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QUESTION
I am trying to run a simple parallel program on a SLURM cluster (4x raspberry Pi 3) but I have no success. I have been reading about it, but I just cannot get it to work. The problem is as follows:
I have a Python program named remove_duplicates_in_scraped_data.py. This program is executed on a single node (node=1xraspberry pi) and inside the program there is a multiprocessing loop section that looks something like:
...ANSWER
Answered 2021-Jun-15 at 06:17Pythons multiprocessing package is limited to shared memory parallelization. It spawns new processes that all have access to the main memory of a single machine.
You cannot simply scale out such a software onto multiple nodes. As the different machines do not have a shared memory that they can access.
To run your program on multiple nodes at once, you should have a look into MPI (Message Passing Interface). There is also a python package for that.
Depending on your task, it may also be suitable to run the program 4 times (so one job per node) and have it work on a subset of the data. It is often the simpler approach, but not always possible.
QUESTION
I am playing with a cluster using SLURM on AWS. I have defined the following parameters :
...ANSWER
Answered 2021-Jun-11 at 14:41In Slurm the number of tasks is essentially the number of parallel programs you can start in your allocation. By default, each task can access one CPU (which can be core or thread, depending on config), which can be modified with --cpus-per-task=#
.
This in itself does not tell you anything about the number of nodes you will get. If you just specify --ntasks
(or just -n
), your job will be spread over many nodes, depending on whats available. You can limit this with --nodes #min-#max/--nodes #exact
.
Another way to specify the number of tasks is --ntasks-per-node
, which does exactly what is says and is best used in conjunction with --nodes
. (not with --ntasks
, otherwise it's the max number of tasks per node!)
So, if you want three nodes with 72 tasks (each with the one default CPU), try:
QUESTION
I need to submit a slurm array that will run the same script 18000 times (for independent genes), and I wanted to do this in a way that won't cause problems for my Uni's cluster.
Currently, the MaxArraySize
set by the admins is 2048
. I was going to manually set my options like:
First array script:
...ANSWER
Answered 2021-Jun-11 at 11:31You can submit two jobs with
QUESTION
What is the proper way of configuring jupyter on a server with slurm? After reading the docs, I am excecuting my python script through slurm like this (I am not sure if this is valid):
...ANSWER
Answered 2021-Jun-11 at 11:20This is the correct way to request an interactive session on a compute node with an rtx2080ti GPU. But as Slurm tells you, your job has been submitted, and srun
will block until Slurm finds 14 CPUs, 64GB and a GPU available for you. Until then, squeue
will show your job as pending (PD
).
Running htop
will only show you the processes running on the login node, you will not see the process you submitted unless your cluster has only one node that happens to be the login node as well.
QUESTION
please would you help me with your suggestions on the following :
<> I am using an account on a SLURM cluster where the storage space of my home directory (ie. /home/user) is maximum 32 GB
<> I am running on the SLURM cluster a singularity container that is working only if the the input files are located in the home directory (/home/user that has 32 GB), instead of using any other location on the SLURM cluster (i.e. /labs/professor where we have 7TB)
The question is : is there any way to set up the large account space (i.e. /labs/professor) as a "home directory" in order for the singularity container to run ?
thanks a lot, with much appreciation,
-- bogdan
...ANSWER
Answered 2021-Jun-07 at 03:13You can change variable HOME
as you like (but i wont recommend that unless you know what things are gonna change)
But simpler way is to mane soft links for the directories you like, which i personally do.
QUESTION
I am new to HPC and SLURM especially, and i ran into some troubles.
I was provided with acces to a HPC cluster with 32 CPUs on each node. In order to do the needed calculations I made 12 Python multiprocessing Scripts, where each Script uses excactly 32 CPU's. How, instead of starting each Script manually in the interactive modus ( which is also an option btw. but it takes a lot of time) I decided to write a Batch Script in order to start all my 12 Scripts automatically.
//SCRIPT//
#!/bin/bash
#SBATCH --job-name=job_name
#SBATCH --partition=partition
#SBATCH --nodes=1
#SBATCH --time=47:59:59
#SBATCH --export=NONE
#SBATCH --array=1-12
module switch env env/system-gcc module load python/3.8.5
source /home/user/env/bin/activate
python3.8 $HOME/Script_directory/Script$SLURM_ARRAY_TASK_ID.py
exit
//UNSCRIPT//
But as far as i understand, this script would start all of the Jobs from the Array on the same node and thus the underlying python scripts might start a "fight" for the available CPU's and thus slow down.
How should i modify my bash file in Order to start each task from the array on a separate node?
Thanks in advance!
...ANSWER
Answered 2021-Jun-03 at 11:17This script will start 12 independent jobs, possibly on 12 distinct nodes at the same time, or all 12 in sequence on the same node or any other combination depending on the load of the cluster.
Each job will run the corresponding Script$SLURM_ARRAY_TASK_ID.py
script. There will be no competition for resources.
Note that if nodes are shared in the cluster, you would add the --exclusive
parameter to request whole nodes with their 32 CPUs.
QUESTION
So I am running a slurm job across 2 laptops (2 nodes), and I notice both laptop gets insanely laggy, to the point that the mouse could not even move. When I uses htop I saw the job was using 4 cores in 100% usage. I know for sure that the job does not take up that many cpu usage. How do I make slurm so that it uses only the required amount of cpu power?
...ANSWER
Answered 2021-Jun-01 at 12:01Slurm does not put any additional load onto the CPUs of your node. Besides what it needs for slurmd/slurmstepd, which is not much. If your job has access to four cores and you only use one, the others will be idle.
Maybe your program does something unexpected?
QUESTION
I have an aws HPC auto scale cluster managed by slurm, I can submit jobs using sbatch, however I want to use spraklyr on this cluster so that slurm increases the cluster size based on the workload of the sparklyr code in the R script. Is this possible?
...ANSWER
Answered 2021-May-24 at 11:07Hi Amir is there a reason you are using slurm here? Sparklyr has better integration with Apache Spark and it would be advisable to run it over a spark cluster. You can follow this Blog to know the steps to setup this up with Amazon EMR which is a Service to run Spark cluster on AWS - https://aws.amazon.com/blogs/big-data/running-sparklyr-rstudios-r-interface-to-spark-on-amazon-emr/
QUESTION
is it possible to use variable expansion in #SBATCH
lines in slurm? for instance I want to have line below:
ANSWER
Answered 2021-May-22 at 07:00No, this isn't possible. But you can overwrite the scripts default --array
by giving it explicitly on the sbatch
command line.
QUESTION
I'm new to SLURM and I'm trying to do something very natural: I have a compiled C program, off.exe
, which takes one variable as input, and I want to run it several times in parallel, each with a different value of the input parameter.
I thought I could use the %a
array iterator as input:
ANSWER
Answered 2021-May-18 at 06:05$a
, %j
etc. are replacement symbols for filenames, for example in the names of the output and error files recorded by Slurm. For your job arrays, you need to use one of Slurm's output environment variables, probably $SLURM_ARRAY_TASK_ID
. You can find the full list in the manpage for sbatch
.
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