Introduction to High Performance Computing for Climate Computing Dr. Jerry Perez Research Associate High Performance Computing Center

www.hpcc.ttu.edu

1-21-2015

Creating, moving and editing data files

•Login to Hrothgar •pwd •mkdir test •cd test •vi test

How to access the supercomputer: Using Putty to access Hrothgar.hpcc.ttu.edu

•Select or type Hrothgar.hpcc.ttu.edu in the server window.

•Select open

How to access the supercomputer: Using Putty to access Hrothgar.hpcc.ttu.edu

•Use your eRaider user name at the “login as” prompt.

•Use your eRaider password at the “ [email protected]’s password:”

pwd

At prompt, type: pwd

mkdir

At the prompt, type: mkdir test Check your work, type: ls

cd

At the prompt, type: cd test Check your work, type: ls Check your work, type: pwd

Vi – using the text editor

We will prepare to write our first code.

But first we must learn how to use the vi editor.

At the prompt, type: vi test.sh

Using the VI editor

To get into and out of vi To Start vi

 To use vi on a file, type in vi filename. If the file named filename exists, then the first page (or screen) of the file will be displayed; if the file does not exist, then an empty file and screen are created into which you may enter text. • vi filename edit filename starting at line 1 • vi -r filename recover filename that was being

edited when system crashed

Using the VI editor

Inserting or Adding Text

 The following commands allow you to insert and add text. Each of these commands puts the vi editor into insert mode; thus, the key must be pressed to terminate the entry of text and to put the vi editor back into command mode. * i insert text before cursor, until hit I insert text at beginning of current line, until hit * a append text after cursor, until hit A append text to end of current line, until hit * o open and put text in a new line below current line, until hit * O open and put text in a new line above current line,

until hit

Deleting Text

 The following commands allow you to delete text. * x delete single character under cursor Nx delete N characters, starting with character under cursor dw delete the single word beginning with character under cursor dNw delete N words beginning with character under cursor; e.g., d5w deletes 5 words D delete the remainder of the line, starting with current cursor position * dd delete entire current line Ndd or dNd delete N lines,

beginning with the current line; e.g., 5dd deletes 5 lines

Using the VI editor

To Exit vi

 Usually the new or modified file is saved when you leave vi. However, it is also possible to quit vi without saving the file. 

Note:

The cursor moves to bottom of screen whenever a colon (:) is typed. This type of command is completed by hitting the (or ) key. • :x quit vi, writing out modified file to file named in

original invocation

• :wq quit vi, writing out modified file to file named in

original invocation

• :q quit (or exit) vi * • :q! quit vi even though latest changes have not been

saved for this vi call

TEST.sh – your first cluster job

#$ -V #$ -cwd #$ -S /bin/bash #$ -N test #$ -o $JOB_NAME.o$JOB_ID #$ -e $JOB_NAME.e$JOB_ID #$ -q normal #$ -pe fill 12 #$ -P hrothgar hostname

Running your cluster job

At the prompt type: qsub test.sh

Check your work, type: qstat

Running your cluster job

How to copy files from the supercomputer: Using PSCP to move files •Obtain PSCP.exe: http://www.chiark.greenend.org.uk/~sgtatham/pu tty/download.html

•Select PSCP for your OS.

•If you have a MAC or a Linux OS, you do not need PSCP.

How to copy files from the supercomputer: Using PSCP to move files

Copying files from your Linux host to your Windows PC.

In order to copy a file from your Linux host to your Windows PC your command line would look like this:

pscp [email protected]:test.sh c:\test.sh

 This command line copies “test.sh" located in your home directory on your Linux host to the temp directory on your C:\ drive.

Copying files from your Windows PC to our Linux host.

In order to copy a file from your Windows PC to your our Unix host your command line would look like this:

pscp -v c:\test.sh [email protected]:/test.sh

  This command line copies “test.sh" located in the C:\ drive to your home directory on our Linux cluster. Remember: Backslashes (

\

) for your DOS and Windows files and forward slashes (

/

) for your Linux files.