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Research Computing At Haas (view source)
Revision as of 22:04, 25 January 2011
, 22:04, 25 January 2011New page: Haas research computing for PhD students currently consists of '''bear''' and '''phd-pgsql'''. This pages details these resources. ==Bear== Bear is a 12 node research computing cluster. ...
Haas research computing for PhD students currently consists of '''bear''' and '''phd-pgsql'''. This pages details these resources.
==Bear==
Bear is a 12 node research computing cluster. [http://groups.haas.berkeley.edu/HCS/research_computing/research-hwsw.html The official blurb] 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 have dual core 3Ghz Xenon processors.
There are three ways of using bear:
===Storing Data on Bear===
Your "R" drive lives on bear. We tested access times to the R drive and found that they are much faster than to HCS-Data or other shares that you have access to (other than your C drive, though the speeds are actually comparable with those to C). You should use R:\bulk as your primary data storage area.
If your R drive isn't mapped already then map a network drive to:
\\bear\username$
===SSH'ing into Bear===
You can use a copy of 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.
The address to connect to bear is:
bear.haas.berkeley.edu
And the connection is on the standard port (22). You can set your username under:
Connection -> Data -> Auto-login Username
And save the connection settings if you want.
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"
Available scripting languages include:
*Perl
*Python
*R
There are also (apparently - I haven't tested them) compilers for:
*C++ (GNU Cpp)
*Fortran 77
To see your files you might want the following simple commands:
*'''ls -alt''' - list the files in the current directory in all their glory
*'''cd bulk''' - change into the bulk directory
*'''cd ..''' - change up a directory
===Using Xwindow Applications on Bear===
There are copies of the following Xwindow applications ready for use on bear:
*Matlab (matlab)
*Stata (xstata)
*Stata-SE (xstata-se)
*SAS (sas)
To use these applications you need an Xwindows client. The eXceed client is [http://software.berkeley.edu available from software.berkeley.edu] for [http://software-central.berkeley.edu/software/42-Exceed/version/143/delivery_methods/297 download here]. Download it and install it.
Now save a bear configuration in PuTTy by entering the following parameters and hitting "Save":
Session -> Host Name (or IP address) '''bear.haas.berkeley.edu'''
Connection -> Data -> Auto-login Username '''Your_Username'''
Connection -> Data -> SSH -> Encryption Cipher '''Move Blowfish to the top'''
Connection -> Data -> SSH -> X11 -> Enable X11 Fowarding '''Tick the box'''
Session -> Saved Sessions '''Bear''' + '''Click Save'''
Now start eXceed running (and leave it running in the background) and SSH onto bear using Putty. At the command line type the name of the program, for example "xstata-se", and the program will launch in an eXceed window on your desktop. Voila!
Remember - Bear is your R drive, so the root of bear, when you login, is the root of your R drive!
==PhD-PGSQL==
'''phd-pgsql''' is a new and experimental database server for PhD students and faculty. It hosts a cope of PostgreSQL with support for R, Perl and C++ scripting inside of the RDMS. At present the server is being deployed. More news will be available here shortly!
==Bear==
Bear is a 12 node research computing cluster. [http://groups.haas.berkeley.edu/HCS/research_computing/research-hwsw.html The official blurb] 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 have dual core 3Ghz Xenon processors.
There are three ways of using bear:
===Storing Data on Bear===
Your "R" drive lives on bear. We tested access times to the R drive and found that they are much faster than to HCS-Data or other shares that you have access to (other than your C drive, though the speeds are actually comparable with those to C). You should use R:\bulk as your primary data storage area.
If your R drive isn't mapped already then map a network drive to:
\\bear\username$
===SSH'ing into Bear===
You can use a copy of 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.
The address to connect to bear is:
bear.haas.berkeley.edu
And the connection is on the standard port (22). You can set your username under:
Connection -> Data -> Auto-login Username
And save the connection settings if you want.
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"
Available scripting languages include:
*Perl
*Python
*R
There are also (apparently - I haven't tested them) compilers for:
*C++ (GNU Cpp)
*Fortran 77
To see your files you might want the following simple commands:
*'''ls -alt''' - list the files in the current directory in all their glory
*'''cd bulk''' - change into the bulk directory
*'''cd ..''' - change up a directory
===Using Xwindow Applications on Bear===
There are copies of the following Xwindow applications ready for use on bear:
*Matlab (matlab)
*Stata (xstata)
*Stata-SE (xstata-se)
*SAS (sas)
To use these applications you need an Xwindows client. The eXceed client is [http://software.berkeley.edu available from software.berkeley.edu] for [http://software-central.berkeley.edu/software/42-Exceed/version/143/delivery_methods/297 download here]. Download it and install it.
Now save a bear configuration in PuTTy by entering the following parameters and hitting "Save":
Session -> Host Name (or IP address) '''bear.haas.berkeley.edu'''
Connection -> Data -> Auto-login Username '''Your_Username'''
Connection -> Data -> SSH -> Encryption Cipher '''Move Blowfish to the top'''
Connection -> Data -> SSH -> X11 -> Enable X11 Fowarding '''Tick the box'''
Session -> Saved Sessions '''Bear''' + '''Click Save'''
Now start eXceed running (and leave it running in the background) and SSH onto bear using Putty. At the command line type the name of the program, for example "xstata-se", and the program will launch in an eXceed window on your desktop. Voila!
Remember - Bear is your R drive, so the root of bear, when you login, is the root of your R drive!
==PhD-PGSQL==
'''phd-pgsql''' is a new and experimental database server for PhD students and faculty. It hosts a cope of PostgreSQL with support for R, Perl and C++ scripting inside of the RDMS. At present the server is being deployed. More news will be available here shortly!
