I am submitting a job on the debug queue on Niagara (Slurm scheduler) and am getting the following error:
SALLOC: error: _fork_command: Unable to exec command "/mypath/test.sh": Permission denied
I have checked the permissions of the file test.sh and it is readable, in fact I have been using the same file for serial jobs with no problems. I am trying to use mpirun for a parallel job and that's when I get the error.
My shell script is as follows:
#!/bin/bash
#SBATCH --account= xxxx
#SBATCH --nodes=2
#SBATCH --ntasks=160
#SBATCH --time=3:30:00
#SBATCH --job-name "sNucRNASeq"
pushd /mypath/
mpirun --np 4 R --no-save < Rscript test.R
Rscript test.R
I have tried chmod -rwx test.sh, it did not make a difference.
Am I missing something with regards to letting all the processors access the file? How can I by-pass the error?
The test.R script referred to above is pretty simple:
library(pbdMPI)
init()
rank<-comm.rank()
size<-comm.size()
myfiles<-load("ListofFiles.RData")
y <- scatter(lapply(myfiles, readRDS))
comm.print(str(y))
finalize()
Related
I am executing an R script on a cluster, using the following sbatch file:
#!/bin/bash
#SBATCH --job-name=ReconstructScans
#SBATCH --mem=4g
#SBATCH --account=XXXXXX
#SBATCH --array=1-1013%5
module load StdEnv/2020
module load gcc/9.3.0
module load r/4.0.2
srun Rscript ReconstructScans.R
ReconstructScans.R calls another R script, using
source("path_to_script.R", local=FALSE)
However, for some reason, the variables declared within path_to_script.R are not accessible to ReconstructScans.R. I get the object 'DataPath' not found error.
Why might this be happening? When I open an interactive R shell and source ReconstructScans.R, everything works fine. It's when ReconstructScans.R is executed through sbatch that the problem arises.
Is it a problem with how I'm executing it using:
srun Rscript ReconstructScans.R?
Thank you,
Mrinmayi
I am completely new to using SLURM to submit jobs to a HPC and I am facing a peculiar problem that I am not able to resolve.
I have a job.slurm file that contains the following bash script
#!/bin/bash
#SBATCH --job-name singularity-mpi
#SBATCH -N 1 # total number of nodes
#SBATCH --time=00:05:00 # Max execution time
#SBATCH --partition=partition-name
#SBATCH --output=/home/users/r/usrname/slurm-reports/slurm-%j.out
module load GCC/9.3.0 Singularity/3.7.3-Go-1.14 CUDA/11.0.2 OpenMPI/4.0.3
binaryPrecision=600 #Temporary number
while getopts i:o: flag
do
case "${flag}" in
i) input=${OPTARG}
;;
o) output=${OPTARG}
;;
*) echo "Invalid option: -$flag" ;;
esac
done
mpirun --allow-run-as-root singularity exec --bind /home/users/r/usrname/scratch/points_and_lines/:/usr/local/share/sdpb/ sdpb_2.5.1.sif pvm2sdp $binaryPrecision /usr/local/share/sdpb/$input /usr/local/share/sdpb/$output
The command pvm2sdp is just some specific kind of C++ executable that converts a XML file to a JSON file.
If I submit the .slurm file as
sbatch ./job.slurm -i /home/users/r/usrname/scratch/points_and_lines/xmlfile.xml -o /home/users/r/usrname/scratch/points_and_lines/jsonfile.json
it works perfectly. However, if I instead submit it using srun as
srun ./job.slurm -i /home/users/r/usrname/scratch/points_and_lines/xmlfile.xml -o /home/users/r/usrname/scratch/points_and_lines/jsonfile.json
I get the following error -
--------------------------------------------------------------------------
A call to mkdir was unable to create the desired directory:
Directory: /scratch
Error: Read-only file system
Please check to ensure you have adequate permissions to perform
the desired operation.
--------------------------------------------------------------------------
I have no clue why this is happening and how I can go about resolving the issue. I tried to mount /scratch as well but that does not resolve the issue.
Any help would be greatly appreciated since I need to use the srun inside another .slurm file that contains multiple other MPI calls.
I generally use srun after salloc. Let's say I have to run a python file on a GPU. I will use salloc to allocate a compute node.
salloc --nodes=1 --account=sc1901 --partition=accel_ai_mig --gres=gpu:2
Then I use this command to directly access the shell of the compute node.
srun --pty bash
Now, you can type any command as would do on your pc. You can try nvidia-smi. You can run Python files python code.py.
In your case, you can simply load modules manually and then run your mpirun command after srun --pty bash. You don't need the job script.
One more thing, sbatch and srun are customised for each HPC, so we can't say what exactly is stopping you from running those commands.
At Swansea University, we are expected to use job scripts with the sbatch only. Have a look at my university's HPC tutorial.
Read this article to know the primary differences between both.
I am trying to get a very basic job array script working using Slurm job scheduler on a HPC. I am getting the error:
slurmstepd: error: execve(): Rscript: No such file or directory
This is similar to this but I am not using any export commands so this isn't the cause here. Some sources say it could be something to do with creating these scripts in Windows so the line ends will not work for Unix. Could this be the issue? If so how can I check for this?
My shell script:
#!/bin/bash
# Example of running R script with a job array
#SBATCH --nodes=1
#SBATCH --array=1-10 # how many tasks in the array
#SBATCH --ntasks-per-node=10
#SBATCH -o hello-%j-%a.txt
#SBATCH --mail-user=user#email.address
# Load software
module load R/4.0.0-foss-2020a
# Run R script with a command line argument
srun Rscript hello.R $SLURM_ARRAY_TASK_ID
The script -hello.R is:
#!/usr/bin/env
# Rscript
# accept command line arguments and save them in a list called args
args = commandArgs(trailingOnly=TRUE)
# print task number
print(paste0('Hello! I am a task number: ', args[1]))
Thanks to some offline help I have got an answer to my question. Seems I didn't need to use srun in the shell script and needed to include Rscript in the shebang line in hello.R
Shell script is:
#!/bin/bash
# Example of running R script with a job array
#SBATCH --nodes=1
#SBATCH --array=1-10 # how many tasks in the array
#SBATCH --ntasks-per-node=10
#SBATCH -o hello-%j-%a.txt
#SBATCH --mail-user=tclewis1#sheffield.ac.uk
# Load software
module load R/4.0.0-foss-2020a
# Run R script with a command line argument
Rscript hello.R $SLURM_ARRAY_TASK_ID
And hello.R is now:
#!/usr/bin/env/Rscript
# accept command line arguments and save them in a list called args
args = commandArgs(trailingOnly=TRUE)
# print task number
print(paste0('Hello! I am a task number: ', args[1]))
I'm trying to run an MPI application with a specific task/node configuration. I need to run a total of 8 MPI tasks 4 of which on one node and 4 on another node.
This is the script file I'm using:
#!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --nodes=2
#SBATCH --ntasks=8
#SBATCH --ntasks-per-node=4
#SBATCH --ntasks-per-socket=1
#SBATCH --cpus-per-task=4
module load autoload scalapack/2.0.2--intelmpi--2018--binary intel/pe-xe-2018--binary
srun <path_to_bin> <options>
I then run this with sbatch:
sbatch mpi_test.sh
but I continue to get this error:
sbatch: error: Batch job submission failed: Requested node
configuration is not available
How can I modify this piece of code to make it run? I'm surely missing something, but I cannot figure what.
I'm using IntelMPI and slurm 20.02
This can be due to the wrong parameters.
Potential issue could be in the following lines:
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=4
If there is not enough cpus that satisfy the requirement. ie. if there is less than 16cores in a single node the above error will be shown.
#SBATCH --ntasks-per-socket=1
As in the comment pointed out by damienfrancois, it can be an issue with the number of sockets. If there are no four sockets, then the same error will also be shown.
As a simple step, you can comment out "#SBATCH --ntasks-per-socket=1" the line and run the batch script. If it fails, then the issue can be due to the invalid mapping of tasks to cpu.
More information about the environment is needed for further analysis.
I try to submit a R script to SLURM in CentOS 7, like this:
#!/bin/bash
#SBATCH -J test
#SBATCH -o test.out
#SBATCH -p compute
#SBATCH --qos=normal
#SBATCH -N 1
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=1
#SBATCH --job-name=rtest
Rscript --vanilla Rhelp.R
Then system will return a jobid, but the R script does not work. I can assure this script can run in command line. Then I have found in test.out, like this:
error while loading shared libraries: libicuuc.so.50:
cannot open shared object file: No such file or directory
I am a freshman in SLURM and Linux, thx!
It looks like the libicu RPM package is not installed on the compute nodes.
Just because it may be installed on the head node doesn't mean it's installed on the compute node(s). You could fire off the same ldconfig command in a Slurm job and view the results to confirm that's the case.
With the module avail command from the head node you list all available modules and loaded modules are marked somehow depending on your OS; for me they are marked with (L). All you need to do is load those loaded modules from your file script each of which is invoked with the line
module load path_to_module. Whereas, path_to_module is as is indicated with the previous command module avail.
Or without resorting to module avail you could use module list for currently loaded modules.