cluster:126
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
cluster:126 [2020/02/27 14:26] hmeij07 |
cluster:126 [2025/04/18 13:53] (current) hmeij07 |
||
|---|---|---|---|
| Line 8: | Line 8: | ||
| ===== Description ===== | ===== Description ===== | ||
| - | The High Performance Compute Cluster (HPCC) is comprised of several login nodes (all are on our domain | + | The High Performance Compute Cluster (HPCC) is comprised of several login nodes (all are on our internal network (vlan 52) |
| - | * primary login node '' | + | * server |
| - | * secondary | + | * primary |
| - | * secondary login node '' | + | * zabbix and ganglia monitoring and alerting servers |
| - | * sandbox | + | * secondary login servers |
| - | * NFS server '' | + | * scratch |
| - | * (only log in when moving conternt) file server | + | * backup Slurm test server '' |
| - | * DR node '' | + | * storage servers '' |
| - | * storage servers '' | + | * storage servers '' |
| - | * storage servers '' | + | * storage servers '' |
| - | * mindstore | + | * storage server '' |
| + | * storage server '' | ||
| - | Several types of compute nodes are available via the OpenLava | + | Several types of compute nodes are available via the scheduler: |
| - | * All are running | + | * All are running |
| - | * All are x86_64, Intel Xeon chips from 2006 onwards | + | * All are x86_64, Intel Xeon chips with OpenHPC compile environment 2.x |
| - | * All are on private networks (192.168.x.x or 10.10.x.x, no internet) | + | * All are on private networks (192.168.x.x |
| - | * All mount /home (10TB, to be replaced by FreeNAS/ZFS 190T appliance | + | * All mount /zfshomes |
| * All have local disks providing varying amounts of / | * All have local disks providing varying amounts of / | ||
| - | * Hyperthreading is on but only 50% of logical cores allocated via scheduler | + | * Hyperthreading is on (can be allocated via scheduler) |
| Compute node categories which usually align with queues: | Compute node categories which usually align with queues: | ||
| Line 46: | Line 47: | ||
| * 12 nodes with dual twelve core chips (Xeon Silver 4214, 2.20 Ghz) in ASUS ESC4000G4 2U rack servers with a memory footprint of 96 GB ( 1,152 GB, about 20 teraflops | * 12 nodes with dual twelve core chips (Xeon Silver 4214, 2.20 Ghz) in ASUS ESC4000G4 2U rack servers with a memory footprint of 96 GB ( 1,152 GB, about 20 teraflops | ||
| - | All queues are available for job submissions via all login nodes. Some nodes on Infiniband switches for parallel computational jobs (queues: me256fd, hp12). | + | * 2 nodes with dual twelve |
| - | Home directory file system are provided | + | * 6 nodes with dual 28 core chips (Xeon Gold 'Ice Lake-SP' |
| - | Two (old) Rstore storage | + | * 10 nodes with dual 12 core chips (Xeon Silver 4410Y CPU @ 3.9 Ghz), Emerald Rapids Microway |
| + | All queues are available for job submissions via cottontail2 login node. Some nodes on Infiniband switches for parallel computational jobs (queues: mw256fd, hp12, mw256). | ||
| - | ===== Our Queues ===== | + | Home directory file system are provided (via NFS or IPoIB) by the node M40ha (our file server) from a direct attached disk array. In total, 500 TB of /zfshomes disk space is accessible to the users. Node '' |
| - | Commercial software has their own queue limited by available licenses. There are no scheduler license resources, just queue jobs up in appropriate queue. Jobs are processed on the nodes of hp12, mwgpu < | ||
| - | ^Queue^Nr Of Nodes^Total GB Mem Per Node^Total Cores In Queue^Switch^Hosts^Notes^ | + | ===== Our Queues ===== |
| - | | stata | // | + | |
| - | Note: Matlab and Mathematica now have " | + | There are no scheduler commercial software license resources. Only stata has a limited 6 user license. |
| ^Queue^Nr Of Nodes^Total GB Mem Per Node^Job SLots In Queue^Switch^Hosts^Notes^ | ^Queue^Nr Of Nodes^Total GB Mem Per Node^Job SLots In Queue^Switch^Hosts^Notes^ | ||
| - | | hp12 | | + | | hp12 | |
| | mwgpu | | | mwgpu | | ||
| | mw256fd | | mw256fd | ||
| | tinymem | | tinymem | ||
| | mw128 | | | mw128 | | ||
| - | | amber128 | + | | amber128 |
| + | | exx96 | | ||
| + | | test | | ||
| + | | mw256 | | ||
| + | | mwgpu256 | ||
| Some guidelines for appropriate queue usage with detailed page links: | Some guidelines for appropriate queue usage with detailed page links: | ||
| Line 75: | Line 79: | ||
| * hp12 is the default queue | * hp12 is the default queue | ||
| * for processing lots of small to medium memory footprint jobs | * for processing lots of small to medium memory footprint jobs | ||
| - | | + | * mwgpu is for GPU (K20) enabled software primarily (Amber, Lammps, NAMD, Gromacs, Matlab, Mathematica) |
| - | * for exclusive use of a node reserve all memory | + | * be sure to reserve one or more job slot for each GPU used [[cluster:192|EXX96]] |
| - | | + | * be sure to use the correct wrapper script to set up mpirun from mvapich2, mpich3 or openmpi |
| - | * be sure to reserve one or more job slot for each GPU used [[cluster:119|Submitting GPU Jobs]] | + | |
| - | * be sure to use the correct wrapper script to set up mpirun from mvapich2 | + | |
| * mw256fd | * mw256fd | ||
| * or requiring lots of threads (job slots) confined to single node (Gaussian, Autodeck) | * or requiring lots of threads (job slots) confined to single node (Gaussian, Autodeck) | ||
| Line 92: | Line 94: | ||
| * mw128 (bought with faculty startup funds) tailored for Gaussian jobs | * mw128 (bought with faculty startup funds) tailored for Gaussian jobs | ||
| * About 2TB / | * About 2TB / | ||
| - | * Priority access for Carlos' | + | * Priority access for Carlos' |
| * amber128 (donated hardware) tailored for Amber16 jobs | * amber128 (donated hardware) tailored for Amber16 jobs | ||
| * Be sure to use mpich3 for Amber | * Be sure to use mpich3 for Amber | ||
| - | * Priority access for Amber jobs | + | * Priority access for Amber jobs till 10/ |
| - | * test (swallowtail, petaltail, cottontail2) | + | * exx96 contains 4 RTX2080S per node |
| - | * wall time of 8 hours of CPU usage | + | * same setup as mwgpu queue |
| + | * test contains 8 RTX5000 gpus | ||
| + | * can be used for production runs | ||
| + | * beware of preemptive events, checkpoint! | ||
| + | * mw1256, NFSoRDMA, bought with faculty startup monies | ||
| + | * beware | ||
| + | * 6 compute nodes | ||
| + | * Priority access for Sarah' | ||
| + | * mwgpu256, contains 40 RTX4070Ti-Super gpus | ||
| + | * same setup as exx96 queue | ||
| - | **There are no wall time limits in our HPCC environment | + | **NOTE**: we are migrating from Openlava to Slurm during summer 2022. All queues |
| - | * [[cluster:147|BLCR Checkpoint in OL3]] Serial Jobs | + | * [[cluster:213|New Head Node]] |
| - | * [[cluster:148|BLCR Checkpoint | + | * [[cluster:218|Getting Started with Slurm Guide]] |
| + | |||
| + | **There are no wall time limits | ||
| ===== Other Stuff ===== | ===== Other Stuff ===== | ||
| Line 110: | Line 123: | ||
| Checkpointing is supported in all queues, how it works [[cluster: | Checkpointing is supported in all queues, how it works [[cluster: | ||
| - | For a list of software installed consult [[cluster: | + | For a list of software installed consult [[cluster: |
| + | |||
| + | For a list of OpenHPC software installed consult [[cluster: | ||
| Details on all scratch spaces consult [[cluster: | Details on all scratch spaces consult [[cluster: | ||
| Line 116: | Line 131: | ||
| For HPCC acknowledgements consult [[cluster: | For HPCC acknowledgements consult [[cluster: | ||
| - | Sample scripts for job submissions (serial, array, parallel, forked and gpu) can be found at ''/ | + | Sample scripts for job submissions (serial, array, parallel, forked and gpu) can be found at ''/ |
| - | From off-campus you need to VPN in first at [[http://webvpn.wesleyan.edu]] | + | From off-campus you need to VPN in first, download GlobalProtect client |
cluster/126.1582813588.txt.gz · Last modified: 2020/02/27 14:26 by hmeij07
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
