Contents 1 Description and Citations 2 IBEST Bioinformatics Core Clusters 3 What's new with the IBEST Clusters 4 Available Applications 5 Tutorials and Exercises 5.1 Basic Tutorials 5.1.1 Logging in 5.1.2 Linux Commands 5.1.3 Using modules 5.1.4 Using the Cluster 5.1.5 Installing applications in your home directory 5.1.6 Application Specific Tutorials 5.1.7 Exercises 6 Example Scripts 7 Tools 7.1 Auto-Bayes 7.2 Blastp2tree 8 Old MPI Tutorials 9 System Administration Notes 10 Upcoming Changes

[edit] Description and Citations

• Bioinformatics Core Description - Long descriptions and summaries to use in your proposals.
• Citations - How to cite us in you papers.

[edit] IBEST Bioinformatics Core Clusters

fourtytwo.ibest.uidaho.edu (production - available)

• 512 AMD64 2.4GHz Cores
• 1GB RAM per core
• OS: Linux (Centos 5)

oceanus.ibest.uidaho.edu (draining - available)

• 192 Intel Xeon 2.8GHz CPUs
• 512MB RAM per cpu
• OS: Linux (Gentoo)

serenity.ibest.uidaho.edu (testing - available)

• 96 PPC G5 CPUs
• 2GB RAM per cpu
• OS: Linux (Debian)

medusa.ibest.uidaho.edu (testing - offline)

• 44 Intel Xeon 2.8GHz CPUs
• 512MB RAM per cpu
• OS: Linux (Centos 5)

[edit] What's new with the IBEST Clusters

• Fourtytwo has now been classified as our primary production cluster.
• Serenity (the remodeled Phlegathon) is now up, running a minimal number of nodes and applications for testing. Please remember that it may still be unstable and we will be fixing errors and modifying configurations as we find issues, so please do not start jobs which will last more than two days and back up your data each time you run. As we progress we will bring up more nodes as needed for testing purposes. You may still access serenity by using its old name phlegathon.ibest.uidaho.edu but that name will be removed in the near future. Serenity uses the same scheduler and batch server as Fourtytwo so you may use the same tutorials on the cluster wiki to run.
• Oceanus is being drained for an update over Christmas break. Please do not start jobs that will not quit by then.

[edit] Available Applications

• Fourtytwo: Installed Applications
• Serenity: Installed Applications

[edit] Tutorials and Exercises

[edit] Basic Tutorials

Note: These tutorials are designed for our new cluster fourtytwo.ibest.uidaho.edu. They will not work on oceanus.

[edit] Logging in

• Tutorials: Logging in for the first time.
• Tutorials: Where am I?.
• Tutorials: Your home directory.

[edit] Linux Commands

• Tutorials: Basic Linux commands.
• Tutorials: Advanced scripting in Bash.
• Tutorials: Useful scripts, commands, and words of wisdom.

[edit] Using modules

• Tutorials: Using modules to load applications.
• Tutorials: Loading modules at login.
• Tutorials: Creating your own modulefiles.

[edit] Using the Cluster

• Tutorial: Check on the status of the cluster or all your jobs.
• Tutorial: Submitting a job using qsub.
• Tutorial: Queues and backfill scheduling.
• Tutorial: Viewing the output of a running job.
• Tutorial: Removing a job from the cluster.
• Tutorial: Distributing a task to nodes (non-parallel).
• Tutorial: Submitting parallel jobs.
• Tutorial: Interactive jobs.
• Tutorial: Using visualization tools.

[edit] Installing applications in your home directory

• Tutorial: Compiling standard applications.
• Tutorial: Compiling parallel applications.

[edit] Application Specific Tutorials

• Tutorial: Interactive Mr. Bayes with multiple processors.
• Tutorial: Using mpiBLAST

[edit] Exercises

• Create a script that submits multiple jobs that are dependent on each other.
• Test your skills by applying the tutorials to a practical biological question.

[edit] Example Scripts

• Cluster Submit Scripts - Mr. Bayes (mb)
• Cluster Submit Scripts - Migrate (migrate-n)
• Cluster Submit Scripts - NWChem (nwchem)
• Cluster Submit Scripts - RaxML (raxmlHPC-MPI)
• Cluster Submit Scripts - clustalw-mpi (clustalw-mpi)
• Cluster Submit Scripts - PaCE (PaCE)
• Cluster Submit Scripts - Garli (Garli - MPI version)
• Cluster Submit Scripts - Paup
• Cluster Submit Scripts - R
• Cluster Submit Scripts - Beast

[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] Blastp2tree

The blastp2tree script takes a protein fasta file and uses mpiblast to search against the nr database. Once complete, it takes the top ten hits, aligns them and creates an ML tree. Only for our PBS based systems.

• Cluster Submit Scripts - Blastp2tree

[edit] Old MPI Tutorials

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

[edit] System Administration Notes

• Installing the Serenity PPC Linux Cluster

[edit] Upcoming Changes

• No major changes scheduled for the time being.