Hardware
The “Michigan Nano Computational Cluster” (MNC2) consists of 14 nodes. Each compute node contains a hexa-core Intel Xeon X5660 processor running at 2.66 GHz, 24 GB of memory. MNC2 contains 168 processing cores linked with Gigabit ethernet, 12 TB of disk space.
Software
Nanoscale science pertains to the regime where the number of atoms or molecules under study are too numerous and arranged in too complex a manner for a single-atom/molecule treatment, on the one hand, and the number and arrangement of atoms is neither regular (periodic) nor sufficiently large so as to make statistical (thermodynamic) treatments meaningful, on the other hand. Nevertheless, the foundations of nanoscale computation consist of electronic structure codes, which are initially appropriate for small atom number or periodic systems, and molecular dynamics codes, which are statistical insofar as they typically require ensembles of initial conditions and treat systems interacting with heat baths. Additionally, photonics and phononics codes address the primary bosonic degrees of freedom of nanoscale matter, processing or fabrication, and multiscale or finite element tools treat micro-fluidics, which while larger than the nanoscale often interfaces with nanoscale structures and are important in their own right.
List of computational codes available at NNIN/C@UM — Some codes require that users register or purchase their own copy before using them on the cluster
| CFD and Finite Element Tools | |
| Elmer | CFD-ACE+ |
| Tahoe | Gerris |
| FEBio | Free CFD |
| Intellisuite | Openfoam |
| Meshfree Method | |
| Uintah | |
| MultiScale Tools | |
| Quasicontinuum | LibMultiScale |
| OCTA | CADD |
| Molecular Dynamics | |
| LAMMPS | CP2K |
| DL_POLY | GULP |
| GROMACS | NAMD |
| MOSAICS | MCCCS Towhee |
| Desmond | |
| Photonics & Phononics | |
| DDSCAT | MIT Photonic Bands (MPB) |
| MULTEL | |
| Electronic Structure | |
| Quantum Espresso | Gaussian |
| Abinit | GAMESS |
| CPMD | Octopus |
| VASP | TurboMol |
| CHAMP | Atomic Simulation Env. |
| Micro/Nano Scale Fabrication | |
| Intellisuite | |
Access Policies
As part of obtaining an account, all users should have completed and be familiar with NNIN@UM Computing Policies. For more information please check “privacy & Legal Notice”
The MNC2 allows incoming user connections only using SSH (Secure Shell). Connections via telnet or rsh are not permitted for security reasons.
Visit the following links to acquire a copy of ssh.
| For Unix/Linux | For Windows |
| Open SSH | Putty |
| Commercial SSH (a free copy is available). | |
SSH Hints:
- SSH timeouts: The following options should be included on your SSH command line if you find that your sessions are being disconnected too quickly due to lack of keyboard interaction:
-o ServerAliveInterval=60 -o ServerAliveCountMax=30
- It’s usually not necessary to define your DISPLAY variable in an SSH session between MNC2 hosts. It should be picked up automatically by SSH.
- If you want to generate XWindows displays from an NNIN/C machine and have them appear on your desktop, you will probably need to configure your desktop SSH client to forward/tunnel X11 connections BEFORE you connect to the MNC2 host. You may also need to configure your XWindows emulator. Use the verbose option to troubleshoot problems:
ssh -v [other options] [host]
