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A command called sbatch and foo for the cloudmesh shell

Project description

Cloudmesh Sbatch

A general purpose HPC Template and Experiment management system

Background

Hyper Performance Computation Clusters (HPCs) are designed around a timesharing principle and are powered by queue-based execution ecosystems such as SchedMD's SLURM and IBM's Platform Load Sharing Facility (LSF). While these ecosystems provide a great deal of control and extension for planning, scheduling, and batching jobs, they are limited in their ability to support parameterization in a scheduled task. While there are facilities in place to execute jobs on an Array, the ability to do permutation based experments are limited to what you integrate into your own batch script. Even then, parameterization of values are only made availabile as environment variables, which can be limited depending on your OS or selected programming language. In many cases limitations set by the deployment trhough the compute center also hinder optimal use while restrictions are placed on duration and number of parallel accessible resources. In some cases these restrictions are soo established that removing them is impractical and takes weks to implement on temporary basis.

Cloudmesh Sbatch is a framework that wraps the SLURM batch processor into a templated framework such that experiments can be generated based on configuration files focusing on the livecycle of generating many permutations of experiments with standard tooling, so that you can focus more on modeling your experiments than how to orchestrate them with tools. A number of batch scripts can be generated that than can be executed according to center policies.

Dependencies

When you install cloudmesh-sbatch, you will also be installing a minimum baseline of the cms command (as part of the Cloudmesh ecosystem). For more details on Cloudmesh, see its documentation on read the docs. However all instalation can be done thorugh pip. After instalation, you will need to initialize cloudmesh with the command

$ cms help

While SLURM is not needed to run the cloudmesh sbatch command, the generated output will not exectue unless your system has slurm installed and you are able to run jobs via the slurm sbatch command.

Documentation

Running Cloudmesh SBatch

The cloudmesh sbatch command takes one of two forms of execution. It is started with

$ cms sbatch <command> <parameters>

Where the command invokes a partiuclar action and parameters include a number of parameters for the command These commands allow you to inspect the generated output to confirm your parameterization functions as expected and as intended.

In general, configuration arguments that appear in multiple locations are prioritized in the following order (highest priority first)

  1. CLI Arguments with cms sbatch
  2. Configuration Files
  3. Preset values

Generating Experiments with the CLI

The generate command is used to generate your experiments based upon either a passed configuration file, or via CLI arguments. You can issue the command using either of the below forms:

cms sbatch generate SOURCE --name=NAME [--verbose] [--mode=MODE] [--config=CONFIG] [--attributes=PARAMS] [--out=DESTINATION] [--dryrun] [--noos] [--nocm] [--dir=DIR] [--experiment=EXPERIMENT]
cms sbatch generate --setup=FILE [SOURCE] [--verbose] [--mode=MODE]  [--config=CONFIG] [--attributes=PARAMS] [--out=DESTINATION] [--dryrun] [--noos] [--nocm] [--dir=DIR] [--experiment=EXPERIMENT] [--name=NAME]

If you have prepared a configuration file that conforms to the schema defined in Setup Config, then you can use the second form which overrides the default values.

  • --name=NAME - Supplies a name for this experiment. Note that the name must not match any existing files or directories where you are currently executing the command

  • --verbose - Enables additional logging useful when troubleshooting the program.

  • --mode=MODE - specifies how the output should be generated. One of: f,h,d.

    • f or flat - specifies a "flat" mode, where slurm scripts are generated in a flattened structure, all in one directory.
    • h or hierarchical - specifies a "hierarchical" mode, where experiments are nested into unique directories from each other.
    • d or debug - instructs the command to not generate any output.
  • --config=CONFIG - specifies key-value pairs to be used across all files for substitution. This can be a python, yaml, or json file.

  • --attributes=PARAMS - specifies key-value pairs that can be listed at the command line and used as substitution across all experiments. Note this command leverages cloudmesh's parameter expansion specification for different types of expansion rules.

  • --out=DESTINATION - specifies the directory to write the generated scripts out to.

  • --dryrun - Runs the command without performing any operations

  • --noos - Prevents the interleaving of OS environemnt variables into the subsitution logic

  • --dir=DIR - specifies the directory to write the generated scripts out to.

  • --experiment=EXPERIMENT - specifies a listing of key-value parameters that establish a unique experiment for each combination of values (a cartisian product across all values for each key).

  • --setup=FILE - provides all the above configuration options within a configuration file to simplify executions.

Form 2 - Generating Submission Scripts

sbatch generate submit --name=NAME [--verbose]

This command uses the output of the generate command and generates a shell script that can be used to submit your previously generated outputs to SLURM as a sequence of sbatch commands.

  • --name=NAME - specifies the name used in the generate command. The generate command will inspect the <NAME>.json file and build the necessary commands to run all permutations that the cloudmesh sbatch command generated.

Note that this command only generates the script, and you must run the outputted file in your shell for the commands to be issued to SLURM and run your jobs.

Sample YAML File

This command requires a YAML file which is configured for the host and gpu. The YAML file also points to the desired slurm template.

slurm_template: 'slurm_template.slurm'

sbatch_setup:
  <hostname>-<gpu>:
    - card_name: "a100"
    - time: "05:00:00"
    - num_cpus: 6
    - num_gpus: 1

  rivanna-v100:
    - card_name: "v100"
    - time: "06:00:00"
    - num_cpus: 6
    - num_gpus: 1

example:

cms sbatch slurm.in.sh --config=a.py,b.json,c.yaml --attributes=a=1,b=4  --noos --dir=example --experiment=\"epoch=[1-3] x=[1,4] y=[10,11]\"
sbatch slurm.in.sh --config=a.py,b.json,c.yaml --attributes=a=1,b=4 --noos --dir=example --experiment="epoch=[1-3] x=[1,4] y=[10,11]"
# ERROR: Importing python not yet implemented
epoch=1 x=1 y=10  sbatch example/slurm.sh
epoch=1 x=1 y=11  sbatch example/slurm.sh
epoch=1 x=4 y=10  sbatch example/slurm.sh
epoch=1 x=4 y=11  sbatch example/slurm.sh
epoch=2 x=1 y=10  sbatch example/slurm.sh
epoch=2 x=1 y=11  sbatch example/slurm.sh
epoch=2 x=4 y=10  sbatch example/slurm.sh
epoch=2 x=4 y=11  sbatch example/slurm.sh
epoch=3 x=1 y=10  sbatch example/slurm.sh
epoch=3 x=1 y=11  sbatch example/slurm.sh
epoch=3 x=4 y=10  sbatch example/slurm.sh
epoch=3 x=4 y=11  sbatch example/slurm.sh
Timer: 0.0022s Load: 0.0013s sbatch slurm.in.sh --config=a.py,b.json,c.yaml --attributes=a=1,b=4 --noos --dir=example --experiment="epoch=[1-3] x=[1,4] y=[10,11]"

Slurm on a single computer ubuntu 20.04

Install

see https://drtailor.medium.com/how-to-setup-slurm-on-ubuntu-20-04-for-single-node-work-scheduling-6cc909574365

32 Processors (threads)

sudo apt update -y
sudo apt install slurmd slurmctld -y

sudo chmod 777 /etc/slurm-llnl

# make sure to use the HOSTNAME

sudo cat << EOF > /etc/slurm-llnl/slurm.conf
# 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.
#
ClusterName=localcluster
SlurmctldHost=$HOSTNAME
MpiDefault=none
ProctrackType=proctrack/linuxproc
ReturnToService=2
SlurmctldPidFile=/var/run/slurmctld.pid
SlurmctldPort=6817
SlurmdPidFile=/var/run/slurmd.pid
SlurmdPort=6818
SlurmdSpoolDir=/var/lib/slurm-llnl/slurmd
SlurmUser=slurm
StateSaveLocation=/var/lib/slurm-llnl/slurmctld
SwitchType=switch/none
TaskPlugin=task/none
#
# TIMERS
InactiveLimit=0
KillWait=30
MinJobAge=300
SlurmctldTimeout=120
SlurmdTimeout=300
Waittime=0
# SCHEDULING
SchedulerType=sched/backfill
SelectType=select/cons_tres
SelectTypeParameters=CR_Core
#
#AccountingStoragePort=
AccountingStorageType=accounting_storage/none
JobCompType=jobcomp/none
JobAcctGatherFrequency=30
JobAcctGatherType=jobacct_gather/none
SlurmctldDebug=info
SlurmctldLogFile=/var/log/slurm-llnl/slurmctld.log
SlurmdDebug=info
SlurmdLogFile=/var/log/slurm-llnl/slurmd.log
#
# COMPUTE NODES # THis machine has 128GB main memory
NodeName=$HOSTNAME CPUs=32 RealMemory==128762 State=UNKNOWN
PartitionName=local Nodes=ALL Default=YES MaxTime=INFINITE State=UP
EOF

sudo chmod 755 /etc/slurm-llnl/

Start

sudo systemctl start slurmctld
sudo systemctl start slurmd
sudo scontrol update nodename=localhost state=idle

Stop

sudo systemctl stop slurmd
sudo systemctl stop slurmctld

Info

sinfo

Job

save into gregor.slurm

#!/bin/bash

#SBATCH --job-name=gregors_test          # Job name
#SBATCH --mail-type=END,FAIL             # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=laszewski@gmail.com  # Where to send mail	
#SBATCH --ntasks=1                       # Run on a single CPU
####  XBATCH --mem=1gb                        # Job memory request
#SBATCH --time=00:05:00                  # Time limit hrs:min:sec
#SBATCH --output=sgregors_test_%j.log    # Standard output and error log

pwd; hostname; date

echo "Gregors Test"
date
sleep(30)
date

Run with

sbatch gregor.slurm
watch -n 1 squeue

BUG

JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
                 2    LocalQ gregors_    green PD       0:00      1 (Nodes required for job are DOWN, DRAINED or reserved for jobs in higher priority partitions)

sbatch slurm manageement commands for localhost

start slurm deamons

cms sbatch slurm start

stop surm deamons

cms sbatch slurm stop

BUG:

srun gregor.slurm

srun: Required node not available (down, drained or reserved)
srun: job 7 queued and waiting for resources
sudo scontrol update nodename=localhost state=POWER_UP

Valid states are: NoResp DRAIN FAIL FUTURE RESUME POWER_DOWN POWER_UP UNDRAIN

Cheatsheet

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