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Change your preferences any time. Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. I've written a python script that requires two arguments and works just fine when I run it on the command line with:.

This is an example of the script I'm using:. I've spent a lot of time trying to figure out exactly what is causing the core dumps, and this is what I've narrowed it down to. It only crashes when run from the batch script and only when I'm trying to run the script with arguments.

When I modify it to run without arguments, it runs properly. The problem was the node where my job was sent. I managed to check in which node my job run without errors with the command:. Learn more. Asked 4 years, 9 months ago.

Active 2 months ago. Viewed 4k times. I've written a python script that requires two arguments and works just fine when I run it on the command line with: pythonscript. This is an example of the script I'm using:!

Jiffy Jiffy 3 1 1 silver badge 3 3 bronze badges. Also does pythonscript. They're not in my working directory, and I'm still waiting to hear back from the HPC person. I've actually sorted out why the core dump is happening, and it has to do with trying to import a recently installed module.

It works fine on the login node but not on the compute node. I'm not sure at this point if the arguments are a problem or not. The python script does have the path to the executable hardcoded with hashbang. Active Oldest Votes. This may seem like a silly question, but is the pythonscript.

SLURM Job Submission Part 1 - Batch Scripts and Components

Also have you tried python pythonscript. Matt Matt 3 3 silver badges 16 16 bronze badges. Not a silly question at all. Yes, it's executable. I might actually end up deleting this question, because I've discovered where the illegal instruction is coming from, and it's not what I thought it was. It turned out to be a problem with a newly installed module on the compute node works fine on the login node. Once that problem is fixed and I'm sure that the arguments are no longer a problem, I'll remove this question.

Thanks for your response. I use the following and I can add any number of arguments. Satyajeet Patil Satyajeet Patil 11 1 1 bronze badge. Sign up or log in Sign up using Google. Sign up using Facebook.Job arrays offer a mechanism for submitting and managing collections of similar jobs quickly and easily; job arrays with millions of tasks can be submitted in milliseconds subject to configured size limits.

All jobs must have the same initial options e. Job arrays are only supported for batch jobs and the array index values are specified using the --array or -a option of the sbatch command. The option argument can be specific array index values, a range of index values, and an optional step size as shown in the examples below. Note that the minimum index value is zero and the maximum value is a Slurm configuration parameter MaxArraySize minus one.

Job arrays will have two additional environment variable set. A set of APIs has been developed to operate on an entire job array or select tasks of a job array in a single function call.

The function response consists of an array identifying the various error codes for various tasks of a job ID. If the job ID of a job array is specified as input to the scancel command then all elements of that job array will be cancelled.

Table of Contents

Alternately an array ID, optionally using regular expressions, may be specified for job cancellation. When a job array is submitted to Slurm, only one job record is created.

Additional job records will only be created when the state of a task in the job array changes, typically when a task is allocated resources or its state is modified using the scontrol command. An option of "--array" or "-r" has also been added to the squeue command to print one job array element per line as shown below. Use of the scontrol show job option shows two new fields related to job array support.

The JobID is a unique identifier for the job. The ArrayTaskID is the array index of this particular entry, either a single number of an expression identifying the entries represented by this job record e. Neither field is displayed if the job is not part of a job array.

The optional job ID specified with the scontrol show job or scontrol show step commands can identify job array elements by specifying ArrayJobId and ArrayTaskId with an underscore between them eg. The scontrol hold, holdu, release, requeue, requeuehold, suspend and resume commands can also either operate on all elements of a job array or individual elements as shown below. A job which is to be dependent upon an entire job array should specify itself dependent upon the ArrayJobID.

Since each array element can have a different exit code, the interpretation of the afterok and afternotok clauses will be based upon the highest exit code from any task in the job array. When a job dependency specifies the job ID of a job array: The after clause is satisfied after all tasks in the job array start. The afterany clause is satisfied after all tasks in the job array complete. The aftercorr clause is satisfied after the corresponding task ID in the specified job has completed successfully ran to completion with an exit code of zero.

The afterok clause is satisfied after all tasks in the job array complete successfully. The afternotok clause is satisfied after all tasks in the job array complete with at least one tasks not completing successfully.

sbatch arguments

The following Slurm commands do not currently recognize job arrays and their use requires the use of Slurm job IDs, which are unique for each array element: sbcast, sprio, sreport, sshare and sstat. The sacct, sattach and strigger commands have been modified to permit specification of either job IDs or job array elements. A new configuration parameter has been added to control the maximum job array size: MaxArraySize.

The smallest index that can be specified by a user is zero and the maximum index is MaxArraySize minus one.You just finished up a really cool analysis, and you need to scale it. In this tutorial, we will walk through a very simple method to do this.

sbatch arguments

You first have some script in R or Python. It likely reads in data, processes it, and creates a result. You will need to turn this script into an executable, meaning that it accepts variable arguments. R actually makes this very easy.

While there are advanced input parsers, you can retrieve your script inputs with just a few lines:. We are going to be using it in our work today! Python is just as easy! Instead of commandArgs, we use the sys module.

The same would look like this:. This would actually coincide to the name of your script. If you are interested in advanced input parsing, then you should look at argparse. You can read about our example using argparse for a module entrypoint hereor go directly to the gist.

But guess what? If you change a location, your script breaks. This generally means the following:. This also means you have a stricter quota, and should use it for scripts and valuables and not data.

Everything would be commit, and if you are a pro, you would have testing. If you have a more long term data storage resource e. Now, arguably if you have a small input file e. The trick here is that you want to create an organizational setup where you can always link an input object subject, sample, timepoint, etc.

In the data organization above, we see that our data is organized based on subjects LizardA and LizardB and you can imagine now having a programmatically defined input and output location for each:. What do you name these folders? There are many known data organization standards e. You then want to loop over some set of input variables for example, csv files with data. You can imagine doing this on your computer - each of the inputs would be processed in serial.

As a graduate student I liked having a record of what I had run, and an easy way to re-run any single job without needing to run my submission script again.

Before we make a job file, let me show you what it looks like:.If your work consists of a large number of tasks which differ only in some parameter, you can conveniently submit many tasks at once using a job array, also known as a task array or an array job.

You set the range of values with the --array parameter. This job will be scheduled as ten independent tasks. Each task has a separate time limit of 3 hours, and each may start at a different time on a different host. Using a job array instead of a large number of separate serial jobs has advantages for you and other users. A waiting job array only produces one line of output in squeue, making it easier for you to read its output. The scheduler does not have to analyze job requirements for each task in the array separately, so it can run more efficiently too.

Note that, other than the initial job-submission step with sbatchthe load on the scheduler is the same for an array job as for the equivalent number of non-array jobs. The cost of dispatching each array task is the same as dispatching a non-array job. You should not use a job array to submit tasks with very short run times, e.

Suppose you have multiple directories, each with the same structure, and you want to run the same script in each directory.

sbatch arguments

If the directories can be named with sequential numbers then the example above can be easily adapted. If the names are not so systematic, then create a file with the names of the directories, like so:.

There are several ways to select a given line from a file; this example uses sed to do so:. Jump to: navigationsearch. Other languages:. Namespaces Page Discussion. Views Read View source View history. Navigation Wiki Main Page. This page was last edited on 22 Januaryat HPC Home. Getting an account. Gentle Introduction to using HPC. Getting started on Prince. Prince How-to Articles.

Logging in. Clusters and Storage. Prince HPC. Dumbo Hadoop. Brooklyn OpenStack. Submitting jobs with sbatch. Available software. Building Software. Slurm Tutorial. Scratch Area Cleanup. Programming for Biologists.

Acknowledge Statement. Research Gallery. HPC People. HPC Policies. Request that a minimum of minnodes nodes be allocated to this job. Upon startup, sbatch will read and handle the options set in the following environment variables. Note that environment variables will override any options set in a batch script, and command line options will override any environment variables.

Set to "quiet" otherwise. Possible values two possible comma separated strings. The first possible string identifies the entity to be bound to: "threads", "cores", "sockets", "ldoms" and "boards".

As stated before there are several arguments that you can use to get your jobs to behave a specific way. This is not an exhaustive list, but some of the most widely used and many that you will will probably need to accomplish specific tasks. If --begin is not specified, sbatch assumes that the job should be run immediately. To define the working directory path to be used for the job --workdir option can be used. If it is not specified, the default working directory is the directory where sbatch command is executed.

To write standard output to a file, specify --output option of sbatch. To write standard error to a file, specify --error option. To illustrate the ability to hold execution of a specific job until another has completed, we will write two submission scripts.A batch job script contains the definitions for the resources to be reserved for the job and the commands the user wants to run.

The first line! These examples only use a small subset of the options. For a list of all possible options, see the Slurm documentation. This argument is mandatory. More information about billing. Time is provided using the format hh:mm:ss optionally d-hh:mm:sswhere d is days. The maximum time depends on the selected queue. When the time reservation ends, the job is terminated regardless of whether it is finished or not, so the time reservations should be sufficiently long.

A job consumes billing units according to its actual runtime. If the requested memory is exceeded, the job is terminated. After defining all required resources in the batch job script, set up the environment. Note that for modules to be available for batch jobs, they need to be loaded in the batch job script.

Serial and shared memory jobs need to be run within one computing node.

Thus, the jobs are limited by the hardware specifications available in the nodes. In Puhti, each node has two processors with 20 cores each, i.

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The Sbatch option --cpus-per-task is used the define the number of computing cores that the batch job task uses. In thread-based jobs, the --mem option is recommended for memory reservation. This option defines the amount of memory required per node. Note that if you use --mem-per-cpu option instead, the total memory request of the job will be the memory request multiplied by the number of reserved cores --cpus-per-task.

Thus, if you modify the number of cores, also check the memory reservation. In most cases, it is the most efficient to match the number of reserved cores to the number of threads or processes the application uses.

Check the documentation for application-specific details.

Requesting resources

Some applications use only one core by default, even if more are reserved. Some other applications may try to use all cores in the node even if only some are reserved. This way, the command does not need to be edited if the --cpus-per-task is changed. In MPI jobs, each task has its own memory allocation.

Thus, the tasks can be distributed between nodes. If more fine-tuned control is required, the exact number of nodes and number of tasks per node can be specified with --nodes and --ntasks-per-noderespectively.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service.

It only takes a minute to sign up. I have a R code that I want to execute on several nodes using Slurm, with each iteration of my paramater which goes on a node.

This is my Slurm code :. Then, for each iteration of iI want that one script which be executed on a node. I don't want to use jobs arrays because it doesn't work correctly on my cluster.

So, I want to create a bash loop which would look like this :. You want to include an srun within a for loop in order to requisition node within your script. If we assume you have five subsets, you can use something along the lines of:. This will allow these processes to run in parallel, and SLURM will wait until everything in that for loop completes.

You'll also need to make sure that your output file specification can be written to in parallel if you choose this route. You would have to add some code after the wait command to stitch your outputs back together into one large file. I believe you'll also want to specify a --nodes value in the sbatch file, indicating the total number of nodes your job will use.

Another option would be to include all of your job code in a shell script that takes command-line arguments, and call that from a for loop using srun within your sbatch file.

Sign up to join this community. The best answers are voted up and rise to the top. Home Questions Tags Users Unanswered. How to execute a script on several nodes using Slurm? Ask Question. Asked 11 months ago. Active 1 month ago. Viewed times. This is my Slurm code :!