- slurm-users - lists.schedmd.com

Re: Restricting local disk storage of jobs
by Tim Schneider 07 Feb '24

07 Feb '24

Hey Jeffrey, thanks for this suggestion! This is probably the way to go if one can find a way to access GRES in the prolog. I read somewhere that people were calling scontrol to get this information, but this seems a bit unclean. Anyway, if I find some time I will try it out. Best, Tim On 2/6/24 16:30, Jeffrey T Frey wrote: > Most of my ideas have revolved around creating file systems on-the-fly > as part of the job prolog and destroying them in the epilog. The > issue with that mechanism is that formatting a file system (e.g. > mkfs.<type>) can be time-consuming. E.g. formatting your local > scratch SSD as an LVM PV+VG and allocating per-job volumes, you'd > still need to run a e.g. mkfs.xfs and mount the new file system. > > > ZFS file system creation is much quicker (basically combines the LVM + > mkfs steps above) but I don't know of any clusters using ZFS to manage > local file systems on the compute nodes :-) > > > One /could/ leverage XFS project quotas. E.g. for Slurm job 2147483647: > > > *[root@r00n00 /]# mkdir /tmp-alloc/slurm-2147483647* > *[root@r00n00 /]# xfs_quota -x -c 'project -s -p > /tmp-alloc/slurm-2147483647 2147483647' /tmp-alloc* > Setting up project 2147483647 (path /tmp-alloc/slurm-2147483647)... > Processed 1 (/etc/projects and cmdline) paths for project > 2147483647 with recursion depth infinite (-1). > *[root@r00n00 /]# xfs_quota -x -c 'limit -p bhard=1g 2147483647' > /tmp-alloc* > *[root@r00n00 /]# cd /tmp-alloc/slurm-2147483647* > *[root@r00n00 slurm-2147483647]# dd if=/dev/zero of=zeroes bs=5M > count=1000* > dd: error writing ‘zeroes’: No space left on device > 205+0 records in > 204+0 records out > 1073741824 bytes (1.1 GB) copied, 2.92232 s, 367 MB/s > > : > > [root@r00n00 /]# rm -rf /tmp-alloc/*slurm-2147483647* > [root@r00n00 /]# *xfs_quota -x -c 'limit -p bhard=0 2147483647' > /tmp-alloc* > > > Since Slurm jobids max out at 0x03FFFFFF (and 2147483647 = 0x7FFFFFFF) > we have an easy on-demand project id to use on the file system. Slurm > tmpfs plugins have to do a mkdir to create the per-job directory, > adding two xfs_quota commands (which run in more or less O(1) time) > won't extend the prolog by much. Likewise, Slurm tmpfs plugins have to > scrub the directory at job cleanup, so adding another xfs_quota > command will not do much to change their epilog execution times. The > main question is "where does the tmpfs plugin find the quota limit for > the job?" > > > > > >> On Feb 6, 2024, at 08:39, Tim Schneider via slurm-users >> <slurm-users(a)lists.schedmd.com> wrote: >> >> Hi, >> >> In our SLURM cluster, we are using the job_container/tmpfs plugin to >> ensure that each user can use /tmp and it gets cleaned up after them. >> Currently, we are mapping /tmp into the nodes RAM, which means that >> the cgroups make sure that users can only use a certain amount of >> storage inside /tmp. >> >> Now we would like to use of the node's local SSD instead of its RAM >> to hold the files in /tmp. I have seen people define local storage as >> GRES, but I am wondering how to make sure that users do not exceed >> the storage space they requested in a job. Does anyone have an idea >> how to configure local storage as a proper tracked resource? >> >> Thanks a lot in advance! >> >> Best, >> >> Tim >> >> >> -- >> slurm-users mailing list -- slurm-users(a)lists.schedmd.com >> To unsubscribe send an email to slurm-users-leave(a)lists.schedmd.com >

2 1

scheme for protected GPU jobs from preemption
by Paul Raines 06 Feb '24

06 Feb '24

After using just Fairshare for over a year on our GPU cluster, we have decided it is not working for us for what we really want to achieve among our groups. We have decided to look at preemption. What we want is for users to NOT have a #job/GPU maximum (if they are only person on the cluster they should be able to use it all), but if another user comes to the "full" cluster they should immediately be able to run some jobs. Thus preemption is needed. In our scheme we want * users to have N protected GPU jobs that cannot be preempted where N is the number of GPUs allocated. * N may not be the same for all users. Some priviledged users get more. * jobs pending in the queue will have lower priority dependent on the number of GPUs allocated to running jobs. Maybe doable somehow with PriorityWeightJobSize though not sure how. * Jobs over N are subject to preemption (and requeued if --requeue is given) with shortest running jobs of the user with most unprotected GPUs preempted first. * another complication is we have a variety of different GPUs and users may ask for specific ones which can limit what unprotected GPU jobs are available for preemption My first attempt to do this in SLURM was to just create two partitions, GPU and GPU-req, with different PriorityTier values and the later partition have PreemptMode=REQUEUE. But N would be set by a MaxTRES on the first partition and be the same for everyone and we need it to be INDEPENDENT for each user. Also users would have to "think" about which partition to submit jobs to. And users want their longest running "unprotected" job to be able to be PROMOTED to a "protected" jobs automatically when a "protected" job finishes. However slurm does not allow running jobs to move between partitions. I am trying to figure out QOS pre-emption which might solve the independent N per user issue but I don't think it will solve the promotion issue. Any ideas how this scheme might be possible in SLURM? Otherwise I might have to write a complicated cron job that tries to do it all "outside" of SLURM issuing scontrol commands. --------------------------------------------------------------- Paul Raines http://help.nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

1 0

Restricting local disk storage of jobs
by Tim Schneider 06 Feb '24

06 Feb '24

Hi, In our SLURM cluster, we are using the job_container/tmpfs plugin to ensure that each user can use /tmp and it gets cleaned up after them. Currently, we are mapping /tmp into the nodes RAM, which means that the cgroups make sure that users can only use a certain amount of storage inside /tmp. Now we would like to use of the node's local SSD instead of its RAM to hold the files in /tmp. I have seen people define local storage as GRES, but I am wondering how to make sure that users do not exceed the storage space they requested in a job. Does anyone have an idea how to configure local storage as a proper tracked resource? Thanks a lot in advance! Best, Tim

3 2

Re: [ext] Restricting local disk storage of jobs
by Tim Schneider 06 Feb '24

06 Feb '24

Hi Magnus, I understand. Thanks a lot for your suggestion. Best, Tim On 06.02.24 15:34, Hagdorn, Magnus Karl Moritz wrote: > Hi Tim, > in the end the InitScript didn't contain anything useful because > > slurmd: error: _parse_next_key: Parsing error at unrecognized key: > InitScript > > At this stage I gave up. This was with SLURM 23.02. My plan was to > setup the local scratch directory with XFS and then get the script to > apply a project quota, ie quota attached to the directory. > > I would start by checking if slurm recognises the InitScript option. > > Regards > magnus > > On Tue, 2024-02-06 at 15:24 +0100, Tim Schneider wrote: >> Hi Magnus, >> >> thanks for your reply! If you can, would you mind sharing the >> InitScript >> of your attempt at getting it to work? >> >> Best, >> >> Tim >> >> On 06.02.24 15:19, Hagdorn, Magnus Karl Moritz wrote: >>> Hi Tim, >>> we are using the container/tmpfs plugin to map /tmp to a local NVMe >>> drive which works great. I did consider setting up directory >>> quotas. I >>> thought the InitScript [1] option should do the trick. Alas, I >>> didn't >>> get it to work. If I remember correctly, slurm complained about the >>> option being present. In the end we recommend our users to make >>> exclusive use a node if they are going to use a lot of local >>> scratch >>> space. I don't think this happens very often if at all. >>> Regards >>> magnus >>> >>> [1] >>> https://slurm.schedmd.com/job_container.conf.html#OPT_InitScript >>> >>> >>> On Tue, 2024-02-06 at 14:39 +0100, Tim Schneider via slurm-users >>> wrote: >>>> Hi, >>>> >>>> In our SLURM cluster, we are using the job_container/tmpfs plugin >>>> to >>>> ensure that each user can use /tmp and it gets cleaned up after >>>> them. >>>> Currently, we are mapping /tmp into the nodes RAM, which means >>>> that >>>> the >>>> cgroups make sure that users can only use a certain amount of >>>> storage >>>> inside /tmp. >>>> >>>> Now we would like to use of the node's local SSD instead of its >>>> RAM >>>> to >>>> hold the files in /tmp. I have seen people define local storage >>>> as >>>> GRES, >>>> but I am wondering how to make sure that users do not exceed the >>>> storage >>>> space they requested in a job. Does anyone have an idea how to >>>> configure >>>> local storage as a proper tracked resource? >>>> >>>> Thanks a lot in advance! >>>> >>>> Best, >>>> >>>> Tim >>>> >>>>

1 0

Re: [ext] Restricting local disk storage of jobs
by Tim Schneider 06 Feb '24

06 Feb '24

Hi Magnus, thanks for your reply! If you can, would you mind sharing the InitScript of your attempt at getting it to work? Best, Tim On 06.02.24 15:19, Hagdorn, Magnus Karl Moritz wrote: > Hi Tim, > we are using the container/tmpfs plugin to map /tmp to a local NVMe > drive which works great. I did consider setting up directory quotas. I > thought the InitScript [1] option should do the trick. Alas, I didn't > get it to work. If I remember correctly, slurm complained about the > option being present. In the end we recommend our users to make > exclusive use a node if they are going to use a lot of local scratch > space. I don't think this happens very often if at all. > Regards > magnus > > [1] > https://slurm.schedmd.com/job_container.conf.html#OPT_InitScript > > > On Tue, 2024-02-06 at 14:39 +0100, Tim Schneider via slurm-users wrote: >> Hi, >> >> In our SLURM cluster, we are using the job_container/tmpfs plugin to >> ensure that each user can use /tmp and it gets cleaned up after them. >> Currently, we are mapping /tmp into the nodes RAM, which means that >> the >> cgroups make sure that users can only use a certain amount of storage >> inside /tmp. >> >> Now we would like to use of the node's local SSD instead of its RAM >> to >> hold the files in /tmp. I have seen people define local storage as >> GRES, >> but I am wondering how to make sure that users do not exceed the >> storage >> space they requested in a job. Does anyone have an idea how to >> configure >> local storage as a proper tracked resource? >> >> Thanks a lot in advance! >> >> Best, >> >> Tim >> >>

2 1

Starting a job after a file is created in previous job (dependency looking for soluton)
by Amjad Syed 06 Feb '24

06 Feb '24

Hello I have the following scenario: I need to submit a sequence of up to 400 jobs where the even jobs depend on the preceeding odd job to finish and every odd job depends on the presence of a file generated by the preceding even job (availability of the file for the first of those 400 jobs is guaranteed). If I just submit all those jobs via a loop using dependencies, then I end up with a lot of pending jobs who might later not even run because no output file has been produced by the preceding jobs. Is there a way to pause the submission loop until the required file has been generated so that at most two jobs are submitted at the same time? Here is a sample submission script showing what I want to achieve. for i in {1..200}; do FILE=GHM_paramset_${i}.dat # How can I pause the submission loop until the FILE has been created???? #if test -f "$FILE"; then jobid4=$(sbatch --parsable --dependency=afterok:$jobid3 job4_sub $i) jobid3=$(sbatch --parsable --dependency=afterok:$jobid4 job3_sub $i) #fi done Any help will be appreciated Amjad

3 2

SLURM configuration for LDAP users
by Richard Chang 05 Feb '24

05 Feb '24

Hi, I am a little new to this, so please pardon my ignorance. I have configured slurm in my cluster and it works fine with local users. But I am not able to get it working with LDAP/SSSD authentication. User logins using ssh are working fine. An LDAP user can login to the login, slurmctld and compute nodes, but when they try to submit jobs, slurmctld logs an error about invalid account or partition for user. Someone said we need to add the user manually into the database using the sacctmgr command. But I am not sure we need to do this for each and every LDAP user. Yes, it does work if we add the LDAP user manually using sacctmgr. But I am not convinced this manual way is the way to do. The documentation is not very clear about using LDAP accounts. Saw somewhere in the list about using UsePAM=1 and copying or creating a softlink for slurm PAM module under /etc/pam.d . But it didn't work for me. Saw somewhere else that we need to specifying LaunchParameters=enable_nss_slurm in the slurm.conf file and put slurm keyword in passwd/group entry in the /etc/nsswitch.conf file. Did these, but didn't help either. I am bereft of ideas at present. If anyone has real world experience and can advise, I will be grateful. Thank you, Richard

4 4

timeout of get_user_env does not obey time limit
by urbanjost 03 Feb '24

03 Feb '24

If I use the sbatch(1) option --export=NONE or wipe the environment with "env -i /usr/bin/sbatch ..." or use --export=NIL then the environment is not properly constructed and I see the message in the /var/log/*slurm* files: [2024-02-03T11:50:33.052] _get_user_env: get env for user jsu here [2024-02-03T11:52:33.152] timeout waiting for /bin/su to complete [2024-02-03T11:52:34.152] error: Failed to load current user environment variables [2024-02-03T11:52:34.153] error: _get_user_env: Unable to get user's local environment, running only with passed environment This occurs at 120 seconds not matter if I add --get-user-env=3600 or adjust many slurm.conf time-related parameters. It is easy to reproduce by adding "sleep 100" into a .cshrc file and sbatch(1) the file #!/bin/csh #SBATCH --export=NONE --propagate=NONE --get-user-env=3600L printenv HOME printenv USER printenv PATH env I have adjust MANY time-related limits in the slurm.conf file to no avail. When the system is unresponsive or heavily loaded or users have prologues that set up complex environments via module commands (which can be notoriously slow) the jobs are failing or producing errors. If I configure Slurm so that jobs that timeout requeue instead of running then a user with a slow login setup can submit a large number of jobs and basically close down a cluster because this option not only requeues jobs that fail but puts the node it occurred on in a DRAIN state. We see this as very dangerous as by defaults jobs proceed to execute even when their environment is not properly constructed. I can see that "slurmrestd getenv" and the procedure get_user_env(3c) are involved, but a preliminary scan of the code looked like the --get-user-env=NNNN value was being parsed, and I did not see a reason the setup always times out at 120 seconds (at least on my system). Does anyone know how to get the time allowed to get the default user environment to use the value on the --get-user-env option when no environment is being exported to a job? This is showing up sporadically and causing intermittent failures that are very confusing and disturbing to the users it occurs with. Sent with [Proton Mail](https://proton.me/) secure email.

1 0

selecting job-specific log messages
by urbanjost 03 Feb '24

03 Feb '24

log files use many strings to identify job, including not having a jobID in the message NUMBER=$SLURM_JOBID egrep "\.\<$NUMBER\>\] |\<$NUMBER\>\.batch|jobid \<$NUMBER\>|JObId=\<$NUMBER\>|job id \<$NUMBER\>|job\.\<$NUMBER\>|job \<$NUMBER\>|jobid \[\<$NUMBER\>\]|task_p_slurmd_batch_request: \<$NUMBER\>" /var/log/slurm* Even that misses cruciall data that does not even contain the jobid [2024-02-03T11:50:33.052] _get_user_env: get env for user jsu here [2024-02-03T11:52:33.152] timeout waiting for /bin/su to complete [2024-02-03T11:52:34.152] error: Failed to load current user environment variables [2024-02-03T11:52:34.153] error: _get_user_env: Unable to get user's local environment, running only with passed environment It would be very useful if all messages related to a job had a consistent string in them for grepping the log files; even better might be a command like "scontrol show jobid=NNNN log_messages But I could not find what I wanted (an easy way to find all daemon log messages related to a specific job). I would find it particularly useful if there were a way to automatically append such information to the stdout of the job at job termination so users would automatically get information about job failures or warnings. Is there such a feature available I have missed? Sent with [Proton Mail](https://proton.me/) secure email.

1 0

after upgrade to 23.11.1 nodes stuck in completion state
by Paul Raines 01 Feb '24

01 Feb '24

I finally had downtime on our cluster running 20.11.3 and decided to upgrade SLURM. All daemons were stopped on nodes and master. Rocky 8 Linux OS was updated but not changed configuration-wise in anyway. On the master, when I first installed 23.11.1 and tried to run slurmdbd -D -vvv at the command line, it balked as the more than 2 major version jump. I then installed 22.05.6 and run slurmdbd -D -vvv which took a long time but completed fine. I reinstalled 23.11.1 and did slurmdbd -D --vvv which went quick. I stopped it then ran slurmdbd normally with systemctl. When I ran slurmctld it complained about incompatable state files. I didn't care about loosing state so ran with the -i option to ignore. Seemed happy. I then started up slurmd on my various GPU and non-GPU nodes. I ran a test interactive job just to see if I would get a shell with expected SLURM environment on the nodes and it worked. Except on the GPU nodes I got errors about not being able to get/set GPU frequences. I removed GpuFreqDef=medium from slurm.conf and that went away. I had my people start running jobs last night. This morning I come in and see a lot of nodes are stuck in completing state. All these are GPU nodes. For example on node 'sevilla' squeue reports JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 3679433 lcna100 sjob_123 sg1526 CG 8:29 1 sevilla 3679432 lcna100 sjob_123 sg1526 CG 8:35 1 sevilla 3679431 lcna100 sjob_123 sg1526 CG 8:42 1 sevilla In the slurmd.log on sevilla I see every minute the lines: [2024-01-28T09:37:52.003] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug: _rpc_terminate_job: uid = 1150 JobId=3679432 [2024-01-28T09:37:52.004] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug: _rpc_terminate_job: uid = 1150 JobId=3679431 [2024-01-28T09:37:52.004] debug2: Finish processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug: _rpc_terminate_job: uid = 1150 JobId=3679433 [2024-01-28T09:37:52.004] debug2: Finish processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T09:37:52.004] debug2: Finish processing RPC: REQUEST_TERMINATE_JOB Back at the time 3679433 was cancelled by the user I see [2024-01-28T00:27:48.658] debug2: Start processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T00:27:48.658] debug2: Processing RPC: REQUEST_TERMINATE_JOB [2024-01-28T00:27:48.658] debug: _rpc_terminate_job: uid = 1150 JobId=3679433 [2024-01-28T00:27:48.658] debug: credential for job 3679433 revoked [2024-01-28T00:27:48.658] debug: _rpc_terminate_job: sent SUCCESS for 3679433, waiting for prolog to finish [2024-01-28T00:27:48.658] debug: Waiting for job 3679433's prolog to complete On sevilla itself there are no processes currently running for user sg1526 so no sign of these jobs. There ARE processes running for user mu40 though [root@sevilla ~]# pgrep -f slurm_script | xargs -n1 pstree -p | grep ^slurm slurm_script(30691)---starter-suid(30764)-+-python3(30784)-+-{python3}(30817) slurm_script(30861)---starter-suid(30873)-+-python3(30888)-+-{python3}(30915) slurm_script(30963)---starter-suid(30975)-+-python3(30992)-+-{python3}(31020) [root@sevilla ~]# strings /proc/30691/cmdline /bin/sh /var/slurm/spool/d/job3679220/slurm_script /usr/bin/sacct -p --jobs=3679220 --format=JobID,User,ReqTRES,NodeList,Start,End,Elapsed,CPUTime,State,ExitCode JobID|User|ReqTRES|NodeList|Start|End|Elapsed|CPUTime|State|ExitCode| 3679220|mu40|billing=6,cpu=3,gres/gpu=1,mem=32G,node=1|sevilla|2024-01-27T22:33:27|2024-01-27T23:26:39|00:53:12|02:39:36|NODE_FAIL|1:0| 3679220.batch|||sevilla|2024-01-27T22:33:27|2024-01-27T23:26:39|00:53:12|02:39:36|CANCELLED|| 3679220.extern|||sevilla|2024-01-27T22:33:27|2024-01-27T23:26:39|00:53:12|02:39:36|CANCELLED|| The slurmd.log has at the time it started lines like: [2024-01-27T22:33:28.679] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30691, probably hasn't started yet or has already finished [2024-01-27T22:33:58.092] [3679220.extern] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30650, probably hasn't started yet or has already finished [2024-01-27T22:33:58.166] [3679220.batch] debug2: profile signaling type Task [2024-01-27T22:33:58.168] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30691, probably hasn't started yet or has already finished [2024-01-27T22:33:58.170] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30764, probably hasn't started yet or has already finished [2024-01-27T22:33:58.172] [3679220.batch] debug2: gpu/nvml: _get_gpuutil: Couldn't find pid 30784, probably hasn't started yet or has already finished ... [2024-01-27T22:46:39.018] debug: _step_connect: connect() failed for /var/slurm/spool/d/sevilla_3679220.4294967292: Connection refused [2024-01-27T22:46:39.018] debug: Cleaned up stray socket /var/slurm/spool/d/sevilla_3679220.4294967292 [2024-01-27T22:46:39.018] debug: _step_connect: connect() failed for /var/slurm/spool/d/sevilla_3679220.4294967291: Connection refused [2024-01-27T22:46:39.018] debug: Cleaned up stray socket /var/slurm/spool/d/sevilla_3679220.4294967291 [2024-01-27T22:46:39.018] _handle_stray_script: Purging vestigial job script /var/slurm/spool/d/job3679220/slurm_script then later at the time of termination [2024-01-27T23:26:39.042] debug: _rpc_terminate_job: uid = 1150 JobId=3679220 [2024-01-27T23:26:39.042] debug: credential for job 3679220 revoked [2024-01-27T23:26:39.042] debug2: No steps in jobid 3679220 to send signal 998 [2024-01-27T23:26:39.043] debug2: No steps in jobid 3679220 to send signal 18 [2024-01-27T23:26:39.043] debug2: No steps in jobid 3679220 to send signal 15 [2024-01-27T23:26:39.044] debug2: set revoke expiration for jobid 3679220 to 1706416119 UTS [2024-01-27T23:26:39.044] debug: Waiting for job 3679220's prolog to complete [2024-01-27T23:26:39.044] debug: Finished wait for job 3679220's prolog to complete [2024-01-27T23:26:39.068] debug: completed epilog for jobid 3679220 [2024-01-27T23:26:39.071] debug: JobId=3679220: sent epilog complete msg: rc = 0 So I have a node stuck in 'comp' state that claims to have jobs completing that are definite NOT running on the box BUT there are jobs running on the box that SLURM thinks are done --------------------------------------------------------------- Paul Raines http://help.nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

4 7

2025

2024