Computing resources
From CCGB
See the Help page for an overview of computing topics.
What do we have here that you can use?
Contents |
Access
Almost all systems here run Debian or Ubuntu Linux or Mac OS X. This means you can access these systems remotely via SSH.
All systems have hostnames ending in .bx.psu.edu, e.g. herbie.bx.psu.edu. To SSH to a system from inside BX, you don't need the .bx.psu.edu, e.g.:
% ssh herbie
Whereas outside the BX network, you'd need:
% ssh herbie.bx.psu.edu
You can get SSH for Windows at downloads.its.psu.edu.
Data
On some systems (including most desktops) there is a partition called /space that is designed to be used for large transient datasets. Since doing huge writes to your home directory can be painful on the central fileserver, you are strongly encouraged to write things to /space and then only copy what you need to keep back to your home directory. This also helps keep backup costs low since home directories are backed up (and we're charged based on how much data we have backed up).
You can find sequences and alignments in /depot/data1/cache. If what you need doesn't exist in /depot/data1/cache, don't download it yourself, just ask nate to download it for you. It's best to work with sequences and alignments DIRECTLY from /depot/data1/cache rather than copying them to your home directory (or /space). For bzip or lzop compressed sequences or alignments, use:
bzcat /depot/data1/cache/foo.axt.bz2 lzop -dc /depot/data1/cache/foo.axt.lzo
This writes the alignment out to stdout instead of a file. Pipe that to a program that can read the alignment from stdin and you won't need to actually have the uncompressed alignments on disk:
bzcat /depot/data1/cache/foo.axt.bz2 | bar.pl
The bx-python package also has libraries for seeking to desired locations in a compressed MAF. Please ask for help if you're not sure how to use the compressed alignments effectively.
The Systems
Public
- coltrane
Central server for email, file serving, etc. This is here so you're aware of coltrane, but you generally should not use coltrane for anything. Coltrane runs Debian Sarge with a mix of testing/unstable.
- herbie
General computing system. This is shared amongst everyone in the center, so please keep this in mind when running resource-intensive jobs. Run commands with a nice level of 10:
herbie% nice 10 <your command>
Herbie runs AMD64 Debian Sarge with a mix of testing/unstable. It has 2 x 2.4GHz AMD Opteron 64-bit CPUs and 4GB of memory.
Private
In addition to the various Ubuntu/Debian/OS X workstations scattered around the Center (if you're a student you'll probably be assigned one of these workstations by your sponsoring faculty member), there are a few servers available to just lab members.
- mulligan - Miller Lab
Shared among members of the Miller Lab, so please keep this in mind when running resource-intensive jobs. Mulligan runs AMD64 Debian Sarge with a mix of testing/unstable. It has 2 x 3.0GHz AMD Opteron 64-bit CPUs and 8GB of memory. Mulligan has a very large /space partition.
- scofield - Nekrutenko Lab
This system is for development of Galaxy. Scofield runs x86 Debian Sarge with a mix of testing/unstable. It has 2 x 2.8GHz Intel Xeon CPUs and 3.5GB of memory.
