Hexagon has updated software and libraries. To get the performance and stability improvements the applications needs to be recompiled.

MPI
xt-mpt 5.1.0 -> 5.1.1

Compilers/wrappers/debug
PGI 10.8.0 -> 10.9.0
chapel 1.1.1 -> 1.2.0
xt-asyncpe 4.3 -> 4.4
stat 1.1.0 -> 1.1.1

Scientific libraries
PETSc 3.1.02 -> 3.1.03

NOTES:

xt-mpt

- New SHMEM environment variable, SHMEM_MEMINFO_DISPLAY, to
display the layout of the SHMEM memory regions.

Several bugs were also fixed in this release and are listed below.

742474,744363,754252,763505,764480 - Prevent attempted
oversubscription
of memory during shmem_init() on XT systems

765571, 760251, 761685 - compiler warning about gethostbyname
for all MPI programs


xt-asyncpe
Bugs fixed in this release:
747448 f77 command for PGI should be deprecated
759747 Add LIBSCI_X86_64 variable for cce PE testing
762235 Intel ftn ld -openmp vs xtpe-barcelona for libsci library
- mult
def libifcore.a & libifcoremt.a
764431 Left over (-p acml) failures from the EDG-MERGE with both
ftn and cc
764491 Add accelerator targeting module
764504 linux-f77 script tries to link in seastar libraries on XE
system
764942 Legal C++ code fails with multiple instance error on esLogin
765602 xt-asyncpe module should define -D__x86_64__ when
PrgEnv-gnu is
loaded

Differences:
------------
Beginning with xt-asyncpe 4.4, the f77 script for pgi is now aliased to ftn. In a future release, it will be removed altogether.

PETSc
PETSc-3.1.03 module includes ParMetis-3.1.1 library, which can be
called
through PETSc's API. The Cray PETSc-3.1.03 is equivalent to the
official
patch release of PETSc-3.1-p4 by Argonne National Laboratory, and
allows
users to install SLEPc-3.1 package (an eigenvalue solver package from
Universidad Politecnica de Valencia).

Bugs fixed in this release:
763837 petsc-complex will not link -dynamic

PGI
Features of PGI 10.9.0 are documented at:
http://www.pgroup.com/doc/pgiwsrn109.pdf
The following bugs are fixed in the PGI 10.9.0 release.
763009 pgcc -O3 PGC-S-0000-Internal compiler error [TPR 17173]
763428 cc20 option on -ta=nvidia causes error [17191]
764082 PGI internal compiler error with COPYIN and THREADPRIVATE
clause [17213]

New cost command is available on hexagon. The new command conforms with the NOTUR standard and has the same basic functionality as on the other NOTUR resources.

cost - will show your used CPU hours for the current allocation period.
cost -p - will show total used CPU hours of your connected projects.
cost -P - will show report for another allocation period.

Reference: http://www.bccs.uni.no/hpcdoc/Job_execution_(Hexagon)#Cost_command

The following software/libraries have been updated on hexagon. Users are encouraged to recompile their programs to gain any performance and stability benefits.

MPI
xt-mpt 5.0.1 -> 5.1.0

Math-libs
xt-libsci 10.4.7 -> 10.4.8
PETSc 3.1.01 -> 3.1.02
GA 4.3.1

Compilers and wrappers
PGI 10.6.0 -> 10.8.0
GCC 4.5.0 -> 4.5.1
xt-asyncpe 4.2 -> 4.3

Performance tools and debuggers
xt-craypat/apprentice2 5.1.1 -> 5.1.2
MRNet 2.2.0.1 -> 3.0.0
stat 1.0.0 -> 1.1.0

NOTES:

xt-craypat
General
* more complete support for PGAS, UPC and CAF programs
pat_build
* the 'caf' and 'upc' trace groups now include tracing the 'pgas' group
* some shared objects of executable files that pat_build executed could
not be found - fixed truncation of LD_LIBRARY_PATH
* update Global Array trace wrappers
* fix tracing pthread functions using GNU PrgEnv
* fix tracing user-defined functions for GNU 4.5.0 Fortran

Bugs closed since 5.1.1 release
763880 App2/5.1.2: HW counters overview shows negative numbers
763877 App2/5.1.2: HW counters overview shows more than 100%
763439 tracing user-defined functions results in seg fault for GNU
Fortran 4.5.0
762905 No CAF specific info is provided when instrumenting a CAF code with -g caf
762904 craypat provides misleading info on PGAS codes running on XE6

MPI
The following features were added to MPT 5.1.0:

- Totalview message queue debugging is now supported on XE systems.
This feature can be enabled by setting the MPICH_MSG_QUEUE_DBG
environment variable. For more information about this feature see
the intro_mpi man page.

- SHMEM users can now get the SHMEM version displayed by setting
the SHMEM_VERSION_DISPLAY environment variable when running on
either XT or XE systems.

In addition the following features were added in MPT updates since
the MPT 5.0.0 release and are also included:

- The MPI single copy optimization feature is now enabled by default.
The feature can be disabled by using the MPICH_SMP_SINGLE_COPY_OFF
env variable. For more information about this feature see the
intro_mpi man page.

- Additional information is also now emitted with MPI tracebacks to
more easily correlate them with console messages. Also certain
memory
registration errors will now have the virtual memory maps dumped to
aid in users debugging their programs.

- Cray SHMEM users also can use the new SHMEM_BTE_THRESHOLD env
variable to adjust when SHMEM uses the Block Transfer Engine(BTE)
for off-node transfers.

Several bugs were also fixed in this release and are listed below.

Bugs fixed:
761094,760949,763512,762928 - Fix bytes_transferred field in the gni
netmod LMT RDMA write path
763677,760868 - Fix for LMT path for MPI_Issend hangs


xt-asyncpe
Bugs fixed in this release
760967 MPICH2 tests failing for -sdefault64 -dynamic calling
MPI_Initialized( flag, ierr ) - bad flag returned
761681 Cannot override PGI -tp option from xtpe-* module
763605 mpi applications using pgi and default64 fail
763724 "ftn -default64" is no longer adding "-i8 -r8" to PGI
compilations.
763787 empty parameter reference causes syntax error

xt-libsci
LibSci 10.4.8 includes bugfixes.
761427 xt-libsci/10.4.3 with dynamic libraries
763728 Remove "conflict xt-libsci-gemini" from xt-libsci modulefiles

PETSc
The PETSc 3.1.02 release contains PETSc 3.1-p4 patch set and provides
performance improvements in ATF-CASK SpMV Multiply Kernels PETSc for
AIJ format.

Bugs fixed in this release:
763445 Problem with PetscSynchronizedFlush
763494 Problem with variable definition files (PETSC_LIB_DIR is not
set in the conf/variables)

More detailed information about the official PETSc-3.1 release is
available at
http://www.mcs.anl.gov/petsc/petsc-as/documentation/changes/31.html
SuperLU-4.0 information can be found at
http://crd.lbl.gov/~xiaoye/SuperLU/#superlu

Known problem:
--------------
Missing library entry points in the PETSc complex dynamic libraries,
for non-GNU libraries only.
763837 petsc-complex will not link -dynamic

MRNet
Update to the 3.0 release of the MRNet library.

MRNet 3.0 release notes:
http://www.paradyn.org/mrnet/release_3.0/README

MRNet 3.0 Programmer's Guide:
http://www.paradyn.org/mrnet/release_3.0/mrnet_3.0.html

GA
This is the initial release of Global Arrays Library.
Global Arrays is a portable Non-Uniform Memory Access (NUMA) shared-
memory programming environment for distributed and shared memory
computers. It augments the message-passing model by providing
a shared-memory like access to distributed dense arrays.

For more information visit:
http://www.emsl.pnl.gov/docs/global/ga.html

GCC
The following bugs are fixed in the gcc 4.5.1 release.
760192 GNU gfortran OpenMP - untied task accesses threadprivate -
non-conforming but no msg [44085]
763453 seg fault in gcc 4.5.0

PGI
Features of PGI 10.8.0 are documented at:
http://www.pgroup.com/doc/pgiwsrn108.pdf
The following bugs are fixed in the PGI 10.8.0 release.
761844 internal compiler error [17079]

Several software libraries and programs have been updated on hexagon.
The full pdf-announcement from Cray can be read from http://docs.cray.com/books/S-9401-1008//S-9401-1008.pdf a summary is given below.

MPI and wrappers
xt-mpt 5.0.1 -> 5.0.2
xt-asyncpe 4.1 -> 4.2

Compilers and debug tools
gcc 4.4.4 -> 4.5.0
ATP 1.0.2 -> 1.0.3
gcc-mpc 0.8.1
gcc-gmp 4.3.2
gcc-mpfr 2.3.1 -> 2.4.2

Scientific libraries
netcdf 4.0.1.3 -> 4.1.1.0
hdf5 1.8.4.1 -> 1.8.5.0
petsc 3.1.00 -> 3.1.01
xt-libsci 10.4.6 -> 10.4.7

Performance tools
xt-craypat 5.1.0 -> 5.1.1
apprentice2 5.1.0 -> 5.1.1
xt-papi 3.7.2.0.5 -> 4.1.0

Notes for xt-mpt
The following features were added to MPT 5.0.2:

- The MPI single copy optimization feature is now enabled by default.
The feature can be disabled by using the MPICH_SMP_SINGLE_COPY_OFF
env variable. For more information about this feature see the
intro_mpi man page.

- Additional information is also now emitted with MPI tracebacks to
more easily correlate them with console messages. Also certain
memory
registration errors will now have the virtual memory maps dumped to
aid in users debugging their programs.

- Cray SHMEM users also can use the new SHMEM_BTE_THRESHOLD env
variable to adjust when SHMEM uses the Block Transfer Engine(BTE)
for off-node transfers.

Several bugs were also fixed in this release.