The following tables supply information about the hardware architecture of the cluster for both the Intel and AMD nodes.
Here are some definitions to help if needed:
- cpu = central processor unit
- core = 1 virtual cpu
- node = 1 physical computer
- RAM = Random Access Memory
- GB = Gigabyte (billion bytes)
- TB = Terabye (trillion bytes)
- Gbps = network speed gigabits per sec
| System Component | Configuration |
|---|---|
| 19 Intel Compute Nodes | |
| Processor Type | Intel Xeon E5-2650v4 |
| Sockets | 2 cpus |
| Cores/socket | 12 |
| Clock speed | 2.2 GHz |
| Flop speed | N/A |
| Memory capacity | 128 GB DDR4 DRAM |
| Flash memory | 480 GB SSD |
| Network interface | 10 Gpbs |
1 Intel Compute node:
| System Component | Configuration |
|---|---|
| 1 Intel Compute Node | |
| Processor Type | Intel Xeon E5-2699v4 |
| Sockets | 2 |
| Cores/socket | 22 |
| Clock speed | 2.2 GHz |
| Flop speed | N/A |
| Memory capacity | 256 GB DDR4 DRAM |
| Flash memory | 500 GB SSD |
| Network interface | 10 Gbps |
System Software Environment (Summer 2017)
| Software Function | Description |
|---|---|
| Cluster Management | OpenHPC |
| Operating System | CentOS 7 |
| File Systems | NFS |
| Scheduler and Resource Manager | SLURM |
| Compilers | GNU Fortran, C, C++ |
| Message Passing | Open MPI |
Partitions
| Queue Name | Max Walltime | Max Nodes | Comments |
|---|---|---|---|
| Instruction | None | 3 | Used for access to compute nodes AMD |
| 96x24gpu4 | None | 1 | 4 Telsa P100 GPUs |
| 256×44 | None | 1 | Intel node 256GBs / 2 x 22 cores |
| 128×24 | None | 3 | Intel nodes 128GBs / 2 x 12 cores |
Supported Software by Science Domain
This is NOT a complete list of all software packages available; some (though very few) may be in progress. To see all available software execute in your shell “module avail”. For how to use these packages, you will use Environmental Modules. If you want certain packages installed that are not a listed module, contact us. (This list may not be complete)
| Domain | Software |
|---|---|
| Biochemistry | |
| Bioinformatics | BamTools, BEAGLE, BEAST, BEAST 2, bedtools, Bowtie, Bowtie2, MrBayes, PhyloBayes, Picard, QIIME, SAMtools, Trimmomatic |
| Compilers | gcc, g++ and gfortran |
| File format libraries | hdf5, netcdf |
| Interpreted languages | R, python (2 and 3) |
| Molecular dynamics | Amber, Gromacs, NAMD |
| MPI libraries | OpenMPI |
| Numerical libraries | FFTW, ScaLAPACK |
| Profiling and debugging | Valgrind |
| Quantum chemistry | GAMESS, Gaussian 09, NWChem, QE |
| Structural mechanics | None |