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CBCB Private Wiki

You have to be on the UMIACS VPN to view the private wiki if you are not on campus!

In addition to this wiki there is also the CBCB private wiki. It contains information internal to CBCB, such as information about how to use the cluster.

IMPORTANT (Read First)

NEW! Read about the CBCB Software Modules

The CBCB computational infrastructure is a shared resource and we all need to pitch in in order to make sure it works well for all of us. Most importantly, we need to ensure that our disk space and computational resources are used responsibly. The disk space, in particular, is a valuable commodity and thus it is important to pay attention to the following:

  • There are three types of disk space available (a full list of volumes is available at CBCB Storage) :
    • Local harddrives (usually mounted as /scratch on the machines that have this resource). These are not backed up, are quite fast (they live physically close to the processor), but can only be 'seen' by the machine where they are mounted and, thus, require data staging in/out (which can take a while)
    • Shared 3Par storage (/fs/szasmg*, /fs/szdata/*, etc.). This is very fast and very expensive disk and thus a limited resource. Please only use this space to store data temporarily, while you are running some analyses on it. As a rule of thumb, if a file or collection of files of any considerable size have lived on this space for more than 1-2 weeks, they should probably be moved to the attic space (see below)
    • Attic storage (/fs/szattic*). This is cheaper and ample, but slow and brittle storage. Your data-sets should primarily live here. Due to it's brittleness, the IT department do not recommend you run any analyses directly in this volume, rather you copy the files over to a local harddrive or the 3Par instead, and copy the results back when done.
  • You should remove any temporary results you don't need in the long term as soon as you've generated them, and compress all of the large files. Bzip2 works better than gzip but either should dramatically improve the space requirements, especially for text files such as fasta or fastq.
  • You should ensure that your files are owned by the cbcb group and that they have group write permissions for any file stored on the 3Par, especially for all those in /fs/szscratch. This will allow your colleagues to remove files in case the disk runs out of space and you are, for example, on vacation (in which case you shouldn't have any major files sitting around on the 3Par).

For more information on the CBCB resources see Getting Started in CBCB.




Getting started

If you have just received a new umiacs account through CBCB, follow the instructions on this page to get the basic information you'll need to start working: