Difference between revisions of "Quick Start Guide"

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All group members are entitled to accounts on the Theory Group Linux Cluster. If you have a workstation on your desk you will usually use that machine for your computing needs.  
 
All group members are entitled to accounts on the Theory Group Linux Cluster. If you have a workstation on your desk you will usually use that machine for your computing needs.  
−
thmath,thmath2 and thmath3 are very fast machines intended for running mathematica, maple, and other cpu intensive tasks.  
+
thmath1, thmath2, thmath3 and thmath4 are very fast machines intended for running mathematica and other cpu intensive tasks.  
  
 
*Mail:
 
*Mail:
−
You may not use your account on your personal workstation as your email address. You should register with the LBL EPO to receive an email address of the form YourName@lbl.gov. You should also apply for a lab IMAP account and use that as your primary email account.  
+
When you are hired you will be automatically assigned an email address of the form YourName@lbl.gov. Be sure that you read emails that are sent to this address, either by accessing the Lab email system at http://gmail.lbl.gov or by setting up forwarding to some other address.  Important email associated with your employment at the lab may be sent to this address.
−
Users may store up to 3GB of email on the lab IMAP server without incurring charges. Exceeding the 3GB quota exposes the group to a per MB charge each month. Please take steps to keep your usage below that quota. Valuable information on how to do that can be found on the lab's IMAP FAQ
+
 
−
You may use any standard email client for accessing your mail. Thunderbird, evolution, pine and kmail all support IMAP mail. You may also access the lab mail server through the web gateway. This has the advantage of working from any platform and any computer without any additional configuration.  
+
Users may store up to 30GB of email on the lab IMAP server without incurring charges. Exceeding the 30GB quota exposes the group to a per MB charge each month. Please take steps to keep your usage below that quota.   
−
Whatever mail client you use, please make sure that your "Reply-To" header is properly defined. If you send mail from a workstation without having set this variable, your recipients may not be able to reply to your mail.
+
You may use any standard email client for accessing your mail. Thunderbird, evolution, pine, kmail and Apple Mail all support IMAP mail, but the most convenient interface is the the web gateway http://gmail.lbl.gov. This has the advantage of working from any platform and any computer without any additional configuration.  
 +
 
 
Note that is it your responsibility to ensure that mail is delivered to an account where you can read it. You should read the [[FAQ#Mail_Information|FAQ]] on mail.  
 
Note that is it your responsibility to ensure that mail is delivered to an account where you can read it. You should read the [[FAQ#Mail_Information|FAQ]] on mail.  
  
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*Connecting:
 
*Connecting:
 
From outside of LBL you must use ssh to connect to any of our machines. You may not use telnet. You may ftp from any of our machines to any other machine, but sftp is a better choice if it is supported by the target computer. ftp to our machines is prohibited, but sftp works. Use sftp or scp where possible.  
 
From outside of LBL you must use ssh to connect to any of our machines. You may not use telnet. You may ftp from any of our machines to any other machine, but sftp is a better choice if it is supported by the target computer. ftp to our machines is prohibited, but sftp works. Use sftp or scp where possible.  
−
On a workstation just enter your username and password, the window manager then takes over.  If you have a workstation, you should be doing most of your work there, i.e. you should not be connecting to thsrv for most of your work.
 
  
−
*Workstations:
+
If you are outside the lab and need access to resources that are only available from within the lab network (e.g., the library, or certain business systems), you may connect to the lab VPN using vpn1.lbl.gov as the gateway.  See https://commons.lbl.gov/display/itdivision/VPN+-+Virtual+Private+Network for instructions.
−
You should not be using your workstation to simply open a window and ssh into thsrv. Performance will usually be better if you run locally and your action is not very considerate to those members of the group who do not have workstations.  Most of the workstations are newer than thsrv and are more powerful.  
+
 
  
 
*Shells:
 
*Shells:
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*Editing:
 
*Editing:
−
Emacs or XEmacs is the probably the best editor. However it's very powerful (i.e. dangerous, hard to learn). It becomes much more effective when customized, but works well "out-of-the-box". Go to Options->Customize in Xemacs, or Help->Customize in GNU Emacs to do so. It has modes to facilitate the editing of TeX, C, fortran and HTML code. Xemacs is a version of Emacs that is slightly prettier (and some say slower). Whether you choose to use Xemacs or GNU Emacs is largely a matter of taste. Xemacs has two mail readers, a built in web browser, support for cvs, make and a boatload of other bells and whistles.  
+
Emacs is the probably the best editor. However it's very powerful (i.e. dangerous, hard to learn). It becomes much more effective when customized, but works well "out-of-the-box". Go to Help->Customize in GNU Emacs to do so. It has modes to facilitate the editing of TeX, C, fortran and HTML code. Xemacs is a version of Emacs that is slightly prettier (and some say slower). Whether you choose to use Xemacs or GNU Emacs is largely a matter of taste. Xemacs has two mail readers, a built in web browser, support for cvs, make and a boatload of other bells and whistles.  
 
One advantage of using emacs (either flavor) is that it runs both under X and in textmode, so you can use the same familiar commands whether you're at home or at your workstation.  
 
One advantage of using emacs (either flavor) is that it runs both under X and in textmode, so you can use the same familiar commands whether you're at home or at your workstation.  
 
vim is an improved version of the UNIX vi editor that we all cursed in years past. Some people like it. Some people like okra.  
 
vim is an improved version of the UNIX vi editor that we all cursed in years past. Some people like it. Some people like okra.  
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The above are all text editors. If you want a word processor with the ability to exchange documents with MS PCs and Macs, use OpenOffice, which is installed on all of the workstations. You can start it by going to the "K button" (left side of the panel) then "Office" See the FAQ for more information.  
 
The above are all text editors. If you want a word processor with the ability to exchange documents with MS PCs and Macs, use OpenOffice, which is installed on all of the workstations. You can start it by going to the "K button" (left side of the panel) then "Office" See the FAQ for more information.  
  
−
*Mathematica and Maple:
+
*Mathematica:
−
They are available for general use on thmath, thmath2 and thmath3 only. Two concurrent kernels may be run on each of these machines. To see which licenses are in use, you may view http://phyweb.lbl.gov/cgi-bin/mathematica.pl
+
This is available for general use on thmath1, thmath2 and thmath4 only. Two concurrent kernels may be run on each of these machines.  
−
Backups and Disk quotas:
+
 
−
The /home is backed up daily. Since space in /home is limited, use the /scratch-local areas for large files that do not need to be backed up, like local copies of files that exist elsewhere. Use the command quota to see your disk quota. Requests for increased disk quotas will not be granted if your space is used ineffectively, See here for some hints on using backed up space effectively.  
+
*Backups and Disk quotas:
 +
The /home is backed up daily. Since space in /home is limited, use the /scratch-local areas for large files that do not need to be backed up, like local copies of files that exist elsewhere. Use the command quota to see your disk quota. Requests for increased disk quotas will not be granted if your space is used ineffectively.
  
 
*Scratch areas:
 
*Scratch areas:

Latest revision as of 18:35, 17 June 2015

The general configuration of the linux cluster is described in the System Configuration document.

When you're done here, please also read through the FAQ.

The Basics

  • What computers can I use?

All group members are entitled to accounts on the Theory Group Linux Cluster. If you have a workstation on your desk you will usually use that machine for your computing needs. thmath1, thmath2, thmath3 and thmath4 are very fast machines intended for running mathematica and other cpu intensive tasks.

  • Mail:

When you are hired you will be automatically assigned an email address of the form YourName@lbl.gov. Be sure that you read emails that are sent to this address, either by accessing the Lab email system at http://gmail.lbl.gov or by setting up forwarding to some other address. Important email associated with your employment at the lab may be sent to this address.

Users may store up to 30GB of email on the lab IMAP server without incurring charges. Exceeding the 30GB quota exposes the group to a per MB charge each month. Please take steps to keep your usage below that quota. You may use any standard email client for accessing your mail. Thunderbird, evolution, pine, kmail and Apple Mail all support IMAP mail, but the most convenient interface is the the web gateway http://gmail.lbl.gov. This has the advantage of working from any platform and any computer without any additional configuration.

Note that is it your responsibility to ensure that mail is delivered to an account where you can read it. You should read the FAQ on mail.

  • What should I use for a password?

Do not use any easily guessed thing. The passwords are checked on a regular basis, if yours fails some simple tests you will be forced to change it. Use at least 8 characters; a mixture of letters, numbers and non alphanumeric characters (such as # or %) is best. Do not use the same passwords on different machines. Do not reuse passwords. Good passwords can often be generated by choosing a phrase, then using the first letter from each word. The password will be easily remembered, but very hard to guess. For example, "Don't use this as your password, silly", would generate the password dutayp,s. Note that I've included the comma to make it harder to guess. You may also want to include some simple, easy to remember substitutions, like du7aYp,s, where I've replaced the t with a 7 because they kind of look alike to me, and I've capitalized the "Y" from "your." Keep in mind that the total space of possible passwords is ~10^16, while the number of entries in the Oxford English Dictionary is ~10^8. This means that the total set of dictionary words and trivial permutations of them is a negligible subset of all possible passwords. Consequently, it is actually quite easy to choose a password that is as good as random. Please take a few minutes to do so.

  • Getting Help:

The primary source of help is the Unix manual, invoked by the command "man." If you use konqueror (the default web browser under KDE) as your webbrowser, you may view man pages by visiting the URL '#commandname'. e.g. typing #ls in the konqueror location field displays the man page for the "ls" command. Within KDE this can also be invoked by pressing "Alt-F2" then typing #ls into the field that appears. The command "help" gives some information about the shell commands. There is extensive documentation packages in /usr/share/doc Linux has many FAQs.

  • Connecting:

From outside of LBL you must use ssh to connect to any of our machines. You may not use telnet. You may ftp from any of our machines to any other machine, but sftp is a better choice if it is supported by the target computer. ftp to our machines is prohibited, but sftp works. Use sftp or scp where possible.

If you are outside the lab and need access to resources that are only available from within the lab network (e.g., the library, or certain business systems), you may connect to the lab VPN using vpn1.lbl.gov as the gateway. See https://commons.lbl.gov/display/itdivision/VPN+-+Virtual+Private+Network for instructions.


  • Shells:

The default shell is bash. The scripts are not checked for the other shells . The csch, tsch, zsh, and ksh are also available. Use chsh to change your shell.

  • Customizing your environment:

If you take no special steps you'll get a default windowing environment that has been customized to our system. In addition, a number of environment variables will be set (e.g., $PRINTER is set to theory2). You may edit your personal copies of the standard unix configuration files as you please. See the FAQ for details.

  • Editing:

Emacs is the probably the best editor. However it's very powerful (i.e. dangerous, hard to learn). It becomes much more effective when customized, but works well "out-of-the-box". Go to Help->Customize in GNU Emacs to do so. It has modes to facilitate the editing of TeX, C, fortran and HTML code. Xemacs is a version of Emacs that is slightly prettier (and some say slower). Whether you choose to use Xemacs or GNU Emacs is largely a matter of taste. Xemacs has two mail readers, a built in web browser, support for cvs, make and a boatload of other bells and whistles. One advantage of using emacs (either flavor) is that it runs both under X and in textmode, so you can use the same familiar commands whether you're at home or at your workstation. vim is an improved version of the UNIX vi editor that we all cursed in years past. Some people like it. Some people like okra. You may also wish to try kate or kwrite. They run only under X, and support syntax highlighting. They are part of KDE, but you don't have to run the full KDE environment to use it. The above are all text editors. If you want a word processor with the ability to exchange documents with MS PCs and Macs, use OpenOffice, which is installed on all of the workstations. You can start it by going to the "K button" (left side of the panel) then "Office" See the FAQ for more information.

  • Mathematica:

This is available for general use on thmath1, thmath2 and thmath4 only. Two concurrent kernels may be run on each of these machines.

  • Backups and Disk quotas:

The /home is backed up daily. Since space in /home is limited, use the /scratch-local areas for large files that do not need to be backed up, like local copies of files that exist elsewhere. Use the command quota to see your disk quota. Requests for increased disk quotas will not be granted if your space is used ineffectively.

  • Scratch areas:

All the machines have large scratch disk areas, mounted at /scratch-local, which are available for general use. They are not backed up. Files left there are not removed automatically by the system. If the space becomes filled, users who have stuff there will be notified. There is also a global scratch area, mounted at /scratch. Files in this area are visible from all workstations (unlike the local /scratch-local areas).

  • Batch Processing:

Background your job, or better yet, use at, cron and batch. Use man to learn how to use these utilities. Be sure to use niceso that your job does not hog the machine resources.

  • Books:

Running Linux by Matt Welsh and Lar Kaufman (O'Reilly)

Unix for Dummies by Levine and Young (IDG)

Learning the Unix Operating system by G. Todino, J. Strank and J Peek

Learning GNU Emacs by Debra Cameron, Bill Rosenblatt and Eric Raymond.

What you need to know when you cannot find your UNIX system administrator by Linda Mui (O'Reilly)...

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