There is a techie page at this location Slurm Techie Page for those of you who are interested in the setup.
This page is intended for users to get started with the Slurm scheduler. greentail52 will be the slurm scheduler test “controller” with several cpu+gpu compute nodes configured. Any jobs submitted should be simple, quick running jobs, like a “sleep” or “hello world” jobs. The configured compute nodes are still managed by Openlava.
Default Environment
Slurm was compiled within this environment
# installer found /usr/local/cuda symbolic link to n37-cuda-9.2 export CUDAHOME=/usr/local/n37-cuda-9.2 export PATH=/usr/local/n37-cuda-9.2/bin:$PATH export LD_LIBRARY_PATH=/usr/local/n37-cuda-9.2/lib64:$LD_LIBRARY_PATH which nvcc # openmpi, just in case export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH which mpirun
Slurm Location
# for now, symbolic link to slurm-21.08.01 export PATH=/usr/local/slurm/bin:$PATH export LD_LIBRARY_PATH=/usr/local/slurm/lib:$LD_LIBRARY_PATH
# sorta like bqueues
$ sinfo -l
Thu Oct 14 09:27:02 2021
PARTITION AVAIL TIMELIMIT JOB_SIZE ROOT OVERSUBS GROUPS NODES STATE NODELIST
test* up infinite 1-infinite no EXCLUSIV all 3 idle n[37,78-79]
mwgpu up infinite 1-infinite no YES:4 all 1 idle n37
amber128 up infinite 1-infinite no YES:4 all 1 idle n78
exx96 up infinite 1-infinite no YES:4 all 1 idle n79
# more node info
$ sinfo -lN
Thu Oct 14 13:57:12 2021
NODELIST NODES PARTITION STATE CPUS S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON
n37 1 test* idle 32 2:8:2 257917 0 1 hasLocal none
n37 1 mwgpu idle 32 2:8:2 257917 0 1 hasLocal none
n78 1 amber128 idle 32 2:8:2 128660 0 1 hasLocal none
n78 1 test* idle 32 2:8:2 128660 0 1 hasLocal none
n79 1 test* idle 48 2:12:2 95056 0 1 hasLocal none
n79 1 exx96 idle 48 2:12:2 95056 0 1 hasLocal none
# sorta like bsub
$ sbatch run
Submitted batch job 1000002
# sorta like bjobs
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1000002 test test hmeij R 0:08 1 n78
# sorta like bhosts -l
$ scontrol show node n78
NodeName=n78 Arch=x86_64 CoresPerSocket=8
CPUAlloc=0 CPUTot=32 CPULoad=0.03
AvailableFeatures=hasLocalscratch
ActiveFeatures=hasLocalscratch
Gres=gpu:geforce_gtx_1080_ti:4(S:0-1)
NodeAddr=n78 NodeHostName=n78 Version=21.08.1
OS=Linux 3.10.0-693.2.2.el7.x86_64 #1 SMP Tue Sep 12 22:26:13 UTC 2017
RealMemory=128660 AllocMem=0 FreeMem=72987 Sockets=2 Boards=1
MemSpecLimit=1024
State=IDLE ThreadsPerCore=2 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A
Partitions=test,amber128
BootTime=2021-03-28T20:35:53 SlurmdStartTime=2021-10-14T13:56:00
LastBusyTime=2021-10-14T13:56:01
CfgTRES=cpu=32,mem=128660M,billing=32
AllocTRES=
CapWatts=n/a
CurrentWatts=0 AveWatts=0
ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
# sorta like bhist -l
$ scontrol show job 1000002
JobId=1000002 JobName=test
UserId=hmeij(8216) GroupId=its(623) MCS_label=N/A
Priority=4294901757 Nice=0 Account=(null) QOS=(null)
JobState=RUNNING Reason=None Dependency=(null)
Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
RunTime=00:03:18 TimeLimit=UNLIMITED TimeMin=N/A
SubmitTime=2021-10-11T13:27:58 EligibleTime=2021-10-11T13:27:58
AccrueTime=2021-10-11T13:27:58
StartTime=2021-10-11T13:27:58 EndTime=Unknown Deadline=N/A
SuspendTime=None SecsPreSuspend=0 LastSchedEval=2021-10-11T13:27:58 Scheduler=Main
Partition=test AllocNode:Sid=greentail52:70776
ReqNodeList=(null) ExcNodeList=(null)
NodeList=n78
BatchHost=n78
NumNodes=1 NumCPUs=2 NumTasks=1 CPUs/Task=1 ReqB:S:C:T=0:0:1:1
TRES=cpu=2,mem=128M,node=1,billing=2
Socks/Node=1 NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
MinCPUsNode=1 MinMemoryNode=128M MinTmpDiskNode=0
Features=(null) DelayBoot=00:00:00
OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
Command=/zfshomes/hmeij/slurm/run
WorkDir=/zfshomes/hmeij/slurm
StdErr=/zfshomes/hmeij/slurm/err
StdIn=/dev/null
StdOut=/zfshomes/hmeij/slurm/out
Power=
TresPerNode=gres:gpu:1
MailUser=hmeij@wesleyan.edu MailType=END
# sorta like bkill
$ scancel 1000003
man lsf.confman sbatch
From the information above it is a matter of learning new terminology and how to control devices. As you can see sinfo shows that nodes can exist in multiple partitions (queues, the '*' denotes default queue). So we could simply rebuild our queues in Slurm. But Slurm also presents node “features” (arbitrary resources like “hasLocalscracth”) and/or node “generic resources” (consumable, boolean, resources, like “gpu”). With a combination of those or just a very specific request for a resource you can control the routing of your job. For example, queue test contains 3 nodes but requesting resource gpu:geforce_rtx_2080_s assures you end up on node n79. Or you can simply request gpu:1 if gpu model is not important.
Same on the cpu only compute nodes. Features could be created for memory footprints (for example “hasMem64”, “hasMem128”, hasMem192“, “hasMem256”, “hasMem32”). Then all the cpu only nodes can go into one queue and we can stick all cpu+gpu nodes in another queue. Or all of them in a single queue. We'll see, just testing.
On the cpu resource requests: You may request 1 or more nodes, 1 or more sockets per node, 1 or more cores (physical) per socket or 1 or more threads (logical + physical) per core. Such a request can be fine grained or not; just request a node with –exclusive (test queue only) or share nodes (other queues, with –oversubscribe)
Note: this oversubscribing is not working yet. I can only get 4 simultaneous jobs running. Maybe there is a conflict with Openlava jobs. Should isolate a node and do further testing. After isolation (n37), 4 jobs with -n 4 exhausts number of physical cores. Is that why 5th job goes pending? Solved, see Changes section.
Slurm has a builtin MPI flavor, I suggest you do not rely on it. The documentation states that on major release upgrades the libslurm.so library is not backwards compatible and all software using it would need to be recompiled. There is a handy parallel job launcher which may be of use, it is called srun.
For now, we'll rely on PATH/LD_LIBRARY_PATH settings to control the environment. This also implies your job should run under Openlava or Slurm. With the new head node deployment we'll introduce modules to control the environment for newly installed software.
srun commands can be embedded in a job submission script but it can also run interactively. Like
$ srun --partition=mwgpu -n 4 -B 1:4:1 --mem=1024 sleep 60 &
For more details on srun consult https://slurm.schedmd.com/srun.html
Putting it all together a job submission script might look like example below. Simply submit to sbatch, assuming the job script name is run
$ sbatch run
Sample Submit Script
#!/bin/bash # [found at XStream] # Slurm will IGNORE all lines after the FIRST BLANK LINE, # even the ones containing #SBATCH. # Always put your SBATCH parameters at the top of your batch script. # Took me days to find, [constraint=|gres=] were not working ... silly behavior -Henk # # GENERAL #SBATCH --job-name="test" #SBATCH --output=out # or both in default file #SBATCH --error=err # slurm-$SLURM_JOBID.out #SBATCH --mail-type=END #SBATCH --mail-user=username@wesleyan.edu # # NODE control #SBATCH -N 1 # default, nodes ###SBATCH --nodelist=n78,n79 ###SBATCH --constraint=hasLocalscratch # n37, n78 ###SBATCH --constraint=hasLocalscratch1tb # n79 ###SBATCH --exclusive # test queue only ###SBATCH --oversubscribe # not on test queue # # CPU control #SBATCH -n 8 # total cpus request is tasks=N(S*C*T) #SBATCH -B 1:4:2 # S:C:T=sockets/node:cores/socket:threads/core # # GPU control ###SBATCH --gres=gpu:geforce_gtx_1080_ti:1 # n78 ###SBATCH --gres=gpu:geforce_rtx_2080_s:1 # n79 ###SBATCH --gres=gpu:tesla_k20m:1 # n37 #SBATCH --gres=gpu:1 # any # ENV control # openmpi export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH which mpirun # unique job scratch dir created(prolog)/cleaned(epilog) export MYSANSCRATCH=/sanscratch/$SLURM_JOBID export MYLOCALSCRATCH=/localscratch/$SLURM_JOBID cd $MYLOCALSCRATCH pwd # CPU serial job example date # look in stdout file datee # look in stderr file env | grep ^SLURM echo "hello world of slurm" touch foo ls -l foo # CPU mpi example, note: no -np flag, no --hostfile mpirun $HOME/slurm/hello_c # GPU docker example, be sure to select rtx2080s gpu # manual "wrapper" setup to find idle gpu, on localhost # cuda 10.2 gpuid="` gpu-free | sed "s/,/\n/g" | shuf | head -1 ` " echo ""; echo "docker running on gpu $HOSTNAME:$gpuid"; echo "" #export CUDA_VISIBLE_DEVICES=$gpuid # or NV_GPU NV_GPU=$gpuid \ nvidia-docker run --rm -u $(id -u):$(id -g) \ -v /$HOME:/mnt/$USER \ -v /home/apps:/mnt/apps \ -v /usr/local:/mnt/local \ nvcr.io/nvidia/tensorflow:19.09-py2 python \ /mnt/$USER/jobs/docker/benchmarks-master/scripts/tf_cnn_benchmarks/run_tests.py \ --num_gpus=1 --batch_size=64 \ --model=resnet50 \ --variable_update=parameter_server > $HOME/slurm/out.docker sleep 5m # so you can query job/node with scontrol
The relevant sections of the script above should generate output like this
err file
# the stderr file starts with /var/spool/slurmd/job1000056/slurm_script: line 47: datee: command not found # lots of tensorflow warnings <snip> # and that apps writes to stderr ---------------------------------------------------------------------- Ran 104 tests in 197.454s OK (skipped=12)
out file
/share/apps/CENTOS7/openmpi/4.0.4/bin/mpirun /localscratch/1000056 Thu Oct 14 10:36:22 EDT 2021 SLURM_NODELIST=n79 SLURM_JOB_NAME=test SLURMD_NODENAME=n79 SLURM_TOPOLOGY_ADDR=n79 SLURM_THREADS_PER_CORE=2 SLURM_PRIO_PROCESS=0 SLURM_NODE_ALIASES=(null) SLURM_GPUS_ON_NODE=4 SLURM_TOPOLOGY_ADDR_PATTERN=node SLURM_JOB_GPUS=0,1,2,3 SLURM_NNODES=1 SLURM_JOBID=1000056 SLURM_NTASKS=8 SLURM_TASKS_PER_NODE=8 SLURM_WORKING_CLUSTER=slurmcluster:greentail52:6817:9472:109 SLURM_CONF=/usr/local/slurm-21.08.1/etc/slurm.conf SLURM_JOB_ID=1000056 SLURM_JOB_USER=hmeij SLURM_JOB_UID=8216 SLURM_NODEID=0 SLURM_SUBMIT_DIR=/zfshomes/hmeij/slurm SLURM_TASK_PID=257975 SLURM_NPROCS=8 SLURM_CPUS_ON_NODE=48 SLURM_PROCID=0 SLURM_JOB_NODELIST=n79 SLURM_LOCALID=0 SLURM_JOB_GID=623 SLURM_JOB_CPUS_PER_NODE=48 SLURM_CLUSTER_NAME=slurmcluster SLURM_GTIDS=0 SLURM_SUBMIT_HOST=greentail52 SLURM_JOB_PARTITION=test SLURM_JOB_NUM_NODES=1 SLURM_MEM_PER_NODE=192 hello world of slurm -rw-r--r-- 1 hmeij its 0 Oct 14 10:36 foo Hello, world, I am 0 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) Hello, world, I am 1 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) Hello, world, I am 4 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) Hello, world, I am 5 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) Hello, world, I am 2 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) Hello, world, I am 3 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) Hello, world, I am 6 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) Hello, world, I am 7 of 8, (Open MPI v4.0.4, package: Open MPI hmeij@greentail52 Distribution, ident: 4.0.4, repo rev: v4.0.4, Jun 10, 2020, 112) docker running on gpu n79:3
and the out.docker file
================ == TensorFlow == ================ NVIDIA Release 19.09 (build 8044706) TensorFlow Version 1.14.0 Container image Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved. Copyright 2017-2019 The TensorFlow Authors. All rights reserved. <snip> Generating training model Initializing graph Running warm up Done warm up <snip> ---------------------------------------------------------------- Generating training model Initializing graph Running warm up Done warm up Step Img/sec total_loss 1 images/sec: 110.3 +/- 0.0 (jitter = 0.0) 1.156250119209290 2 images/sec: 213.2 +/- 1096.9 (jitter = 2299.9) 7.638743400573730 3 images/sec: 309.0 +/- 822.7 (jitter = 246.5) -2.596951484680176 4 images/sec: 398.6 +/- 649.2 (jitter = 123.3) -35.271511077880859 ---------------------------------------------------------------- total images/sec: 378.12 ----------------------------------------------------------------
If there are errors on this page, or mistatements, let me know. As we test and improve the setup to mimic a production environment I will update the page (and mark those entries with newer timestamp/signature).
— Henk 2021/10/15 09:16
export CUDA_VISIBLE_DEVICES=`shuf -i 0-3 -n 1`Newer 2022 version seems to have reversed the override options for oversubscribe. So here is our testing…back to CR_CPU_Memory and OverSubscribe=No — Henk 2022/11/02 13:23
CR_Socket_Memory PartitionName=test Nodes=n[100-101] Default=YES MaxTime=INFINITE State=UP OverSubscribe=No DefCpuPerGPU=12 MPI jobs with -N 1, -n 8 and -B 2:4:1 no override options, cpus=48 --mem=2048, cpus=48 and --cpus-per-task=1, cpus=48 and --ntasks-per-node=8, cpus=24 MPI jobs with -N, -n 8 and -B 1:8:1 --mem=10240 cpus=48 and --cpus-per-task=1, cpus=48 and --ntasks-per-node=8, cpus=24 GPU jobs with -N 1, -n 1 and -B 1:1:1 no override options, no cuda export, cpus=48 --cpus-per-gpu=1, cpus=24 and --mem-per-gpu=7168, cpus=1 (pending while other gpu runs in queue but gpus are free???) GPU jobs with -N 1, -n 1 and -B 1:1:1 no override options, yes cuda export, cpus=48 --cpus-per-gpu=1, cpus=24 and --mem-per-gpu=7168, cpus=1 (resources pending while a gpu job runs, gpus are free, then it executes) ...suddenly the cpus=1 turns into cpus=24 when submitting, slurm confused becuase of all the job cancellations? CR_CPU_Memory test=no, mwgpu=force:16 PartitionName=test Nodes=n[100-101] Default=YES MaxTime=INFINITE State=UP OverSubscribe=No DefCpuPerGPU=12 MPI jobs with -N 1, -n 8 and -B 2:4:1 no override options, cpus=8 (queue fills across nodes, but only one job per node, test & mwgpu) --mem=1024, cpus=8 (queue fills first node ..., but only three jobs per node, test 3x8=24 full 4th job pending & mwgpu 17th job goes pending on n33, overloaded with -n 8 !!) (not needed) --cpus-per-task=?, cpus= (not needed) --ntasks-per-node=?, cpus= GPU jobs with -N 1, -n 1 and -B 1:1:1 on test no override options, no cuda export, cpus=12 (one gpu per node) --cpus-per-gpu=1, cpus=1 (one gpu per node) and --mem-per-gpu=7168, cpus=1 (both override options required else all mem allocated!, max 4 jobs per node, fills first node first...cuda export not needed) with cuda export, same node, same gpu, with "no" enabled multiple jobs per gpu not accepted GPU jobs with -N 1, -n 1 and -B 1:1:1 on mwgpu --cpus-per-gpu=1, and --mem-per-gpu=7168, cpus=1 (same node, same gpu, cuda export set, with "force:16" enabled 4 jobs per gpu accepted, potential for overloading!)
OverSubscribe
Suggestion was made to set OverSubcribe=No for all partitions (thanks, Colin). We now observe with a simple sleep script that we can run 16 jobs simultaneously (with either -n or -B). So that's 16 physical cores, each has a logical core (thread) for a total of 32 cpus for n37.
for i in `seq 1 17`;do sbatch sleep; done
#!/bin/bash #SBATCH --job-name=sleep #SBATCH --partition=mwgpu ###SBATCH -n 1 #SBATCH -B 1:1:1 #SBATCH --mem=1024 sleep 60
— Henk 2021/10/15 15:18
GPU-CPU cores
Noticed this with debug level on in slurmd.log. No action taken.
# n37: old gpu model bound to all physical cpu cores GRES[gpu] Type:tesla_k20m Count:1 Cores(32):0-15 Links:-1,0,0,0 /dev/nvidia0 GRES[gpu] Type:tesla_k20m Count:1 Cores(32):0-15 Links:0,-1,0,0 /dev/nvidia1 GRES[gpu] Type:tesla_k20m Count:1 Cores(32):0-15 Links:0,0,-1,0 /dev/nvidia2 GRES[gpu] Type:tesla_k20m Count:1 Cores(32):0-15 Links:0,0,0,-1 /dev/nvidia3 # n78: somewhat dated gpu model, bound to top/bot of physical cores (16) GRES[gpu] Type:geforce_gtx_1080_ti Count:1 Cores(32):0-7 Links:-1,0,0,0 /dev/nvidia0 GRES[gpu] Type:geforce_gtx_1080_ti Count:1 Cores(32):0-7 Links:0,-1,0,0 /dev/nvidia1 GRES[gpu] Type:geforce_gtx_1080_ti Count:1 Cores(32):8-15 Links:0,0,-1,0 /dev/nvidia2 GRES[gpu] Type:geforce_gtx_1080_ti Count:1 Cores(32):8-15 Links:0,0,0,-1 /dev/nvidia3 # n79, more recent gpu model, same bound pattern of top/bot (24) GRES[gpu] Type:geforce_rtx_2080_s Count:1 Cores(48):0-11 Links:-1,0,0,0 /dev/nvidia0 GRES[gpu] Type:geforce_rtx_2080_s Count:1 Cores(48):0-11 Links:0,-1,0,0 /dev/nvidia1 GRES[gpu] Type:geforce_rtx_2080_s Count:1 Cores(48):12-23 Links:0,0,-1,0 /dev/nvidia2 GRES[gpu] Type:geforce_rtx_2080_s Count:1 Cores(48):12-23 Links:0,0,0,-1 /dev/nvidia3
Partition Priority
If set you can list more than one queue…
srun --partition=exx96,amber128,mwgpu --mem=1024 --gpus=1 --gres=gpu:any sleep 60 &
The above will fill up n79 first, then n78, then n36…
Node Weight Priority
Weight nodes by the memory per logical core: jobs will be allocated the nodes with the lowest weight which satisfies their requirements. So CPU jobs will be routed last to gpu queues because they have the highest weight (=lowest priority).
hp12: 12/8 = 1.5 tinymem: 32/20 = 1.6 mw128: 128/24 = 5.333333 mw256: 256/16 = 16 exx96: 96/24 = 4 amber128: 128/16 = 8 mwgpu = 256/16 = 16
Or more arbitrary (based on desired cpu node comsumption of cpu jobs. No action taken.
tinymem 10 mw128 20 mw256fd 30 + HasMem256 feature so cpu jobs can directly target large mem mwgpu 40 + HasMem256 feature amber128 50 exx96 80
CR_CPU_Memory
Makes for a better 1-1 relationship of physical core to ntask yet the “hyperthreads” are still available to user jobs but physical cores are consumed first, if I got all this right.
Deployed. My need to set threads=1 and cpus=(quantity of physical cores)…this went horribly wrong it resaulted in sockets=1 setting and threads=1 for each node. — Henk 2021/10/18 14:32
We did set number of cpus per gpu (12 for n79) and minimum memory settings. Now we experience 5th job pending with 48 cpus consumed. When using sbatch set -n 8 because sbatch will override defaults.
srun --partition=test --mem=1024 --gres=gpu:geforce_rtx_2080_s:1 sleep 60 &