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| abstract:farber:runjobs:queues [2018-05-22 07:59] – sraskar | abstract:farber:runjobs:queues [2018-10-08 16:01] (current) – anita |
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| ===== The job queues on Farber ===== | ====== The job queues on Farber ====== |
| |
| Each investing-entity on a cluster an //owner queue// that exclusively use the investing-entity's compute nodes. (They do not use any nodes belonging to others.) Grid Engine allows those queues to be selected only by members of the investing-entity's group. | Each investing-entity on a cluster an //owner queue// that exclusively use the investing-entity's compute nodes. (They do not use any nodes belonging to others.) Grid Engine allows those queues to be selected only by members of the investing-entity's group. |
| ^ <<//investing_entity//>>''.q'' | The default queue for all jobs.| | ^ <<//investing_entity//>>''.q'' | The default queue for all jobs.| |
| ^ ''standby.q'' | A special queue that spans all standard nodes, at most 200 slots per user. Submissions will have a lower priority than jobs submitted to owner-queues, and standby jobs will only be started on lightly-loaded nodes. These jobs will not be preempted by others' job submissions. Jobs will be terminated with notification after running for 8 hours of elapsed (wall-clock) time. //Also see the ''standby-4h.q'' entry.// | | ^ ''standby.q'' | A special queue that spans all standard nodes, at most 200 slots per user. Submissions will have a lower priority than jobs submitted to owner-queues, and standby jobs will only be started on lightly-loaded nodes. These jobs will not be preempted by others' job submissions. Jobs will be terminated with notification after running for 8 hours of elapsed (wall-clock) time. //Also see the ''standby-4h.q'' entry.// | |
| ^ ::: | You must specify **–l standby=1** as a **qsub** option. You must also use the **-notify** option if your jobs traps the USR2 termination signal. [[general:jobsched:standby |(Details)]] | | ^ ::: | You must specify **–l standby=1** as a **qsub** option. You must also use the **-notify** option if your jobs traps the USR2 termination signal.| |
| ^ ''standby-4h.q'' | A special queue that spans all standard nodes, at most 800 slots per user. Submissions will have a lower priority than jobs submitted to owner-queues, and 4hr standby jobs will only be started on lightly-loaded nodes. These jobs will not be preempted by others' job submissions. Jobs will be terminated with notification after running for 4 hours of elapsed (wall-clock) time. | | ^ ''standby-4h.q'' | A special queue that spans all standard nodes, at most 800 slots per user. Submissions will have a lower priority than jobs submitted to owner-queues, and 4hr standby jobs will only be started on lightly-loaded nodes. These jobs will not be preempted by others' job submissions. Jobs will be terminated with notification after running for 4 hours of elapsed (wall-clock) time. | |
| ^ ::: | You must specify **–l standby=1** as a **qsub** option. And, if more than 200 slots are requested, you must also specify a maximum run-time of 4 hours or less via the **-l h_rt=//hh:mm:ss//** option. Finally, use the **-notify** option if your jobs traps the USR2 termination signal. [[general:jobsched:standby |(Details)]] | | ^ ::: | You must specify **–l standby=1** as a **qsub** option. And, if more than 200 slots are requested, you must also specify a maximum run-time of 4 hours or less via the **-l h_rt=//hh:mm:ss//** option. Finally, use the **-notify** option if your jobs traps the USR2 termination signal.| |
| ^ ''spillover.q'' | A special queue that spans all standard nodes and is used by Grid Engine to map jobs when requested resources are unavailable on standard nodes in owner queues, e.g., other standby or spillover jobs are using owner resources. | | ^ ''spillover.q'' | A special queue that spans all standard nodes and is used by Grid Engine to map jobs when requested resources are unavailable on standard nodes in owner queues, e.g., other standby or spillover jobs are using owner resources. | |
| |
| </note> | </note> |
| |
| ===== The "standby" queues ===== | ===== Farber "standby" queues ===== |
| | |
| | Farber has two standby queues, ''standby.q'' and ''standby-4h.q'', that span all **"standard"** nodes on the cluster. A "standard" node has 20 cores and 64GB of memory. |
| |
| The "standby" queues span nodes of the cluster to allow you to use unused compute cycles on other groups' nodes in addition to those from your own group's nodes. All standby jobs have a run-time limit specific to a cluster in order to be fair to node owners. | The "standby" queues span nodes of the cluster to allow you to use unused compute cycles on other groups' nodes in addition to those from your own group's nodes. All standby jobs have a run-time limit specific to a cluster in order to be fair to node owners. |
| </code> | </code> |
| |
| ====Grid Engine resources governing these queues==== | ==== Grid Engine resources governing these queues ==== |
| The "standby" queues are assigned based on the number of slots and the maximum (wall-clock) //hard// run-time you specify. Typically each cluster defines a default //hard// run-time limit as well as a maximum number of slots allowed per user for standby jobs. | The "standby" queues are assigned based on the number of slots and the maximum (wall-clock) //hard// run-time you specify. Typically each cluster defines a default //hard// run-time limit as well as a maximum number of slots allowed per user for standby jobs. |
| | |
| | The differences between the two queues is tied to the number of slots and the maximum (wall-clock) //hard// run-time you specify. |
| | |
| | * If you specify a maximum run-time of 4 hours or less (e.g.,''h_rt=4:00:00''), your job will be assigned to ''standby-4h.q''. |
| | |
| | * If you do **not** specify a maximum run-time **or** if you specify a run-time greater than 4 hours but not exceeding 8 hours, then you may request up to 200 slots for any job. The job will be assigned to ''standby.q''. |
| | |
| | The total number of concurrent slots in the ''standby.q'' jobs may not exceed 200, and the total in both ''standby.q'' and ''standby-4h.q'' may not exceed 800. The limit is by user, and all other jobs will wait for your jobs to finish. |
| | |
| | For example, you could concurrently run 25 20-slot jobs (500 slots). This would leave 300 slots available for any other concurrent standby jobs you may submit. |
| | |
| | Job script example: |
| | <code bash> |
| | # |
| | # The standby flag asks to run the job in a standby queue. |
| | #$ -l standby=1 |
| | # |
| | # This job needs an openmpi parallel environment using 500 slots. |
| | #$ -pe openmpi 500 |
| | # |
| | # The h_rt flag specifies a 4-hr maximum (hard) run-time limit. |
| | # The flag is required because the job needs more than 240 slots. |
| | #$ -l h_rt=4:00:00 |
| | ... |
| | </code> |
| |
| ==== Mapping jobs to nodes ==== | ==== Mapping jobs to nodes ==== |
| |
| Once Grid Engine determines the appropriate standby queue, it maps the job to available, idle, nodes (hosts) to fill all the slots. For MPI jobs, Grid Engine is configured to use the //fill up// allocation rule, by default. This will keep the number of nodes down, and may reduce the amount of inter-node communication. However in some cases, it may be useful to control the number of nodes and the number of processes per node for MPI jobs. | Once Grid Engine determines the appropriate standby queue, it maps the job to available, idle, nodes (hosts) to fill all the slots. For openmpi jobs, Grid Engine is configured to use the //fill up// allocation rule, by default. This will keep the number of nodes down, and thus reduce the amount of inter-node communication. |
| | |
| | It may be useful to control the number of nodes and the number of processes per node. |
| | For example: |
| | qsub -l standby,h_rt=4:00:00 myopenmpi.qs |
| | The MPI processes (ranks) will be mapped to **''ceiling(NSLOTS/20)''** hosts. All hosts, except possibly the last host, will have exactly 20 processes. |
| | The MPI_FLAG ''--display_map'' will display details of the allocations in your Grid Engine output. The MPI_FLAG ''--loadbalance'' will spread the processes out among the assigned hosts, without changing the number of hosts. |
| | |
| | <note important>If you do not specify an exact multiple of 20, there will be slots available to other queued Grid Engine jobs. |
| | If these jobs are assigned to your nodes (you have them for up to 8 hours), they will compete for shared resources: |
| | ^ Resource ^ Shared ^ |
| | | cores | 20 | |
| | | memory |64 GBs | |
| | If you add the ''exclusive'' resource in your queue script file |
| | #$ -l exclusive=1 |
| | then Grid Engine will round up your slot request to a multiple of 20 and thus keep other jobs off the node. |
| | </note> |
| | |
| | <note tip>The allocation rule and the group names are configured in Grid Engine. You can use the ''qconf'' command to show |
| | the current configuration. |
| | |
| | To see the current allocation rule for ''mpi'': |
| | |
| | $ qconf -sp mpi | grep allocation_rule |
| | allocation_rule $fill_up |
| | |
| | To see a list of all group names: |
| | |
| | $ qconf -shgrpl |
| | @128G |
| | @256G |
| | ... |
| | |
| | To see the nodes in a group name: |
| | $ qconf -shgrp @128G |
| | group_name @128G |
| | hostlist n068 n069 n070 n071 n106 n108 n109 n110 n113 |
| | </note> |
| |
| ====Actions at the run-time limit==== | ==== Actions at the run-time limit ===== |
| When a standby job reaches its maximum run time, Grid Engine kills the job. The process depends on your use of Grid Engine's ''-notify'' flag and how your job handles the resulting ''USR2'' notification signal. | When a standby job reaches its maximum run time, Grid Engine kills the job. The process depends on your use of Grid Engine's ''-notify'' flag and how your job handles the resulting ''USR2'' notification signal. |
| |
| User = traine | User = traine |
| Queue = standby.q@n015 | Queue = standby.q@n015 |
| Host = n015.mills.hpc.udel.edu | Host = n015.farber.hpc.udel.edu |
| Start Time = 06/01/2012 12:38:51 | Start Time = 06/01/2012 12:38:51 |
| End Time = 06/01/2012 16:43:53 | End Time = 06/01/2012 16:43:53 |
| ==== What if my program does not catch USR2? ==== | ==== What if my program does not catch USR2? ==== |
| |
| <note>The following information comes from a lengthy troubleshooting session with a Mills user. IT thanks the user for his patience while all the details were hashed out.</note> | <note>The following information comes from a lengthy troubleshooting session with a farber user. IT thanks the user for his patience while all the details were hashed out.</note> |
| |
| When a program that does not handle the ''USR2'' signal receives that signal, the default action is to abort. This will raise a ''CHLD'' signal in the program's parent process. Typically, a Grid Engine job script (the parent process) will react to ''CHLD'' by itself aborting. | When a program that does not handle the ''USR2'' signal receives that signal, the default action is to abort. This will raise a ''CHLD'' signal in the program's parent process. Typically, a Grid Engine job script (the parent process) will react to ''CHLD'' by itself aborting. |
| The first ''trap'' command tells the job shell (and child processes) to ignore the ''USR2'' signal. Appending the ampersand (&) character to the ''mpirun'' command runs it in the background and the job script continues to execute immediately. Thus, ''mpirun'' has been started and will ignore ''USR2'' signals. Now, the job shell is set to execute the ''runtimeLimitReached'' function when it itself receives ''USR2'' -- this //does not// change the behavior of the ''mpirun'' that is executing in the background, though (it will still ignore ''USR2''). Finally, the ''wait'' command puts the job shell to sleep (no CPU usage) until all child processes have exited (namely, ''mpirun''). The ''wait'' command is a function built-in to BASH and not an external program, so it does not cause the job shell to block and delay reaction to ''USR2'' like ''mpirun'' did in the previous example. | The first ''trap'' command tells the job shell (and child processes) to ignore the ''USR2'' signal. Appending the ampersand (&) character to the ''mpirun'' command runs it in the background and the job script continues to execute immediately. Thus, ''mpirun'' has been started and will ignore ''USR2'' signals. Now, the job shell is set to execute the ''runtimeLimitReached'' function when it itself receives ''USR2'' -- this //does not// change the behavior of the ''mpirun'' that is executing in the background, though (it will still ignore ''USR2''). Finally, the ''wait'' command puts the job shell to sleep (no CPU usage) until all child processes have exited (namely, ''mpirun''). The ''wait'' command is a function built-in to BASH and not an external program, so it does not cause the job shell to block and delay reaction to ''USR2'' like ''mpirun'' did in the previous example. |
| |
| | ===== Farber Exclusive access ===== |
| |
| | If a job is submitted with the ''-l exclusive=1'' resource, Grid Engine will |
| |
| | * promote any serial jobs to 20-core threaded (-pe threads 20) |
| | * modify any parallel jobs to round-up the slot count to the nearest multiple of 20 |
| | * ignore any memory resources and make all memory available on all nodes assigned to the job |
| |
| | A job running on a node with ''-l exclusive=1'' will block any other jobs from making use of resources on that host. |
| | |
| ===== Farber "standby" queues ===== | |
| | |
| Farber has two standby queues, ''standby.q'' and ''standby-4h.q'', that span all **"standard"** nodes on the cluster. A "standard" node has 20 cores and 64GB of memory. | |
| | |
| ====Grid Engine resources governing these queues==== | |
| The differences between the two queues is tied to the number of slots and the maximum (wall-clock) //hard// run-time you specify. | |
| | |
| * If you specify a maximum run-time of 4 hours or less (e.g.,''h_rt=4:00:00''), your job will be assigned to ''standby-4h.q''. | |
| | |
| * If you do **not** specify a maximum run-time **or** if you specify a run-time greater than 4 hours but not exceeding 8 hours, then you may request up to 200 slots for any job. The job will be assigned to ''standby.q''. | |
| | |
| The total number of concurrent slots in the ''standby.q'' jobs may not exceed 200, and the total in both ''standby.q'' and ''standby-4h.q'' may not exceed 800. The limit is by user, and all other jobs will wait for your jobs to finish. | |
| | |
| For example, you could concurrently run 25 20-slot jobs (500 slots). This would leave 300 slots available for any other concurrent standby jobs you may submit. | |
| |
| Job script example: | Job script example: |
| <code bash> | <code bash> |
| # | # |
| # The standby flag asks to run the job in a standby queue. | # The exclusive flag asks to run this job only on all nodes required to fulfill requested slots |
| #$ -l standby=1 | #$ -l exclusive=1 |
| # | # |
| # This job needs an openmpi parallel environment using 500 slots. | # This job needs an openmpi parallel environment using 32 slots = 2 nodes exclusively. |
| #$ -pe openmpi 500 | #$ -pe openmpi 32 |
| # | # |
| # The h_rt flag specifies a 4-hr maximum (hard) run-time limit. | # By default the slot count granted by Grid Engine will be |
| # The flag is required because the job needs more than 240 slots. | # used, one MPI worker per slot. Set this variable if you |
| #$ -l h_rt=4:00:00 | # want to use fewer cores than Grid Engine granted you (e.g. |
| | # when using exclusive=1): |
| | # |
| | #WANT_NPROC=0 |
| ... | ... |
| </code> | </code> |
| |
| ==== Mapping jobs to nodes ==== | <note tip>In the script example, this job would be rounded up to 40 and would be assigned 2 nodes. If you really want your job to run with only 32 slots, uncomment and set ''WANT_NPROC=32''.</note> |
| Once Grid Engine determines the appropriate standby queue, it maps the job to available, idle, nodes (hosts) to fill all the slots. For openmpi jobs, Grid Engine is configured to use the //fill up// allocation rule, by default. This will keep the number of nodes down, and thus reduce the amount of inter-node communication. | |
| | |
| It may be useful to control the number of nodes and the number of processes per node. | |
| For example: | |
| qsub -l standby,h_rt=4:00:00 myopenmpi.qs | |
| The MPI processes (ranks) will be mapped to **''ceiling(NSLOTS/20)''** hosts. All hosts, except possibly the last host, will have exactly 20 processes. | |
| The MPI_FLAG ''--display_map'' will display details of the allocations in your Grid Engine output. The MPI_FLAG ''--loadbalance'' will spread the processes out among the assigned hosts, without changing the number of hosts. | |
| | |
| <note important>If you do not specify an exact multiple of 20, there will be slots available to other queued Grid Engine jobs. | |
| If these jobs are assigned to your nodes (you have them for up to 8 hours), they will compete for shared resources: | |
| ^ Resource ^ Shared ^ | |
| | cores | 20 | | |
| | memory |64 GBs | | |
| If you add the ''exclusive'' resource in your queue script file | |
| #$ -l exclusive=1 | |
| then Grid Engine will round up your slot request to a multiple of 20 and thus keep other jobs off the node. | |
| </note> | |
| | |
| <note tip>The allocation rule and the group names are configured in Grid Engine. You can use the ''qconf'' command to show | |
| the current configuration. | |
| | |
| To see the current allocation rule for ''mpi'': | |
| | |
| $ qconf -sp mpi | grep allocation_rule | |
| allocation_rule $fill_up | |
| | |
| To see a list of all group names: | |
| | |
| $ qconf -shgrpl | |
| @128G | |
| @256G | |
| ... | |
| | |
| To see the nodes in a group name: | |
| $ qconf -shgrp @128G | |
| group_name @128G | |
| hostlist n068 n069 n070 n071 n106 n108 n109 n110 n113 | |
| </note> | |
| | |
| | |
| | |
| ====== Farber Exclusive access ====== | |
| |
| Grid Engine is configured to "fill up" nodes by allocating as many slots as possible before proceeding to another node to fulfill the total number of requested slots for the job. Unfortunately, Grid Engine may not do what you expect, evenly distribute and fill up across the total number of nodes needed for your job. For example, if you submit four Open MPI jobs each requesting 20 slots and there are four free nodes each with 20 cores on the cluster, you would expect each job to be assigned on a single node, but in fact, the first job may land on a single node, the second, third, and fourth may wind up straddling the remaining three nodes. | Grid Engine is configured to "fill up" nodes by allocating as many slots as possible before proceeding to another node to fulfill the total number of requested slots for the job. Unfortunately, Grid Engine may not do what you expect, evenly distribute and fill up across the total number of nodes needed for your job. For example, if you submit four Open MPI jobs each requesting 20 slots and there are four free nodes each with 20 cores on the cluster, you would expect each job to be assigned on a single node, but in fact, the first job may land on a single node, the second, third, and fourth may wind up straddling the remaining three nodes. |
| qsub -l exclusive=1 ... | qsub -l exclusive=1 ... |
| </code> | </code> |
| |
| |
| |
| |
| <note tip>In the script example, this job would be rounded up to 40 and would be assigned 2 nodes. If you really want your job to run with only 32 slots, uncomment and set ''WANT_NPROC=32''.</note> | <note tip>In the script example, this job would be rounded up to 40 and would be assigned 2 nodes. If you really want your job to run with only 32 slots, uncomment and set ''WANT_NPROC=32''.</note> |
| |
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