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BioHPC Lab:
User Guide

 


Storage

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).

Local storage. 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, etc.

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 deleted

  • 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 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 Storage Guide.

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 Lab Computers.

 

 

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