The XL-fortran and Visual Age C/C++ compilers was updated with the latest maintenance packages from december-2004.
Updated packages:
memdbg.aix50.adt 4.4.3.3
vac.C 6.0.0.10
vac.msg.en_US.C 6.0.0.2
vacpp.cmp.aix50.lib 6.0.0.9
vacpp.cmp.core 6.0.0.11
vacpp.cmp.include 6.0.0.9
vacpp.cmp.tools 6.0.0.9
vacpp.memdbg.aix50.lib 6.0.0.6
vacpp.memdbg.aix50.rte 6.0.0.9
vacpp.msg.en_US.cmp.core 6.0.0.7
vacpp.samples.ansicl 6.0.0.6
xlfcmp 8.1.1.8
xlfcmp.msg.en_US 8.1.1.3
xlfrte 8.1.1.8
xlfrte.aix51 8.1.1.7
xlopt.aix50.lib 1.3.2.5
xlopt.tools 1.3.2.4
xlsmp.aix50.rte 1.5.0.0
xlsmp.msg.en_US.rte 1.5.0.0
xlsmp.rte 1.5.0.0
Software
distcc + ccache on fimm
The distributed C/C++ compiler distcc and compiler cache ccache was installed on the linux cluster fimm.bccs.uib.no. Both are by default calling the system 'gcc' compiler, but can also call other compilers.
distcc will speed up compile jobs by distributing the build over a cluster of nodes (currently 3 dual cpu Pentium4 Xeon nodes = 12 virtual cpus). To speed up builds using distcc, simply specify 'make -j12 CC=distcc'.
ccache will keep a cache of object files generated during builds, and re-use them when it sees that the exact same source is being rebuilt using the exact same compiler switches. If you're doing lots of "make clean; make" on the same sources, ccache will speed it up a lot! All you need to do is to specify 'make CC=ccache'.
distcc and ccache can also be used together via 'make -j12 CC="ccache distcc"'.
distcc will speed up compile jobs by distributing the build over a cluster of nodes (currently 3 dual cpu Pentium4 Xeon nodes = 12 virtual cpus). To speed up builds using distcc, simply specify 'make -j12 CC=distcc'.
ccache will keep a cache of object files generated during builds, and re-use them when it sees that the exact same source is being rebuilt using the exact same compiler switches. If you're doing lots of "make clean; make" on the same sources, ccache will speed it up a lot! All you need to do is to specify 'make CC=ccache'.
distcc and ccache can also be used together via 'make -j12 CC="ccache distcc"'.
Mathematical Acceleration Subsystem libraries upgraded
The Mathematical Acceleration Subsystem (MASS) libraries was upgraded from v3.1 to v4.1.
Ref:
Features and benefits
The Mathematical Acceleration SubSystem (MASS) library is an approach to increase the performance of a code. It provides high performance versions of a subset of mathematical intrinsic functions. To do this, it sacrifices a small amount of accuracy. Compared to the standard mathematical library, libm.a, the MASS library can only differ in the last bit. This is not significant in most programs. The libmass.a library can be used with either Fortran or C applications and runs under AIX. As all functions in the MASS library use the same syntax as the standard functions it replaces, you do not have to make any changes in the source code to use it. MASS also offers a vector version for some of the functions. The vector functions are more efficient than the scaler ones, but require that the source code is rewritten. There are two versions of the vector MASS library. The first library, libmassv.a, contains vector function subroutines that run on the entire IBM RS/6000 family. The second library, libmassvp4.a, contains the subroutines of libmassv.a and adds a set that is tuned for and based upon the Power4 architecture.
Example of use:
To use the standard MASS library, link your program with -lmass. For example,
% xlf90 -O3 -qarch=auto -qtune=auto x.f -lmass
% cc -O3 -qarch=auto -qtune=auto x.c -lmass -lm
As -lmass replaces some of the functions in -lm, you must always link it before you link with -lm. xlf90 and its variants link automatically with -lm.
Ref:
Features and benefits
The Mathematical Acceleration SubSystem (MASS) library is an approach to increase the performance of a code. It provides high performance versions of a subset of mathematical intrinsic functions. To do this, it sacrifices a small amount of accuracy. Compared to the standard mathematical library, libm.a, the MASS library can only differ in the last bit. This is not significant in most programs. The libmass.a library can be used with either Fortran or C applications and runs under AIX. As all functions in the MASS library use the same syntax as the standard functions it replaces, you do not have to make any changes in the source code to use it. MASS also offers a vector version for some of the functions. The vector functions are more efficient than the scaler ones, but require that the source code is rewritten. There are two versions of the vector MASS library. The first library, libmassv.a, contains vector function subroutines that run on the entire IBM RS/6000 family. The second library, libmassvp4.a, contains the subroutines of libmassv.a and adds a set that is tuned for and based upon the Power4 architecture.
Example of use:
To use the standard MASS library, link your program with -lmass. For example,
% xlf90 -O3 -qarch=auto -qtune=auto x.f -lmass
% cc -O3 -qarch=auto -qtune=auto x.c -lmass -lm
As -lmass replaces some of the functions in -lm, you must always link it before you link with -lm. xlf90 and its variants link automatically with -lm.
batch scheduler upgraded on linux cluster
The Maui scheduler was upgraded from v3.2.5 to v3.2.6p9. This should help with the fair-share scheduling and backfill. Give lower priority to those who use a lot of cputime, and prioritize the once who run less.
Check 'showq' or 'showq -i' to see what priority your job has to get started. Complain to hpc-support@hpc.uib.no if you feel you're not getting high enough priority.
NFR-users should get top priority as long as they're not using more than 75% of the cputime.
Check 'showq' or 'showq -i' to see what priority your job has to get started. Complain to hpc-support@hpc.uib.no if you feel you're not getting high enough priority.
NFR-users should get top priority as long as they're not using more than 75% of the cputime.
Intel compilers patched
The intel 'icc' and 'ifort' compilers on the linux cluster was patched with the latest fixes:
l_cc_pc_8.0.066_pe070.1
l_fc_pc_8.0.046_pe050.1
GSL upgraded on the linux cluster
GSL - GNU Scientific Librarywas upgraded to v1.5 on the linux cluster.
It's installed in /localnet/gsl/.
CC=icc ./configure --prefix=/localnet/gsl-1.5
make
make check
make install
It's installed in /localnet/gsl/.
CC=icc ./configure --prefix=/localnet/gsl-1.5
make
make check
make install
ADF 2004.01 installed on regatta
ADF version 2004.01 has been installed and made the default version on the regatta. Use 'module load adf' to use it.
Major improvements with respect to the 2003 version include:
- New modules for the ADF graphical user interface, now more user-friendly than ever
- Various improvements for geometry optimizations and (analytic) Hessian calculations
- Availability of hybrid xc energy functionals, such as B3LYP
- Much new functionality: chiral optical properties, NBO interface, many speed-ups, ...
For complete list of changes, please see http://www.scm.com/Doc/Doc2004.01/Updates/page2.html
Gaussian 03 C.02 installed on regatta
Gaussian 02 C.02 has been installed on the regatta. Use 'module load g03c02' to set up your environment for this version. Please test it, and report any problems to hpc-support@hpc.uib.no.
For information on new features and bugfixes in this release, read http://www.gaussian.com/g_tech/g03_rel.htm.
For information on new features and bugfixes in this release, read http://www.gaussian.com/g_tech/g03_rel.htm.
OpenSSH upgraded (with S/Key)
OpenSSH was upgraded to version 3.8.1p1 and configured to support S/Key autentication (OTP). S/Key autentication is a one-time password system that makes it possible to log in securely from any internet cafe without worrying about anybody logging the password that was used during log-in.
maui scheduler minor upgrade
The Maui batch scheduler was upgraded from version 3.2.6p6-snap.1070912066 to 3.2.6p6-snap.1079990700. Hopefully this should fix a memory leak, which has forced us to restart the scheduler every second week to keep it from crashing.