On the Linux workstations, you have access to two kinds of storage:
networked storage and local storage.
Networked storage, typically your home directory, e.g. /home/abc123 (where "abc123" is your login ID).
This is where you end up right after you log in to a machine. All home directories
reside physically on a file server and are network-mounted on each of the workstations.
This means that you will always see the same home directory, no matter which of the
workstations you log in to. This also means that access to files in the home directory
is slower than access to local disks (i.e., the ones physically attached to a given
workstation). Therefore, I/O-intensive programs (such as all Next-Gen tools, for example)
should NEVER be run in the home directory (i.e., they should not read or write large
files located in the home directory). Instead, you should use the local storage for
this purpose (see below). Your home directory will be subject to a quota, i.e.
only limited amount of data can be stared there. Please refer to the
Lab storage guide for
more information on the networked storage. Other directories that are
network mounted on all workstations are /programs (where most of the
software is installed) and /shared_data (where copies of genomic
databases reside, see databases).
Each machine has an available local storage located in the
directory /workdir (regular disks) or /SSD (SSD storage on selected
workstations). Actual amount of storage available is listed on the
Reservations page under the machine name (e.g. "4TB HDD; 1TB SSD" means
4TB regular disk storage under /workdir and 1TB of SSD storage under
/SSD). After logging in, each user should create
his/her own subdirectory under /workdir or /SSD (e.g., /workdir/abc123)
and put all the files to be processed in that subdirectory rather
than in the home directory. When launching an application, make sure that
it always reads/writes files from/to local disk - this is usually
accomplished by executing a "change directory" command similar to "cd /workdir/abc123"
and starting the application from there. When your session ends, the content of
/workdir may be wiped out automatically
to make space for next user's data. Therefore, any important files
(calculation results, for example) have to be transferred to your home
directory before you log out. Note:
The directory /workdir (and its subdirectories) are local to each
machine, i.e., /workdir on cbsuwrkst2 is not accessible from cbsuwrkst3,
NOTE. Files in /workdir or /SSD directory should be transferred out of the
workstation and deleted after the computations are done. Unfortunately
many users leave these files behind creating disk space problems for
other users in the future. To prevent this we have implemented automated
cleaning procedure that removes old files from /workdir at 3:00am every
day. The rules for removing old files are:
Files of the current reservation are NEVER
FIles for reservations that ended more
than 7 days ago are ALWAYS deleted.
If there is more than 50% of free disk space
available files of the 2 most recent previous reservations are not
deleted in addition to the current reservation (if any).
If there is less than 50% but more than 10% of
free disk space available files of the 2 most recent
reservations are not deleted (including current reservation, if any)
If there is less than 10% of free disk space
available files of the most recent reservation are not deleted
(including current reservation, if any).
See our FAQ for more information about file transfer methods. If
you need to clean /workdir at other time than 3:00am you can do it by
running script /programs/config/clean_workdir - it will start the same
procedure as is run periodically at 3:00am.
Each user is assigned a free storage quota on their home
directory, depending on the user type. Users associated with
active Lab Credit Accounts (i.e. with non-zero hour balance)
have 200GB storage quota. Users without active Lab Credit
Account can store up to 20GB (e.g. workshop users). Any user can
purchase additional storage, which can be applied to his/her
home directory, or to group of directories, or to a dedicated
storage directory shared by group of users. The cost of
additional storage is 91.35 per 1TB per year. NOTE: free storage
quotes cannot be combined, added to purchased storage or used for multiple accounts.
They are just to make sure users can carry out common
computations without purchasing extra storage. For details
please refer to Lab
Local data cache
The BioHPC lab computers keep copies of some of the commonly used
reference genomes. For detailed information on how to access these
databases please go to Genome Databases on BioHPC