calcoloscientifico:cluster:softwareapplicativo:relion
Differenze
Queste sono le differenze tra la revisione selezionata e la versione attuale della pagina.
| Entrambe le parti precedenti la revisioneRevisione precedenteProssima revisione | Revisione precedente | ||
| calcoloscientifico:cluster:softwareapplicativo:relion [22/04/2022 15:19] – [Table] fabio.spataro | calcoloscientifico:cluster:softwareapplicativo:relion [29/05/2023 11:55] (versione attuale) – federico.prost | ||
|---|---|---|---|
| Linea 3: | Linea 3: | ||
| === Short guide to using Relion (compiled with GNU tools) === | === Short guide to using Relion (compiled with GNU tools) === | ||
| - | Connect to the server [[calcoloscientifico: | + | Connect to the server [[calcoloscientifico: |
| + | using: | ||
| + | |||
| + | ssh -X nome.cognome@gui.hpc.unipr.it (with linux) | ||
| + | |||
| + | or | ||
| + | |||
| + | | ||
| Open a terminal and enter the following commands: | Open a terminal and enter the following commands: | ||
| Linea 11: | Linea 19: | ||
| newgrp: group '< | newgrp: group '< | ||
| - | [user@ui03 | + | (< |
| - | [user@ui03 | + | (< |
| - | [user@ui03 | + | (< |
| - | [user@ui03 | + | (< |
| - | Currently Loaded Modules: | + | (< |
| - | 1) gnu8/ | + | |
| - | 2) openmpi3/ | + | |
| - | [user@ui03 test]$ echo $RELION_QSUB_TEMPLATE | + | (< |
| - | / | + | |
| + | Currently Loaded Modules: | ||
| + | 1) gnu8/ | ||
| + | 2) libfabric/ | ||
| + | |||
| + | (< | ||
| + | / | ||
| - | [user@ui03 test]$ relion | + | (< |
| </ | </ | ||
| We assume that the directory | We assume that the directory | ||
| - | ''/ | + | ''/ |
| contains an example case to test how Relion works. | contains an example case to test how Relion works. | ||
| < | < | ||
| - | Replace < | + | Replace < |
| </ | </ | ||
| The file | The file | ||
| - | ''/ | + | ''/ |
| is the script to submit the job to the SLURM queue manager. | is the script to submit the job to the SLURM queue manager. | ||
| Linea 60: | Linea 72: | ||
| | Which GPUs to use: | | Which GPUs to use: | ||
| - | {{ : | + | {{ : |
| Set the various parameters in | Set the various parameters in | ||
| Linea 78: | Linea 90: | ||
| | | | | ||
| | Real memory required per node: | < | | Real memory required per node: | < | ||
| - | | | + | | |
| | Additional (extra5) SBATCH directives: | --nodes=< | | Additional (extra5) SBATCH directives: | --nodes=< | ||
| | Additional (extra6) SBATCH directives: | --ntastks-per-node=< | | Additional (extra6) SBATCH directives: | --ntastks-per-node=< | ||
| | Additional (extra7) SBATCH directives: | --reservation=< | | Additional (extra7) SBATCH directives: | --reservation=< | ||
| - | | | + | | |
| | Current job: | <job name> | | Current job: | <job name> | ||
| | Additional argumets: | <options to add to the command that will be execute> (optional) | | Additional argumets: | <options to add to the command that will be execute> (optional) | ||
| - | {{ : | + | {{ : |
| Submit the job with " | Submit the job with " | ||
| Linea 100: | Linea 112: | ||
| Cancel the job with " | Cancel the job with " | ||
| - | {{ : | + | {{ : |
| - | + | ||
| - | {{ : | + | |
| Cancel the job in the queue (Relion does not do this automatically): | Cancel the job in the queue (Relion does not do this automatically): | ||
| Linea 112: | Linea 122: | ||
| To submit the job to the '' | To submit the job to the '' | ||
| - | | Queue name: | + | | Queue name: | **gpu_guest** |
| - | | Standard submission script: | + | | Standard submission script: | / |
| === CPU processing === | === CPU processing === | ||
| - | == Submit to bdw partition == | + | == Submit to cpu partition == |
| < | < | ||
| Linea 135: | Linea 145: | ||
| | Use GPU acceleration? | | Use GPU acceleration? | ||
| - | {{ : | + | {{ : |
| Set the various parameters in | Set the various parameters in | ||
| Linea 148: | Linea 158: | ||
| | Submit to queue? | Yes | | | Submit to queue? | Yes | | ||
| - | | Queue name: | **bdw** | | + | | Queue name: | **cpu** | |
| | Queue submit command: | sbatch | | Queue submit command: | sbatch | ||
| | Total run time: | D-HH:MM:SS (estimated) | | Total run time: | D-HH:MM:SS (estimated) | ||
| Linea 157: | Linea 167: | ||
| | Additional (extra6) SBATCH directives: | --ntastks-per-node=< | | Additional (extra6) SBATCH directives: | --ntastks-per-node=< | ||
| | Additional (extra7) SBATCH directives: | --reservation=< | | Additional (extra7) SBATCH directives: | --reservation=< | ||
| - | | | + | | |
| | Current job: | <job name> | | Current job: | <job name> | ||
| | Additional argumets: | <options to add to the command that will be execute> (optional) | | Additional argumets: | <options to add to the command that will be execute> (optional) | ||
| - | {{ : | + | {{ : |
| Submit the job with " | Submit the job with " | ||
| Linea 175: | Linea 185: | ||
| Cancel the job with " | Cancel the job with " | ||
| - | {{ : | + | {{ : |
| - | + | ||
| - | {{ : | + | |
| Cancel the job in the queue (Relion does not do this automatically): | Cancel the job in the queue (Relion does not do this automatically): | ||
| '' | '' | ||
| - | |||
| - | == Submit to vrt partition == | ||
| - | |||
| - | To submit the work on the '' | ||
| - | |||
| - | | Queue name: | ||
| - | | Standard submission script: | ||
| == Submit to knl partition == | == Submit to knl partition == | ||
| Linea 194: | Linea 195: | ||
| To submit the work on the ''' | To submit the work on the ''' | ||
| - | | Queue name: | + | | Queue name: | **knl** |
| - | | Standard submission script: | + | | Standard submission script: | / |
| - | + | ||
| - | == Submit to skl partition == | + | |
| - | + | ||
| - | To submit the work on the '' | + | |
| - | + | ||
| - | | Queue name: | + | |
| - | | Standard submission script: | + | |
| - | + | ||
| - | == Submit to skl_guest partition == | + | |
| - | + | ||
| - | To submit the work on the '' | + | |
| - | + | ||
| - | | Queue name: | + | |
| - | | Standard submission script: | + | |
| == The choice of parameters == | == The choice of parameters == | ||
| Linea 220: | Linea 207: | ||
| | gpu | >= 1 | 1-6 | | | gpu | >= 1 | 1-6 | | ||
| | gpu_guest | | gpu_guest | ||
| - | | vrt | 1 | 0 | | + | | cpu |
| - | | bdw | + | |
| | knl | >= 2 | 0 | | | knl | >= 2 | 0 | | ||
| - | | skl | >= 2 | 0 | | ||
| - | | skl_guest | ||
| The number of allocated nodes depends on the number of CPUs required, the number of CPUs per node (depending on the [[calcoloscientifico: | The number of allocated nodes depends on the number of CPUs required, the number of CPUs per node (depending on the [[calcoloscientifico: | ||
calcoloscientifico/cluster/softwareapplicativo/relion.1650633570.txt.gz · Ultima modifica: 22/04/2022 15:19 da fabio.spataro