Access the Cluster
ssh - secure terminal service for account login
sftp/scp - file transfers
Default shell account is bash.
echo $PATH - view current directory paths for your account
Add paths to your account temporarily: PATH=$PATH:/directory/path/to_add
Add paths to your account permanently: Edit path statement (shown below) in "~/.bash_profile". Separate paths with colons.
# User specific environment and startup programs
set - useful information about path and other account settings
gsh uptime - see the uptime of each compute node
gsh ps U username - see processes you have running on compute nodes
pbsnodes -a - see the current state of all the compute nodes
Intel Fortran F77, F90 Compiler
For Fortran 77 use: ifort my_program.f [ flags ] -o executable
For Fortran 90 use: ifort my_program.f90 [ flags ] -o executable
Intel C/C++ Compiler
For C use: icc my_program.c [ flags ] -o executable
For C++ use: icpc my_program.cpp [ flags ] -o executable
GNU Scientific Compilers
For Fortran use: f77 my_program.f
For C use: gcc my_program.c
mpicc –c my_program.c or mpicc –c my_program my_program.c
mpif77 –c my_ program.f or mpif77 –c my_program my_program.f
mpicxx –c my_program.cxx or mpicxx –c my_program my_program.cxx
mpif90 –c my_program.f90 or mpif90 –c my_program my_program.f90
mpicc –o my_program my_program.o –lm
mpicc –o my_program my_program.c
mpif77 –o my_program my_program.f
mpicxx –o my_program my_program.cxx
mpif90 –o my_program my_program.f90
The Portable Batch System (PBS) is used to allocate nodes for your job and run it. It is the preferred method to run jobs on the compute nodes.
To use the PBS queue, you run jobs with qsub and monitor using qstat commands. The qsub command is used to submit a job to the PBS queue, and the qstat command is used to check on the status of a job in the PBS queue.
In order to run a job through PBS, you first create a PBS script that contains the commands to be executed. This script is then submitted to PBS using the qsub command.
The file pbs_mpi_cpi.sh is a sample file automatically created in your user area. Issue the command, “qsub pbs_mpi_cpi.sh” to submit the file to PBS. Note: The sample PBS script specifies the use of all 16 compute nodes. You should change the number of compute nodes to four (4) when you create your own PBS scripts. Otherwise, you may have a long wait until all nodes are available.
Commonly Used PBS Commands:
qstat - Shows status of PBS batch jobs.
Use 'qstat -a' for more detailed output, 'qstat -f' for full job details, or 'qstat -n' to see the nodes used by a particular job.
qsub - Submits a job to the PBS queuing system.
qdel - Delete a PBS job from the queue.
Other PBS Commands:
qalter - Modifies the attributes of a job.
qhold - Requests that the PBS server place a hold on a job.
qmove - Remove a job from the queue in which it resides and place the job in another queue.
qmsg - Send message to PBS batch job. To send a message to a job is to write a message string into one or more output files of the job.
qorder - Exchange the order of two PBS batch jobs in a queue.
qrerun - Reruns a PBS batch job.
qrls - Release hold on PBS batch job.
qselect - List the job identifier of those jobs which meet a list of selection criteria.
qsig - Requests that a signal be send to the session leader of a batch job.