Clusters

From WikIBEST

Contents 1 What's new with the IBEST Clusters 1.1 New Development Cluster 1.2 Changes to Existing Clusters 2 Instructions 2.1 Cluster Utilities 3 Tutorials 3.1 MPI Tutorials 3.2 Application Specific Tutorials 4 Scripts 5 Tools 5.1 Auto-Bayes 6 Cluster Status 6.1 Oceanus 6.2 Phlegathon 6.3 Medusa 7 Coming up

[edit] What's new with the IBEST Clusters

[edit] New Development Cluster

Our new development cluster is now operational. We are still in the process of installing applications and fine tuning the system. It will require some adjustments to your submission scripts as it is a PBS based system rather than an SGE based system. It has fully functional process check-pointing available which is also integrated into the grid management software. Over the next few weeks as I install all the required software, I will be documenting the use and sample submission scripts of various programs. You may temporarily access these documents here on the New Cluster Documentation Links page

[edit] Changes to Existing Clusters

There are changes in the way you will be submitting your scripts to the clusters. Qsub is the same but we are now starting to use the modules environment manipulation package to set paths to the different mpi libraries. These changes will make your submission scripts less complex.

When using the new scripts append '-new' to the '-pe' option (ie. -pe mpich2-smpd would be -pe mpich2-smpd-new). By the beginning of the fall semester the clusters will be completely switched over and your old scripts will not work. Please contact the system administrators if you have trouble converting your scripts.

[edit] Instructions

[edit] Cluster Utilities

• mpienv - Deprecated in favor or the environment modules package
• mpils - Deprecated
• mpishow - Deprecated in favor of 'module list'
• mpichange - Deprecated in favor of 'module load'
• qscreen
• qattach
• qlogin
• module

[edit] Tutorials

[edit] MPI Tutorials

• Manually create an MPI Ring using SGE.
• Using the new MPI environment tools.
• Submit a MPICH2 SMPD job through SGE.

[edit] Application Specific Tutorials

• Tutorial: Interactive Mr. Bayes with multiple processors.

[edit] Scripts

• Cluster Submit Scripts - Mr. Bayes (mb)
• Cluster Submit Scripts - Migrate (migrate-n)
• Cluster Submit Scripts - NWChem (nwchem)
• Cluster Submit Scripts - RaxML (raxmlHPC-MPI)

[edit] Tools

[edit] Auto-Bayes

The Auto-Bayes scripts will take a list of Mr. Bayes instruction files and submit them to the cluster, reserving the appropriate number of nodes for the amount of chains.

• Cluster Submit Scripts - Auto-Bayes

[edit] Cluster Status

[edit] Oceanus

Intel/Linux Cluster

• Total Nodes: 96 (384 slots)
• Operational: 80
• Down: 16

[edit] Phlegathon

PPC/OSX

• Total Nodes: 48 (192 slots)
• Operational: 47
• Down: 1

[edit] Medusa

Intel/Linux Cluster

• Total Nodes: 22
• Operational: 21
• Down: 1

[edit] Coming up

• At the end of the summer, reconfiguration begins on phlegathon. Phlegathon will be converted to a PPC/Linux system using the Torque/Maui setup that Medusa is currently using.

• The hardware for the new cluster is here! Once our power upgrades are completed we will be bringing the new 128 core system on line. Once we receive the year two funds we will be expanding it to a 512 core cluster.