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There are three ways of using bear:To find out this information yourself (and for other reasons), you'd like to be able to shell on to a node. I currently can't (I get permission denied requests). However, you can dispatch a shell command to a node through bsub though!
'''phd-pgsql''' is a new and experimental database Details on how to work with this server for PhD students and faculty. It hosts a copy of are on the [[Working with PostgreSQL with support for R, Perl and C++ scripting inside of the RDMS. At present the server is being deployed]] page. More news will be available here shortly!
Research Computing At Haas (view source)
Revision as of 19:56, 26 October 2011
, 19:56, 26 October 2011→Bear
Haas research computing for PhD students currently consists of '''bear.haas.berkeley.edu''' and '''phd-pgsqlpostgres.haas.berkeley.edu'''. This pages page details these resources.
==Bear==
Bear is a 12 8 node research computing cluster. [http://groups.haas.berkeley.edu/HCS/research_computing/research-hwsw.html The official blurb] is out of date (it still says that bear has two sets of 5 compute nodes, one set with 64Gb of RAM per node, and one with 16Gb of RAM per node). Nodes All nodes have dual quad core 3Ghz Xenon processorsat about 3Ghz.
The following commands are valuable:
free #list memory available
cat /proc/meminfo #see the memory specs
cat /proc/cpuinfo #see the chip specs
uname -a #see the system info
/sbin/ifconfig -a #see the network tables
The IP addresses of the nodes are:
*Bear (login node): 128.32.67.85, 128.32.67.86, 192.168.1.42, 192.168.1.43, 10.1.1.42, 10.1.1.43
*cn-06 to 11: 10.1.1.105 to 10.1.1.111
The memory and chips are:
*The login node(s) have 2 dual-core Xeon 5150 chips @2.66Ghz, with 38G of RAM
*cn-06 to cn-10 each have 2 quad-core Xeon 5570 chips @2.93Ghz with 48G of RAM
*cn-11 has 8 physical cores (16 cores through hyperthreading) with 196GB of RAM
Previously, we also had:
*(Disabled) cn-01 to cn-05 have 2 single core Xeon chips @3.2Ghz with 16G of RAM
'''There are three ways of using bear''':
===Storing Data on Bear===
===SSH'ing into Bear===
You can use a copy of PuTTy PuTTY to SSH onto bear. PuTTY is a free SSH client that you can [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html download from its author]. You don not need to 'install' it - it is a standalone executable file. [http://groups.haas.berkeley.edu/hcs/howdoi/install_putty.pdf Details for the configuration] are available from the [http://groups.haas.berkeley.edu/HCS/howdoi.html howdoi section] of the haas website, but none is really needed.
And save the connection settings if you want.
====Screen====
You may want to use the 'screen' command to create a screen that can be detached from your SSH session or to run multiple shells within a single session.
Just type:
screen
To control screen, rather than the shell you are given, use the Ctrl-A (C-A) commands. Type:
C-A ?
to get the screen help. The command 'exit' will exit you from (your last) screen and dump you back to the original shell. Crucially, screen's can be 'detached' and left running in the background, and if your SSH (putty) connection drops for some reason but if you are running your commands within a screen, they will stay running and can be picked up again later on. Screens can also be shared across multiple users.
Useful commands are:
'''Within Screen:'''
C-a c Create a new screen
C-a 0 Move to screen 0
C-a 1 Move to screen 1 (and so on)
C-a n Move to next screen
C-a d Detach screen from the SSH session and return to the shell
exit Terminate screen and return to the shell
'''From the shell:'''
screen -ls List all screen sessions available
screen -r session_name Reattach to a screen session
See also:
*[http://www.rackaid.com/resources/linux-screen-tutorial-and-how-to/ A quick tutorial on screen].
====Bsub====
If you are running scripts then you should use the ''bsub'' to have them execute on the compute nodes, rather than the login node, as otherwise a runaway script can bring the entire of bear to a stand still. An example syntax for running a perl script is:
bsub -Is "perl Script.pl"
When a process launches it reports the compute node that is being used (cn-02 to cn-10), and a process id (p_id). You can kill a process (that wasn't launched interactively) by typing:
bkill p_id
You can set the memory allocation and target a node. Memory is in Kb, so 48Gigs is 50331648 (48 * 1024 * 1024) and 40G is 41943040. To target a node use the -m switch and the node name. Nodes cn-06 to cn-10 have 48Gb (see the specs above).
bsub -M 41943040 -m cn-06 -Is "..."
To decide which node to target, you'll need to know who is running what where. To get this list of jobs run by '''all''' '''u'''sers you type:
bjobs -u all
To see the actual utilization on a particular node you can run top on the node with the commands
top-cn-06
top-cn-07
etc... Note that top-cn-11 isn't defined (yet) so you can give the command directly:
bsub -m cn-11 -Ip top
Also, note that if the top command isn't being dispatched to the node then it is probably because it thinks the node is full. You can probably get around this by giving top higher priority.
If you are running many jobs simultaneously (and please, be respectful when you do) it seems that bsub will only submit 3 jobs to compute nodes at once, and will queue the rest up as pending. Submitting jobs to individual nodes bypasses this.
====Stata====
Note that there are both stata and stata-se versions on bear. And Versions 9, 10, and 11. When you give the command
stata
or
stata-se
You automatically run the latest version and it passes the command to bsub so that you are running stata on one of the commute nodes.
If you want to manually control bsub options give the command (this one runs stata se version 11:
bsub "/usr/local/stata11/stata-se -b dofile.do"
====Languages====
Available scripting languages include:
*Fortran 77
====Unix Commands====
To see your files you might want the following simple commands:
*'''cd bulk''' - change into the bulk directory
*'''cd ..''' - change up a directory
*'''top''' - look at the top processes
*'''ps -aux''' show all processes running
====Useful Tricks====
If you want to change the color scheme used by the 'ls' command then:
cp /etc/DIR_COLORS.xterm .dir_colors
And edit the .dir_colors file to suit your tastes. Note that the changes won't take effect until you start a new session!
===Using Xwindow Applications on Bear===
To use these applications you need an Xwindows client. The eXceed client is available from available from [http://software.berkeley.edu software.berkeley.edu] for [http://software-central.berkeley.edu/software/42-Exceed/version/143/delivery_methods/297 download here]. '''Download it and install it'''. You can accept a typical installation for just one user. There is [http://groups.haas.berkeley.edu/hcs/howdoi/exceed.asp a very old set-up guide from HCS] that may be useful, but the details below should suffice. Note that there is a security notice warning of risks when you use eXceed. We are partly protected from these risks by the design of the Haas network, but you might want to consider following the advanced configuration instructions.
Remember - Bear is your R drive, so the root of bear, when you login, is the root of your R drive!
==Postgres.Haas.Berkeley.Edu== '''Postgres.Haas''' is a new and experimental database server for PhDstudents and faculty. It hosts a copy of PostgreSQL with support for R, Perl and C++ scripting inside of the RDMS. At present the server is being tested and new users are welcome. Those with permission can see the [[Haas PhD Server Configuration]] page to view the set-PGSQL==up.
