For an account on phillips, please send a request to Michael(dot)Sprague(at)colorado(dot)edu
If you need support/help on the Bowling Alley machines, please send a
message to trouble@eady.colorado.edu
If you need support/help on phillips, please send a message to
trouble@phillips.colorado.edu
Please be aware that there is no backup of user data on the Bowling
Alley and phillips machines. Please backup important data to another
server.
Queueing System
PBSpro job submission to queue: qsub pbs_script
The script file includes the information that PBS needs to place your job in a priority queue, including the executable name, expected wall time, number of cpus, and designamed output files. The command returns a job id for that job. job status: qstat jobid kill job: qdel jobid Further PBS documentation Also type man pbs, man qsub, man qstat, man qdel, etc at unix prompt.
Compilers
Intel Fortran Compiler 8.0 command: /usr/local/intel/bin/ifort documentation: /usr/local/intel/doc or man /usr/local/intel/bin/ifort
Intel c/c++ Compiler 8.0 command: /usr/local/intel/bin/ecc documentation: /usr/local/intel/doc or man /usr/local/intel/bin/ecc
MPICHmanual and
commands Compile using mpif90, mpif77 or mpiCC located in /usr/local/mpich/bin.
These are mpi wrappers for the Intel 8.0 compilers.
You will need /usr/local/intel/lib/ in your LD_LIBRARY_PATH
and /usr/local/intel/bin/ in your path.
run executable using /usr/local/mpich/bin/mpirun
(not the default /usr/bin/mpirun)
use -machinefile flag on mpirun to specify machines
OpenMP
On Intel compiler, use -openmp flag to invoke OpenMP.
For Fortran, use -fpp as well to invoke the text preprocessor. example codehello_OpenMP.f90
phillips> /usr/local/intel/bin/ifort hello_OpenMP.f90 -openmp -fpp -i_dynamic
phillips> a.out see output
timing test: OpenMP_timing_test.f90 Compares parallel and serial timing for a simple loop.
phillips> /usr/local/intel/bin/ifort OpenMP_timing_test.f90 -openmp -fpp -i_dynamic
phillips> a.out see output
NAG Fortran 77 library for intel compiler location: /usr/local/lib/libnag-mkl.a, libnag.so.20, libnag.a, libnag-mkl.so.20 documentation: /usr/local/NAG/asliR7/fll6420dbl/doc example code: /usr/local/NAG/asliR7/fll6420dbl/examples
NAG Fortran 90 librarylocation: /usr/local/lib/libnagfl90* documentation: /usr/local/NAG/asliR7/fnl6404dbl/doc example code: /usr/local/NAG/asliR7/fnl6404dbl/examples
NAG c library location: /usr/local/lib/libnagc.so.6 documentation: /usr/local/NAG/asliR7/cll6406da/doc example code: /usr/local/NAG/asliR7/cll6406da/examples
FFTw, the "Fastest Fourier Transform in the West"
manual at /usr/local/fftw-3.0.1/doc/html/index.html location: /usr/local/fftw-3.0.1/lib/libfftw3.* to compile:/usr/local/intel/bin/ifort my_code.f90 -i_dynamic -lfftw3 -L/usr/local/fftw-3.0.1/lib -I/usr/local/fftw-3.0.1/include/
Also, make sure /usr/local/fftw-3.0.1/lib is in LD_LIBRARY_PATH
Ogle command: /usr/local/ogle-2001nov06/ogle documentation: less /usr/local/ogle-2001nov06/ogle.man
To run Ogle, you may use the GUI interface or an
Ogle script file
To use the script, type ogle ogle_script at the unix prompt.
