Versions Compared

Old Version 47

changes.mady.by.user Anna Battenhouse

Saved on

compared with

New Version Current

changes.mady.by.user Daryl Barth

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

TACC compute clusters now share a common Work file system called stockyard. So files in your Work area do not have to be copied, for example from to stampede2 stampede3 to ls6 – they can be accessed directly from either cluster.

...

  • $STOCKYARD - This refers to the root of your shared Work area
    • e.g. /work/01063/abattenh
  • $WORK - Refers to a sub-directory of the shared Work area that is different for different clusters, e.g.:
    • /work/01063/abattenh/ls6 on lonestar6
    • /work/01063/abattenh/stampede2stampede3 on stampede2 stampede3

A mechanism is being developed for purchasing larger stockyard allocations (above the 1 TB basic quota) from TACC are in development.

The UT Austin BioInformatics Team, a loose group of bioinformatics researchers, maintains a common directory area on stockyard.

...

corral is a gigantic (multiple PB) storage system (spinning disk) where researchers can store data. UT researchers may request up to 5 TB of corral storage through the normal TACC allocation request process. Additional space on corral can be rented for ~$80~$43/TB/year. See https://docs.tacc.utexas.edu/hpc/corral/

A couple of things to keep in mind regarding corral:

...

There is currently no charge for ranch storage. However, since the data is stored on tape it is not immediately available – robots find and mount appropriate tapes when the data is requested, and it can take minutes to hours for the data to appear on disk. The metadata about your data – the directory structures and file names – is always accessible, but the actual data in the files is not on disk until unless "staged". See the ranch user guide for more information: https://wwwdocs.tacc.utexas.edu/user-services/user-guides/ranch-user-guidehpc/ranch/.

Once that data is staged to the ranch disk it can be copied to other places. However, the ranch file system is not mounted as a local file system from the stampede2 stampede3 or ls6 clusters. So remote copy commands are always needed to copy data to and from ranch (e.g. scp, rsync).

...

Code Block
languagebash
titleGet ready to wget
mkdir -p $SCRATCH/archive/original/20212024.core_ngs
cd $SCRATCH/archive/original/20212024.core_ngs
wget

Here are two web links:

...

Now press Enter to get the command going. Repeat for the 2nd link. Check that you now see the two files (ls), or tree tree $SCRATCH to see your Scratch directory hierarchy:

...

  • -a means "archive mode", which implies the following options (and a few others)
    • -p – preserve file permissions
    • -t – preserve file times
    • -l – copy symbolic links as links
    • -r – recursively copy sub-directories
  • -v means verbose
  • -W means transfer Whole file only
    • Normally the rsync algorithm compares the contents of files that need to be copied and only transfers the different parts.
    • For large files and binary files, figuring out what has changed (diff-ing) can take more time than just copying the whole file.
    • The -W option disables file content comparisons (skips diff-ing).
      • Files are only copied if their modification date is more recent or the file size is different

Since these are all single-character options, they can be combined after one option prefix dash ( - ). You could also use options -ptlrvW, separately, instead of using -a for "archive mode".

Tip
titleAlways add a trailing slash ( / ) after directory names

The trailing slash ( / ) on the source and destination directories are very important for rsync – and for other Linux copy commands also!

rsync will create the last directory level for you, but earlier levels must already exist.

Let's copy a directory using rsync. We'll also add the -P option to show Progress as the copy progresses.

Code Block
languagebash
titlersync (local directory)
mkdir -p $SCRATCH/data
cds
rsync -avrWavW -P $CORENGS/custom_tracks/ data/custom_tracks/

...

Tip

The bash shell has several convenient line editing features:

  • use the Up arrow to scroll back through the command line history; Down arrow goes forward
  • use Ctrl-a to move the cursor to the beginning start of a line; Ctrl-e to the end end
  • Ctrl-k ("kill") to delete all text on your command line after the cursor
  • Ctrl-y ("yank") to copy the last killed text to where the cursor is

Once the cursor is positioned where you want it:

  • Just type in any additional text you want
  • To delete text after the cursor, use:
    • Delete key on Windows
    • Function-Delete keys on Macintosh
  • To delete text before the cursor, use:
    • Backspace key on Windows
    • Delete key on Macintosh

(Read more about Command line history and editing)

...

Code Block
titlesingle remote file copy with scp
cat $CORENGS/tacc/dragonfly_access.txt
cds
mkdir -p data/test2
scp -p corengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test2/
tree ./data/test2

Notes:

  • The 1st time you access a new host the SSH security prompt will appear
  • You will be prompted for your remote host password
    • for security reasons characters will not be echoed
  • The  -r recursive argument works for scp also, just like for cp
  • The  -p argument says to preserve the file's last modification time
    • otherwise the last modification time of the local copy will be when the copy was done

...