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services:cluster:start [2015/06/16 12:09] – [Table] dreger | services:cluster:start [2020/06/24 13:14] – remove sheldon and yoshi behrmj87 |
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====== Information about the HPC-Cluster ====== | ====== Information about the HPC-Cluster ====== |
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In order to get access to the department of physics HPC resources you need to send an email to hpc@physik.fu-berlin.de. Please give some information on the kind of jobs you are planing to run and software you plan to use, if possible. | ===== Access to the Cluster ===== |
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**2015-06-16**: Currently there are two HPC clusters in production at the physics department. One is located in the HLRN datacenter, the other is located at ZEDAT. See the table below for further information on available resources. Both cluster only share a common /home. Everything else like the queuing system ot /scratch are distinct. Both are running Debian/Wheezy and utilize the Slurm scheduling system. | In order to get access to the department of physics HPC resources you need to send an email to hpc@physik.fu-berlin.de. Please supply the following information: |
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| - Your ZEDAT account username |
| - The group you are using the system for (e.g. ag-netz,ag-imhof,...) |
| - The software you are using for your simulations (e.g. gromacs, gaussian, self-written code in language XYZ, ...) and whether you use MPI or OpenCL/CUDA. |
| - Software that you happen to know so well that other HPC users within the department may ask you for help. |
| - A self-contained example job that is typical for the workload you will be using the HPC systems for, ideally with a small README describing how to run it and a job script. If possible scale it so it runs between a few minutes and an hour at maximum. |
| - If you are no longer a member of the physics department, we would like to get an estimate on how much longer you will need access to the systems (e.g. to finish some paper) |
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===== Slurm documentation ===== | ===== Slurm documentation ===== |
* [[important|Important notes]] on cluster usage | * [[important|Important notes]] on cluster usage |
* Start with the [[slurm|Introduction to the Slurm HPC cluster]]. | * Start with the [[slurm|Introduction to the Slurm HPC cluster]]. |
| * Using [[interactivesessions|interactive sessions]] with the queuing system. |
| * How to make use of the [[gpunodes|GPU-nodes]]. |
| * Here is a [[nodes|list of special nodes]] that are currently not part of slurm. |
| * Here is a [[userlist|list of HPC users]] and the software they use |
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===== General documentation ===== | ===== General documentation ===== |
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* Robert Hübener from AG-Eisert has written a HOWTO for using [[mmacluster|Mathematica on a HPC-Cluster]]. | * Robert Hübener from AG-Eisert has written a HOWTO for using [[mmacluster|Mathematica on a HPC-Cluster]]. |
* A current python version as been built for cluster usage. The [[pythoncluster|Python on the HPC-Cluster]] tutorial describes how to set it up. | * A more current Python version has been built for cluster usage. The [[pythoncluster|Python on the HPC-Cluster]] tutorial describes how to set it up. |
| * Try to [[usetmpforio|use /tmp for I/O intensive single node jobs]] |
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===== Overview of available resources ===== | ===== Overview of available resources ===== |
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The following table lists all HPC resources available at the physics department. At the end of the table we also list the resources for the ZEDAT [[http://www.zedat.fu-berlin.de/HPC/Soroban|soroban]] cluster. The torque system will soon be replaced by SLURM. All torque nodes are running Debian/Squeeze, while all SLURM nodes are running Debian/Wheezy. | The following table lists some HPC resources available at the physics department. At the end of the table we also list the resources for the ZEDAT [[http://www.zedat.fu-berlin.de/HPC/Soroban|soroban]] cluster. The tron cluster at Takustrasse 9 is currently restructured. We also have some [[nodes|special purpose nodes]] that are currently not managed by Slurm. |
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^ Hosts ^ Manager ^ Nodes ^ Form ^ Hardware ^ CPU ^ Speed ^ Core/Node ^ RAM/Core ^ RAM/Node ^ #RAM ^ #Cores ^ | |
| @#cfc:**tron cluster** - FB Physik - Location: Takustrasse 9 |||||||||||| | |
| @#cfc:n010-n041 | offline | 32 | 2U Twin<sup>2</sup> | Dell C6100 | 2x Xeon X5650 | 2.66GHz | 12 | 8G | 96G | 3072G | 384 | | |
| @#cfc:n110-n111 | offline | 2 | 2U | Dell C6145 | 4x Opteron 6128HE | 2.0GHz | 32 | 4G | 128G | 256G | 64 | | |
| @#cfc:n112-n127 | offline | 16 | Blade | Dell M600 | 2x Xeon E5450 | 3.00GHz | 8 | 2G | 16G | 256G | 128 | | |
| @#cfc:n128-n143 | offline | 16 | Blade | Dell M600 | 2x Xeon E5450 | 3.00GHz | 8 | 2G | 16G | 256G | 128 | | |
| @#cfc:n144-n175 | offline | 32 | Blade | Dell M610 | 2x Xeon X5570 | 2.93GHz | 8 | 6G | 48G | 1536G | 256 | | |
| @#cfc:n176-n183 | offline | 8 | 4U | HP DL580 | 4x Xeon X7560 | 2.26Ghz | 32 | 8G | 256G | 2048G | 256 | | |
| @#cfc:**#Taku9** | | **~~=sum(range(col(),1,col(),row()-1))~~** | | | | | | | | **~~=sum(range(col(),1,col(),row()-1))~~G** | **~~=sum(range(col(),1,col(),row()-1))~~** | | |
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| @#ced:**sheldon cluster** - FB Physik - Location: HLRN |||||||||||| | |
| @#ced:x001-x192 | SLURM<sup>1)</sup> | 192 | Blade | SGI Altix ICE 8200 | 2x Xeon X5570 | 2.93GHz | 8 | 6G | 48G | 9216G | 1536 | | |
| @#ced:uv1000 | none | 1 | 42U | SGI UV 1000 | 64x Xeon X7560 | 2.26Ghz | 512 | 4G | 2T | 2048G | 512 | | |
| @#ced:**#HLRN** | | **193** | | | | | | | | **11264G** | **2048** | | |
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| @#cef:**yoshi cluster** - FB Physik - Location: ZEDAT |||||||||||| | |
| @#cef:y001-y128 | SLURM<sup>1)</sup> | 128 | Blade | HP BL460c G6 | 2x Xeon X5570 | 2.93GHz | 8 | 6G | 48G | 6144G | 1024 | | |
| @#cef:ygpu01-ygpu31 | SLURM<sup>2)</sup> | 31 | 2U GPU Nodes (2x Nvidia Tesla M2070) | IBM iDataPlex dx360 M3 | 2x Xeon X5570 | 2.93GHz | 8 | 3G | 24G | 744G | 248 | | |
| @#cef:**#Ph-ZEDAT** | | **159** | | | | | | | | **6888G** | **1272** | | |
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| @#ccf:**soroban cluster** - ZEDAT-HPC - Location: ZEDAT |||||||||||| | |
| @#ccf:node001-002 | SLURM | 2 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 8G | 48G | 96G | 24 | | |
| @#ccf:node003-030 | SLURM | 28 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 4G | 24G | 672G | 336 | | |
| @#ccf:node031-100 | SLURM | 70 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 8G | 48G | 3360G | 840 | | |
| @#ccf:node101-112 | SLURM | 12 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 16G | 96G | 1152G | 144 | | |
| @#ccf:**#ZEDAT** | | **112** | | | | | | | | **5280G** | **1344** | | |
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| @#ccc:**ausgemusterte Systeme** |||||||||||| | |
| @#ccc:Abacus4 | | 8 | | IBM p575 | 16x POWER 5+ | 1.9Ghz | 32 | 4G | 128G | 1024G | 256 | | |
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| The name of the login node for each of our clusters has the same name as the cluster, e.g. the tron login node is reachable via ssh under the hostname ''tron''. |
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| ^ Hosts ^ Manager ^ Nodes ^ Form ^ Hardware ^ CPU ^ Speed ^ Core/Node ^ RAM/Core ^ RAM/Node ^ #RAM ^ #Cores ^ |
| | @#cfc:**tron cluster** - FB Physik - Location: Takustrasse 9 - OS: Debian/Stretch |||||||||||| |
| | @#cfc:z001-z020 | SLURM | 20 | 1U | IBM iDataPlex dx360 M4 | 2x Xeon E5-2680v2 | 2.8GHz | 20 | 25G | 512G | 10024G | 400 | |
| | @#cfc:z021-z040 | SLURM | 20 | 1U | IBM iDataPlex dx360 M4 | 2x Xeon E5-2680v2 | 2.8GHz | 20 | 12G | 256G | 5120G | 400 | |
| | @#cfc:z041-z113 | SLURM | 72 | 2U GPU Nodes (2x Nvidia Tesla K20x) | IBM iDataPlex dx360 M4 | 2x Xeon E5-2680v2 | 2.8GHz | 20 | 6G | 128G | 9216G | 1440 | |
| | @#cfc:z163-z166 | SLURM | 4 | 2U | HP DL560 G8 | 4x Xeon E5-4650L | 2.6GHz | 32 | 24G | 768G | 3072G | 128 | |
| | @#cfc:**#Taku9** | | **~~=sum(range(col(),1,col(),row()-1))~~** | | | | | | | | **~~=sum(range(col(),1,col(),row()-1))~~G** | **~~=sum(range(col(),1,col(),row()-1))~~** | |
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| | @#ccf:**soroban cluster** - ZEDAT-HPC - Location: ZEDAT |||||||||||| |
| | @#ccf:node001-002 | SLURM | 2 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 8G | 48G | 96G | 24 | |
| | @#ccf:node003-030 | SLURM | 28 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 4G | 24G | 672G | 336 | |
| | @#ccf:node031-100 | SLURM | 70 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 8G | 48G | 3360G | 840 | |
| | @#ccf:node101-112 | SLURM | 12 | 1U Twin | Asus Z8NH-D12 | 2x Xeon X5650 | 2.66GHz | 12 | 16G | 96G | 1152G | 144 | |
| | @#ccf:**#ZEDAT** | | **112** | | | | | | | | **5280G** | **1344** | |
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| | @#ccc:Abacus4 | | 8 | | IBM p575 | 16x POWER 5+ | 1.9Ghz | 32 | 4G | 128G | 1024G | 256 | |
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Operating System: Debian Linux Squeeze (x64)\\ | |
<sup>1)</sup> in production but still experimental\\ | |
<sup>2)</sup> work in progress | |
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(15.03.2014) | (06.11.2018) |
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