I have a setup/installation of SLURM on my desktop computer to do some testing and understand how it works before deploying it to a cluster. The desktop computer is running Ubuntu 18.10 (Cosmic), as the nodes in the cluster are all running on. The used version of SLURM is 17.11.9. I have tested some of the features of SLURM, e.g. job-arrays and its deployment of tasks. However I would like to communicate with the different tasks sent out to each node or CPU in the cluster, in order to collect its results (without disk I/O). For that reason, I have looked in how manage that with e.g. message queuing, and MPI, or OpenMPI. (Any other implementation strategy, as an advice or recommendation is much appreciated.)
I have tested MPI with a simple Python snippet, starting a communication between two processes. I am using MPI4PY to handle this communication. This code snippet runs fine with mpiexec-command, but running it via SLURM and sbatch-command I cannot get it to work. SLURM is configured with OpenMPI and opmi_info states that SLURM is supported.
OpenMPI version 3.1.2-6 (from dpkg -l | grep mpi) SLURM_VERSION 17.11.9 Ubuntu 18.10 (Cosmic) MPI4PY version 3.0.1. (from pip list)
This is the Python3.6 code snippet:
$cat mpi_test.py
from mpi4py import MPI
if __name__=='__main__':
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
if rank==0:
data={'param1':1, 'param2':2, 'param3':3}
destinationNode = 1
print('Im', rank, 'sending to ', destinationNode)
comm.send(data, dest=destinationNode, tag=11)
elif rank!=0:
sourceNode = 0
dataRx=comm.recv(source=sourceNode, tag=11)
print('Im', rank, 'recieving from ', sourceNode)
for keys in dataRx.keys():
print('Data recieved: ',str(dataRx[keys]))
The python.mpi.sbatch used at the call with sbatch is:
$cat python.mpi.sbatch
#!/bin/bash -l
#SBATCH --job-name=mpiSimpleExample
#SBATCH --nodes=1
#SBATCH --error=slurm-err-%j.err
#SBATCH --export=all
#SBATCH --time=0-00:05:00
#SBATCH --partition=debug
srun -N 1 mpiexec -n 2 python3 mpi_test.py
#mpiexec -n 2 python3 mpi_test.py
exit 0
Running "sbatch python.mpi.sbatch" with this setup yields the following output:
$sbatch python.mpi.sbatch
$cat slurm-err-104.err
----------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 2
slots
that were requested by the application:
python3
Either request fewer slots for your application, or make more slots
available for use.
--------------------------------------------------------------------
Modifying python.mpi.sbatch to instead use:
"srun -n 1 mpiexec -n 1 python3 mpi_test.py" yields the error:
$cat slurm-err-105.error
Traceback (most recent call last):
File "mpi_test.py", line 18, in <module>
comm.send(data, dest=destinationNode, tag=11)
File "mpi4py/MPI/Comm.pyx", line 1156, in mpi4py.MPI.Comm.send
File "mpi4py/MPI/msgpickle.pxi", line 174, in mpi4py.MPI.PyMPI_send
mpi4py.MPI.Exception: MPI_ERR_RANK: invalid rank
---------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero
status, thus causing the job to be terminated. The first process to do
so was:
Process name: [[44366,1],0]
Exit code: 1
---------------------------------------------------------------------
Which is expected since it is only started with 1 node.
Running mpirun hostname, yields four instances of the machine, thus there should be four slots available for this machine. I may run the Python3.6 with up to four (after modification of mpi_test.py) processess with the command "mpiexec -n 4 python3 mpi_test.py", with success.
Any help is much appreciated.
slurm.conf-file:
# slurm.conf file generated by configurator.html.
# Put this file on all nodes of your cluster.
# See the slurm.conf man page for more information.
#
ControlMachine=desktop-comp
#ControlAddr=
#BackupController=
#BackupAddr=
#
AuthType=auth/munge
#CheckpointType=checkpoint/none
CryptoType=crypto/munge
#DisableRootJobs=NO
#EnforcePartLimits=NO
#Epilog=
#EpilogSlurmctld=
#FirstJobId=1
#MaxJobId=999999
#GresTypes=
#GroupUpdateForce=0
#GroupUpdateTime=600
#JobCheckpointDir=/var/slurm/checkpoint
#JobCredentialPrivateKey=
#JobCredentialPublicCertificate=
#JobFileAppend=0
#JobRequeue=1
#JobSubmitPlugins=1
#KillOnBadExit=0
#LaunchType=launch/slurm
#Licenses=foo*4,bar
#MailProg=/bin/mail
#MaxJobCount=5000
#MaxStepCount=40000
#MaxTasksPerNode=128
MpiDefault=openmpi
#MpiParams=ports=#-#
#PluginDir=
#PlugStackConfig=
#PrivateData=jobs
#ProctrackType=proctrack/cgroup
#Prolog=
#PrologFlags=
#PrologSlurmctld=
#PropagatePrioProcess=0
#PropagateResourceLimits=
#PropagateResourceLimitsExcept=
#RebootProgram=
ReturnToService=1
#SallocDefaultCommand=
SlurmctldPidFile=/var/run/slurm-llnl/slurmctld.pid
SlurmctldPort=6817
SlurmdPidFile=/var/run/slurm-llnl/slurmd.pid
SlurmdPort=6818
SlurmdSpoolDir=/var/lib/slurm-llnl/slurmd
SlurmUser=slurm
#SlurmdUser=root
#SrunEpilog=
#SrunProlog=
StateSaveLocation=/var/lib/slurm-llnl/slurmd
SwitchType=switch/none
#TaskEpilog=
#TaskPlugin=task/affinity
#TaskPluginParam=Sched
#TaskProlog=
#TopologyPlugin=topology/tree
#TmpFS=/tmp
#TrackWCKey=no
#TreeWidth=
#UnkillableStepProgram=
#UsePAM=0
#
#
# TIMERS
#BatchStartTimeout=10
#CompleteWait=0
#EpilogMsgTime=2000
#GetEnvTimeout=2
#HealthCheckInterval=0
#HealthCheckProgram=
InactiveLimit=0
KillWait=30
#MessageTimeout=10
#ResvOverRun=0
MinJobAge=300
#OverTimeLimit=0
SlurmctldTimeout=120
SlurmdTimeout=300
#UnkillableStepTimeout=60
#VSizeFactor=0
Waittime=0
#
#
# SCHEDULING
#DefMemPerCPU=0
FastSchedule=1
#MaxMemPerCPU=0
#SchedulerTimeSlice=30
SchedulerType=sched/backfill
SelectType=select/cons_res
SelectTypeParameters=CR_Core
#
#
# JOB PRIORITY
#PriorityFlags=
#PriorityType=priority/basic
#PriorityDecayHalfLife=
#PriorityCalcPeriod=
#PriorityFavorSmall=
#PriorityMaxAge=
#PriorityUsageResetPeriod=
#PriorityWeightAge=
#PriorityWeightFairshare=
#PriorityWeightJobSize=
#PriorityWeightPartition=
#PriorityWeightQOS=
#
#
# LOGGING AND ACCOUNTING
#AccountingStorageEnforce=0
#AccountingStorageHost=
#AccountingStorageLoc=
#AccountingStoragePass=
#AccountingStoragePort=
AccountingStorageType=accounting_storage/none
#AccountingStorageUser=
AccountingStoreJobComment=YES
ClusterName=cluster
#DebugFlags=
#JobCompHost=
#JobCompLoc=
#JobCompPass=
#JobCompPort=
JobCompType=jobcomp/none
#JobCompUser=
#JobContainerType=job_container/none
JobAcctGatherFrequency=30
JobAcctGatherType=jobacct_gather/none
SlurmctldDebug=3
#SlurmctldLogFile=
SlurmdDebug=3
#SlurmdLogFile=
#SlurmSchedLogFile=
#SlurmSchedLogLevel=
#
#
# POWER SAVE SUPPORT FOR IDLE NODES (optional)
#SuspendProgram=
#ResumeProgram=
#SuspendTimeout=
#ResumeTimeout=
#ResumeRate=
#SuspendExcNodes=
#SuspendExcParts=
#SuspendRate=
#SuspendTime=
#
#
# COMPUTE NODES
NodeName=desktop-comp CPUs=1 State=UNKNOWN
PartitionName=debug Nodes=desktop-compDefault=YES MaxTime=INFINITE State=UP
In your update question you have in your slurm.conf the line
NodeName=desktop-comp CPUs=1 State=UNKNOWN
This tells slurm that you have only one CPU available on your node. You can try running slurmd -C to see what slurm discovers about your computer and copypaste the CPUs, CoresPerSocket etc. values to your slurm.conf.