Running Programs on the Cray SV1

1. ssh cray (or cray.tjhsst.edu or seymour.tjhsst.edu)
   From home:
   • 1. ssh remote.tjhsst.edu
   • 2. ssh cray.tjhsst.edu from remote
   • Use putty.exe for an xterm connection from home
   • Use Winscp for a window ftp connection to transfer files
2. Same system commands as the workstations, for example:
   • ls lists files
   • pwd shows the directory path - yours should be /local/yourname
   • mkdir directory creates directories (folders) to categorize your files
   • cd directory - puts you into directory
   • cd ../ moves back one directory
3. Transfer files from a workstation to the SV1:
   • run gftp from another xterm
   • choose SSH2 from the upper right of the gftp window and connect to the Cray with username/password
   • For a non-window file transfer use ftp cray
     put file transfers your file from our lab to the SV1
     get file gets the files from the SV1 to the workstation
     Note: you can use "ls", "cd" inside ftp
4. Editing programs - the SV1 has only emacs or vim
   • Workstation option: use an editor on the workstation. Transfer the source file to the SV1 using gftp or ftp
   • vim filename
     • You start out in "command" mode
     • : linenumber
       goes to a line number
     • :i
       Enters "insert" mode - use this mode to type into your file
       :a is similar, appends to the end of a line
     • ESC
       goes back to "command" mode
     • In command mode:
       x - deletes one char
       dd - deletes one line
     • :w saves the file
     • :wq saves and quits
     • :q! quits without saving
   • emacs filename
     • CTRL x CTRL s
       saves your file, no exit
     • CTRL x CTRL c
       exits emacs, asks if you want to save
     • CTRL x CTRL h
       Gets a preliminary help file
       q - quits the help
       t - gives you a tutorial
       space bar scrolls
5. C and C++
   Specifying the name of your executable:
   • cc -o filename filename.c ("-o filename" generates the output/executable file)
   • ./filename (runs the executable)
     Not specifying the name of your executable:
   • cc filename.c generates the generic a.out as an executable
   • use ./a.out to run the executable

     C++

   • CC -o filename filename.cpp
   • ./filename (runs the executable)
   • CC filename.cpp for a.out as the executable

6. Fortran 90
   • f90 -o filename filename.f90 or f90 filename.f90 for a.out
   • ./filename or ./a.out (runs the executable)

7. MPI (Message Passing Interface) (SV1 has the C and Fortran versions of MPI, no C++ version for MPI)
   • cc -o filename filename.c
   • mpirun -np 4 filename
     (runs the executable with 4 processes, "np" = number of processes)
   • mpirun -nt 4 filename
     (runs the executable with 4 tasks, "nt" = number of tasks,
     tasks use shared memory, may be faster than processes)

8. OpenMP (Fortran 90 version, no C version)
   Example file:
   • omp_hello.f90 from OpenMP exercises (scroll down to "Fortran files")
   • f90 omp_hello.f90 compiles an a.out executable
     ./a.out runs the executable
   • OMP_NUM_THREADS=8 changes the number of threads to 8 from the default (probably 4 threads default)

9. PVM - for any interested, the SV1 also has Parallel Virtual Machine. This is similar to MPI; we won't be using it in class