Biowulf High Performance Computing at the NIH
Online class: Introduction to Biowulf

Hands-On: Disk Storage, Checkquota, Snapshots

Get a listing of files in your home and data areas:

ls -la /home/$USER

ls -l /data/$USER

Check your disk space allocation and usage:

Create a directory for yourself in /scratch and copy a file into that area:
mkdir /scratch/$USER
cp /fdb/blastdb/nt.nal  /scratch/$USER

Important: Copy the scripts that will be used in this class to your own area. The utility 'hpc-classes' will do this:

hpc-classes biowulf
The copy takes about 4 mins – be patient. You should now have a directory /data/$USER/hpc-classes/biowulf containing a few GB of data.


# change directory to your /home/$USER
# cd to the .snapshot directory
cd .snapshot
# see what snapshots are available
# cd to a specific snapshot -- replace [date] with the date of an available nightly snapshot
cd Nightly.[date]
# copy a file from that snapshot to your home directory -- replace 'somefile' with the name of a real file
cp somefile /home/$USER
# check the newly copied file
ls -l /home/$USER/somefile
# copy the same file, preserving the timestamp
cp -p somefile /home/$USER


Question 1: how much disk space is used by /data/$USER/hpc-classes/biowulf?


Type 'du -sh /data/$USER/hpc-classes/biowulf'. It should show 3-4 GB.

Question 2: how large is your home directory and how much unused space is in /home/$USER?


Type 'checkquota'.

Question 3: Can you write to your .snapshot area?


No. Try it and see.

Question 4: how many nightly snapshots are available in the /home area?


Type 'ls -ld /home/$USER/.snapshot/Nightly*'. You should see 6 Nightly snapshots.

Question 5: How many weekly snapshots are available in your data area?


Type 'ls -ld /data/$USER/.snapshot/weekly*'. You should see 2 Nightly snapshots.