New to the Lab: Difference between revisions

From Center for Cognitive Neuroscience
Jump to navigation Jump to search
(Undo revision 2788 by Manson (talk))
 
m (44 revisions)
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
=Getting Work Done=
=Computer Resources=
==Computer Resources==
Please see [[FAQ#Shared_Resources | FAQ: Shared Resources]] for in depth list of available resources.  
Please see [[FAQ#Shared_Resources | FAQ: Shared Resources]] for in depth list of available resources.  


Virtually all work in the lab is done in one of four ways:
Virtually all work in the lab is done in one of three ways:
<ol>
<ol>
<li>On a group resource lab computer
<li>On a group resource lab computer
<li>On the hoffman2 cluster
<li>On the hoffman2 cluster
<li>On the miles cluster
<li>On another lab member's computer
<li>On another lab member's computer
</ol>
</ol>
Line 14: Line 12:


===Group Resource Lab Computer===
===Group Resource Lab Computer===
These are computers available for reserving by anyone in the lab. So far, we have approximately 5 of these. To gain an account on these computers, you must send a request email to:
These are computers available for reserving by anyone in the lab. So far, we have approximately 5 of these. To gain an account on these computers, ask for the local lab manager/administrator <del> or shoot an email at [mailto:support@ccn.ucla.edu CCN Support]</del>.
[mailto:support@ccn.ucla.edu CCN Support] with the following information
 
  Email Subject: Lab Account Request
Prepare the following information:
  Subject: Lab Account Request
  Name: Your Name
  Name: Your Name
  Email: Your preferred email  
  Email: Your preferred email  
Line 22: Line 21:
  AIM: your aim chat account if you don't mind being reached this way
  AIM: your aim chat account if you don't mind being reached this way


You receive a confirmation email with any specific instructions once your account is created.
You will receive a confirmation email with any specific instructions once your account is created.


===Backups===
===Hoffman2 Cluster===
Every time you log out of or into a lab computer, your homes are sync'd to the main server *each time you log out*. So, if you have a computer assigned to you make a point of logging out (a safe and practical thing to do) to ensure all your data is backed up.
A very detailed, step by step walk through on obtaining an account on Hoffman2 is found on the [[Getting a Hoffman2_Account]] wiki page.  
 
If you accidentally delete a file or folder, send an email to [mailto:support@ccn.ucla.edu support] and request that it be restored. Please provide
* the full path to the file or directory you want restored
* whether you'd like it copied back to your computer or emailed to you separately.
 
If you have a personal computer you would like backed up, please send an email to [mailto:support@ccn.ucla.edu support] requesting it be configured for you.
 
If you have a personal backup account, all backups can be accessed and schedules set at:
 
[https://npih-monk.lab.ccn.ucla.edu/cgi-bin/BackupPC_Admin CCN Lab Backup Server]
 
Accessing the backup server '''requires''' a lab account.  


===Hoffman2 Cluster===
A very detailed, step by step walk through on obtaining an account on Hoffman2 is found on the [[Getting_a_Miles_or_Hoffman2_Account]] wiki page.
<b>Please remember that all support issues, lost passwords, forgotten accounts, and  more regarding Hoffman2 should be directed to the [mailto:accounts@ats.ucla.edu ATS Support].</b>
<b>Please remember that all support issues, lost passwords, forgotten accounts, and  more regarding Hoffman2 should be directed to the [mailto:accounts@ats.ucla.edu ATS Support].</b>


Read their [http://www.ats.ucla.edu/clusters/hoffman2/faq.htm FAQ] first!
Read their [http://www.ats.ucla.edu/clusters/hoffman2/faq.htm FAQ] first!
Once you've obtained an account, you may wish to look over the [[Every Day UNIX and Working with Hoffman]] page.
Once you've obtained an account, you may wish to look over the [[Every Day UNIX and Working with Hoffman]] page.


===Another Lab Member's Comptuer===
===Another Lab Member's Comptuer===
Although it may sound wild, the only person who can help you with this is the person who owns the computer. :)
Although it may sound wild, the only person who can help you with this is the person who owns the computer. :)
Also, ask permission first.


==Tools & Utilities==
If you are working on Hoffman2, miles, or a lab computer all the utilities you need to get working are already available. If this is not the case, please send a request to [mailto:support@ccn.ucla.edu CCN Support] requesting the program be added.


===Editors===
=Tools & Utilities=
A word on editors. Just about any editor is sufficient. However, some are less prone to user error than others when used for tasks such as programming or scripting.
During the course of your work for the lab, you'll often need to perform various tasks that revolve around using image analysis software, scripting, shell scripting (bash, zsh), and use of clusters (qsub, qstat, and writing job submission scripts).
If you are working on Hoffman2, miles, or a lab computer all the utilities you need to get working are already available. If this is not the case, please send a request to <del>[mailto:support@ccn.ucla.edu CCN Support]</del> or the local administrator requesting the program be added.


====TextEdit====
===Text Editors===
TextEdit is the built in OSX editor. By default, the files it creates are Rich Text. These are entirely unworkable for scripting or programming use. It also has a bad habit of leaving off appropriate UNIX end of line characters (this means a file looks like one big line to the operating system).  
Just about any editor is sufficient. Know how to use them. More information at [[Text Editors]].
Popular Editors:
*Vim
*Emacs
*TextEdit


Though a decent general purpose editor, it's highly discouraged to use this editor for scripting, programming, or editing of system files (like your bash_profile).
===Shell Scripting===
 
BASH is the shell you'll most likely be using in the lab and on our clusters. Knowing the shell and how to write simple scripts is absolutely essential to get your work done without suffering the ails of Repetitive Stress Syndrome. Ask around the office about Carpal Tunnel if you need inspiration to learn how to script. :)
====Vim====
Vim is an old standby, it's the default editor on many, many unix based systems. It is a full featured editor with many plugins to extend functionality (if you need them). It's usable in the Terminal and has several GUI editors based on it as well. For the mac, the best one I've found is [http://code.google.com/p/macvim/ MacVim].
 
Vim is a modal editor. This method of editing puts off some users. If you're interested, you can access the built in tutorial called (ingeniously) vimtutor.
$ vimtutor
 
====Emacs====
Emacs is the other big player in editors. It's a first class editor with very powerful features, but easy enough to use for simple tasks as well. It also is usable in both the terminal and has several GUI options like [http://aquamacs.org/ AquaEmacs]
 
You can access the emacs tutorial by
$ emacs
Once inside emacs, use the following key combo:
Control-h, t


====Komodo Edit====
Here are the basics:
From the site:
*[[BASH]]
Dynamic language expertise for Perl, PHP, Python, Ruby, and Tcl, plus JavaScript, CSS, HTML, and XML, and template languages like RHTML, Template-Toolkit, HTML-Smarty and Django.
*[[Unix Tools]]
*[[Python]]


[http://www.activestate.com/komodo_edit/ Komodo Edit] runs on every platform and supports both Vim and Emacs keybindings. It's really a first class editor by any definition of the word.
====TextMate====
TextMate is a very popular OSX editor. It has all the features you'd expect such as syntax highlighting, auto-indenting, etc. It's only draw back is that it does not have a terminal interface and does not work on other platforms besides OSX. It also costs money, which might turn away a starving student or two. For more information see [http://macromates.com/ TextMate].
====Others====
These are just a few and by no means meant to be exhaustive. However, there are some "essential features" you should look for when choosing your editor of choice. A few are:
# Syntax Coloring for source code and scripts
# Auto-indentation
# Plugable (e.g. others can extend it via plugins)
Though worthy of simple usage, the common basic editors Nano, Pico, and friends often do not provide the tools or functionality for writing error free, easy to read code or scripts. For anything beyond the ridiculously trivial the user should seriously consider a more feature rich editor.


=Keeping "In the Loop"=
=Keeping "In the Loop"=
Lab meetings, mail outs, notifications, where do they come from and how do you get them? Easy.
Lab meetings, mail outs, notifications, where do they come from and how do you get them? Easy.


==Mailing Lists==
===Mailing Lists===
*The Cohen-Bookheimer Lab mailing list receives all email specific to our lab. This includes notifications of hardware issues, software updates, general notifications, meetings, filed trips, and picnics.
*The Cohen-Bookheimer Lab mailing list receives all email specific to our lab. This includes notifications of hardware issues, software updates, general notifications, meetings, filed trips, and picnics.
**[http://www.ccn.ucla.edu/mailman/listinfo/cblab CBLAB]
**[http://www.ccn.ucla.edu/mailman/listinfo/cblab CBLAB]
Line 102: Line 66:
*Classes. If you're taking a course from Susan or Mark, there may be a mailing list specifically for that class. Please check with your professor for details.
*Classes. If you're taking a course from Susan or Mark, there may be a mailing list specifically for that class. Please check with your professor for details.


==Lab Meetings==
===Lab Meetings===
{| class="wikitable" border='1'  
{| class="wikitable" border='1'  
! Lab !!Time !!Location
! Lab !!Time !!Location
|-  
|-  
| Bookheimer || 1pm Thursdays || C8-369
| Bookheimer || 10pm Tuesdays || ---
|-
|-
| Cohen          || 1pm Every Other Thursday ||C8-885
| Cohen          || 2pm Thursday || ---
|}
|}


==Blogs & Wikis==
If you're here you found one of them! Here's the full list:
*[http://www.ccn.ucla.edu/wiki CCN Wiki]
**HowTo pages, pages for classes, and for image analysis.
*[http://www.ccn.ucla.edu/groups Lab Groups Blog/Wiki]
**Honestly, this one isn't much used. But it may be worth wasting 5m to see if anything interesting is there.
*[http://www.ccn.ucla.edu/users Lab Users Blog/Wii]
**Except for the James Kyle blog, these aren't used much. If you're a lab member, you can create your own blog/wiki here if that interests you. Just sign in using the username and password that you were given for logging into lab computers.
=Other Sources of Information (What You Should Know)=
During the course of your work for the lab, you'll often need to perform various tasks that revolve around using image analysis software, scripting, shell scripting (bash, zsh), and use of clusters (qsub, qstat, and writing job submission scripts).
In addition to the above resources, here are some links to get started.
==Sun Grid Engine (The Cluster)==
For information on the most commonly used commands for managing and submitting cluster jobs, see the [http://www.ats.ucla.edu/clusters/common/computing/batch/sge.htm ATS SGE] page.
==Python==
Python is the official scripting language of the lab. Anything beyond trivial work should use python to ensure homogeneity, interoperability, and future use of that work.
===Experienced in Programming, New to Python===
If you're already an experienced programmer, but new to Python. The free online book [http://diveintopython.org/ Dive Into Python] is right up your alley. It only lightly focuses on basic controllers like iterators, loops, conditional branching (if/else), and common data structures (arrays, hashes, etc). It focuses on specific Python idioms and linguistic sugar to get you from 0 to coding in as short a time as possible.
Please note the book was written for Python 2.2, so some of the behavior may vary slightly from that given in the book. For example, dir() lists both built-ins and public methods rather than just public methods. However, the differences aren't that significant and it still servers well as a quickie introduction.
===New to Programming===
If you're new to programming in general, the [http://www.greenteapress.com/thinkpython/thinkpython.html Think Python] free online book was written with you in mind. It's a gentle introduction to Object Oriented design principles...the python way. Don't worry, if you don't know what that means this manual will teach you.
===Standard Documentation===
Finally, there are the standard Python resources of [http://docs.python.org/tutorial/ Official Python Tutorial], [http://effbot.org/pyfaq/ The Semi-Official Python FAQ], and [http://python.org/ Python.org].
==Shell Scripting==
BASH is the shell you'll most likely be using in the lab and on our clusters. Knowing the shell and how to write simple scripts is absolutely essential to get your work done without suffering the ails of Repetitive Stress Syndrome. Ask around the office about Carpal Tunnel if you need inspiration to learn how to script. :)
===New to UNIX and BASH===
Here's a general list of useful sites to get you started on bash and unix
*[http://wooledge.org:8000/BashFAQ Bash FAQ]
*[http://wooledge.org:8000/BashGuide Bash Guide]
*[http://www.gnu.org/software/bash/manual/bashref.html Bash Reference Manual]
*[http://bash-hackers.org/wiki/doku.php Bash Hackers Wiki]
*[http://www.grymoire.com/Unix/Quote.html Learn to Quote] Everything you'd want to know about how quotes work in bash....and probably a lot more you don't.
*[http://billharlan.com/pub/papers/Bourne_shell_idioms.html Bourne Shell Idioms]
*[http://www.shelldorado.com/ Shelldorado] Collection of tutorials, guides, articles, and more about the Bash shell.
===Familiar with UNIX and BASH, But No Expert===
If you're familiar with the Terminal, Bash, and getting around, but are no scripting Guru there's one stop to get you from n00b to whiz.
*[http://tldp.org/LDP/abs/html/ Advanced Bash-Scripting Guide]
==Getting, Sending, and Transferring Files, Logging In, and All That Jazz==
The main method of transferring files back and forth and logging into remote servers is [http://openssh.org/ OpenSSH].
*[http://www.stocksy.co.uk/articles/Mac/ssh_on_mac_os_x/ SSH On Mac OSX]


=Finding More Information=
=Finding More Information=
Line 178: Line 92:
It may sound funny, but Google is an amazing resource. Often simply typing in the error you receive in google is enough to find a solution.  
It may sound funny, but Google is an amazing resource. Often simply typing in the error you receive in google is enough to find a solution.  


===Boolean, AND Searches===
====Boolean, AND Searches====
In my experience, one powerful feature of Google that many are not aware of is its Boolean search methods. By default, the AND operator is used. For example, a search for <i>red dog</i> is translated as "red AND dog". This means google looks for all pages that contain both the words Red and the word Dog, but not pages with only red or only dog.
In my experience, one powerful feature of Google that many are not aware of is its Boolean search methods. By default, the AND operator is used. For example, a search for <i>red dog</i> is translated as "red AND dog". This means google looks for all pages that contain both the words Red and the word Dog, but not pages with only red or only dog.


===Quoted Searches===
====Quoted Searches====
Any set of words placed in quotes is taken as a literal search. For example, by quoting the above search "red dog" google finds all pages with the exact string "red dog", but ignores pages that may have red and dog at different parts of the page. The quoted string is very useful for finding information about errors.  
Any set of words placed in quotes is taken as a literal search. For example, by quoting the above search "red dog" google finds all pages with the exact string "red dog", but ignores pages that may have red and dog at different parts of the page. The quoted string is very useful for finding information about errors.  


===Broadening and Narrowing Searches===
====Broadening and Narrowing Searches====
The technique of broadening and narrowing searches is the most important for efficient Googling. Here are some tips:
The technique of broadening and narrowing searches is the most important for efficient Googling. Here are some tips:
*If you search for the word "analysis" and find nothing, try a variation of the word such as "analyze".  
*If you search for the word "analysis" and find nothing, try a variation of the word such as "analyze".  

Latest revision as of 03:44, 16 January 2014

Computer Resources

Please see FAQ: Shared Resources for in depth list of available resources.

Virtually all work in the lab is done in one of three ways:

  1. On a group resource lab computer
  2. On the hoffman2 cluster
  3. On another lab member's computer

Let's cover each of these in detail and how you can gain access to that resource.

Group Resource Lab Computer

These are computers available for reserving by anyone in the lab. So far, we have approximately 5 of these. To gain an account on these computers, ask for the local lab manager/administrator or shoot an email at CCN Support.

Prepare the following information: 

Subject: Lab Account Request
Name: Your Name
Email: Your preferred email 
Phone: Phone Number to reach you when out of the office
AIM: your aim chat account if you don't mind being reached this way

You will receive a confirmation email with any specific instructions once your account is created.

Hoffman2 Cluster

A very detailed, step by step walk through on obtaining an account on Hoffman2 is found on the Getting a Hoffman2_Account wiki page.

Please remember that all support issues, lost passwords, forgotten accounts, and more regarding Hoffman2 should be directed to the ATS Support.

Read their FAQ first! Once you've obtained an account, you may wish to look over the Every Day UNIX and Working with Hoffman page.

Another Lab Member's Comptuer

Although it may sound wild, the only person who can help you with this is the person who owns the computer. :) Also, ask permission first.


Tools & Utilities

During the course of your work for the lab, you'll often need to perform various tasks that revolve around using image analysis software, scripting, shell scripting (bash, zsh), and use of clusters (qsub, qstat, and writing job submission scripts). If you are working on Hoffman2, miles, or a lab computer all the utilities you need to get working are already available. If this is not the case, please send a request to CCN Support or the local administrator requesting the program be added.

Text Editors

Just about any editor is sufficient. Know how to use them. More information at Text Editors. Popular Editors:

  • Vim
  • Emacs
  • TextEdit

Shell Scripting

BASH is the shell you'll most likely be using in the lab and on our clusters. Knowing the shell and how to write simple scripts is absolutely essential to get your work done without suffering the ails of Repetitive Stress Syndrome. Ask around the office about Carpal Tunnel if you need inspiration to learn how to script. :)

Here are the basics:


Keeping "In the Loop"

Lab meetings, mail outs, notifications, where do they come from and how do you get them? Easy.

Mailing Lists

  • The Cohen-Bookheimer Lab mailing list receives all email specific to our lab. This includes notifications of hardware issues, software updates, general notifications, meetings, filed trips, and picnics.
  • The Cluster-Users mailing list receives notifications about various cluster issues and updates. These are mostly hardware related or may involve software specific to the cluster, e.g. a scheduled down time for updating FSL.
  • Classes. If you're taking a course from Susan or Mark, there may be a mailing list specifically for that class. Please check with your professor for details.

Lab Meetings

Lab Time Location
Bookheimer 10pm Tuesdays ---
Cohen 2pm Thursday ---


Finding More Information

Man Pages

For further information there is one resource above all others. I'm going to repeat it 3 times (each repetition imbues the phrase with deeper meaning...I learned this from top 40 music):

  • Man Pages
  • Man Pages
  • Man Pages

Man Pages are the be all end all of information for UNIX programs. Man is short for "Manual" or as Websters likes to chirp: 

1. a book of instructions, esp. for operating a machine or learning a subject; a handbook : a computer manual | a training

And that's just what man pages do, they instruct you on all the ins and outs of how to use a specific program. Man pages are a formal language. They require a rigid format that is unambiguous and succinct in its interpretation. It's not as bad as it sounds, but may look confusing at first. Fear not! Our friendly O'Reilly members have written a tutorial on how to use the built in UNIX manuals and documentation to uncover the mystery:

Google

It may sound funny, but Google is an amazing resource. Often simply typing in the error you receive in google is enough to find a solution.

Boolean, AND Searches

In my experience, one powerful feature of Google that many are not aware of is its Boolean search methods. By default, the AND operator is used. For example, a search for red dog is translated as "red AND dog". This means google looks for all pages that contain both the words Red and the word Dog, but not pages with only red or only dog.

Quoted Searches

Any set of words placed in quotes is taken as a literal search. For example, by quoting the above search "red dog" google finds all pages with the exact string "red dog", but ignores pages that may have red and dog at different parts of the page. The quoted string is very useful for finding information about errors.

Broadening and Narrowing Searches

The technique of broadening and narrowing searches is the most important for efficient Googling. Here are some tips:

  • If you search for the word "analysis" and find nothing, try a variation of the word such as "analyze".
  • Use the shortest variation of a word in your search that is still unique or pertinent to increase the number of results. For example, instead of searching for "programming" search for "program". The key here is that all pages that contain "programming" also contains "program", thus you have broadened the possible number of hits. Some other results:
    • instead of scanning, search for scan
    • instead of unfolding, search for unfold
    • instead of boolean, search for bool
  • Narrow your search with quotes
    • For example, if you search for functional magnetic resonance and get far too many hits, you can narrow the results by searching for the exact string "functional magnetic resonance"
  • Use acronym and synonyms liberally. e.g. MRI instead of magnetic resonance imaging
  • Eliminate terms from your search that are obviously specific to your individual case.
    • For example, say you get an error: "FSL Fubar Error 521: some_file_I_named.txt". Now, obviously not everyone in the world has a file named "some_file_I_named.txt". Thus, it is a frivolous search term that does little in helping google find a solution for us. Trimming this down to the terms that would be common to any error of this time produces much better results. e.g. "FSL Fubar Error 521"

AHHHHH HELP ME!!: How to Get Help

You've read the docs, you've searched google, you've read the man pages....and yet cannot find a solution. What do you do now?

First off, it's worth looking over this informative write up on the process of How_to_Ask_for_Help. Often in our frustration we overlook the obvious. How_to_Ask_for_Help serves as a nice guide on the steps to take in building a good help request (good for you and good for the person you're asking). It helps cut through the frustration and confusion in order to get to what we're really looking for. . . Answers!

After you've got a well formed support question, fire an email off to CCN Support. You'll receive updates on the status of your inquiry, notification by email when the issue is resolved, and links to possible solutions.

Retrieved from "https://www.ccn.ucla.edu/wiki/index.php?title=New_to_the_Lab&oldid=1683"