scenario, but rather expected behaviour. A parameter with exactly the same start date and operating conditions has previously been injected into the calibration database. The database is now refusing to overwrite it. Check if you are characterizing the correct data with the correct conditions.

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