Differences
This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revisionBoth sides next revision | ||
doku:vsc3_queue [2021/09/11 18:40] – removed goldenberg | doku:vsc3_queue [2022/06/23 12:11] – [Hardware types] msiegel | ||
---|---|---|---|
Line 1: | Line 1: | ||
+ | ====== Queue | Partition setup on VSC-3+ ====== | ||
+ | On VSC-3+, the type of hardware and the quality of service (QOS) where the jobs run on may be selected. Nodes of the same type of hardware are grouped to partitions, the QOS defines the maximum run time of a job and the number and type of allocable nodes. | ||
+ | ===== Hardware types ===== | ||
+ | Three different types of compute nodes, nodes with 64 GB and 256 GB, GPU nodes and | ||
+ | bioinformatics nodes (very high memory) are available. | ||
+ | |||
+ | On VSC-3+, the hardware is grouped into so-called < | ||
+ | |||
+ | ^partition name^ description^ | ||
+ | |vsc3plus_0064 | default, nodes with 64 GB of memory | | ||
+ | |vsc3plus_0256 | nodes with 256 GB of memory| | ||
+ | |gpu_xxxx | ||
+ | |binf | Bioinformatics nodes | | ||
+ | |jupyter| reserved for the JupyterHub | | ||
+ | |||
+ | For the specific GPU partitions, see [[doku: | ||
+ | |||
+ | The partitions of the oil-cooled nodes (normal_0064, | ||
+ | ===== Quality of service (QOS) ===== | ||
+ | |||
+ | Access to node partitions is granted by the so-called < | ||
+ | < | ||
+ | |||
+ | The QOSs that are assigned to a specific user can be viewed with: | ||
+ | < | ||
+ | sacctmgr show user `id -u` withassoc format=user, | ||
+ | </ | ||
+ | The default QOS and all QOSs usable are also shown right after login. | ||
+ | |||
+ | Generally, it can be distinguished in QOS defined on the ordinary compute nodes (vsc4plus_0064/ | ||
+ | |||
+ | The < | ||
+ | ==== Run time limits ==== | ||
+ | |||
+ | |||
+ | ^ The QOS's hard run time limits ^ | | ||
+ | | | | | ||
+ | | vsc3plus_0064 / vsc3plus_0256 | ||
+ | | idle_0064 / idle_0256 | ||
+ | | GPU queues gpu_..... | ||
+ | | normal_binf | ||
+ | | private queues | ||
+ | | devel_0064 (up to 4 nodes available) | ||
+ | The QOS's run time limits can also be requested via the command | ||
+ | < | ||
+ | SLURM allows for setting a run time limit //below// the default QOS's run time limit. After the specified time is elapsed, the job is killed: | ||
+ | < | ||
+ | Acceptable time formats include " | ||
+ | |||
+ | ==== Backfilling ==== | ||
+ | |||
+ | Furthermore, | ||
+ | < | ||
+ | |||
+ | ==== sbatch parameters ==== | ||
+ | For submitting jobs, three parameters are important: | ||
+ | |||
+ | < | ||
+ | #SBATCH --partition=mem_xxxx | ||
+ | #SBATCH --qos=xxxxx_xxxx | ||
+ | #SBATCH --account=xxxxxx | ||
+ | </ | ||
+ | The core hours will be charged to the specified account. If not specified, the default account ('' | ||
+ | |||
+ | === ordinary projects === | ||
+ | |||
+ | For ordinary projects the QOSs are: | ||
+ | ^QOS name ^ gives access to partition ^description^ | ||
+ | | | | | ||
+ | |vsc3plus_0064 | vsc3plus_0064| default | | ||
+ | |vsc3plus_0256 | vsc3plus_0256| | | ||
+ | |gpu_.... | ||
+ | |normal_binf | binf| | | ||
+ | |devel_0064 | 4 nodes on vsc3plus_0064 | | ||
+ | |||
+ | == examples == | ||
+ | < | ||
+ | #SBATCH --partition=vsc3plus_0064 | ||
+ | #SBATCH --qos=vsc3plus_0064 | ||
+ | #SBATCH --account=p7xxxx | ||
+ | </ | ||
+ | < | ||
+ | #SBATCH --partition=gpu_a40dual | ||
+ | #SBATCH --qos=gpu_a40dual | ||
+ | #SBATCH --account=p7xxxx | ||
+ | </ | ||
+ | * Note that partition, qos, and account have to fit together. | ||
+ | * If the account is not given, the default account ('' | ||
+ | * If partition and qos are not given, default values are vsc3plus_0064 for both. | ||
+ | |||
+ | === private nodes projects === | ||
+ | |||
+ | == example == | ||
+ | |||
+ | < | ||
+ | #SBATCH --partition=vsc3plus_xxxx | ||
+ | #SBATCH --qos=p7xxx_xxxx | ||
+ | #SBATCH --account=p7xxxx | ||
+ | </ | ||
+ | |||