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— | doku:vsc3_queue [2021/05/14 13:44] – [Queue | Partition setup on VSC-3] goldenberg | ||
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+ | ====== 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 (ver 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 | | ||
+ | ===== 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, | ||
+ | </ | ||
+ | |||
+ | Have a look on the < | ||
+ | ==== Run time limits ==== | ||
+ | |||
+ | |||
+ | ^ The QOS's hard run time limits ^ | | ||
+ | | | | | ||
+ | | normal_0064 / normal_0128 / normal_0256 | ||
+ | | idle_0064 / idle_0128 / idle_0256 | ||
+ | | private queues | ||
+ | | devel queue (up to 10 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^ | ||
+ | | | | | ||
+ | |normal_0064 | mem_0064| default | | ||
+ | |normal_0128 | mem_0128| | | ||
+ | |normal_0256 | mem_0256| | | ||
+ | |devel_0128 | ||
+ | |||
+ | == examples == | ||
+ | < | ||
+ | #SBATCH --partition=mem_0128 | ||
+ | #SBATCH --qos=normal_0128 | ||
+ | #SBATCH --account=p7xxxx | ||
+ | </ | ||
+ | < | ||
+ | #SBATCH --partition=mem_0128 | ||
+ | #SBATCH --qos=devel_0128 | ||
+ | #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 mem_0064 and normal_0064. | ||
+ | |||
+ | === private nodes projects === | ||
+ | |||
+ | == example == | ||
+ | |||
+ | < | ||
+ | #SBATCH --partition=mem_xxxx | ||
+ | #SBATCH --qos=p7xxx_xxxx | ||
+ | #SBATCH --account=p7xxxx | ||
+ | </ | ||
+ | |||