| Your Account |
|
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
PATH=$PATH:$HOME/bin
export PATH |
|
| set - useful
information about path and other account
settings |
| |
| |
| Compiling |
|
| To compile without the MPI
libraries: |
|
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 |
| |
|
LAPACK Libraries,
BLAS Libraries |
| Under Construction |
| |
|
MPICH - Compiling, Linking and Running |
| Under Construction |
| |
| |
| To compile with the MPI
libraries: |
| 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 |
| |
| |
| Linking
(C compiler example): mpicc –o my_program
my_program.o –lm |
| |
| For compiling and linking
in one step: |
| 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 |
| |
| |
| Submitting Jobs |
|
| Using mpirun |
To run the program a.out on
four (4) processors use the following
mpirun –np 4 a.out (note: We prefer users to
use PBS to run programs.) |
| |
|
The Portable Batch System (PBS) is used to allocate
nodes for a job and run it.
You should use PBS to run jobs on the compute nodes. |
| |
To use the PBS queue,
you run the qsub and 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 already 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. |
| |
| 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. |
| |
