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ceci tutorial
Resource sharing on a supercomputer dedicated to technical and/or scientific computing is often organized by a piece of software called a resource manager or job scheduler. Users submit jobs, which are scheduled and allocated resources (CPU time, memory, etc.) by the resource manager.
Slurm is a resource manager and job scheduler designed to do just that, and much more. It was originally created by people at the Livermore Computing Center, and has grown into a full-fledge open-source software backed up by a large community, commercially supported by the original developers, and installed in many of the Top500 supercomputers.
Slurm offers many commands you can use to interact with the system. For instance, the sinfo command gives an overview of the resources offered by the cluster, while the squeue command shows to which jobs those resources are currently allocated.
By default, sinfo lists the partitions that are available. A partition is a set of compute nodes (computers dedicated to ... computing,) grouped logically. Typical examples include partitions dedicated to batch processing, debugging, post processing, or visualization.
# sinfo
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
batch up infinite 2 alloc node[8-9]
batch up infinite 6 idle node[10-15]
debug* up 30:00 8 idle node[0-7]
In the above example, we see two partitions, named batch and debug. The latter is the default partition as it is marked with an asterisk. All nodes of the debug partition are idle, while two of the batch partition are being used.
The command sinfo can output the information in a node-oriented fashion, with the argument -N
# sinfo -N -l
NODELIST NODES PARTITION STATE CPUS MEMORY TMP_DISK WEIGHT FEATURES REASON
node[0-1] 2 debug* idle 2 3448 38536 16 (null) (null)
node[2,4-7] 5 debug* idle 2 3384 38536 16 (null) (null)
node3 1 debug* idle 2 3394 38536 16 (null) (null)
node[8-9] 2 batch allocated 2 246 82306 16 (null) (null)
node[10-15] 6 batch idle 2 246 82306 16 (null) (null)
Note that with the -l argument, more information about the nodes is provided: number of CPUs, memory, temporary disk (also called scratch space), node weight (an internal parameter specifying preferences in nodes for allocations when there are multiple possibilities), features of the nodes (such as processor type for instance) and the reason, if any, for which a node is down.
You can actually specify precisely what information you would like sinfo to output by using its \--format argument. For more details, have a look at the sinfo manpage with man sinfo.
The squeue command shows the list of jobs which are currently running (they are in the RUNNING state, noted as 'R') or waiting for resources (noted as 'PD').
# squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
12345 debug job1 dave R 0:21 4 node[9-12]
12346 debug job2 dave PD 0:00 8 (Resources)
12348 debug job3 ed PD 0:00 4 (Priority)
The above output show that is one job running, whose name is job1 and whose jobid is 12345. The jobid is a unique identifier that is used by many Slurm commands when actions must be taken about one particular job. For instance, to cancel job job1, you would use scancel 12345. Time is the time the job has been running until now. Node is the number of nodes which are allocated to the job, while the Nodelist column lists the nodes which have been allocated for running jobs. For pending jobs, that column gives the reason why the job is pending. In the example, job 12346 is pending because resources (CPUs, or other) are not available in sufficient amounts, while job 12348 is waiting for job 12346, whose priority is higher, to run. Each job is indeed assigned a priority depending on several parameters whose details are beyond the scope of this document. Note that the priority for pending jobs can be obtained with the sprio command.
There are many switches you can use to filter the output by user (\--user), by partition (\--partition) by state (\--state), etc. As with the sinfo command, you can choose what you want sprio to output with the \--format parameter.
Now the question is: How do you create a job?
A job consists in two parts:resource requests and job steps. Resource requests consist in a number of CPUs, computing expected duration, amounts of RAM or disk space, etc. Job steps describe tasks that must be done, software which must be run.
The typical way of creating a job is to write a submission script. A submission script is a shell script, e.g. a Bash script, whose comments, if they are prefixed with SBATCH, are understood by Slurm as parameters describing resource requests and other submissions options. You can get the complete list of parameters from the sbatch manpage (man sbatch)
The script itself is a job step. Other job steps are created with the srun command.
For instance, the following script, hypothetically named submit.sh,
#!/bin/bash
#
#SBATCH --job-name=test
#SBATCH --output=res.txt
#
#SBATCH --ntasks=1
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
srun hostname
srun sleep 60
would request one CPU for 10 minutes, along with 100 MB of RAM, in the default queue.. When started, the job would run a first job step srun hostname, which will launch the UNIX command hostname on the node on which the requested CPU was allocated. Then, a second jobs step will start the sleep command. Interestingly, you can get near-realtime information about your program (memory consumption, etc.) with the sstat command. Note that the \--job-name parameter allows giving a meaningful name to the job and the \--output parameter defines the file to which the output of the job must be sent.
Once the submission script is written properly, you need to submit it to slurm through the sbatch command, which, upon success, responds with the jobid attributed to the job. (The dollar sign below is the shell prompt)
$ sbatch submit.sh
sbatch: Submitted batch job 99999999
The job then enters the queue in the PENDING state. Once resources become available and the job has highest priority, an allocation is created for it and it goes to the RUNNING state. If the job completes correctly, it goes to the COMPLETED state, otherwise, it is set to the FAILED state.
Upon compeltion, the output file contains the result of the commands run in the script file. In the above example, you can see it with cat res.txt.
Note that you can create an interactive job with the salloc command or by issuing a srun command directly.
But, still, the real question is: How do you create a parallel job?
There are several ways a parallel job, one whose tasks are run simultaneously, can be created:
- by running a multi-process program (SPMD paradigm, e.g. with MPI)
- by running a multithreaded program (shared memory paradigm, e.g. with OpenMP or pthreads)
- by running several instances of a single-threaded program (so-called embarrassingly parallel paradigm)
- by running one master program controling several slave programs (master/slave paradigm)
In the Slurm context, a task is to be understood as a process. So a multi-process program is made of several tasks. By contrast, a multithreaded program is composed of only one task, which uses several CPUs.
Tasks are requested/created with the \--ntasks option, while CPUs, for the multithreaded programs, are requested with the \--cpus-per-task option. Tasks cannot be split across several compute nodes, so requesting several CPUs with the \--cpus-per-task option will ensure all CPUs are allocated on the same compute node. By contrast, requesting the same amount of CPUs with the \--ntasks option may lead to several CPUs being allocated on several, distinct compute nodes.
Here are some quick sample submission scripts. For more detailed information, make sure to have a look at the Slurm FAQ and to follow our training sessions. There is also Script Generation Wizard you can use to help you in submission scripts creation.
#!/bin/bash
#
#SBATCH --job-name=test_mpi
#SBATCH --output=res_mpi.txt
#
#SBATCH --ntasks=4
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
module load openmpi
mpirun hello.mpi
Request four cores on the cluster for 10 minutes, using 100 MB of RAM per core. Assuming my_mpi_program was compiled with MPI support, mpirun will create four instances of it, on the nodes allocated by Slurm.
You can try the above example by downloading the example hello world program from Wikipedia (name it for instance wiki_mpi_example.c), and compiling it with
module load openmpi
mpicc wiki_mpi_example.c -o hello.mpi
The res_mpi.txt file should contain something like
0: We have 4 processors
0: Hello 1! Processor 1 reporting for duty
0: Hello 2! Processor 2 reporting for duty
0: Hello 3! Processor 3 reporting for duty
#!/bin/bash
#
#SBATCH --job-name=test_omp
#SBATCH --output=res_omp.txt
#
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
./hello.omp
The job it will be run in an allocation where four cores have been reserved on the same compute node.
You can try it by using the hello world program from Wikipedia (name it for instance wiki_omp_example.c) and compiling it with
gcc -fopenmp wiki_omp_example.c -o hello.omp
The res_omp.txt file should contain something like
Hello World from thread 0
Hello World from thread 3
Hello World from thread 1
Hello World from thread 2
There are 4 threads
#!/bin/bash
#
#SBATCH --job-name=test_emb
#SBATCH --output=res_emb.txt
#
#SBATCH --ntasks=4
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
srun printenv SLURM_PROCID
In that configuration, the printenv command will be run four times, and each will have its environment variable SLURM_PROCID set to a distinct value.
This setup is useful if the program is based on random draws (e.g. Monte-Carlo simulations): the application permitting, you can have four programs drawing 1000 samples and combine their output (with another program) to get the equivalent of drawing 4000 samples.
Another typical use of this setting is parameter sweep where the same computation is carried on by each program except that some high-level parameter has distinct values in each case. Examples include optimisation of an integer-valued parameter through range scanning. In the latter case, each instance of the program simply has to lookup the $SLURM_PROCID environment variable and decide, accordingly, what values of the parameter to test.
The same can be set up to process several data files for instance. Each instance of the program just has to decide which file to read based upon the value set in its $SLURM_PROCID environment variable.
Upon completion, the above job will create a file test_emp with four lines:
0
1
2
3
#!/bin/bash
#
#SBATCH --job-name=test_ms
#SBATCH --output=res_ms.txt
#
#SBATCH --ntasks=4
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100
srun --multi-prog multi.conf
With file multi.conf being, for example, as follows
0 echo 'I am the Master'
1-3 bash -c 'printenv SLURM_PROCID'
The above instructs Slurm to create four tasks (or processes), one running echo 'I am the Master', and the other 3 running bash -c 'printenv SLURM_PROCID'. This is typically used in a producer/consumer setup where one program (the master) create computing tasks for the other program (the slaves) to perform.
Upon completion of the above job, file res_ms.txt will contain
I am the Master
1
2
3