On Tuesday, May 16th, SCV will perform a major operating system
upgrade to its linux cluster, along with login nodes: skate and
cootie. The systems will be upgraded to BU Linux 4.5 Server Edition,
also known as Zodiac.  Zodiac is based on a variant of the Red Hat
Enterprise Linux 4 distribution.

Some of the major software changes are as follows:

  Software                 Old Version     New Version
  Operating System         RH 7.2          BU Linux 4.5 Server
  Linux Kernel             2.4.20          2.6.9
  Glibc                    2.2.4           2.3.4
  System gcc               2.96            3.4.5
  Intel compilers          8.0.1           9.0
  Portland Group Compilers 3.2             no longer available
  MPICH                    1.2.5..10       1.2.6..14b

Any code compiled using the Portland Group compilers will have to be
recompiled using either gcc or Intel (Intel will be the only option
for Fortran 90).  All programs using mpi will have to be recompiled to
use the new version of mpich.  While other code may run as is, it
should be recompiled using the new compilers in order to take
advantage of compiler improvements and fixes.

Slight changes will need to be made to the parallel job batch
submission scripts.  The ROOT variable pointing to the old version of
mpich will have to be replaced by one of the two new versions of mpich
(/usr/local/mpichgm/gcc/bin or /usr/local/mpichgm/intel/bin).
Alternatively you can leave the ROOT variable blank and use the mpich
defined by your environment settings.  Your environment settings can
be easily controlled using 'modules' command
(http://scv.bu.edu/SCV/linux-cluster/module.html) Also the --gm-recv
and --gm-kill arguments to mpirun are no longer required.

You can review these mpi submit script changes by comparing provided
examples:
 old:  http://scv.bu.edu/pbs_scripts/pbsmpi.sh.old.txt
 new:  http://scv.bu.edu/pbs_scripts/pbsmpi.sh.new.txt

If you would like to test your code and work on porting ahead of the
upgrade, we will be able to provide you access to a test system upon
request.  Please e-mail help@skate.bu.edu if you need assistance.

- SCV Sysadmins