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Queues
Slurm has queues to ..allocate ....In altamira, there are some queues configured. This table resume the main queues and the principal properties of each of them:
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| Directive | Description | Default value |
|---|---|---|
--job-name=value | The name of the job that appears in the batch queue | script_name |
--output=... | The name of the file to collect the standard output of the job. The %j part in the job directives will be sustitute by the job ID. | file-%j.out |
--error=... | The name of the file to collect the standard error of the job. The %j part in the job directives will be sustitute by the job ID. | file-%j.err |
--workdir=... | The working directory of your job (i.e. where the job will run). If not specified, it is the current working directory at the time the job was submitted. | submitting directory |
--qos=... | Quality of Service (or queue) where the job is allocated. By default, a queue is assigned for the user so this variable is not mandatory. | main |
--time=... | The limit of wall clock time. This is a mandatory field and you must set it to a value greater than the real execution time for your application and smaller than the time limits granted to the user. Notice that your job will be killed after the elapsed period. | qos default time limit |
--ntasks=... | The number of processes to alocated as parallel tasks. | 1 |
--cpus-per-task=... | Number of processors for each task. Without this option, the controller will just try to allocate one processor per task. The number of cpus per task must be between 1 and 16, since each node has 16 cores (one for each thread). | 1 |
--ntasks-per-node | The number of tasks allocated in each node. When an application uses more than 3.8 GB of memory per process, it is not possible to have 16 processes in the same node and its 64GB of memory. It can be combined with the cpus_per_task to allocate the nodes exclusively, i.e. to allocate 2, processes per node, set both directives to 2. The number of tasks per node must be between 1 and 16. | 1 |
--mem-per-cpu | Minimum memory required per allocated CPU. Default units are megabytes unless the SchedulerParameters configuration parameter includes the "default_gbytes" option for gigabytes. | DefMemPerCPU |
Job environment variables
There are also a few SLURM environment variables you can use in your scripts:
| Variable | Description |
|---|---|
SLURM_JOBID | Specifies the job ID of the executing job |
SLURM_NPROCS | Specifies the total number of processes in the job. Same as -n, --ntasks |
SLURM_NNODES | Is the actual number of nodes assigned to run your job |
SLURM_PROCID | Specifies the MPI rank (or relative process ID) for the current process. The range is from 0-(SLURM_NPROCS-1) |
SLURM_NODEID | Specifies relative node ID of the current job. The range is from 0-(SLURM_NNODES-1) |
SLURM_LOCALID | Specifies the node-local task ID for the process within a job |
SLURM_NODELIST | Specifies the list of nodes on which the job is actually running |
| SLURM_SUBMIT_DIR | The directory from which sbatch was invoked. |
SLURM_MEM_PER_CPU | Memory available per CPU used |
Job examples
Example for a sequential job:
| Code Block | ||
|---|---|---|
| ||
#!/bin/bash # #SBATCH --job-name=hello #SBATCH --output=hello.out # #SBATCH --ntasks=1 #SBATCH --time=10:00 # From here the job starts echo hostname sleep 60 |
Example for a parallel job:
| Code Block | ||
|---|---|---|
| ||
#/bin/bash # #SBATCH ---mem-per-cpu=100 job-name=hello #SBATCH --output=hello.out #SBATCH --ntasks=1 #SBATCH --time=10:00 # From here the job starts srun hostname srun sleep 60 |
Software
Modules Enviroment
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