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You normally want to prevent over-subscription of cores on execution hosts by limiting the slots allocated on a host to its CPU cores ( processors) count — where “processors” might mean hardware threads.
If you only have a single queue, you can get away with specifying the slot counts in the queue for each host (qconf -mconf). You can do it also by host group
slots 0,[@hexcore=12],[@quadcore=8]...
With multiple queues on the same hosts, you may need to avoid over-subscription due to contributions from each queue.
An easy way for an inhomogeneous cluster is with the following RQS (with qconf -arqs), although it may lead to slow scheduling in a large cluster:
{
Name host-slots
description restrict slots to core count
enabled true
limit hosts {*} to slots=$num_proc
}
This would probably be the best solution if num_proc, the processor count, is variable by turning hardware threads on and off.
Alternatively, with a host group for each hardware type, you can use a set of limits like
limit hosts {@hexcore} to slots=12
limit hosts {@quadcore} to slots=8
which will avoid the possible scheduling inefficiency of the $num_proc dynamic limit.
Finally, and possibly the most foolproof way in normal situations is to set the complex on each host, e.g.
$ for n in 8 16; do qconf -mattr exechost complex_values slots=$n \ `qconf -sobjl exechost load_values "*num_proc=$n*"`; done
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RQS
Max user jobs on a particular execution host
{ name max_per_host enabled TRUE limit users dag hosts chrisdag-laptop to slots=2 }The RQS Design Specification document contains the following more complicated example:
- All users together should never take more than 20 slots
- All users should maximal take 5 slots on all linux hosts
- Every user is restricted to one slot per linux host, only user "roland" is restricted to 2 slots and all other slots on hosts are set to 0
In that case, the ruleset would look like this, note that "@linux" is a predefined hostgroup:
{ name maxujobs limit users * to slots=20 } { name max_linux limit users * hosts @linux to slots=5 } { name max_per_host limit users roland hosts {@linux} to slots=2 limit users {*} hosts {@linux} to slots=1 limit users * hosts * to slots=0 }
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Am 03.01.2012 um 11:34 schrieb Ben De Luca:
> I wonder if I am miss remembering, but is there a way to
> configure a queue to have the same number of slots as there are NCOR
> (or even NCPU) as per machine. I seem to remember doing this though I
> may have set this with hostlist some how? I am running SGE 8.0.0e
> (son of gridengine)
If you want to have it generic, you could define 999 slots and use an RQS per hosts to define it to match the number of cores automatically, but it will make the output longer and give a (IMO) confusing output for qstat.To define it in the queue definition:
$ qconf -sq all.q
...
slots 1,[node01=4],[node02=8],[@hexacore=6]
[gridengine users] queue slots per machine
Reuti reuti at staff.uni-marburg.de
Tue Jan 3 16:42:46 UTC 2012
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Dave Love d.love at liverpool.ac.uk
Wed Jan 4 17:39:03 UTC 2012
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Reuti <reuti at staff.uni-marburg.de> writes: >>> In `qstat -f` you see the number of resv/used/tot. slots. All slots >>> show up with the value of the queue configuration if I'm not mistaken, >>> reading 999 then. >> >> I see this for a couple of nodes: >> >> -------------------------------------------------------------------------------- >> - >> parallel at node063 BIPC 0/4/4 3.82 lx-amd64 >> 122440 0.67089 NVT5job2a ******** r 01/03/2012 16:50:25 4 >> -------------------------------------------------------------------------------- >> - >> parallel at node064 BIPC 0/0/4 0.00 lx-amd64 > > Not for me, I have 999 in the queue configuration and get: > > $ qstat -f > queuename qtype resv/used/tot. load_avg arch states > --------------------------------------------------------------------------------- > a at b BIPC 0/0/999 0.01 lx24-x86 > ------------------------------------------------------------------------------ Oh, right. I have $ qconf -sq parallel | grep slots slots 0,[@quadcore=8],[@octcore=16],[@dualcore=4],[@hexcore=12],[@ibsdr4=4] as opposed (I assume) to your 999 there. I'll clarify the doc.
Am 03.01.2012 um 17:38 schrieb Dave Love: > Reuti <reuti at staff.uni-marburg.de> writes: > >> Am 03.01.2012 um 11:34 schrieb Ben De Luca: >> >>> I wonder if I am miss remembering, but is there a way to >>> configure a queue to have the same number of slots as there are NCOR >>> (or even NCPU) as per machine. I seem to remember doing this though I >>> may have set this with hostlist some how? I am running SGE 8.0.0e >>> (son of gridengine) > > [Beware that's not released.] > >> If you want to have it generic, you could define 999 slots and use an >> RQS per hosts to define it to match the number of cores automatically, >> but it will make the output longer and give a (IMO) confusing output >> for qstat. > > I.e. > > $ qconf -srqs host-slots > { > name host-slots > description "restrict slots to core count" > enabled TRUE > limit hosts {*} to slots=$num_proc > } > > How is it confusing, exactly? In `qstat -f` you see the number of resv/used/tot. slots. All slots show up with the value of the queue configuration if I'm not mistaken, reading 999 then. -- Reuti > In case it's not clear, it isn't the same as just doing this with > multiple queues on the host. > >> To define it in the queue definition: >> >> $ qconf -sq all.q >> ... >> slots 1,[node01=4],[node02=8],[@hexacore=6] >
XXX
-pe high 10-20requests a high-priority "parallel environment" that spans several machines, in this case any number of CPUs between 10 and 20 (inclusive), a single number will request exactly that many CPUs. Note that if you request more CPUs than you actually have high-priority access to, your job will hang. See Submitting OpenMP Jobs or Submitting MPI Jobs
-q *@machineName-n*request a specific machine, or machine group
-l slots=2requests that the job be given 2 slots (or 2 cpus) instead of 1; you MUST use this if your program is multi-threaded, you should NOT use it otherwise
-l mem_free=1.5Grequests that only machines with 1.5GB (=1536MB) or more be used for this job; ie. the job requires a lot of memory and thus is not suitable for all hosts. Note that 1G is equal to 1024M (How do I determine how much memory my program needs? See the FAQ)
MPI
Applications that use Message Passing Interface (MPI) consist of multiple tasks that rely on a communication infrastructure. The orte (Open Run-Time Environment) parallel environment supports Open MPI applications.
% qsub -pe orte 4 runmeIn the example above, the runme script calls mpirun to start the tasks, which GridEngine distributes to 4 separate machines.
There is an example MPI application to help you get started. Also there is much more information at open-mpi.org.
Sun Grid Engine Plugin - StarCluster 0.95.5 documentation
Advanced Options¶
The SGE plugin has advanced options that some users may wish to tune for their needs. In order to use these advanced options you must first define the SGE plugin in your config:
[plugin sge] setup_class = starcluster.plugins.sge.SGEPlugin
Disabling Job Execution on Master Node¶
By default StarCluster configures the master node as an execution host which means that the master node can accept and run jobs. In some cases you may not wish to run jobs on the master due to resource constraints. For example, if you're generating a lot of NFS traffic in your jobs you may wish to completely dedicate the master to serving NFS rather than both running jobs and serving NFS.
To disable the master node being used as an execution host set master_is_exec_host=False in your sge plugin config:
[plugin sge] setup_class = starcluster.plugins.sge.SGEPlugin master_is_exec_host = FalseNow whenever a new cluster is created with the SGE plugin enabled the master will not be configured as an execution host.
Setting the Number of Slots Per Host¶
By default StarCluster configures each execution host in the cluster with a number of job 'slots' equal to the number of processors on the host. If you'd like to manually set the number of slots on each execution host set slots_per_host=<num_slots_per_host> in your SGE plugin config:
[plugin sge] setup_class = starcluster.plugins.sge.SGEPlugin slots_per_host = 10Sun Grid Engine Quick-Start¶
The following sections give an overview of how to submit jobs, monitor job and host status, and how to use the SGE parallel environment.
Submitting Jobs¶
A job in SGE represents a task to be performed on a node in the cluster and contains the command line used to start the task. A job may have specific resource requirements but in general should be agnostic to which node in the cluster it runs on as long as its resource requirements are met.
Note
All jobs require at least one available slot on a node in the cluster to run.
Submitting jobs is done using the qsub command. Let's try submitting a simple job that runs the hostname command on a given cluster node:
sgeadmin@master:~$ qsub -V -b y -cwd hostname Your job 1 ("hostname") has been submitted
- The -V option to qsub states that the job should have the same environment variables as the shell executing qsub (recommended)
- The -b option to qsub states that the command being executed could be a single binary executable or a bash script. In this case the command hostname is a single binary. This option takes a y or n argument indicating either yes the command is a binary or no it is not a binary.
- The -cwd option to qsub tells Sun Grid Engine that the job should be executed in the same directory that qsub was called.
- The last argument to qsub is the command to be executed (hostname in this case)
Notice that the qsub command, when successful, will print the job number to stdout. You can use the job number to monitor the job's status and progress within the queue as we'll see in the next section.
Monitoring Jobs in the Queue¶
Now that our job has been submitted, let's take a look at the job's status in the queue using the command qstat:
sgeadmin@master:~$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ------------------------------------------------------------------- 1 0.00000 hostname sgeadmin qw 09/09/2009 14:58:00 1 sgeadmin@master:~$From this output, we can see that the job is in the qw state which stands for queued and waiting. After a few seconds, the job will transition into a r, or running, state at which point the job will begin executing:
sgeadmin@master:~$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------- 1 0.00000 hostname sgeadmin r 09/09/2009 14:58:14 1 sgeadmin@master:~$Once the job has finished, the job will be removed from the queue and will no longer appear in the output of qstat:
sgeadmin@master:~$ qstat sgeadmin@master:~$Now that the job has finished let's move on to the next section to see how we view a job's output.
Viewing a Job's Output¶
Sun Grid Engine creates stdout and stderr files in the job's working directory for each job executed. If any additional files are created during a job's execution, they will also be located in the job's working directory unless explicitly saved elsewhere.
The job's stdout and stderr files are named after the job with the extension ending in the job's number.
For the simple job submitted above we have:
sgeadmin@master:~$ ls hostname.* hostname.e1 hostname.o1 sgeadmin@master:~$ cat hostname.o1 node001 sgeadmin@master:~$ cat hostname.e1 sgeadmin@master:~$Notice that Sun Grid Engine automatically named the job hostname and created two output files: hostname.e1 and hostname.o1. The e stands for stderr and the o for stdout. The 1 at the end of the files' extension is the job number. So if the job had been named my_new_job and was job #23 submitted, the output files would look like:
my_new_job.e23 my_new_job.o23Monitoring Cluster Usage¶
After a while you may be curious to view the load on Sun Grid Engine. To do this, we use the qhost command:
sgeadmin@master:~$ qhost HOSTNAME ARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS ------------------------------------------------------------------------------- global - - - - - - - master lx24-x86 1 0.00 1.7G 62.7M 896.0M 0.0 node001 lx24-x86 1 0.00 1.7G 47.8M 896.0M 0.0The output shows the architecture (ARCH), number of cpus (NCPU), the current load (LOAD), total memory (MEMTOT), and currently used memory (MEMUSE) and swap space (SWAPTO) for each node.
You can also view the average load (load_avg) per node using the '-f' option to qstat:
sgeadmin@master:~$ qstat -f queuename qtype resv/used/tot. load_avg arch states --------------------------------------------------------------------------------- [email protected] BIP 0/0/1 0.00 lx24-x86 --------------------------------------------------------------------------------- [email protected] BIP 0/0/1 0.00 lx24-x86Creating a Job Script¶
In the 'Submitting a Job' section we submitted a single command hostname. This is useful for simple jobs but for more complex jobs where we need to incorporate some logic we can use a so-called job script. A job script is essentially a bash script that contains some logic and executes any number of external programs/scripts:
#!/bin/bash echo "hello from job script!" echo "the date is" `date` echo "here's /etc/hosts contents:" cat /etc/hosts echo "finishing job :D"As you can see, this script simply executes a few commands (such as echo, date, cat, etc.) and exits. Anything printed to the screen will be put in the job's stdout file by Sun Grid Engine.
Since this is just a bash script, you can put any form of logic necessary in the job script (i.e. if statements, while loops, for loops, etc.) and you may call any number of external programs needed to complete the job.
Let's see how you run this new job script. Save the script above to /home/sgeadmin/jobscript.sh on your StarCluster and execute the following as the sgeadmin user:
sgeadmin@master:~$ qsub -V jobscript.sh Your job 6 ("jobscript.sh") has been submittedNow that the job has been submitted, let's call qstat periodically until the job has finished since this job should only take a second to run once it's executed:
sgeadmin@master:~$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ------------------------------------------------------------------- 6 0.00000 jobscript. sgeadmin qw 09/09/2009 16:18:43 1 sgeadmin@master:~$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ------------------------------------------------------------------- 6 0.00000 jobscript. sgeadmin qw 09/09/2009 16:18:43 1 sgeadmin@master:~$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ------------------------------------------------------------------- 6 0.00000 jobscript. sgeadmin qw 09/09/2009 16:18:43 1 sgeadmin@master:~$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ------------------------------------------------------------------- 6 0.00000 jobscript. sgeadmin qw 09/09/2009 16:18:43 1 sgeadmin@master:~$ qstat job-ID prior name user state submit/start at queue slots ja-task-ID ------------------------------------------------------------------- 6 0.55500 jobscript. sgeadmin r 09/09/2009 16:18:57 [email protected] 1 sgeadmin@master:~$ qstat sgeadmin@master:~$Now that the job is finished, let's take a look at the output files:
sgeadmin@master:~$ ls jobscript.sh* jobscript.sh jobscript.sh.e6 jobscript.sh.o6 sgeadmin@master:~$ cat jobscript.sh.o6 hello from job script! the date is Wed Sep 9 16:18:57 UTC 2009 here's /etc/hosts contents: # Do not remove the following line or programs that require network functionality will fail 127.0.0.1 localhost.localdomain localhost 10.252.167.143 master 10.252.165.173 node001 finishing job :D sgeadmin@master:~$ cat jobscript.sh.e6 sgeadmin@master:~$We see from looking at the output that the stdout file contains the output of the echo, date, and cat statements in the job script and that the stderr file is blank meaning there were no errors during the job's execution. Had something failed, such as a command not found error for example, these errors would have appeared in the stderr file.
Deleting a Job from the Queue¶
What if a job is stuck in the queue, is taking too long to run, or was simply started with incorrect parameters? You can delete a job from the queue using the qdel command in Sun Grid Engine. Below we launch a simple 'sleep' job that sleeps for 10 seconds so that we can kill it using qdel:
sgeadmin@master:~$ qsub -b y -cwd sleep 10 Your job 3 ("sleep") has been submitted sgeadmin@master:~$ qdel 3 sgeadmin has registered the job 3 for deletionAfter running qdel you'll notice the job is gone from the queue:
sgeadmin@master:~$ qstat sgeadmin@master:~$OpenMPI and Sun Grid Engine¶
Note
OpenMPI must be compiled with SGE support (–with-sge) to make use of the tight-integration between OpenMPI and SGE as documented in this section. This is the case on all of StarCluster's public AMIs.
OpenMPI supports tight integration with Sun Grid Engine. This integration allows Sun Grid Engine to handle assigning hosts to parallel jobs and to properly account for parallel jobs.
OpenMPI Parallel Environment¶
StarCluster by default sets up a parallel environment, called "orte", that has been configured for OpenMPI integration within SGE and has a number of slots equal to the total number of processors in the cluster. You can inspect the SGE parallel environment by running:
sgeadmin@ip-10-194-13-219:~$ qconf -sp orte pe_name orte slots 16 user_lists NONE xuser_lists NONE start_proc_args /bin/true stop_proc_args /bin/true allocation_rule $fill_up control_slaves TRUE job_is_first_task FALSE urgency_slots min accounting_summary FALSEThis is the default configuration for a two-node, c1.xlarge cluster (16 virtual cores).
Parallel Environment Allocation Rule¶
Notice the allocation_rule setting in the output of the qconf command in the previous section. This rule defines how to assign slots to a job. By default StarCluster uses the fill_up allocation rule. This rule causes SGE to greedily take all available slots on as many cluster nodes as needed to fulfill the slot requirements of a given job. For example, if a user requests 8 slots and a single node has 8 slots available, that job will run entirely on one node. If 5 slots are available on one node and 3 on another, it will take all 5 on that node, and all 3 on the other node.
The allocation rule can also be configured to distribute the slots around the cluster as evenly as possible by using the round_robin allocation_rule. For example, if a job requests 8 slots, it will go to the first node, grab a slot if available, move to the next node and grab a single slot if available, and so on wrapping around the cluster nodes again if necessary to allocate 8 slots to the job.
Finally, setting the allocation_rule to an integer number will cause the parallel environment to take a fixed number of slots from each host when allocating the job by specifying an integer for the allocation_rule. For example, if the allocation_rule is set to 1 then all slots have to reside on different hosts. If the special value $pe_slots is used then all slots for the parallel job must be allocated entirely on a single host in the cluster.
You can change the allocation rule for the orte parallel environment at any time using:
$ qconf -mp orteThis will open up vi (or any editor defined in the EDITOR environment variable) and let you edit the parallel environment settings. To change from fill_up to round_robin in the above example, change the allocation_rule line from:
allocation_rule $fill_upto:
allocation_rule $round_robinYou can also change the rule to the pe_slots mode:
allocation_rule $pe_slotsor specify a fixed number of slots per host to assign when allocating the job:
allocation_rule 1After making the change and saving the file you can verify your settings using:
sgeadmin@ip-10-194-13-219:~$ qconf -sp orte pe_name orte slots 16 user_lists NONE xuser_lists NONE start_proc_args /bin/true stop_proc_args /bin/true allocation_rule $round_robin control_slaves TRUE job_is_first_task FALSE urgency_slots min accounting_summary FALSESubmitting OpenMPI Jobs using a Parallel Environment¶
The general workflow for running MPI code is:
- Compile the code using mpicc, mpicxx, mpif77, mpif90, etc.
- Copy the resulting executable to the same path on all nodes or to an NFS-shared location on the master node
Note
It is important that the path to the executable is identical on all nodes for mpirun to correctly launch your parallel code. The easiest approach is to copy the executable somewhere under /home on the master node since /home is NFS-shared across all nodes in the cluster.
Run the code on X number of machines using:
$ mpirun -np X -hostfile myhostfile ./mpi-executable arg1 arg2 [...]where the hostfile looks something like:
$ cat /path/to/hostfile master slots=2 node001 slots=2 node002 slots=2 node003 slots=2However, when using an SGE parallel environment with OpenMPI you no longer have to specify the -np, -hostfile, -host, etc. options to mpirun. This is because SGE will automatically assign hosts and processors to be used by OpenMPI for your job. You also do not need to pass the –byslot and –bynode options to mpirun given that these mechanisms are now handled by the fill_up and round_robin modes specified in the SGE parallel environment.
Instead of using the above formulation create a simple job script that contains a very simplified mpirun call:
$ cat myjobscript.sh mpirun /path/to/mpi-executable arg1 arg2 [...]Then submit the job using the qsub command and the orte parallel environment automatically configured for you by StarCluster:
$ qsub -pe orte 24 ./myjobscript.shThe -pe option species which parallel environment to use and how many slots to request. The above example requests 24 slots (or processors) using the orte parallel environment. The parallel environment automatically takes care of distributing the MPI job amongst the SGE nodes using the allocation_rule defined in the environment's settings.
You can also do this without a job script like so:
$ cd /path/to/executable $ qsub -b y -cwd -pe orte 24 mpirun ./mpi-executable arg1 arg2 [...]
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