-I starts an interactive job
-q specifies a queue (cpuq or gpuq for Euclid and cpui or gpui for Cy-Tera)
-l number of nodes and cores per node needed by a job
This will open a shell on the first node assigned. This is useful for jobs that have graphical interfaces or setting up job scripts.
h5. Example MPI code: hello.c
{code}
#include <stdio.h>
#include <mpi.h>
int main(int argc, char ** argv) {
int size,rank;
int length;
char name[80];
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
MPI_Comm_size(MPI_COMM_WORLD,&size);
MPI_Get_processor_name(name,&length);
printf(
"Hello MPI World! Proc %d out of %d on %s\n", rank, size, name);
MPI_Finalize();
return 0;
}
{code}
h5. To compile a parallel job
{code:bgColor=#c0c0c0}
module load openmpi
mpicc -o hello hello.c
{code}
h5. To create a job script
A job script is a list of instructions that tell PBS how to run your job. You can modify a job script in a text editor such as Vim, nano, joe, pico, emacs etc. You should do such work on the head node.
*On Euclid*
{code}
#!/bin/bash -l
# Fix: job name; merge stdout & stderr; environment; ask cores
#PBS -N mpi-hello_world
#PBS -j oe
#PBS -q batch
#PBS -l nodes=2:ppn=8
cd $PBS_O_WORKDIR
module load openmpi # without this, mpiexec may not be in path
mpiexec ./hello # execution depends on Software Environment
env|grep ^BC_ # print Baseline Configuration related variables
env|grep ^HOME
env|grep ^WORK
sleep 15 # Wait a bit otherwise the job runs too fast
{code}
*On Cy-Tera*
{code}
#!/bin/bash -l
# Fix: job name; merge stdout & stderr; environment; ask cores
#PBS -N mpi-hello_world
#PBS -j oe
#PBS -q cpuq
#PBS -l nodes=2:ppn=12,walltime=00:15:00
cd $PBS_O_WORKDIR
module load openmpi # without this, mpiexec may not be in path
mpiexec ./hello # execution depends on Software Environment
env|grep ^BC_ # print Baseline Configuration related variables
env|grep ^HOME
env|grep ^WORK
sleep 15 # Wait a bit otherwise the job runs too fast
{code}
h5. To submit a job
*On Euclid*
{code:bgColor=#c0c0c0}
qsub <name of script> # To submit a job in PBS
{code}
*On Cy-Tera*
{code:bgColor=#c0c0c0}
msub <name of script> # To submit a job in PBS
{code}
h5. Makefile Example
{code}
CC=g++
CFLAGS=-c -Wall
LDFLAGS=
SOURCES=main.cpp hello.cpp factorial.cpp
OBJECTS=$(SOURCES:.cpp=.o)
EXECUTABLE=hello
all: $(SOURCES) $(EXECUTABLE)
$(EXECUTABLE): $(OBJECTS)
$(CC) $(LDFLAGS) $(OBJECTS) -O $@
.cpp.o:
$(CC) $(FLAGS) $< -O $@
{code}
{info}
The examples mentioned hereby can be found in euclid:
/opt/examples/coreskills
{info}
...