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?

Type these commands:
ssh bambam
passwd
Put in your old password and then new when prompted. Changes will be propagated 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 wilma, stone, slate, betty, lava, gravel, bambam, bronto, energy, nano, bobcat, lynx. More details about the workstations are 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 and faster Desktop experience, in addition to Mobaxterm, see Faq 4e about how to use X2go.

Gaussview note: Some graphics libraries may be incompatible. A work-around is to type mesagl immediately before starting GaussView. This will set the USE_MESAGL environment variable. However, really try Faq 4e about how to use X2go. It will be much better.

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?

You must first install XQuartz.

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.


You can use use graphics programs like Maestro and Gaussview from XQuartz (slow, basic) or X2Go (faster, complete desktop).

We include the basic XQuartz instructions here but strongly recommend you use X2Go as describe in Faq 4e.

XQuartz: Open XQuartz (Applications > Utilities > XQuartz) and then open a Terminal from within XQuartz (XQuartz menu: > Applications > Terminal). In that XQuartz Terminal, type:

ssh -XY username@machinename.cchem.berkeley.edu

A basic XQuartz installations will allow you to use most graphical programs such as gedit (type gedit), Maestro (type maestro), and Gaussview, but they will run much more slowly than when you are in 175 Tan Hall. Instead, see Faq 4e about how to use X2go. It will be much better.


Gaussview note: Most remote connections from Mac/Windows have GaussView display bugs over MobaXterm or XQuartz. Type mesagl immediately before starting GaussView (type gv6). This sets the USE_MESAGL environment variable and uses alternate graphics libraries.

However, really see Faq 4e about how to use X2go. It will be much better.


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.

We used to recommend MacFusion but it may not work on recent MacOS. It mounts remote servers as local drives within finder allowing normal drag an drop operation. Connect to "machinename.cchem.berkeley.edu" (see section above). Use your MGCF username and the ssh protocol ("22" is the Port).


4c) How about Ubuntu or other Linux?

Basically follow the MacOS instructions except you don't need XQuartz.

In X2Go, look for the Ubuntu or other Linux client at the download page. Note, you only need the client, not the Server. Then follow the X2Go configuration instructions.


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 X2Go.

Recently people have reported touble dowloading X2Go. If this happens, please try a different browser. Some browsers are overly sentive to http vs https in downloads.

On Windows, in addition to Mobaxterm, download the X2Go Client. Choose the mswin link for X2GoClient_latest_mswini32-setup.exe and install it.
Install the Recommended components. Be sure to let all processes/connections go through Windows Defender.

On Mac, in addition to XQuartz, download the X2Go Client. Most people will want the MacOS 10.13 and higher DMG. Install the dmg on your Mac.

Once you have X2Go installed, start the X2Go client, and choose the menu Session > New Session. This will open a series of Tabs to configure the session.

Change the Session name to mgcf-machinename and type in a Host which should be machinename.cchem.berkeley.edu replacing machinename with one of the MGCF workstations:

where "username" is your MGCF username and "machinename" is one of the workstations listed here.

For example, your Session name could be mgcf-wilma and the Host could be wilma.cchem.berkeley.edu
Type in your MGCF username in the Login field, change the Session type to MATE (a basic desktop environment, note that most of the other choices in this Menu DO NOT WORK).
On Windows, the MATE selection looks slightly different but is otherwise the same as on Mac.

On the Input/Output Tab, set the Display to Custom and set the Width:800 and Height:600. You can later adjust the Display to suit your monitor but this is a good set of values to start with.

On the Media Tab, unset the Enable sound support and also unset Client side printing support.

Click OK and return to the Main Screen.

Double click on the Session (face icon) to start it.

Then click Yes or Allow Access to all questions and type your username and password when prompted. One Windows, be sure to let all connections, such as the ssh app, the server app and other features go through Windows Defender.
You should get to a normal looking MGCF Desktop although you may have to right click and Organize Desktop by Name. You can also try the Places > Desktop if you have trouble seeing your icons.

Troubleshooting: Please see our Tips on using Maestro via X2Go

Please quit all programs and double click the green Logout button when you are finished. Maestro is very sensitive to this. Be sure to quit the program so your data is correctly saved. Also Comsol will leave stray processes and fail to return the license token if you don't explicitly quit the program. Please quit all programs. Then Logout.


5) How do I track or kill calculation processes?

Please look at the MGCF diagram. When you login via 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 Tiger.

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 Tiger. Tiger 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 Tiger.

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 Tiger 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 Tiger 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 grep
The 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 Tiger. 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 Tiger computing cluster. This is only for the MGCF workstations.

The command:
qstat | grep gpu
will show gpu jobs on Tiger. Tiger 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?

As of March 2021, we are retiring our Windows Virtual Machine. All users who need Windows software in the MGCF should review our Windows page.

We offer options to help you setup your own Windows VM, and/or request access to our new Windows server.