Introduction to the HPCC Dirk Colbry Research Specialist Institute for Cyber Enabled Research

HPCC Online Resources – HPCC home wiki.hpcc.msu.edu – Public/Private Wiki forums.hpcc.msu.edu – User forums rt.hpcc.msu.edu – Help desk request tracking mon.hpcc.msu.edu – System Monitors

HPCC Cluster Overview Linux operating system Primary interface is text based though Secure Shell (ssh) All Machines in the main cluster are binary compatible (compile once run anywhere) Each user has 50Gigs of personal hard drive space. /mnt/home/username/ Users have access to 33TB of scratch space. /mnt/scratch/username/ A scheduler is used to manage jobs running on the cluster A submission script is used to tell the scheduler the resources required and how to run a job A Module system is used to manage the loading and unloading of software configurations

gateway Access to HPCC is primarily though the gateway machinie: ssh Access to all HPCC services uses MSU username and password.

HPCC System Diagram

Hardware Time Line YearNameDescriptionCoresMemoryTotal Cores 2005green1.6GHz Itanium2 (very old) (shared) 128 Main Cluster 2005amd05Dule-core 2.2GHz AMD Opterons48GB intel07Quad-core 2.3GHz Xeons88GB intel08Sun x4450s (Fat Node)1664GB amd09Sun Fire X4600 Opterons (Fat Node)32256GB We are currently investigating two new purchases for 2009/2010 Graphics Processing Unit (GPU) Cluster New General Purpose Large Cluster

HPCC System Diagram

Cluster Developer Nodes Developer Nodes are accessible from gateway and used for testing. ssh dev-amd05 – Same hardware as amd05 ssh dev-intel07 – Same hardware as intel07 ssh dev-amd09 – Same hardware as amd09 We periodically have some test boxes. These include: ssh dev-intel09 – 8 core intel Xeon with 24GB of memory ssh gfx-000 – Nvidia Graphics Processing Node Jobs running on the developer nodes should be limited to two hours of walltime. Developer nodes are shared by everyone.

HPCC System Diagram

Available Software Center Supported Development Software Intel compilers, openmp, openmpi, mvapich, totalview, mkl, pathscale, gnu... Center Supported Research Software Matlab, R, fluent, abaqus, HEEDS, amber, blast, ls- dyna, starp... Center Unsupported Software (module use.cus) gromacs, cmake, cuda, imagemagick, java, openmm, siesta...

Steps in Using the HPCC 1. Connect to HPCC 2. Transfer required input files and source code 3. Determine required software 4. Compile programs (if needed) 5. Test software/programs on a developer node 6. Write a submission script 7. Submit the job 8. Get your results and write a paper!!

Module System To maximize the different types of software and system configurations that are available to the users. HPCC uses a Module system. Key Commands module avail – show available modules module list – list currently loaded modules module load modulename – load a module module unload modulename – unload a module

Getting Help Documentation and User Manual - wiki.hpcc.msu.edu User Forums - forums.hpcc.msu.edu Contact HPCC and iCER Staff for: Reporting System Problems HPC Program writing/debugging Consultation Help with HPC grant writing System Requests Other General Questions Primary form of contact - HPCC Request tracking system – rt.hpcc.msu.edu HPCC Phone – (517) am-5pm HPCC Office – Engineering Building am-5pm

Next Week - Getting Connected Secure Shell - hpc.msu.edu Putty Windows Secure Shell X11 Server (windowing) xming cygwin File transfers Mapped Network Drives - files.hpc.msu.edu