Caltech Center for Advanced Computing Research » Page 'Cellcenter1 Server System Guide'
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Cellcenter1 Server System Guide


1. How to Get An Account

2. How to Access the Machine

Connect to the front end, cellcenter1.cacr.caltech.edu:

ssh -l username cellcenter1.cacr.caltech.edu

Please edit, compile, build and run your jobs on cellcenter1; for “long” production runs, please use the cellcenter agenda at http://www.henge.caltech.edu to indicate your runtime plans. Your IMSS/ITS userID/password gives you acess to the cellcenter agenda.

NOTE: password entry into the Sun Fire X4600 is not allowed, but rather access is permitted via ssh public keys. If you do not have a public key, please see SSH Key Instructions.

3.  System Configuration Information / Technical Summary

The cellcenter1 Sun Fire X4600 provides computing capabilities specifically configured to meet the needs of applications from Caltech’s Kennedy Lab, studying biochemical signal transduction systems in central nervous system synapses. The configuration, integrated by Sun Microsystems and CACR’s technical support team, consists of 4 AMD Opteron 8218 dual core processors, with 64 GB main memory.

Technical Summary:

Architecture
  • Opteron Linux Server
Memory
  • 64 GB DDR2-667 main memory
Processors
  • 4 dual core AMD Opteron 8218, 2.6 GHz
  • 1 MB Level 2 cache per core
Network Interconnect
  • PCI-x, PCI-Express
  • Gigabit Ethernet
Disk
  • nfs project work area data-store01/project-id
  • 400 GB SAS home dirs
  • zfs project work areas, /zfs[1,2]/project-id
Operating System
  • Red Hat Linux 2.6.9-42.0.3
Compilers
  • GNU: Fortran77, C, C++
  • PGI: F77, F90, C, C++
  • Pathscale 2.5: F90, C, C++
MPI
  • MPICH

4.  Available File Systems and Descriptions/Intended Usage

  • nfs mounted project work area, /data-store01/compbio, seen globally. RAID6, not backed up
    • Each project has a quota’d partition under this mount point, with subdirectories for each user within the project.
    • data-store01 is nfs exported from a dual processor, dual core AMD Opteron 870 (2 GHz) system with 16 GB of memory. A 16 port Areca controller hosts an 8 TB (raw) RAID6 disk array.
    • local home – seen globally
    • zfs[1,2] is exported from X4500’s hosting zfs file sistems, using virtual storage pools to support high performance and capacity.

5. Compiling/Preparing to Run

Available Compilers:

  • PGI: pgcc, pgCC, pgf90, pgf77
    • install root = /usr/local/PGI
  • PathScale: pathcc, pathCC, pathf90
    • install root = /usr/local/PathScale
  • Gnu: gcc, g++, g77
    • install root = /usr/bin

Available MPI:

  • mpich

Useful “home grown” commands for accessing the compilers and MPI utilities:

/usr/local/bin/pkgs  lists available packages on cellcenter1. Packages are items on the software stack which are commonly used, and necessarily need to have environment variables and pathes updated in order to be used properly. Available packages are:

  • mpich – Portable MPI from ANL
  • pathscale – The PathScale compiler suite – default compilers (v3.1)
  • python -[2.3.3]
  • pgi – The Portland Group compilers (v7.1 )
  • use –list (shows available packages)
  • use –what (shows what packages you are using )

In order to set your environment to use a particular package, do use pkgname. For example, to use the PathScale compilers do

use pathscale

which will update your PATH, LD_LIBRARY_PATH, MANPATH and set the PathScale enviroment variable to the appropriate installation base directory. To drop a package from your environment, do  drop pkgname. For example, to drop the PGI compilers from your environment do  drop pgi

6. Supported Debuggers and Debugging Tips

  • pathdb (PathScale Debugger)
  • pgdebug (PGI Debugger)

7. Getting Help/Communicationg with Other Users/Staff

Send mail to cacr-cellcenter1-support at cacr.caltech.edu. CACR technical support is available during standard business hours (M-F, 8am to 5pm); after hours responses are as time permits.

8. Expectations About System Down Times/News

Scheduled Preventive Maintenance (PM) is Monday from 0900 to 1300. CACR Operations will not always take the full PM for systems work. If you would like to schedule benchmarking or test runs with dedicated access to the entire system, asking cacr-cellcenter1-support for a portion of PM time is fine and encouraged.

News about operational changes (e.g. system software upgrades, file system policy changes, dedicated runs) will be posted using news. New news items since last ssh’ing to the head node will be displayed automatically.

Using news:

  • /usr/local/bin/news -help
  • Usage:
    • news  prints all new news items
    • news X  prints news item “X”
    • news -a prints all news items
    • news -l prints names of all news items
    • news -h prints this message

9. Miscellaneous System Software

  • Tell us what you’d like!

10. Performance

Coming Soon.

11. Policies

All users are expected to adhere to the CACR Computing Policies.