CLUSTER
The platform ABiMS offers resources around a dedicated data center (Marine Genomic Data Center).
This data center is destined to data storage and security, as well as their analyses.
It represents :
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1864 processors handled by Sun Grid Engine middle-ware (SGE),
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a secure data storage (RAID) of 2 PB,
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a record robot with two LTO5 players for the daily record of critical data.
This infrastructure has been financed by multiple sources :
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Région Bretagne - BioGenOuest
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Conseil Général - CG29
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ANR projects
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Station Biologique de Roscoff: FR2424, UMR7139, UMR7144, UMR7150
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Investissements d'Avenir projects: EMBRC-France, IDEALG, Océanomics, IFB
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GRSIBI projects.
In 2013, 90% of the CPU resources involved collaborative projects with at less one partner from the "Station Biologique de Roscoff"; 10 % were used for fully external projects.
Training Materials
Please have a look at this Training Material before using the Cluster.
RESOURCES
This group structure allows to submit jobs on a specific computer type.
DIFFERENTS TYPES OF NODE
| Group | Node | Type | Function | Processor | RAM |
|---|---|---|---|---|---|
| @@bigcpu | n40-n55 | Dell blade M630 | Multithreaded treatements |
Intel 32 x 2.4 GHz |
128 GB |
| n80-n95 | Dell C6220 | Multithreaded treatements |
Intel 32 x 2.2 GHz |
128 GB | |
| @@bignode | n56-n59 | Dell R630 |
Multithreaded treatements Memory usage |
Intel 48 x 2.3 GHz |
256 GB |
| n76-n79 | Dell R815 |
Multithreaded treatements Memory usage |
AMD 48 x 2.2 GHz |
256 GB | |
| n115-n118 | Dell R630 |
Multithreaded treatements Memory usage |
Intel 48 x 2.2 GHz |
256 GB | |
| @@bigmem | n99 | Dell R910 | Memory usage |
Intel 40 x 2.0 GHz |
1 TB |
| n100 | Dell R930 | Memory usage |
Intel 128 x 2.1 GHz |
2 TB | |
| @@blade8 | n60-n75 | Dell blade M605 |
Reserved for galaxy |
AMD 8 x 2.4 GHz |
32 GB |
A queue system managed by the SGE scheduler allows the job submission and monitoring.
The available queues are :
| Time out | Available resources | Purpose | |
|---|---|---|---|
| short.q | 12 hours | High priority - 50 % of all CPU (- n99) | Regular jobs |
| long.q | 10 days | Standard priority - 50 % of all CPU (- n99) | Long jobs |
| infinite.q | no limit | Low priority - 25 % of all CPU (- n99) | Really really long jobs |
| bigmem.q | For treatements requiring a lot of RAM | ||
| qlogin.q | 2 days | For connections in qlogin mode | |
| clc.q | n76 | For CLC use (please contact support.abims@sb-roscoff.fr). | |
| galaxy.q | For Galaxy instances. |
A dedicated queue, named iprscan.q, is for InterProScan applications. It is automatically used by the application without having to use the qsub submission command.
MAXIMUM NUMBER OF SLOTS AVAILABLE PER QUEUE FOR EACH GROUP
| @@bignode | @@bigcpu | @@bigmem | @@blade8 | |
|---|---|---|---|---|
| short.q | 24 | 16 | 0 | 0 |
| long.q | 24 | 16 | 0 | 0 |
| infinite.q | 12 | 8 | 0 | 0 |
| bigmem.q | 0 | 0 | 128 | 0 |
| galaxy.q | 12 | 16 | 8 | 8 |
In case of competition during treatements in parallel (for example : jobs on three queues), treatements on the short.q queue have priority, followed by those running on long.q, and then by those running on infinite.q.