Remote Data Collection
Contents |
[edit] Introduction
This webpage provides some instructions on how to setup remote operation of the beamlines.
[edit] User actions
As a user you must have an NX client installed. Our administrative or beamline staff will send you exact details on which machine to contact with your NX client. Typically you should use NX to connect directly to the ccd2 machine on the beamline you intend to use (the path for this will be given to you by the beamline staff). Processing the data should be done in a separate instance of NX that is logged in to bcsb-nx instead of the beamline machine. This is to prevent resource intensive computations from interfering with data collection.
Your login will be a designated LDAP uid and password that will be given to you before your shift starts.
Our beamline staff will give you a phone call as soon as the beamline is ready. Please make sure you know which pucks you want to have loaded and in which dewar they are. Please leave clear instructions with your dewars in which order you want to have your pucks loaded. Our beamline staff will loads pucks for you in the dewar in batches of 3. When you are done screening/collection your batch of pucks, please call your beamline representative to change pucks out. Changing pucks after 4.30 pm Pacific time, will be handled by our evening and night staff. During weekdays, we typically have coverage between 10am and 5am.
Details on who to call, backup numbers and details regarding night support will be posted on the beamline for your inspection.
[edit] Staff actions
When starting the beamline for the remote users, follow normal startup procedures. When the beamline is ready, login to the UserAdmin webapp at https://bcsb.als.lbl.gov/UserAdmin2/ with your staff credentials. You can also access this app from the "Staff" menu on the BCSB site.
Find the user's account by typing some or all of the username in the upper left hand box. Find the username in the list and click it. The users' information should appear in the right hand side. Look at the "User Host Attributes" section of the page, and find the "Add Host Attribute" button. After clicking this button, a blank should appear below. Type in one of the following host attributes, depending on the beamline:
bl501 -> 501remote bl502 -> 502remote bl503 -> 503remote bl821 -> 821remote bl822 -> 822remote
So, if the user is going to use beamline 502, type "502remote" into the blank and click submit.
The user should be ready to login. Remember to LOGOUT after you're done.
When the user is finished, remember to remove this host attribute by clicking the "X" next to it. This will revoke the users' ability to NX to that beamline's ccd2 machine.
[edit] User Names
The user can tell you his username, or you can check it from this page. If you must create an account, you can do that here: User Administration
Be sure to set the download and remote user host attributes for new remote accounts.
At this moment, the beamline is ready for remote operation. Load the first couple of pucks as specified by the user. Contact the user and give him the go-ahead for data collection. Make sure you interlock the hutch and leave the signs indicating that remote data collection is taking place.
[edit] Login issues
Check the Not So Frequently Asked Questions about trouble shooting NX.
[edit] Path
Any user can be a remote user when the following is followed:
You can do a "echo $SHELL" to see if you're using tcsh or bash.
The .tcshrc file needs to contain this (place it close to the bottom, just before the last endif) :
# setup for remote data collection if (-f /prod/BOS/setupRemote.csh) then source /prod/BOS/setupRemote.csh endif
if you use bash, then your .bashrc file should contain these lines:
# setup for remote data collection if [ -f /prod/BOS/setupRemote.csh ]; then /prod/BOS/setupRemote.csh fi
[edit] Permissions
The user should have a 'host attribute' named remote. To check if this attribute is set, staff can go to the user-admin interface and add the host attribute 'remote'.
[edit] NX issues
If for some reason the user cannot log in (please get specifics, such as a screen shot of the NX fault) try to restart the NX server by typing
service nxserver restart
on the ccd2 machine of that particular beamline as root.
A common error is that NX complains about the number of users is to much. This can be due to the fact that other users are logged in. The addtonx < userid > command, will restart the server subsequently.
Another issue observed is a message complaining about not being able to run cdwm. If the users use a KDE desktop, this problem goes away.
[edit] Practical issues
After connecting to our data collection machines, you will be able to control your designated beamline.
Please be aware that due to network issues, there might be some delays/sluggishness in certain operations. Please set the NX connection to ADSL for smooth operation. Setting it to LAN might cause increased lag, although ADXV will work properly. BOS (and Mini) on the ccd2 machine are configured in such a way that it will display jpegs of the diffraction images rather than using adxv. Running an external adxv for detailed image inspection can be usefull.
To get adxv to display on one of the bl50n-ccd2 machines, you may (most likely not though) have to set this environment variable on your machine (bl50n-ccd2):
setenv XFORMSTATUSFILE /data/dcsuser/xf_status
You can then run adxv using:
/prod/BOS/bin/adxv -autoload
If this alsop doesn't work, the last resort is the following:
ssh -Y -C < userid >@bcsb-nx.als.lbl.gov setenv XFORMSTATUSFILE /data/bl50*/dcsuser/xf_status /usr/bin/adxv -autoload
(replace * with 1,2 or 3 depending on the beamline)
Regular paths and environmental variables should have been set by the staff in your .tcshrc file.
As usual, stopping and starting the BOS data collection server is done by typing
stopBOS.csh startBOS.csh
Typically, a server is already started for you by the beamline staff. You just have to start a GUI (BOS client) by typing
BOS.csh
One could use our fancy new gui as well:
Mini.csh
When running remotely, please lauch a PZT terminal (menu option Camera->PZT) so that you have a view of what is happening inside the hutch. This is usefull to make sure that your crystal is mounted properly or spot other problems.
On a separate desktop, you can connect to our processing machine:
ssh -Y -C bcsb-nx.als.lbl.gov
to use crystallographic software such as HKL2000.
[edit] Beamline staff and user communication
Beamline staff can communicate with the user (and vice versa) via the Chat window in BOS. The Chat window is launched from the "View" pulldown menu, option "Chat".
On the beamline, two pieces of paper will be posted. One paper has experimenter info (your name and phone numbers) and staff info (our name and phone number). The other paper has a puck table listed: in this way, we (and you) keep track of which puck is where.
Use the beamline cameras to view this information. web addresses and login info will be send to you before your beamtime starts.
Night Support can be contacted after 6pm at 510-495-2500.
[edit] Data backup
The easiest way to back up data is to use scp, sftp or rsync from bcsb-nx.als.lbl.gov.