[slurm-users] How to request for the allocation of scratch .

Thu Apr 16 16:12:31 UTC 2020

That all seems fine to me.

I would check into your slurm logs to try and determine why slurm put your nodes into drain state.

Erik

---
Erik Ellestad
Wynton Cluster SysAdmin
UCSF
________________________________
From: slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf of navin srivastava <navin.altair at gmail.com>
Sent: Wednesday, April 15, 2020 10:37 PM
To: Slurm User Community List <slurm-users at lists.schedmd.com>
Subject: Re: [slurm-users] How to request for the allocation of scratch .

Thanks Erik.

Last night i made the changes.

i defined in slurm.conf on all the nodes as well as on the slurm server.

TmpFS=/lscratch

 NodeName=node[01-10]  CPUs=44  RealMemory=257380 Sockets=2 CoresPerSocket=22 ThreadsPerCore=1 TmpDisk=1600000 State=UNKNOWN Feature=P4000 Gres=gpu:2

These nodes having 1.6TB local scratch. i did a scontrol reconfig on all the nodes but after sometime we saw all nodes went into drain state.then i revert back the changes with old one.

on all nodes jobs were running and the localsctratch is 20-25% in use.
we have already cleanup script in crontab which used to clean the scratch space regularly.

is anything wrong here?

Regards
Navin.

On Thu, Apr 16, 2020 at 12:26 AM Ellestad, Erik <Erik.Ellestad at ucsf.edu<mailto:Erik.Ellestad at ucsf.edu>> wrote:
The default value for TmpDisk is 0, so if you want local scratch available on a node, the amount of TmpDisk space must be defined in the node configuration in slurm.conf.

example:

NodeName=TestNode01 CPUs=8 Boards=1 SocketsPerBoard=2 CoresPerSocket=4 ThreadsPerCore=1 RealMemory=24099 TmpDisk=150000

The configuration value for the node definition is in MB.

https://slurm.schedmd.com/slurm.conf.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__slurm.schedmd.com_slurm.conf.html&d=DwMFaQ&c=iORugZls2LlYyCAZRB3XLg&r=Ct3zEADMmPgyUYfpHDJQWaWsE9mNbEHEhGxpsYoThbE&m=S4Dlg4-bVtpN7A5uGS3U053sTbGLQhWWqF7czJWRhO8&s=-q_lB4fzIj8i2PkR5NfWJomcaoDnRlBuyvyxkf4V0hQ&e=>

TmpDisk
Total size of temporary disk storage in TmpFS in megabytes (e.g. "16384"). TmpFS (for "Temporary File System") identifies the location which jobs should use for temporary storage. Note this does not indicate the amount of free space available to the user on the node, only the total file system size. The system administration should ensure this file system is purged as needed so that user jobs have access to most of this space. The Prolog and/or Epilog programs (specified in the configuration file) might be used to ensure the file system is kept clean. The default value is 0.

When requesting --tmp with srun or sbatch, it can be done in various size formats:

--tmp=<size[units]>
Specify a minimum amount of temporary disk space per node. Default units are megabytes unless the SchedulerParameters configuration parameter includes the "default_gbytes" option for gigabytes. Different units can be specified using the suffix [K|M|G|T].

https://slurm.schedmd.com/sbatch.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__slurm.schedmd.com_sbatch.html&d=DwMFaQ&c=iORugZls2LlYyCAZRB3XLg&r=Ct3zEADMmPgyUYfpHDJQWaWsE9mNbEHEhGxpsYoThbE&m=S4Dlg4-bVtpN7A5uGS3U053sTbGLQhWWqF7czJWRhO8&s=yF9k9ysKRaVnu_ZnNdHsxj8Yc6X7PXTlId7i3XgZ5V4&e=>

---
Erik Ellestad
Wynton Cluster SysAdmin
UCSF
________________________________
From: slurm-users <slurm-users-bounces at lists.schedmd.com<mailto:slurm-users-bounces at lists.schedmd.com>> on behalf of navin srivastava <navin.altair at gmail.com<mailto:navin.altair at gmail.com>>
Sent: Tuesday, April 14, 2020 11:19 PM
To: Slurm User Community List <slurm-users at lists.schedmd.com<mailto:slurm-users at lists.schedmd.com>>
Subject: Re: [slurm-users] How to request for the allocation of scratch .

Thank you Erik.

To define the local scratch on all the compute node is not mandatory? only on slurm server is enough right?
Also the TMPdisk should be defined in MB or can be defined in GB as well

while requesting --tmp , we can use the value in GB right?

Regards
Navin.

On Tue, Apr 14, 2020 at 11:04 PM Ellestad, Erik <Erik.Ellestad at ucsf.edu<mailto:Erik.Ellestad at ucsf.edu>> wrote:
Have you defined the TmpDisk value for each node?

As far as I know, local disk space is not a valid type for GRES.

https://slurm.schedmd.com/gres.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__slurm.schedmd.com_gres.html&d=DwMFaQ&c=iORugZls2LlYyCAZRB3XLg&r=Ct3zEADMmPgyUYfpHDJQWaWsE9mNbEHEhGxpsYoThbE&m=qpy9RbpYHEmd6jqfs9j8b4IiRJf3GkO-X_v05nL-8Bo&s=B5wXNgnl6EdXIaS0QQpITnBTSxcjnAHJENyJGLyWltI&e=>

"Generic resource (GRES) scheduling is supported through a flexible plugin mechanism. Support is currently provided for Graphics Processing Units (GPUs), CUDA Multi-Process Service (MPS), and Intel® Many Integrated Core (MIC) processors."

The only valid solution I've found for scratch is to:

In slurm.conf, define the location of local scratch globally via TmpFS.

And then the amount per host is defined via TmpDisk=xxx.

Then the request for srun/sbatch via --tmp=X

---
Erik Ellestad
Wynton Cluster SysAdmin
UCSF
________________________________
From: slurm-users <slurm-users-bounces at lists.schedmd.com<mailto:slurm-users-bounces at lists.schedmd.com>> on behalf of navin srivastava <navin.altair at gmail.com<mailto:navin.altair at gmail.com>>
Sent: Tuesday, April 14, 2020 7:32 AM
To: Slurm User Community List <slurm-users at lists.schedmd.com<mailto:slurm-users at lists.schedmd.com>>
Subject: Re: [slurm-users] How to request for the allocation of scratch .

Any suggestion on the above query.need help to understand it.
Does TmpFS=/scratch   and the request is #SBATCH --tmp=500GB  then it will reserve the 500GB from scratch.
let me know if my assumption is correct?

Regards
Navin.

On Mon, Apr 13, 2020 at 11:10 AM navin srivastava <navin.altair at gmail.com<mailto:navin.altair at gmail.com>> wrote:
Hi Team,

i wanted to define a mechanism to request the local disk space while submitting the job.

we have dedicated /scratch of 1.2 TB file system for the execution of the job on each of the compute nodes other than / and other file system.
i have defined in slurm.conf as TmpFS=/scratch  and then wanted to use  #SBATCH --scratch =10GB   in the request.
but it seems it is not accepting this variable except /tmp.

Then i have opted the mechanism of gres.conf

GresTypes=gpu,scratch

and defined each node the scratch value and then requested using --gres=lscratch:10GB
but in this scenario if requesting both gres resources gpu as well as scratch it show me only scratch in my Gres resource not gpu.
does it using the gpu also as a gres resource?

could anybody please advice which is the correct method to achieve the same?
Also, is scratch will be able to calculate the actual usage value on the node.

REgards
Navin.

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