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The queuing system

The queueing system currently installed on Hagrid is OpenPBS/Maui.

Useful commands

qsub to submit a job
qstat to check the status of the queue
qdel to delete a job
checkjob what does the scheduler think about a job

Less useful commands

qhold to place a hold on a job
qrls to release a hold on a job
qselect to list all jobs meeting certain creteria
qmove to move a job to a different queue
qorder to change the ordering of two jobs in a queue
qrerun to terminate a job and return it to the queue
qsig to send a signal to a job

Scalar (single) jobs

The qsub job files are simple shell scripts with PBS directives in form of shell comments.

 

#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -q grawp
cd /home/user/scalar
scalartest

 

This script executes the programm scalartest on one node of the queue grawp. The line beginning with #PBS marks a PBS directive. Here, the job needs one node and one processor (per node). It is important to note the change in the correct directory using the cd command.

 

Parallel (MPI) jobs

To start an MPI job the mpiexec command is used.

 

#!/bin/bash
#PBS -l nodes=4:ppn=2
#PBS -q grawp
cd /home/user/mpi
mpiexec -n 8 ./mpitest

 

This jobs takes four nodes with two processor per node, i.e. a total of eight cpus. The argument to mpiexec (-n) is the total number of processes (4*2). The actual program exectuted on the nodes is mpitest.

 

For an odd number of nine cpus the corresponding PBS directive is

 

#PBS -l nodes=4:ppn=2+1:ppn=1:grawp

 

Note: this directive allocates 2 processors on 4 nodes and 1 processor on 1 node. The directive grawp after ppn=1 is necessary, otherwise torque/maui allocates nodes of any queue-type. To change the node-type of the first set of processors, in this case 4:ppn=2 use the -q directive.

 

Actually torque/maui has the freedom to pack the nodes, i.e. it might allocate 2 nodes with 4 processors and 1 node with 1 processor.

Useful PBS directives

-l resources (cpu time, memory, ...) required by the job
-e standard error stream
-o standard output stream
-N name of the job
-p priority of the job
-q destination of the job (queue)
-S shell that exectutes the job script

Queues

PBS can control different queues which differe on criteria like the wall clock time etc.

In order to have a fair share of the resources (cpu time) consummed by the users the Maui sheduler reorders the execution sequence.

To get an overview of the available queues the qstat command can be used

 

qstat -Q -f

qstat -q

 

Jobs can be submitted (-q directive) to the following queues:

queue name default CPU Time default no. of CPUs machine size
hagrid 12h 1 32 bit
hermione 24h 1 64 bit
grawp 2h 1 64 bit

Obtaining an account

For technical questions or an account on grawp ask the system administrators.

 

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