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For assistance, please contact the Help Desk at help@hpc.unm.edu or (505)  277-8348 (Monday through Friday, 9 a.m. to 5 p.m. Mountain Time)

Login using secure-shell (ssh):

%  ssh loslobos.alliance.unm.edu

Transfer files to the Linux cluster from your home machine  using secure copy protocol (scp):

%  scp <file> <user>@loslobos.alliance.unm.edu:<dest>

Change your password on the Linux cluster:

%  yppasswd

Change your login shell on the Linux cluster:

%  ypchsh

Please forward your mail to your local system. To forward mail,  create a .forward file in your Linux cluster home directory and put your email address in it:

<username>@<host.domain>

Compilers from GNU, PGI are installed.

GNU C

%  gcc –o exec [options] filename(s).c

GNU C++

%  g++ –o exec [options] filename(s).C

GNU Fortran77

%  g77 –o exec [options] filename(s).f

PGI Fortran77

%  pgf77 –o exec [options] filename(s).f

PGI Fortran90/95

%  pgf90 –o exec [options] filename(s).f90

Source code debuggers:

GNU

%  gdb

PGI

%  pgdbg

Performance profiler:

PGI

%  pgprof

For example:

%  which mpirun

/usr/parallel/mpich-gm.pgi/bin/mpirun

shows that you are using MPICH with the GM interface, and the corresponding MPICH compiling scripts mpif77 and mpif90 will use the PGI Fortran compilers.

C

%  mpicc –o exec [options] filename(s).c

C++

%  mpiCC –o exec [options] filename(s).C

Fortran77

%  mpif77 –o exec [options] filename(s).f

Fortran90

%  mpif90 -o exec [options] filename(s).f90

ATLAS BLAS

%  -L/usr/local/lib -lcblas -lf77blas -latlas

LAPACK

%  -L/usr/local/lib -llapack -lcblas -lf77blas -latlas

FFTW release 2, complex input

%  -L/usr/local/lib -lfftw

FFTW release 2, real input

%  -L/usr/local/lib -lrfftw

FFTW release 3, real or complex input

%  -L/usr/local/lib -lfftw3

MPICH P4 Compatible Libraries:

FFTW release 2, complex input

%  -L/usr/parallel/lib/p4 -lfftw_mpi -lfftw

FFTW release 2, real input

%  -L/usr/parallel/lib/p4 -lrfftw_mpi -lrfftw

Scalapack

%  -L/usr/parallel/lib/p4 -lscalapack -lblacsf77init -lblacs -lblacsf77init -L/usr/local/lib -lf77blas -latlas

MPICH GM Compatible Libraries:

FFTW release 2, complex input

%  -L/usr/parallel/lib/gm -lfftw_mpi -lfftw

FFTW release 2, real input

%  -L/usr/parallel/lib/gm -lrfftw_mpi -lrfftw

Scalapack

%  -L/usr/parallel/lib/gm -lscalapack -lblacsf77init -lblacs -lblacsf77init -L/usr/local/lib -lf77blas -latlas

PBS supports two modes for running jobs – batch  and interactive. With batch mode, a user submits a job, and the job is queued, scheduled and run without any further interaction.  With interactive mode, a user submits a request for an interactive session on a set of compute nodes assigned by the PBS job manager.

The following examples show simple scripts for batch mode jobs.  

Portable Batch System (PBS)

PBS Batch Mode Sample Scripts:

Request 16 nodes and start one mpi process on each node:

#PBS -l nodes=16:ppn=2
mpirun -machinefile $PBS_NODEFILE -np 16 myprog.exe

Request 8 nodes and start 2 mpi processes on each node:

#PBS -l nodes=8:ppn=2
mpirun -machinefile $PBS_NODEFILE -np 16 myprog.exe

Standard output and error files will be written to your working directory.  To submit the script to PBS, use the following command:

% qsub <pbs_script_file>

PBS Interactive Mode Sample Session:
Request an interactive session with 8 nodes:

% qsub –I –l nodes=8

Run your program as follows:

Start one mpi process on each node: 

% mpirun -machinefile $PBS_NODEFILE -np 8 myprog.exe

Start two mpi processes on each node:

% mpirun -machinefile $PBS_NODEFILE -np 16 myprog.exe

Release your nodes when finished by typing:

% exit

Display contents and status of queue:

% qstat -a

Remove job from queue:

% qdel <job_id>