Seaborg Decommissioned January 2008

• Overview
• Archiving & Retrieving User Disk Storage
• Moving to Other NERSC Systems
• Software Considerations
• Additional Information

The NERSC IBM SP RS/6000 Power3 system, named Seaborg, was made available to NERSC users in January 2001. It was retired after the end of the 2007 Allocation Year, on January 8, 2008. Seaborg is not available as an MPP Resource for Allocation Year 2008.

Users should back up all valuable /scratch data to HPSS as it will be DELETED when Seaborg is decommissioned.

• October 18, 2007 - Begin Archiving of inactive user home directories to HPSS (see below)
• November 1, 2007 - No new user accounts will be added; USG supported software will be frozen.
• January 1, 2008 - Seaborg running with limited support contract. All important /scratch data should be moved to HPSS prior to January 1st as a precautionary measure. If Seaborg were to suffer a major outage it is likely the machine would not be restored.
• January 7, 2008 - Last day of Allocation Year 2007.
• January 7, 2008 16:00 Pacific Time - Seaborg Batch Queues and Running Jobs Stopped.
• January 7, 2008 16:00 - 23:59 Pacific Time - All MPP Production systems down for end of year accounting.
• January 8, 2008 00:01 Pacific Time - Seaborg User Logins Re-enabled for users to backup /scratch data only (no running jobs).
• January 8, 2008 16:00 Pacific Time - Seaborg User Logins Disabled for final time. Users will have until 16:00 PT to back up all data from /scratch directories.

Archiving User Disk Storage

User $HOME directories will be backed up to user HPSS accounts by January 15, 2008. User logins will be disabled on January 8th, 2008 so there is a one week interval where users may not have access Seaborg $HOME directory data. If there are files from your Seaborg $HOME directory to which you must have immediate access, please copy them to HPSS or another system before access to Seaborg is terminated.

All files in $SCRATCH will be deleted after January 8, 2008. Please copy any files you wish to retain from $SCRATCH to HPSS or another system before that date.

User home directories will be archived to the HPSS storage system as a tar file in the user's HPSS directory. The name of the file will be [username].seaborg.[date].tar.gz. Users can retrieve this file from the NERSC HPSS storage system in order to use files from their Seaborg home directory on other systems.

Retrieving Archived Data

Moving to Other NERSC Systems

After the decommission of Seaborg, it is expected that the largest, most powerful system at NERSC will be the Cray XT system Franklin. At the present time, Franklin is configured to favor jobs running on more than 4,000 CPU's. Seaborg codes running at more modest scales, such as 1-64 CPU's, might be a better fit on one of the other NERSC systems, such as Bassi or Jacquard.

Seaborg codes which rely heavily on mathematical libraries such as NAG or IMSL should be moved to Bassi (NAG) or Jacquard (NAG or IMSL). There is no expectation at this time that IMSL or NAG will ever be available on Franklin.

Seaborg codes which make heavy use of scripting languages (Perl, Python, Java) should be moved to Bassi or Jacquard, as these sorts of scripts cannot be run on the compute nodes of Franklin.

Hybrid MPI/OpenMP codes will run on Franklin, but there are only two cores per node on Franklin. Pure OpenMP codes should probably move to Bassi with 8 CPU's per node.

Users who wish to continue working on an IBM system with the AIX environment and LoadLeveler batch system can move to Bassi. While Bassi provides a similar user environment, users should be aware of significant differences such as:

• 8 processors per node instead of 16 on seaborg
• particular memory considerations
• Machine Charge Factor of 6.0
• regular batch jobs up to 384 processors

An overview of other systems at NERSC, such as the Linux cluster Jacquard and the SGI Altix DaVinci can be found at the NERSC Science-Driven Systems page. Both Jacquard and DaVinci are significantly different from Seaborg:

• Jacquard has 2 processors per node, and DaVinci has a single node with 32 CPU's
• Both Jacquard and DaVinci run Linux operating system
• Jacquard uses the PBS batch system and the PathScale compiler suite
• DaVinci is generally intended for interactive visualization use, and the Intel compilers are available

Software Considerations

The following software at NERSC will be retiring along with Seaborg

• KAI compiler products such as KCC were actually retired by the vendor, Intel, in 2002
• pghpf compiler for SMP-style HPF fortran codes
• bvi "binary vi" text editor
• nano text editor
• xemacs
• ddd debugger
• vampir and vampirtrace performance analysis tools
• xprofiler
• MPE
• hpmtoolkit
• CEPBA tooklit
• totmem
• CMake
• Atlas 3.7.2
• ccSHT
• WSMP Watson Sparse Matrix package.
• Cernlib (except on PDSF)
• Gaussian98
• MCTDH
• Vast f77 to f90 translator
• MPPL f77 to f90 translator
• SPIKE
• SvPablo and sddf
• Zori
• ZeroFault
• Cumulvs
• Pvode (replaced by SUNDIALS)
• dx
• MDSplus
• xdiff
• (Watch for Updates)

The basic IBM SP software environment will remain available on Bassi: AIX, LoadLeveler, POE, LAPI, as, xlf, xlc, xlC, pdbx, PE Benchmarker, ESSL, ESSL-SMP, PESSL, MASS libraries, sptools, etc.. Versions of software on Bassi will, in many case, be newer than the final versions on Seaborg. See the Bassi Software Page for a full list of available software.

The general Linux/GNU environment, including emacs, gcc, java, cvs, perl, python, tcl/tk, autoconf, automake, vim, etc., will be available in part on the AIX system Bassi (often through modules) and also part of the native Linux environment on Franklin, Jacquard and Davinci. See the full software listings for Franklin, Jacquard, and DaVinci,

The DDT debugger is available on Franklin, Bassi, Jacquard and Davinci through a module. The Totalview debugger will be available on Bassi and Jacquard. The GNU gdb debugger is available on Franklin, Jacquard and DaVinci.

The performance monitoring tool IPM is available through a module on Bassi, Jacquard and Davinci. It is planned for Franklin. The TAU toolset is available on Franklin, Bassi and Jacquard through modules. The PAPI toolset is available on Franklin, Bassi, Jacquard and DaVinci through modules.

Mathematical Libraries

The NAG, Hypre and SLEPc libraries are available through modules on Bassi and Jacquard. NAG Mark 19 will not longer be available.

The Parpack and Petsc libraries are available on Franklin, Bassi and Jacquard through modules.

The Aztec library is available on Franklin and Bassi through a module.

The Lapack library is available on Bassi through a module, and on Franklin and Jacquard as part of the ACML library.

The Scalapack Library is available on Bassi and Jacquard through a module, and it is part of the Libsci library on Franklin.

The SPRNG random number library is available on Jacquard through a module.

The SuperLU libraries are available on Franklin, Bassi and Jacquard through modules.

The FFTW library is available on Franklin, Bassi, Jacquard and DaVinci through a module.

The GNU Scientific Library, gsl, is available on Jacquard through a module.

Visualization Libraries and Applications

In regard to the NCAR visualization library, version 4.4.0 and 4.4.2 are available on Bassi in both 32- and 64-bit addressing. On DaVinci version 4.3.1 in double precision, and version 4.4.0 and 4.4.2 are available. On Jacquard, version 4.4.0 and 4.4.2 are available. The ncaru utilities are available on Bassi through a module. Version 4.1.1 will not longer be available.

The visualization application IDL is available on Franklin, Bassi, Jacquard and DaVinci through a module. The visualization application vmd is available on DaVinci and Jacquard through a module. The visualization applications AVS-Express, Ensight and Rasmol are available on DaVinci through modules. The Imagemagick visualization tools are available on Jacquard through a module, and in the native environment of DaVinci. The visualization application Grace is available on Bassi, Jacquard and DaVinci through a module. Gnuplot is part of the environment on Franklin, Jacquard and Davinci, and available through a module on Bassi. The PGPlot graphics library is available on Bassi and Jacquard through a module. gs, Ghostscript, is part of the native Linux environment on Franklin and DaVinci, and available through a module on Bassi and Jacquard. xv is available on Jacquard. The PGPLOT library is available on both Bassi and Jacquard through a module.

Other Libraries and Applications

The HDF, HDF5 netCDF and NCO I/O libraries are available through modules on Franklin, Bassi, Jacquard and DaVinci. The netCDF browser ncview and the CFITSIO library are available on Bassi, Jacquard and DaVinci through modules.

Global Arrays (ga) is available through a module on Franklin, Bassi and Jacquard.

Titanium, UPC and Blast will be available on both Bassi and Jacquard.

The climate model CCSM, supported by NCAR, is available on Bassi and Jacquard, and NCAR is working on a port to Franklin. Contact NCAR for details.

Globus is available on Bassi and Davinci through a module.

Other parts of the ACTS Collection, such as Trilinos, SUNDIALS and TAO, should be available soon on Bassi and Jacquard through modules. Some additional parts of ACTS may also be available on Franklin. Overture will only be available on Jacquard.

Zoltan is available on Bassi through a module.

The XML2 library is available on Bassi, Jacquard and Davinci through a module.

Acroread will be available on Bassi (through a module) and Jacquard (native).

MySQL will be available on Bassi & Jacquard through a module, and on Franklin as part of the normal user environment.

The CTSS utilities for reading old CTSS format files in HPSS is available on Bassi.

The udunits software is available on Davinci through a module.

The chemistry application Amber is available on Franklin, Bassi and Jacquard through a module. The chemistry application Namd is available on Bassi, Jacquard and Davinci through a module. The chemistry applications Gamess, Gaussian (g03), Molpro, NWChem and Q-Chem are available on Bassi and Jacquard through modules. The chemistry application Gromacs is available on Jacquard through a module.

The materials science application Vasp is available on Franklin, Bassi and Jacquard through a module. The applications Wien2k and Lammps are available on Bassi through modules.

For more information on software, see the NERSC Software Page.

Additional Information

NUG Presentation by Jim Craw, September 17, 2007, Seaborg Decommission: Timeline and Data Retention Issues (PDF).     (PPT version).

Article "Goodbye Seaborg: IBM Supercomputer Workhorse That Has Produced Great Scientific Results Will Retire," in the September 2007 NERSC News (PDF).

Article "Cray Wins $52 Million Supercomputer Contract with NERSC" from LBNL Computing Sciences News, August 10, 2006.

As details of the process develop, this page will be updated.