Launching the software manually:

This section will guide you through each window opened and will show you how to re-open it manually in case of problems.

Connecting to the beamline computer and starting MxCUBE

Use the green terminal window, which is logged in to the beamline control PC, and type mxcube at the command prompt. If that window has been closed, open another terminal window and connect to the control PC (see this page to find the control PC name):

ssh -X opidname@controlpcname, e.g. ssh -X opid29@id29control

then at the command prompt type mxcube.

Once mxCuBE v2 has started log in to mxCuBE2 as if you were on the beamline, i.e., use your experiment number and password.

remote access tet.jpg

orange.bmp

Once logged in to mxCuBE, the top bar will become yellow and you can then ask for control of the beamline by clicking the "Ask for control" button on the bottom right of the mxCuBE window. Before you do this, however, it is best to inform your local contact - either by phone or using the 'chat' tab -  that you are ready to take control of the beamline.

Upon being given control of the beamline you will be asked to give details including your name, home laboratory name, contact telephone number and e-mail address. These are required by the ESRF Safety Group and will allow the ESRF's Exerimental Hall Operators to contact you in case of problems outside normal local contacting hours. You will also be asked whether users from your group are at the ESRF to help in case of minor problems.  

Once you've taken control of the beam-line the top bar of mxCuBE will turn green. You should also see in the bottom right corner of mxCuBE who is accessing the beamline. You can give control to other members of the same BAG group.  There "chat" tab at the top of the mxCuBE window can be used to communicate with your Local Contact.

green.bmp

If for any reason an intervention by the Local Contact requires that he/she takes control of MxCuBE, he/she will inform you of this and a message to this effect will appear. Note that upon losing control of MxCuBE, the top bar becomes yellow.

yellow.bmp

Experimental hutch cameras

In the NXClient session, use a new terminal window on the rnice cluster and start firefox if it is not already running. Then navigate to one of the following URLs to access the cameras to see what is happening in the experimental hutch. Note that these web addresses are only accessible from inside the ESRF firewall.

Beamline           Web Camera Address

ID23-1                http://id23video03.esrf.fr/

ID23-2                http://id232video1/view/index.shtml

ID29                   http://id29video1/view/index.shtml

ID30A3               http://id30aeh2video1.esrf.fr/view/viewer_index.shtml for a hutch overview

                           http://id30aeh2video2/view/viewer_index.shtml for the sample view

ID30B                 http://id30beh3video1.esrf.fr/view/viewer_index.shtml for a hutch overview

                           http://id30beh3video3.esrf.fr/view/viewer_index.shtml for the sample view

 

You can also connect these web cams using the ESRF ssl gateway with your experiment account and usual password. 

Starting image visualisation software

The adxv window that is automatically started at the beginning of a remote experiment is running on rnice. To restart it, type adxv either in the control PC terminal window, or in an rnice terminal window.

Note that for remote access, adxv is not started in "follow" mode as this oftentimes overloads the network connection.

Alternatively, you may want to try the image viewer Albula (by Dectris) by typing albula .

Starting data collection

Here is a link to some of things you should know before collecting data on the ESRF MX-beamlines.

By default, the Local Contact will load the user baskets from top to bottom (from the transport dewar) in sample changer position 1 to position 5.

Starting data processing

For manual data processing, you can log in to our computational cluster using the ssh -X mxproc command.

Starting data transfer

  • Use rsync to copy data from the ESRF to a remote machine (e.g., the user's home institute) while you're at the ESRF, use something like this:

rsync -r -p -t -l -e ssh --exclude='*.tmp' --progress --stats --compress /data/visitor/mx9999/id231/20160401 user_name@host_address:directory_name

The command above will connect to the host_address with the login user_name, and will compare the local directory /data/visitor/mx9999/id231/20160401 with the remote directory directory_name/ (if it exists, otherwise it will be created). It will then copy the differences from the ESRF to the remote computer.

The various rsync options mean that directories are copied recursively ("-r"), permissions, creation time and soft links are preserved ("-p", "-t", "-l"), the connection is secured through ssh ("-e ssh"), files with the extension .tmp are ignored ("--exclude='*.tmp'"), the transfered data is compresssed ("--compress"), and transfer progress and statistics are shown ("--progress", "--stats").

Note: If you need to remove the host key for the remote host (in case the machine was changed) you can run : ssh-keygen -R firewall.esrf.fr

  • Use rsync to copy data from the ESRF while you are logged in to a remote machine, use something like this:

rsync -r -p -t -l -e 'ssh -p5022' --exclude='*.tmp' --progress --stats --compress mx9999@firewall.esrf.fr:/data/visitor/mx9999/id23eh1/20160401 .

  • Besides rsync, other options are scp:

scp -r -P 5022 mx9999@firewall.esrf.fr:/data/visitor/mx9999/id23eh1/20160401 .

or sFTP.