MGCF FAQS
1) I accidentally deleted a file. Can I get it back?
2) How do I capture an image from the screen?
3) How do I change my password?
4a) How do I connect via terminal from my computer running Windows ?
4a.1) How do I file transfer to/from my computer running Windows ?
4b) How do I connect via terminal from my computer running Mac OSX?
4b.1) How do I file transfer to/from my computer running Mac OSX?
4c) How about Ubuntu or other Linux?
4d) How do I connect from my off campus computer?
4e) How do use Graphical based programs remotely (Maestro, Gaussian, Comsol etc).
5) How do I track or kill calculation processes?
5a) How do I track or kill gpu calculation processes?
6) How do I use Windows software within the MGCF?
1) I accidentally deleted a file. Can I get it back?
Please email mgcf@berkeley.edu with the details like file and folder names along with dates.
We do not archive files but we have nightly backups for the last few months.
Note: Our backups disregard files that are >15GB in size and *.rwf files since those are usually temporary scratch files that clog the backup process.
2) How do I capture an image from the screen in 175 Tan Hall?
If you connect in via X2Go, here are Mac instructions, although Kathy finds Command-Shift-5 works best for her. On Windows, there are many ways and this is easy to find online.
If you are physically in 175 Tan Hall, begin by making sure the target window or area is not obscured by any other window or image.
The import command is part of the ImageMagick suite of tools.
You use it by typing import filename.jpg followed by the Enter key.
Then either click once on the window of interest or click-drag to specify a rectangle.
You will hear a beep and the file called filename.jpg is created.
Type display filename.jpg to open the editing tool of ImageMagick. Clicking anywhere in the ImageMagick window will then bring up a control panel which can be used to edit and resave the image.
Import can save the image in different formats (gif, tiff, jpg, png) if you specify the desired format at the import step. For example: import filename.tiff
ImageMagick is extensive, powerful and scriptable. Check it out for more sophisticated image editing needs.
3) How do I change my password?
Login to the MGCF via your usual process. Then type these commands:
ssh wilma
passwd
Put in your old password and then new when prompted.
Changes will be propagated from wilma to other machines in a few hours.
4a) How do I connect via terminal from a computer running Windows?
We recommend Mobaxterm.
Choose the Free, Personal version. Then install as usual (the Installer edition is better for most people). Make sure you allow Mobaxterm to get through the Windows firewall. Start a new Session. See mobaxterm-1.png.
Choose SSH for a normal login terminal. Chose SFTP for file transfer (more below). See mobaxterm-2.png.
See mobaxterm-7.png.
For Remote Host type any MGCF workstation name: machinename.cchem.berkeley.edu
replacing "machinename" with the one of the workstation names listed here.
Type your MGCF username in the Username box. Port 22 is correct.
Give your MGCF password at the prompt, and you will access your home directory just like you would in the facilty.
If you want a more complete desktop experience, in addition to Mobaxterm, see Faq 4e about how to use remote desktop tools.
File transfers: On Windows, Mobaxterm has a built in file transfer tool called SFTP. See mobaxterm-3.png.
Use an MGCF workstation name in the Remote host field, and use your MGCF username. Type your password when prompted. Then you will see a screen as below:
You can toggle the View > Show/hide sidebar to get a cleaner view. See mobaxterm-6.png.
Your Windows file system is on the left and your MGCF workstation file system is on the right. Note that MobaXterm shows otherwise hidden files and folders that begin with a "." dot, for example .anaconda, .config, etc. DO NOT DELETE OR MOVE THE DOT files/folders. These are critical system files. Scroll down past these to find the other folders and files.
See also Filezilla which is an alternative free file transfer tool, where one can easily use View > Directory Listing Filters to hide the dot files. The Port number is 22.
See also the Mac section for Cyberduck.
4b) How do I connect from a computer running Mac OSX?
If you mainly want to do command line steps like qstat or run_g16 then open a Mac Terminal (Applications > Utilities > Terminal). In that Mac Terminal, type:
ssh username@machinename.cchem.berkeley.edu
where "username" is your MGCF username and "machinename" is one of the workstations listed here.
The first time you ssh to an MGCF machine, you will get a message asking whether you want to continue logging in. Type yes. Type your MGCF password when prompted. This puts you on a command prompt in your MGCF home directory.
If you want more than a command line, see Faq 4e about how to use remote desktop tools.
File transfers: We currently recommend CyberDuck. See cyberduck-conf1.png. Click Open Connection in the left corner, then choose SFTP from the pulldown. Type in a server name (one of the MGCF workstations), a username and a password. Then click Connect. In cyberduck-conf2.png you can see a user's mgcf home folder on the left and a mac folder on the right. This allows drag and drop.
4c) How about Ubuntu or other Linux?
Basically follow the MacOS instructions for the command line and the remote desktop instructions. As you download those remote desktop tools, you only need the client side, not the server.
4d) How do I connect from my off campus computer?
We only accept connections from berkeley.edu and lbl.gov networks. If you are off campus, you need to start a VPN session before starting your ssh, MobaXterm, X2Go, Cyberduck, etc connection.
4e) How do use Graphical based programs remotely (Maestro, Gaussian, Comsol etc).
If you want a more complete and faster Desktop experience, try:
Thinlinc (Maestro requires this).
or
X2go (Most apps work but not Maestro).
5) How do I track or kill calculation processes?
Please look at the MGCF diagram. When you login via remote desktop (thinlinc or X2Go) or Mobaxterm, or a Mac terminal, you are working on one of the MGCF workstations. Depending on what you do while logged in, you might have processes on one or more of the MGCF workstations, or you might have processes (each is normally called a "job") on the computing cluster named Panther.
In general, if you are running Gaussian, QChem, Orca, or any calculation using a run_program (run_castep, run_amber, run_comsol, etc) script, then calculations are sent to Panther. Panther has a queueing system to allocate jobs to different nodes of the computing cluster. Thus you use the queue commands, qstat and qdel, to manage those jobs. You use an MGCF workstation to setup/review the calculations, but they run on Panther.
You can delete a calculation from the queue on Panther using qdel job_id where job_id is the number in the first column of output from qstat.
This is described on the New User Instructions (UCB only).
In contrast, if you are submit a simulation from the Comsol (GUI), Maestro (Macromodel, Glide), or any hand scripted job with nohup, then your process is likely running on one of the MGCF workstations. To follow processes running on the MGCF workstations, the main commands are top, topw, ps -x, and ws_ps.
The top and topw commands are described on our New User Instructions.
The top command shows the largest few processes on the current workstation where you are logged in. Press q to end top.
The column highlighted in green shows the total cpu core usage for the biggest few processes. This is as a percentage of the total available, so in this case
process number 1522 is using 1800% of 1 cpu core (= 18 core). Most MGCF workstations have 24 cpu core and 128GB ram, and these percentage numbers
can range up to 2400.
If you detect that the current machine is too busy (infrequent but occasional) type exit and then reconnect to a different machine. In general, if you’re logged into one workstation, you can login to another one by simply typing “ssh machinename”, with the specific workstation name substituted for “machinename”.
The topw command shows the largest few processes on all MGCF workstations. This does NOT include the Panther computing cluster. This
is only for the MGCF workstations.
The ps -x command shows your processes running on the current workstation where you are logged in
(note the space between ps and -x).
The ws_ps command will
show your processes running on all MGCF workstations (this command has no spaces). This does NOT include the Panther computing cluster. This
is only for the MGCF workstations.
Note that if you are using X2Go, then there will be ~20 processes associated with the basic desktop. This is fine.
The left column for top, topw and ws_ps shows a number called the process ID, called the PID.
To kill a process, the command to type is:
kill -9 PID
replacing PID with the actual number. For example, to kill a process that looks like this in the ws_ps output:
20480 user 00:00:00 grepThe command to type is:
kill -9 20480
If you have lots of stray processes on MGCF workstations and want to kill them all, the command is: ws_kill
This will kill all of your processes on every MGCF workstation, including logging you out of your current X2Go or terminal connection. This happens immediately at the end of the command. Be careful! As long as you have no unsaved changes in some open program, then it is safe, if a bit brutal.
This will not affect jobs in the queue on Panther. You still need qstat and qdel for that.
If you want to kill all your processes running on a single workstation, open a terminal and, if you're not logged into that workstation, type ssh machinename, where machinename is the name of the particular workstation. Then type pkill -U username, where username is your username. You will then automatically be logged out of that workstation.
5a) How do I track or kill gpu calculation processes?
The command:
gpuw
command will
show gpu processes running on MGCF workstations (this command has no spaces). This does NOT include the Panther computing cluster. This
is only for the MGCF workstations.
The command:
qstat | grep gpu
will show gpu jobs on Panther. Panther has 8 gpus so you can count the running jobs and decide your calculation strategy.
To kill jobs, use the instructions above for cpu processes
.
6) How do I use Windows software within the MGCF?
We have a very non powerful Windows server for only a handful of special applications that don't run on Linux. See Windows page.