Advanced OAR

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Note.png Note

This page is actively maintained by the Grid'5000 team. If you encounter problems, please report them (see the Support page). Additionally, as it is a wiki page, you are free to make minor corrections yourself if needed. If you would like to suggest a more fundamental change, please contact the Grid'5000 team.

This tutorial consists of various independent sections describing various details of OAR useful for advanced usage, as well as some tips and tricks. It assumes you are familiar with OAR and Grid5000 basics. If not, please first look at the Getting Started page.

This OAR tutorial focuses on command line usages. It assumes you are using the bash shell (but should be easy to adapt to another shell). It can be read linearly, but you also may pick some random sections. Begin at least by #useful tips.

OAR

Useful tips

  • Take the time to carefully configure ssh, as described in the SSH page.
  • Use screen or tmux so that your work is not lost if you lose the connection to Grid5000. Moreover, having a screen session opened with one or more shell sessions allows you to leave your work session when you want then get back to it later and recover it exactly as you leaved it.
  • Most OAR commands (oarsub, oarstat, oarnodes) can provide output in various formats:
    • text (this is the default mode)
    • PERL dumper (-D)
    • XML (-X)
    • Yaml (-Y)
    • json (-J)
  • Direct access to the OAR database: users can directly access the PostgreSQL OAR database oar2 on the server oardb.site.grid5000.fr with the read-only account oarreader. The password is read.
  • Regarding the oarsub command line, you should mostly only see the "host" word, but the oarsub command can use both the word "host" or "nodes" indifferently in Grid'5000, as nodes is just an alias for host. Prefer using "host". Besides, the word "host" is also to be preferred to the longer "network_address" word in the resources filters (both properties have sometime the same value, but not always).

Connection to the job's nodes

You will normally use the oarsh command to connect to nodes instead of ssh, and oarcp instead of scp to copy files to/from the nodes. If you use taktuk for parallel executions (or a similar tools like pdsh) or rsync to synchronize files to/from a node, you have to configure the connector so the command uses oarsh instead of ssh underneath (see the man pages of the command to find out how to change the connector, e.g. using -c or -e). Please also note that Grid'5000 also provide a mode (allow_classic_ssh job type) where ssh allows to connect to nodes, with some restrictions, see below.

oarsh and job keys

By default, OAR generates an SSH key pair for each job, and oarsh is used to connect the job's nodes. oarsh uses either the OAR_JOB_ID or OAR_JOB_KEY_FILE environment variables to know what job to connect. If outside a job shell (e.g. on the frontend), you have to set one of those enrionment variable. But oarsh works directly if you are already in a job shell as the variables are set.

Using OAR_JOB_ID

For instance, create a job requesting 3 hosts (3 nodes):

Terminal.png fontend.site:
oarsub -I -l host=3
[ADMISSION RULE] Set default walltime to 3600.
[ADMISSION RULE] Modify resource description with type constraints
Generate a job key...
OAR_JOB_ID=<JOBID>
...

Then, in another terminal, assuming the 2nd host in the job is named node-2:

Terminal.png fontend.site:
OAR_JOB_ID=JOBID oarsh node-2
Using OAR_JOB_KEY_FILE

OAR can expose the job key, using the -e option of oarsub

Terminal.png fontend.site:
oarsub -I -l host=3 -e my_job_key

Then, in another terminal, assuming the 2nd host in the job is named node-2:

Terminal.png fontend.site:
OAR_JOB_KEY_FILE=my_job_key oarsh node-2
Alternative

Note that the following command also allows getting a shell in a job, but only on the first default resource (i.e. node).

Terminal.png fontend.site:
oarsub -C JOBID

sharing keys between jobs

Telling OAR to always use the same key may be very convenient.

For that, you must have a passphrase-less ssh key (e.g. dedicated for navigating inside grid5000, do not use your general purpose SSH private key!) to serve as a job key: In your ~/.profile or ~/.bash_profile, set:

export OAR_JOB_KEY_FILE=path_to_your_private_key

Then, OAR will always use that key for all jobs, allowing you to connect to your nodes with oarsh seamlessly from outside the jobs (without worrying about setting the environment variable for each job).

Moreover, if that key is replicated between all Grid5000 sites, and assuming the environment variable OAR_JOB_KEY_FILE is exported in ~/.profile or ~/.bash_profile in all sites, you will be able to connect directly from any frontend to any reserved node in any site.

Warning.png Warning

If using the same job key for all jobs, be warned that this will be an issue if two jobs share nodes, each reserving one of the cpus, gpus, or cores of the node, for instance. Indeed, in that case, commands run thanks to oarsh may not be executed in the expected job context (i.e. cgroup/cpuset). You may look at the OAR_JOB_ID to notice that.

oarsh vs ssh: tips and tricks

Some internals

oarsh is a frontend to ssh (the oarsh command wraps the OpenSSH ssh command to add some required functions to connect to a job, but provides mostly the same interface, albeit not all option are available). oarsh internal mechanism at a glance:

  • It opens an ssh connection as the oar user to the OAR dedicated SSH server running on a node (listening on port 6667)
  • It detects who you are based on the job key: if you indeed have the right to connect to the node (you reserved it in an OAR job), it switches to your user for the execution of the shell or command on the node in the job's context (cgroup/cpuset).
1st tip - hide oarsh, rename it ssh

Creating a symlink from ~/bin/ssh (assuming it is in the execution PATH) to /usr/bin/oarsh allows hidding the wrapper use (as long as the OAR_JOB_ID or OAR_JOB_KEY_FILE environment variables are set when connecting from a frontend to a node).

2nd tip - using ssh directly, without oarsh

If using oarsh does not suit your need, because you would like to use some of the options of ssh that oarsh does not support, you can also connect to reserved nodes by using the real ssh by adding the right set of options to the command. It can also allow a connection to reserved nodes directly from some place where oarsh is not available (e.g. from outside Grid'5000):

Assuming you have a passphrase-less SSH key (preferably just for internal uses in Grid5000), you can tell oarsub to use that key as a job key instead of letting OAR generate a new one (see #sharing keys between jobs). Then you can use that key to connect to nodes, even from outside Grid'5000.

  • Copy the key to your workstation, for instance outside of Grid5000:
Terminal.png workstation:
scp site.g5k:.ssh/your_internal_private_key_file ~/
  • In Grid5000, submit a job using this key:
Terminal.png fontend.site:
oarsub -i ~/.ssh/your_internal_private_key_file -I
  • Wait for the job to start. Then in another terminal, from outside Grid5000, try connecting to the node:
Terminal.png workstation:
ssh -i ~/your_internal_private_key_file -p 6667 [any other ssh options] oar@reserved-node.site.g5k

Finally, this can be hidden in a SSH ProxyCommand (See also SSH#Using_SSH_ProxyCommand_feature_to_ease_the_access_to_hosts_inside_Grid.275000):

After adding the following configuration in your OpenSSH configuration file on your workstation (~/.ssh/config):

Host *.g5koar
ProxyCommand ssh g5k-username@access.grid5000.fr -W "$(basename %h .g5koar):%p"
User oar
Port 6667
IdentityFile ~/your_internal_private_key_file
ForwardAgent no

Warning: the ProxyCommand line works if your login shell is bash. If not you may have to adapt it.

You can just ssh to a reserved node directly from your workstation as follows:

Terminal.png workstation:
ssh reserved-node.site.g5koar

allow_classic_ssh

To complete the previous section, creating a job with the -t allow_classic_ssh option allows to use ssh directly (with no special options this time) instead of oarsh to connect to the nodes. But the cost is not being able to reserve resources at a finer level than a host (not possible to reserve at the cpu, gpu or core levels).

Terminal.png fontend.site:
oarsub -t allow_classic_ssh -I

Then just ssh to one of the reserved node

Terminal.png fontend.site:
ssh node

Passive and interactive job modes

Interactive mode

In interactive mode, a shell is opened on the first default resource (i.e. node) of the job (or on the frontend, if the job is of type deploy or cosystem). In interactive mode, the job will be terminated as soon as this job's shell is closed or will be killed earlier if the job's walltime is reached. It can also be killed by an explicit oardel.

You can experiment with 3 shells. On first shell, to see the list of your running jobs, regularly run:

Terminal.png fontend.site:
oarstat -u

To see your own jobs. On the second shell, run an interactive job:

Terminal.png fontend.site:
oarsub -l walltime=walltime -I

Wait for the job to start, run oarstat, then leave the job, run oarstat again. Submit another interactive job, and on the third shell, kill it:

Terminal.png fontend.site:
oardel JOBID

Passive mode

In passive mode, the command that is given to oarsub is executed on the first default resource (i.e. node) of the job (or on the site's frontend if the job is of type deploy or cosystem). The job's duration will be the shorter of the execution time of the command and the job's given walltime. That unless the job is terminated beforehand by an explicit oardel call from the user or administrator.

Terminal.png fontend.site:
oarsub -l host=3,walltime=walltime "commnad"

Special case for jobs of type noop which are always passive jobs: no command is executed for them. The duration of the job is the given walltime.

Terminal.png fontend.site:
oarsub -t noop -l host=3,walltime=walltime

Interactive mode without shell

You may not want a job to open a shell or to run a script when the job starts, for example because you will use the reserved resources from a program whose lifecycle is longer than the job (and which will use the resources by connecting to the job).

One trick to achieve this is to run the job in passive mode with a long sleep command. One drawback of this method is that the job may terminate with status error if the sleep is killed. This can be a problem in some situations, eg. when using job dependencies.

Another solution is to use an advance reservation (see below) with a starting date very close in the future, or even with the current date and time.

Submission and reservation modes

Submission (aka batch jobs)

If you don't specify the job's start date (oarsub -r option), then your job is a submission, which lets OAR choose the best schedule and resources.

Reservation (aka advance reservations)

If you specify the job's start date, that is a reservation. OAR will just try to find resources for the given schedule, fixed by you.

There are some consequences:

  • Current Grid5000 usage policy allows no more than 2 reservations per site (excluding reservations that start in less than one hour)
  • in submission mode you're almost guaranteed to get your wanted resources, because oar can decide what resources to allocate at the last moment. You cannot get the list of resources until the job starts.
  • in reservation mode, you're not guaranteed to get your wanted resources, because oar has to plan the allocation of resources at reservation time. If later resources become not available, you lose them for your job. You can get the list of resources as soon as the reservation starts.
  • in submission mode, you cannot know the date at which your job will start until it starts. But OAR can give you an estimation of that date.
  • to coordinate oar submissions on several sites, OARGrid has to do OAR reservations.

Example: a reservation for a job in one week from now

$ oarsub -r "$(date +'%Y-%m-%d %H:%M:%S' --date='+1 week')"

For reservations, there is no interactive mode. You can give OAR a command to execute or nothing. If you don't give a command, you'll have to connect to the jobs once the reservation starts (using oarsub -C <jobid> or oarsh).

Getting information about a job

The oarstat command gets jobs informations. By default it lists the current jobs of all users. You can restrict it to your own jobs or someone else's jobs with option -u:

$ oarstat -u

You can get full details of a job:

$ oarstat -fj <JOBID>

If scripting OAR and regularly polling job states with oarstat, you can cause a high load on the OAR server (because default oarstat invocation causes costly SQL request in the OAR database). In this case, you should use option -s which is optimized and only queries the current state of a given job:

$ oarstat -s -j <JOBID>

Complex resources selection

The complete selector format syntax (oarsub -l option) is:

"-l {sql1}/name1=n1/name2=n2+{sql2}/name3=n3/name4=n4/name5=n5+...,walltime=hh:mm:ss"

where

  • sqlN are optional SQL predicates on the resource properties (e.g. mem, ib_rate, gpu_count, ...)
  • nameN=n are the wanted number of given resources of name nameN (e.g. host, cpu, core, disk...).
  • slashes (/) between resources express resource subtree selection
  • + allows aggregating different resource specifications
  • walltime=hh:mm::ss (separated by a comma) sets the job walltime (expected duration), which defaults to 1 hour
List resource properties

You can get the list of resource properties for SQL predicates by running the oarprint -l command on a node:

sagittaire-1 $ oarprint -l
List of properties:
disktype, gpu_count, ...

You can get the property values set to resources using the oarnodes:

flyon $ oarnodes -Y --sql="host = 'sagittaire-1.lyon.grid5000.fr'"

These OAR properties are described in the OAR Properties page.

Note.png Note

A SQL predicate on the resource properties can also be set using the -p <...> syntax, in which case it applies to all aggregated resource specifications. It can also be combined with the -l <...> syntax (curly brackets), for some possible common parts among all aggragates. Please refer to a SQL syntax manual in order to build a correct SQL predicate syntax, which technically speaking is a WHERE clause of a resource selection SQL matching.

Using the resources hierarchies

The OAR resources define implicit hierarchies to be used on the resource requests (oarsub -l). These hierarchies are specific to Grid'5000.

For instance:

  • ask for 1 core on 15 hosts (nodes) on a same cluster (total = 15 cores)
$ oarsub -I -l /cluster=1/host=15/core=1
  • ask for 1 core on 15 hosts (nodes) on 2 clusters (total = 30 cores)
$ oarsub -I -l /cluster=2/host=15/core=1
  • ask for 1 core on 2 cpus on 15 hosts (nodes) on a same cluster (total = 30 cores)
$ oarsub -I -l /cluster=1/host=15/cpu=2/core=1
  • ask for 10 cpus on 2 clusters (total = 20 cpus, the number of hosts and cores depends on the topology of the machines)
$ oarsub -I -l /cluster=2/cpu=10
  • ask for 1 core on 3 different network switches (total = 3 cores)
$ oarsub -I -l /switch=3/core=1

Valid resource hierarchies are:

  • Compute and disk resources
    • both switch > cluster, or cluster > switch can be valid (some clusters spread their hosts (nodes) on many switches, some clusters share a same switch), we note below cluster|switch to reflect that ambiguity.
    • cluster|switch > chassis > host > cpu > gpu > core
    • cluster|switch > chassis > host > disk
  • vlan resources
    • vlan only
  • subnet resources
    • slash16 > slash17 > slash18 > slash19 > slash20 > slash21 > slash22

Of course not all hierarchy levels have to be given in a resource request.

Note.png Note

Please mind that the nodes keyword (plural!) is an alias for host (singular!). A node or host is one server (computer). For instance, -l /cluster=X/nodes=Y/core=Z is exactly the same as -l /cluster=X/host=Y/core=Z.

Selecting resources using properties

The properties of the resources are described in the OAR Properties page.

Selecting nodes from a specific cluster

For example in Nancy:

$ oarsub -I -l {"cluster='graphene'"}/host=2

Or, alternative syntax:

$ oarsub -I -p "cluster='graphene'" -l /host=2
Selecting specific nodes

For example in Lyon:

$ oarsub -I -l {"host in ('sagittaire-10.lyon.grid5000.fr', 'sagittaire-11.lyon.grid5000.fr', 'sagittaire-12.lyon.grid5000.fr')"}/host=1

or, alternative syntax:

$ oarsub -I -p "host in ('sagittaire-10.lyon.grid5000.fr', 'sagittaire-11.lyon.grid5000.fr', 'sagittaire-12.lyon.grid5000.fr')" -l /nodes=1

By negating the SQL clause, you can also exclude some nodes.

Other examples using properties

Ask for 10 cores of the cluster graphene

$ oarsub -I -l core=10 -p "cluster='graphene'"

Ask for 2 nodes with 16384 GB of memory and Infiniband 20G

$ oarsub -I -p "memnode='16384' and ib_rate='20'" -l host=2

Ask for any 4 nodes except graphene-12

$ oarsub -I -p "not host like 'graphene-12.%'" -l host=4
Examples of joint resources requests

Ask for 2 nodes with virtualization capability, on different clusters + IP subnets:

  • We want 2 nodes (hosts) and 4 /22 subnets with the following constraints:
    • Nodes are on 2 different clusters of the same site (Hint: use a site with several clusters :-D)
    • Nodes have virtualization capability enabled
    • /22 subnets are on two different /19 subnets
    • 2 subnets belonging to the same /19 subnet are consecutive
$ oarsub -I -l /slash_19=2/slash_22=2+{"virtual!='none'"}/cluster=2/host=1

Lets verify the reservation:

 $ uniq $OAR_NODE_FILE
 graphene-43.nancy.grid5000.fr
 graphite-3.nancy.grid5000.fr
 $ g5k-subnets -p
 10.144.32.0/22
 10.144.36.0/22
 10.144.0.0/22
 10.144.4.0/22
 $ g5k-subnets -ps
 10.144.0.0/21
 10.144.32.0/21

Another example, ask for both

  • 1 core on 2 hosts (nodes) on the same cluster with 16384 MB of memory and Infiniband 20G
  • 1 cpu on 2 hosts (nodes) on the same switch with 8 cores processors for a walltime of 4 hours
$ oarsub -I -l "{memnode=16384 and ib_rate='20'}/cluster=1/host=2/core=1+{cpucore=8}/switch=1/host=2/cpu=1,walltime=4:0:0"

Walltime must always be the last argument of -l <...>

Note.png Note

If no resource matches your request, oarsub will exit with the message

Generate a job key...
[ADMISSION RULE] Set default walltime to 3600.
[ADMISSION RULE] Modify resource description with type constraints
There are not enough resources for your request
OAR_JOB_ID=-5
Oarsub failed: please verify your request syntax or ask for support to your admin.
Check that what you are requesting is actually relevant.

Handling the resources allocated to my job with oarprint

The oarprint allows to print nicely the resources of a job.

We first submit a job

$ oarsub -I -l host=4
...
OAR_JOB_ID=178361
Retrieve the nodes list

We want the list of the nodes (hosts) we got, identified by unique hostnames

$ oarprint host
sagittaire-32.lyon.grid5000.fr
capricorne-34.lyon.grid5000.fr
sagittaire-63.lyon.grid5000.fr
sagittaire-28.lyon.grid5000.fr

(We get 1 line per host, not per core !)

Retrieve the core list
$ oarprint core
63
241
64
163
243
244
164
242

Obviously, retrieving OAR internal core Id might not help much. Hence the use of a customized output format

Retrieve core list with host and cpuset Id as identifier

We want to identify our cores by their associated host names and cpuset Ids:

$ oarprint core -P host,cpuset
capricorne-34.lyon.grid5000.fr 0
sagittaire-32.lyon.grid5000.fr 0
capricorne-34.lyon.grid5000.fr 1
sagittaire-28.lyon.grid5000.fr 0
sagittaire-63.lyon.grid5000.fr 0
sagittaire-63.lyon.grid5000.fr 1
sagittaire-28.lyon.grid5000.fr 1
sagittaire-32.lyon.grid5000.fr 1
A more complex example with a customized output format

We want to identify our cores by their associated host name and cpuset Id, and get the memory information as well, with a customized output format

$ oarprint core -P host,cpuset,memnode -F "NODE=%[%] MEM=%"
NODE=capricorne-34.lyon.grid5000.fr[0] MEM=2048
NODE=sagittaire-32.lyon.grid5000.fr[0] MEM=2048
NODE=capricorne-34.lyon.grid5000.fr[1] MEM=2048
NODE=sagittaire-28.lyon.grid5000.fr[0] MEM=2048
NODE=sagittaire-63.lyon.grid5000.fr[0] MEM=2048
NODE=sagittaire-63.lyon.grid5000.fr[1] MEM=2048
NODE=sagittaire-28.lyon.grid5000.fr[1] MEM=2048
NODE=sagittaire-32.lyon.grid5000.fr[1] MEM=2048
From the submission frontend

If you are not in a job shell ($OAR_RESOURCE_PROPERTIES_FILE is not defined), running oarprint will give:

$ oarprint 
/usr/bin/oarprint: no input data available

In that case, you can however pipe the output of the oarstat command in oarprint, e.g.:

$ oarstat -j <JOB_ID> -p | oarprint core -P host,cpuset,memnode -F "%[%] (%)" -f -
capricorne-34.lyon.grid5000.fr[0] (2048)
sagittaire-32.lyon.grid5000.fr[0] (2048)
capricorne-34.lyon.grid5000.fr[1] (2048)
sagittaire-28.lyon.grid5000.fr[0] (2048)
sagittaire-63.lyon.grid5000.fr[0] (2048)
sagittaire-63.lyon.grid5000.fr[1] (2048)
sagittaire-28.lyon.grid5000.fr[1] (2048)
sagittaire-32.lyon.grid5000.fr[1] (2048)
List the OAR properties to use with oarprint

Properties are descibed in the OAR Properties page, but they can also be listed using the oarprint -l command:

$ oarprint -l
List of properties:
disktype, gpu_count, ...
Note.png Note

Those properties can also be used in oarsub using the -p switch for instance.

X11 forwarding

X11 forwarding is enabled in the shell opened in interactive job (oarsub -I). X11 forwarding can also be enabled in a shell opened on a node of a job with oarsh, just like with a classic ssh command: The -X or -Y option must be passed to oarsh.

Note.png Note

Please mind that for X11 forwarding to work in the job, X11 forwarding must already work in the shell from which the OAR commands are run. Check the DISPLAY environment variable !

We will use xterm to test X11.

Enabling X11 forwarding up to the frontend

Connect to a frontend with ssh (reminder: read the getting started tutorial about the use of the ssh proxycommand), and make sure the X11 forwarding is operational so far:

Look at the DISPLAY environment variable, which ssh should have set to localhost:10.0 or the like (the 10.0 part may vary from hop to hop in the X11 forwarding chain, with numbers greater than 10).

It requires to use the -X or -Y option in the ssh command line, or to have ForwardX11=yes set in your SSH configuration.

In any case, check:

Terminal.png frontend.site:
echo $DISPLAY
localhost:11.0
Using X11 forwarding in the oarsub job shell

If the DISPLAY environment variable is set in the calling shell, oarsub will automatically enable the X11 forwarding.

Terminal.png frontend.site:
oarsub -I -l core=1
[ADMISSION RULE] Set default walltime to 7200.
[ADMISSION RULE] Modify resource description with type constraints
OAR_JOB_ID=4926 
Interactive mode : waiting...
[2007-03-07 09:01:16] Starting...

Initialize X11 forwarding...
Connect to OAR job 4926 via the node idpot-8.grenoble.grid5000.fr
jdoe@idpot-8:~$ 

Then from the shell of the job, check again the display:

jdoe@idpot-8:~$ echo $DISPLAY
localhost:10.0

And run xterm

jdoe@idpot-8:~$ xterm

Wait for the window to open: it may be pretty long!

Using X11 forwarding in a job via oarsh

With oarsh, the -X or -Y option must be used to enable the X11 forwarding:

Terminal.png frontend.site:
OAR_JOB_ID=4928 oarsh -X idpot-8

Then in the opened shell, you can again check that the DISPLAY is set, and run xterm.

You can also just run the xterm command directly in the oarsh call:

Terminal.png frontend.site:
OAR_JOB_ID=4928 oarsh -X idpot-8 xterm
Note.png Note

X11 forwarding will suffer from the latency between your local network and the Grid'5000 network.

  • Mind using a site local access to Grid'5000 to lower that latency: see External access ;
  • And/or prefer using another remote display service, such as VNC for instance

Using best effort mode jobs

Best effort job campaign

OAR 2 provides a way to specify that jobs are best effort, which means that the server can delete them if room is needed to fit other jobs. One can submit such jobs using the besteffort type of job.

For instance you can run a job campaign as follows:

for param in $(< ./paramlist); do
    oarsub -t besteffort -l core=1 "./my_script.sh $param"
done

In this example, the file ./paramlist contains a list of parameters for a parametric application.

The following demonstrates the mechanism.

Note.png Note

Please have a look at the UsagePolicy to avoid abuses.

Best effort job mechanism

Running a besteffort job in a first shell
frennes:~$ oarsub -I -l host=10 -t besteffort
[ADMISSION RULE] Automatically redirect in the besteffort queue
[ADMISSION RULE] Automatically add the besteffort constraint on the resources
[ADMISSION RULE] Set default walltime to 3600.
[ADMISSION RULE] Modify resource description with type constraints
Generate a job key...
OAR_JOB_ID=988535
Interactive mode : waiting...
Starting...
Connect to OAR job 988535 via the node parasilo-26.rennes.grid5000.fr
parasilo-26:~$ uniq $OAR_FILE_NODES
parasilo-26.rennes.grid5000.fr
parasilo-27.rennes.grid5000.fr
parasilo-28.rennes.grid5000.fr
parasilo-3.rennes.grid5000.fr
parasilo-4.rennes.grid5000.fr
parasilo-5.rennes.grid5000.fr
parasilo-6.rennes.grid5000.fr
parasilo-7.rennes.grid5000.fr
parasilo-8.rennes.grid5000.fr
parasilo-9.rennes.grid5000.fr


Running a non best effort job on the same set of resources in a second shell
frennes:~$ oarsub -I -l {"host in ('parasilo-9.rennes.grid5000.fr')"}/host=1
[ADMISSION RULE] Set default walltime to 3600.
[ADMISSION RULE] Modify resource description with type constraints
Generate a job key...
OAR_JOB_ID=988546
Interactive mode : waiting...
[2018-01-15 13:28:24] Start prediction: 2018-01-15 13:28:24 (FIFO scheduling OK)
Starting...
Connect to OAR job 988546 via the node parasilo-9.rennes.grid5000.fr


As expected, meanwhile the best effort job was stopped (watch the first shell):

parasilo-26:~$ Connection to parasilo-26.rennes.grid5000.fr closed by remote host.
Connection to parasilo-26.rennes.grid5000.fr closed.
[ERROR] An unknown error occured : 65280
Disconnected from OAR job 988545

Using the checkpointing trigger mechanism

Writing the test script

Here is a script which features an infinite loop and a signal handler trigged by SIGUSR2 (default signal for OAR's checkpointing mechanism).

#!/bin/bash

handler() { echo "Caught checkpoint signal at: `date`"; echo "Terminating."; exit 0; }
trap handler SIGUSR2

cat <<EOF
Hostname: `hostname`
Pid: $$
Starting job at: `date`
EOF
while : ; do sleep 10; done
Running the job

We run the job on 1 core, and a walltime of 5 minutes, and ask the job to be checkpointed if it lasts (and it will indeed) more than walltime - 150 sec = 2 min 30.

$ oarsub -l "core=1,walltime=0:05:00" --checkpoint 150 ./checkpoint.sh 
[ADMISSION RULE] Modify resource description with type constraints
OAR_JOB_ID=988555
$
Result

Taking a look at the job output:

$ cat OAR.988555.stdout 
Hostname: parasilo-9.rennes.grid5000.fr
Pid: 12013
Starting job at: Mon Jan 15 14:05:50 CET 2018
Caught checkpoint signal at: Mon Jan 15 14:08:30 CET 2018
Terminating.

The checkpointing signal was sent to the job 2 minutes 30 before the walltime as expected so that the job can finish nicely.

Interactive checkpointing

The oardel command provides the capability to raise a checkpoint event interactively to a job.

We submit the job again

$ oarsub -l "core=1,walltime=0:05:0" --checkpoint 150 ./checkpoint.sh 
[ADMISSION RULE] Modify resource description with type constraints
OAR_JOB_ID=988560

Then run the oardel -c #jobid command...

$ oardel -c 988560
Checkpointing the job 988560 ...DONE.
The job 988560 was notified to checkpoint itself (send SIGUSR2).

And then watch the job's output:

$ cat OAR.988560.stdout 
Hostname: parasilo-4.rennes.grid5000.fr
Pid: 11612
Starting job at: Mon Jan 15 14:17:25 CET 2018
Caught checkpoint signal at: Mon Jan 15 14:17:35 CET 2018
Terminating.

The job terminated as expected.

Using jobs dependency

A job can wait for the termination of a previous job.

First Job

We run a first interactive job in a first Shell

 frennes:~$ oarsub -I 
[ADMISSION RULE] Set default walltime to 3600.
[ADMISSION RULE] Modify resource description with type constraints
Generate a job key...
OAR_JOB_ID=988571
Interactive mode : waiting...
Starting...
Connect to OAR job 988569 via the node parasilo-28.rennes.grid5000.fr
parasilo-28:~$

And leave that job pending.

Second Job

Then we run a second job in another Shell, with a dependence on the first one

jdoe@idpot:~$ oarsub -I -a 988571
[ADMISSION RULE] Set default walltime to 3600.
[ADMISSION RULE] Modify resource description with type constraints
Generate a job key...
OAR_JOB_ID=988572
Interactive mode : waiting...
[2018-01-15 14:27:08] Start prediction: 2018-01-15 15:30:23 (FIFO scheduling OK)
Job dependency in action

We do a logout on the first interactive job...

parasilo-28:~$ logout
Connection to parasilo-28.rennes.grid5000.fr closed.
Disconnected from OAR job 988571

... then watch the second Shell and see the second job starting

[2018-01-15 14:27:08] Start prediction: 2018-01-15 15:30:23 (FIFO scheduling OK)
Starting...
Connect to OAR job 988572 via the node parasilo-3.rennes.grid5000.fr

Container jobs

With the container job functionality, OAR allows for someone to execute inner jobs within the boundaries of the container job. Inner jobs are scheduled using the same algorithm as other jobs, but restricted to the container job's resources and timespan.

A typical use case is to submit first a container job, then have inner jobs submitted, with referring to the container job_id.

Mind that the inner jobs that will not fit in the container's boundaries will stay in the waiting state in the queue, not scheduled and not executed. They will be deleted when the container job is terminated.

Container jobs are especially useful when organizing tutorial of teaching labs, with the container job created by the organizer, and inner jobs created by the attendees.

Mind that if in your use case, all inner job are to be created by the same user as the container job, it is preferable to use a tool such as GNU Parallel.

Inner job are killed when the container job is terminated.

Note.png Note

A container job must ally both the container job type and any of the cosystem or noop job types. This is mandatory for the reason that inner jobs could be of type deploy and reboot the nodes hosting the container itself. container jobs are usable with passive (batch, scripted), interactive (oarsub -I) and advance reservations (oarsub -r <date>) jobs. But inner jobs cannot be advance reservations.

First a job of the type container must be submitted
Terminal.png frontend:
oarsub -I -t cosystem -t container -l host=10,walltime=2:00:00
...
OAR_JOB_ID=42
...
Then it is possible to use the inner type to schedule the new jobs within the previously created container job
Terminal.png frontend:
oarsub -I -t inner=42 -l host=7,walltime=00:10:00
Terminal.png frontend:
oarsub -I -t inner=42 -l host=1,walltime=00:20:00
Terminal.png frontend:
oarsub -I -t inner=42 -l host=10,walltime=00:10:00
Note.png Note

A job created with:

Terminal.png frontend:
oarsub -I -t inner=42 -l host=11
will never be scheduled because the container job "42" only reserved 10 nodes.

cosystem and noop jobs

cosystem
  • Jobs of type cosystem, just like jobs of type deploy, do not execute on the first node assigned to the job but on the frontend.
  • But unlike deploy jobs, cosystem jobs do not grant any special privileges (e.g. no kareboot right).
noop
  • Jobs of type noop do not execute anything at all. They just allocate resources for a time frame.
  • noop jobs cannot be interactive (oarsub -I).
  • noop jobs have the advantage over the cosystem job that they are not affected by a reboot (e.g. due to a maintenance or a failure) of the frontend.

If running a script on the frontend is not required, noop job a probably to be preferred over the cosystem jobs.

Changing the walltime of a running job (oarwalltime)

Starting with OAR version 2.5.8, users can request a change to the walltime (duration of the resource reservation) of a running job. This can be achieved using the oarwalltime command or Grid'5000's API.

This change can be an increase or a decrease, and specified giving either a new walltime value, or an increase value (begin with +) or a decrease value (begin with -).

Please note that a request may stay partially or completely unsatisfied if a next job occupies the resources.

Job must be running for a walltime change. For Waiting job, delete and resubmit.

Note.png Note

Walltime change is not possible in the production queue (Nancy).

Warning.png Warning

While changes of walltime are not limited a priori (by the oarwalltime command or the API), the resulting characteristics of the jobs must comply with the Grid5000:UsagePolicy. Enforcement checks happen as usual, a posteriori.

Command line interface

Querying the walltime change status:

Terminal.png frontend:
oarwalltime 1743185
Walltime change status for job 1743185 (job is running):
  Current walltime:       1:0:0
  Possible increase:  UNLIMITED
  Already granted:        0:0:0
  Pending/unsatisfied:    0:0:0

Requesting the walltime change:

Terminal.png frontend:
oarwalltime 1743185 +1:30
Accepted: walltime change request updated for job 1743185, it will be handled shortly.

Querying right afterward:

Terminal.png frontend:
oarwalltime 1743185
Walltime change status for job 1743185 (job is running):
  Current walltime:       1:0:0
  Possible increase:  UNLIMITED
  Already granted:        0:0:0
  Pending/unsatisfied:  +1:30:0

The request is still to be handled by OAR's scheduler.

Querying again a bit later:

Terminal.png frontend:
oarwalltime 1743185
Walltime change status for job 1743185 (job is running):
  Current walltime:      2:30:0
  Possible increase:  UNLIMITED
  Already granted:      +1:30:0
  Pending/unsatisfied:    0:0:0

May a job exist on the resources and partially prevent the walltime increase, the query output would be:

Terminal.png frontend:
oarwalltime 1743185
Walltime change status for job 1743185 (job is running):
  Current walltime:      2:30:0
  Possible increase:  UNLIMITED
  Already granted:      +1:10:0
  Pending/unsatisfied:  +0:20:0

Changes events are also reported in oarstat.

See man oarwalltime for more information.

Using the REST API

Requesting the walltime change:

curl -i -X POST https://api.grid5000.fr/stable/sites/grenoble/internal/oarapi/jobs/1743185.json -H'Content-Type: application/json' -d '{"method":"walltime-change", "walltime":"+0:30:0"}'

Querying the status of the walltime change:

curl -i -X GET https://api.grid5000.fr/stable/sites/grenoble/internal/oarapi/jobs/1743185/details.json -H'Content-Type: application/json'

See the walltime-change and events keys of the output.

Restricting jobs to daytime or night/week-end time

To help submitting batch jobs fitting inside the time frames defined in the usage policy (day vs. night and week-end), the types day and night can be used (oarsub -t <type>…).

Submit a job to run during the current day time
Terminal.png frontend:
oarsub -t day

As such:

  • It will be forced to run between 9:00 and 19:00, or the next day if the job is submitted during the night.
  • If the job did not succeed to run before 19:00, it will be deleted.
Submit a job to run during the coming (or current) night (or week-end on Friday)
Terminal.png frontend:
oarsub -t night

As such:

  • It will be forced to run after 19:00, and before 9:00 for week nights (Monday to Thursday nights), or before 9:00 on the next Monday for a job which runs during a week-end.
  • If a job could not be scheduled during the current night (not enough resources available), it will be kept in the queue and then postponed in the morning for a retry the next night (hour constraints will be changed to the next night slot), that for 7 days.
  • If the walltime of the job is more than 13h59, the job will obviously not run before a weekend.

Note that:

  • the maximum walltime for a night is 14h, but due to some overhead in the system (resources state changes, reboots...), it is strongly advised to limit walltime to at most 13h30. Furthermore, a shorter walltime (max a few hours)? will result in more chances to get a job scheduled in case many jobs are already in queue.
  • jobs with a walltime greater than 14h will be required to run during the week-ends. But even if submitted at the beginning of the week, they will not be scheduled before the Friday morning. Thus, any advance reservation done before Friday will take precedence. Also, given that the rescheduling happens on a daily basis for the next night, advance reservations take precedence if they are submitted before the daily rescheduling. In practice, this mechanism thus provides a low priority way to submit batch jobs during nights and week-ends.
  • a job will be kept 7 days before deletion (if it cannot be run because of lack of resources within a week)

Multi-site jobs with OARGrid

oargrid alows submitting OAR jobs to several Grid'5000 sites at once.

For instance, we are going to reserve 4 nodes on 3 different sites for half an hour

Terminal.png frontend:
oargridsub -t allow_classic_ssh -w '0:30:00' SITE1:rdef="/nodes=2",SITE2:rdef="/nodes=1",SITE3:rdef="nodes=1"

Note that in grid reservation mode, no script can be specified. Users are in charge to:

  1. connect to the allocated nodes.
  2. launch their experiment.

OAR Grid connects to each of the specified clusters and makes a passive submission. Cluster job ids are returned by OAR. A grid job id is returned by OAR Grid to bind cluster jobs ids together.

You should see an output like this:

SITE1:rdef=/nodes=2,SITE2:rdef=/nodes=1,SITE3:rdef=nodes=1
[OAR_GRIDSUB] [SITE3] Date/TZ adjustment: 0 seconds
[OAR_GRIDSUB] [SITE3] Reservation success on SITE3 : batchId = SITE_JOB_ID3
[OAR_GRIDSUB] [SITE2] Date/TZ adjustment: 1 seconds
[OAR_GRIDSUB] [SITE2] Reservation success on SITE2 : batchId = SITE_JOB_ID2
[OAR_GRIDSUB] [SITE1] Date/TZ adjustment: 0 seconds
[OAR_GRIDSUB] [SITE1] Reservation success on SITE1 : batchId = SITE_JOB_ID1
[OAR_GRIDSUB] Grid reservation id = GRID_JOB_ID
[OAR_GRIDSUB] SSH KEY : /tmp/oargrid//oargrid_ssh_key_LOGIN_GRID_JOB_ID
       You can use this key to connect directly to your OAR nodes with the oar user.

Fetch the allocated nodes list to transmit it to the script we want to run:

Terminal.png frontend:
oargridstat -w -l GRID_JOB_ID | sed '/^$/d' > ~/machines
Note.png Note

The -w command-line argument makes oargridstat wait for the start of every cluster reservation.

  • Nodes list can be incomplete otherwise.

(1) Select the node to launch the script (ie: the first node listed in the ~/machines file).

If (and only if) this node does not belong to the site where the ~/machines file was saved, copy the ~/machines to this node:

Terminal.png frontend:
OAR_JOB_ID=SITE_JOB_ID oarcp -i /tmp/oargrid/oargrid_ssh_key_LOGIN_GRID_JOB_ID ~/machines `head -n 1 machines`:

(2) Connect to this node using oarsh:

Terminal.png frontend:
OAR_JOB_ID=SITE_JOB_ID oarsh -i /tmp/oargrid/oargrid_ssh_key_LOGIN_GRID_JOB_ID `head -n 1 machines`
Note.png Note

Do not forget to indicate the location of the temporary private key generated by the oargridsub command when you want to connect to one of your allocated nodes

  • In previous snippets, this is done by using the -i option.

And then run the script:

Terminal.png node:
~/hello/helloworld ~/machines


The Grid counterpart of oarstat gives information about the grid job:

Terminal.png frontend:
oargridstat GRID_JOB_ID

Our grid submission is interactive, so its end time is unrelated to the end time of our script run. The submission ends when the submission owner requests that it ends or when the submission deadline is reached.

We are going to ask for our submission to end:

Terminal.png frontend:
oargriddel GRID_JOB_ID

Funk

funk is grid resources discovery tool that works at nodes level and generate complex oarsub/oargridsub commands. It can help you in three cases:

  • to know the number of nodes availables for 2 hours at run time, on sites lille, rennes and on clusters taurus and suno
Terminal.png frontend:
funk -m date -r lille,rennes,taurus,suno -w 2:00:00
  • to know when 40 nodes on sagittaire and 4 nodes on taurus will be available, with deploy job type and a subnet
Terminal.png frontend:
funk -m free -r sagittaire:40,taurus:4 -o "-t deploy" -n slash_22=2
  • to find the time when the maximum number of nodes are available during 10 hours, before next week deadline, avoiding usage policy periods, and not using genepi
Terminal.png frontend:
funk -m max -w 10:00:00 -e "2013-12-31 23:59:59" -c -b genepi

More information on its dedicated page.

OAR in the Grid'5000 API

An other way to visualize nodes/jobs status is to use the Grid'5000 API