JuliaParallel / ClusterManagers.jl

ClusterManagers

Support for different job queue systems commonly used on compute clusters.

Currently supported job queue systems

Job queue system	Command to add processors
Load Sharing Facility (LSF)	addprocs_lsf(np::Integer; bsub_flags=``, ssh_cmd=``) or addprocs(LSFManager(np, bsub_flags, ssh_cmd, retry_delays, throttle))
Sun Grid Engine	addprocs_sge(np::Integer; qsub_flags=``) or addprocs(SGEManager(np, qsub_flags))
SGE via qrsh	addprocs_qrsh(np::Integer; qsub_flags=``) or addprocs(QRSHManager(np, qsub_flags))
PBS	addprocs_pbs(np::Integer; qsub_flags=``) or addprocs(PBSManager(np, qsub_flags))
Scyld	addprocs_scyld(np::Integer) or addprocs(ScyldManager(np))
HTCondor	addprocs_htc(np::Integer) or addprocs(HTCManager(np))
Slurm	addprocs_slurm(np::Integer; kwargs...) or addprocs(SlurmManager(np); kwargs...)
Local manager with CPU affinity setting	addprocs(LocalAffinityManager(;np=CPU_CORES, mode::AffinityMode=BALANCED, affinities=[]); kwargs...)
Kubernetes (K8s) via K8sClusterManagers.jl	addprocs(K8sClusterManagers(np; kwargs...))

You can also write your own custom cluster manager; see the instructions in the Julia manual

Slurm: a simple example

using Distributed, ClusterManagers

# Arguments to the Slurm srun(1) command can be given as keyword
# arguments to addprocs.  The argument name and value is translated to
# a srun(1) command line argument as follows:
# 1) If the length of the argument is 1 => "-arg value",
#    e.g. t="0:1:0" => "-t 0:1:0"
# 2) If the length of the argument is > 1 => "--arg=value"
#    e.g. time="0:1:0" => "--time=0:1:0"
# 3) If the value is the empty string, it becomes a flag value,
#    e.g. exclusive="" => "--exclusive"
# 4) If the argument contains "_", they are replaced with "-",
#    e.g. mem_per_cpu=100 => "--mem-per-cpu=100"
addprocs(SlurmManager(2), partition="debug", t="00:5:00")

hosts = []
pids = []
for i in workers()
	host, pid = fetch(@spawnat i (gethostname(), getpid()))
	push!(hosts, host)
	push!(pids, pid)
end

# The Slurm resource allocation is released when all the workers have
# exited
for i in workers()
	rmprocs(i)
end

SGE - a simple interactive example

julia> using ClusterManagers

julia> ClusterManagers.addprocs_sge(5; qsub_flags=`-q queue_name`)
job id is 961, waiting for job to start .
5-element Array{Any,1}:
2
3
4
5
6

julia> @parallel for i=1:5
       run(`hostname`)
       end

julia>  From worker 2:  compute-6
        From worker 4:  compute-6
        From worker 5:  compute-6
        From worker 6:  compute-6
        From worker 3:  compute-6

Some clusters require the user to specify a list of required resources. For example, it may be necessary to specify how much memory will be needed by the job - see this issue. The keyword qsub_flags can be used to specify these and other options. Additionally the keyword wd can be used to specify the working directory (which defaults to ENV["HOME"]).

julia> using Distributed, ClusterManagers

julia> addprocs_sge(5; qsub_flags=`-q queue_name -l h_vmem=4G,tmem=4G`, wd=mktempdir())
Job 5672349 in queue.
Running.
5-element Array{Int64,1}:
 2
 3
 4
 5
 6

julia> pmap(x->run(`hostname`),workers());

julia>  From worker 26: lum-7-2.local
        From worker 23: pace-6-10.local
        From worker 22: chong-207-10.local
        From worker 24: pace-6-11.local
        From worker 25: cheech-207-16.local

julia> rmprocs(workers())
Task (done)

SGE via qrsh

SGEManager uses SGE's qsub command to launch workers, which communicate the TCP/IP host:port info back to the master via the filesystem. On filesystems that are tuned to make heavy use of caching to increase throughput, launching Julia workers can frequently timeout waiting for the standard output files to appear. In this case, it's better to use the QRSHManager, which uses SGE's qrsh command to bypass the filesystem and captures STDOUT directly.

Load Sharing Facility (LSF)

LSFManager supports IBM's scheduler. See the addprocs_lsf docstring for more information.

Using LocalAffinityManager (for pinning local workers to specific cores)

• Linux only feature.
• Requires the Linux taskset command to be installed.
• Usage : addprocs(LocalAffinityManager(;np=CPU_CORES, mode::AffinityMode=BALANCED, affinities=[]); kwargs...).

where

• np is the number of workers to be started.
• affinities, if specified, is a list of CPU IDs. As many workers as entries in affinities are launched. Each worker is pinned to the specified CPU ID.
• mode (used only when affinities is not specified, can be either COMPACT or BALANCED) - COMPACT results in the requested number of workers pinned to cores in increasing order, For example, worker1 => CPU0, worker2 => CPU1 and so on. BALANCED tries to spread the workers. Useful when we have multiple CPU sockets, with each socket having multiple cores. A BALANCED mode results in workers spread across CPU sockets. Default is BALANCED.

Using ElasticManager (dynamically adding workers to a cluster)

The ElasticManager is useful in scenarios where we want to dynamically add workers to a cluster. It achieves this by listening on a known port on the master. The launched workers connect to this port and publish their own host/port information for other workers to connect to.

On the master, you need to instantiate an instance of ElasticManager. The constructors defined are:

ElasticManager(;addr=IPv4("127.0.0.1"), port=9009, cookie=nothing, topology=:all_to_all, printing_kwargs=())
ElasticManager(port) = ElasticManager(;port=port)
ElasticManager(addr, port) = ElasticManager(;addr=addr, port=port)
ElasticManager(addr, port, cookie) = ElasticManager(;addr=addr, port=port, cookie=cookie)

You can set addr=:auto to automatically use the host's private IP address on the local network, which will allow other workers on this network to connect. You can also use port=0 to let the OS choose a random free port for you (some systems may not support this). Once created, printing the ElasticManager object prints the command which you can run on workers to connect them to the master, e.g.:

julia> em = ElasticManager(addr=:auto, port=0)
ElasticManager:
  Active workers : []
  Number of workers to be added  : 0
  Terminated workers : []
  Worker connect command : 
    /home/user/bin/julia --project=/home/user/myproject/Project.toml -e 'using ClusterManagers; ClusterManagers.elastic_worker("4cOSyaYpgSl6BC0C","127.0.1.1",36275)'

By default, the printed command uses the absolute path to the current Julia executable and activates the same project as the current session. You can change either of these defaults by passing printing_kwargs=(absolute_exename=false, same_project=false)) to the first form of the ElasticManager constructor.

Once workers are connected, you can print the em object again to see them added to the list of active workers.