It is possible to set different maximum allocation times for jobs started with sbatch and with srun? Or will both the script submitted with sbatch or srun respect the MaxTime of the partition?
I looked in the documentation, but I didn't find anything that makes it clear if it's possible to do this. If anyone knows, I'll be very grateful :)
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I often run many jobs on slurm. Some finish faster than others. However, it is always hard to keep track which job is which. Can I give custom job names on slurm? If so what is the command on the batch script? Would that show up when I do squeue --me?
The parameter is --job-name (or -J), for instance:
#SBATCH --job-name=exp1_run2
The squeue output will list exp1_run2 for the corresponding job ID under column NAME.
My slurm job uses several nodes, and I want to know the maximum memory usage of each node for a running job. What can I do?
Right now, I can ssh into each node and do free -h -s 30 > memory_usage, but I think there must be a better way to do this.
The Slurm accounting will give you the maximum memory usage over time over all tasks directly. If that information is not sufficient, you can setup profiling following this documentaiton and you will receive from Slurm the full memory usage of each process as a time series for the duration of the job. You can then aggregate per node, find the maximum, etc.
Let's say I want to submit a slurm job just assigning the total amount of tasks (--ntasks=someNumber), without specifying the number of nodes and the tasks per node. Is there a way to know within the launched slurm script how many cores are assigned by slurm for each of the reserved nodes? I need to know this info to properly create a machinefile for the program I'm launching, that must be structured like this:
node02:7
node06:14
node09:3
Once the job is launched, the only way I figured out to see what cores have been allocated on the nodes is using the command:
scontrol show jobid -dd
In its output the abovementioned info is stored (together with plenty of other details).
Is there a better way to get this info?
The way the srun documentation illustrates creating a machine file is by running srun hostname. To get the output you want you could run
srun hostname -s | sort | uniq -c | awk '{print $2":"$1}' > $MACHINEFILE
You should check the documentation of your program to see if it accepts a machine file with repetitions rather than a suffix count. If so you can simplify the command as
srun hostname -s > $MACHINEFILE
And of course the first step is actually to make sure you indeed need a machine file in the first place as many parallel programs/libraries have Slurm support and can gather the needed information from the environment variables setup by Slurm upon job start.
I would like to distribute my job evenly across multiple nodes and have specified the --distribution=cyclic in my sbatch file, but slurm ignores that and uses the block distribution instead.
Before, the tasks were distributing evenly across the nodes. From reading the docs, this is what I expect the default behavior to be, unless otherwise specified in slurm.conf.
Starting today, the tasks are clustering on the first node with only one task on each of the other nodes. I've obviously changed something in the config, but can't figure out where to fix it. I did make a change to the image for the compute nodes and rebooted them today.
When I try to stop the slurmctld on the head node, it is restarted immediately by my Bright Cluster Manager monitor. Not sure if this is preventing configuration updates or not.
I've investigated the slurm.conf file but it looks OK. I've tried both SelectTypeParameters=CR_Core and CR_CPU but get the same result.
To try and work around this I added the --distribution=cyclic to my sbatch file, but slurm is still allocation using the 'block' method. But adding this to the sbatch should not be necessary, at leas according to my understanding of the docs.
Here are the relevant lines from slurm.conf and my sbatch script:
# RESOURCES
SelectType=select/cons_res
SelectTypeParameters=CR_Core
# Node Description
NodeName=DEFAULT Sockets=2 CoresPerSocket=20 ThreadsPerCore=1
# Scheduler
SchedulerType=sched/backfill
#SBATCH --ntasks=12
#SBATCH --nodes=3
#SBATCH --distribution=cyclic:cyclic
I would expect the tasks to be distributed evenly between the nodes, with 4 tasks on each of the 3 nodes.
Here is how the tasks are actually getting distributed:
NODELIST STATE CPUS(A/I/O/T) MEMORY TMP_DISK REASON
compute001 mixed 10/30/0/40 192006 2038 none
compute002 mixed 1/39/0/40 192006 2038 none
compute003 mixed 1/39/0/40 192006 2038 none
compute004 idle 0/40/0/40 192006 2038 none
According to https://slurm.schedmd.com/sbatch.html, the distribution flag is only useful for srun:
Specify alternate distribution methods for remote processes. In sbatch, this only sets environment variables that will be used by subsequent srun requests.
(As to why it's like this… I have no idea. But it does appear it's by design.)
Depending on your configuration, you may be able to approximate what you want by setting SelectType=cons_res or cons_tres and SelectTypeParameters=CR_LLN. If either of these parameters changed recently, that might be the reason the behavior changed, as well.
I managed to manually distribute my processes across the nodes by modifying the sbatch file to limit the number of tasks assigned to each node:
#SBATCH --ntasks=12
#SBATCH --nodes=3
#SBATCH --tasks-per-node=4
This results in the expected distribution of the tasks across the nodes:
NODELIST STATE CPUS(A/I/O/T) MEMORY TMP_DISK REASON
compute001 mixed 4/36/0/40 192027 2038 none
compute002 mixed 4/36/0/40 192027 2038 none
compute003 mixed 4/36/0/40 192027 2038 none
compute004 idle 0/40/0/40 192027 2038 none
I have set of an array job as follows:
sbatch --array=1:100%5 ...
which will limit the number of simultaneously running tasks to 5. The job is now running, and I would like to change this number to 10 (i.e. I wish I'd run sbatch --array=1:100%10 ...).
The documentation on array jobs mentions that you can use scontrol to change options after the job has started. Unfortunately, it's not clear what this option's variable name is, and I don't think it is listed in the documentation of the sbatch command here.
Any pointers well received.
You can change the array throttling limit with the following command:
scontrol update ArrayTaskThrottle=<count> JobId=<jobID>