MSE 4270/6270: Getting started with Unix and computing

Transcription

1 MSE 4270/6270: Getting started with Unix and computing Research computing accounts on ITS Linux Cluster Fir : ITS at UVA operates a Linuxbased commodity cluster with a frontend named Fir. Access to Fir is available to anyone with a research computing account. All graduate students should already have research computing accounts. Undergraduate students and those who needs to activate their research accounts should ask me and I will send the requests to ITS. More information on research accounts can be found here: You can connect to Fir by using SecureCRT and transfer files using SecureFX software that you can get from Instructions on the installation and use of SecureCRT and SecureFX can be found on & Space you can use on Fir: Computation directories: After you login to Fir using SecureCRT, you are automatically located in the Home directory (/home/loginid). All users have a maximum quota of 4 Gigabytes (GB) of space on Home Directory, which should be sufficient for small-scale computation to complete all your homework assignments. For your term projects, some of you may need more space to run simulations in this case you need to move to the temporary scratch storage by cd /bigtmp and create your own directories there by mkdir loginid. Pay attention to the purge policy - the files older than two weeks will be removed from /bigtmp. More information can be found on To edit files you can use vi, pico, jove, emacs, nedit, nano, xemacs,... or any other editor. In particular, emacs seems to be convenient and easy to learn To open file with emacs, enter $ emacs filename If you use emacs, it is convenient to have a separate popup window for each file you edit. To enable the pop-up window you should follow the following three steps: Step 1: Enable Forward X11 packets in the Session Options of SecureCRT

2 Step 2: Install Xming for Windows operating system. To download Xming, go to the official download page ( and download and install the latest version of the two packages called Xming and Xming-fonts. For Mac system, X11 should already be installed. Just start the Xming program before you connect with your SecureCRT program. Step 3: $ emacs filename & Some simple unix commands/help File management ls : list directories and files ls -la : list directories and files, how big they are, creation date, etc. mkdir dirname: make directory named dirname cd dirname : change to directory dirname cd.. : go up one directory cd : cd to your home dir mv file1 file2 : move file1 to file2 (or rename file file1 to file2) cp file1 file2 : copy file1 to file2 rm file1 : delete file1 rm file1 file2 : delete file1 file2...

3 rmdir dirname : delete directory dirname which is empty mkdir dirname : make directory dirname ftp machinename: to transfer files to remote machines ssh machinename: connects to remote machines using secure shell (better than telnet) Compilers c/c++ compilers: cc, gcc, c++, CC, gcc, gc++,... Fortran compilers: pgf90, f90, gf90, xlf,... Generally one adds "flags" to compile a code: $ pgf90 o execname file.f -o execname: name the output executable "execname" To run the executable: $ execname To be able to type other commands while the code is running (run in the background) $ execname & To be able to log out and leave the code running: $ nohup execname & To show your running processes $ps -fu loginid That will show the process ID (PID). Then you can kill the process by typing $ kill -9 PID Miscellanea: "*" are wild cards. For instance "ls *.C" will list only files ending in.c. "man command" gets the online help for command "man -k topic" show me commands dealing with topic. "Ctrl c" generally kills the current program being executed. "more file" shows all file one screen at a time "cat filename" shows the whole file "head file" shows the top part of the file "tail file" shows the last few lines of a file "grep hello *.f90 " returns all lines containing the word hello in any file named *.f90 "command >> out.dat" sends output of command to out.dat More information for you to get started can be found on and ITS Help can be contacted from

4 Loading the module for PGI compiler: Before we can compile the code, we need to load the module for the compiler. In our case, PGI compiler is recommended and it can be loaded by module load pgi. In order to avoid typing this command every time when you login to Fir, you can add the following lines in the end of.kshrc file for ksh shell or.bashrc file for bash shell: # source module commands source /opt/modules/default/init/sh module load pgi Your shell type can be checked by typing the command echo $0 or echo $SHELL..kshrc file and.bashrc file are located in your home directory and can be edited. After you load the module for the compiler, you can compile the class code by make in the code directory. Instructions to compile and run the code shown in the next page 1. Create an input file with name test.in: In the same directory where you are planning to run the code open new file test.in using your favorite editor (vi, nedit, emacs, pico, etc.). Enter values of the input variables, e.g., and save the file. 2. Write a code using the same editor (or cut-and-paste the code listed in the next page). Save it to a file with extension.f, e.g., test.f 3. Compile the code. To get an executable named test.x from file test.f: pgf90 -o test.x test.f 4. To run the executable just type test.x or./test.x 5. As a result of the execution, you should get new file test.out with the output data. You can then plot the output data using your favorite graphics package. You can also transfer this file to your PC using SecureFX and use your favorite graphics package in MS Windows or Mac environment. If you have any problems, please do not hesitate to ask me.

5 Example Fortran code: PROGRAM Test! Lines that start with exclamation mark are ignored by Fortran90 compiler IMPLICIT NONE! By making this statement you are announcing that you will define types of all variables! used in the code. An alternative is to use default type declarations. REAL, PARAMETER :: PI = ! The above line defines a named constant of type REAL.! Named constants cannot be changed later in the code REAL :: X, Y, dx, Xfinish! This line declares several variables of type REAL INTEGER step! This line declares an integer variable step OPEN (UNIT = 15, FILE='test.in')! Open input file test.in Read (15,*) Xfinish, dx! Read the data from the input file OPEN (UNIT = 16,FILE='test.out')! Open output file step=0 X=0.0! We are starting a DO loop below X_loop: DO! Below we are performing some calculations X=X+dx step=step+1 Y=sin(X*PI)! Writing data to the disc (to file test.out) WRITE(16,*) step, X, Y End do X_loop IF (X.GE.Xfinish) EXIT X_loop CLOSE (UNIT = 15) CLOSE (UNIT = 16) END