OS Upgrade

This page will provide information on caveats after specific OS upgrades. Please, refer to this information of you encounter problem as described.

Scientific Linux 4.4 from 3.0.5


Natively compiled libraries

Under Scientific Linux 44, the following library versions (and greater) are natively compiled: SL06g, SL07a, SL07b, SL07c, ... etc ... You can safely compile your code and work with those libraries.

Information for site administrators: In order to provide native support, the following tag had to be released
 SL06g -> SL06g_2
SL07a -> SL07a_3
SL07b -> SL07b_2
SL07c -> SL07c_2

Please, update your libraries rec-compile your libraries before and after the upgrade for consistency.

Non natively compiled libraries

There are however no guarantees that a mix of non-natively compiled libraries and natively compiled private code would work. Hence, the instructions below may work for some users but in no case represents a confirmation of full functionality. Especially, if you encounter a symbol mangling issue (symbols not being found in STAR libraries), it would likely be an indication of an incompatibility.

Library SL05e < version <= SL06f

Are supported via backward compatibility links to Scientific Linux 3.0.5 natively compiled libraries.

Information for users/all: the following issues are known:
  • The compiler may spit the following warning while compiling
    error: extra `;'
    This problem appears due to the use of the -pedantic option in our compilation options. Unfortunately, not all the pedantic issues were caught and SL44 compiler is stricter in that regard.
    To circumvent this problem, either fix your user code or use the following recipe - the example is given for STAR Library SL05c (please adapt for other libraries) ; this needs to be done only once
    cvs co -rSL05c mgr/
    sed "s/-pedantic //" mgr/ConsDefs.pm >mgr/ConsDefs.pm.new
    mv -f mgr/ConsDefs.pm.new mgr/ConsDefs.pm
    compile as usual ...

Library SL05f < versions <= SL05e

Are supported via backward compatibility link through Scientific Linux 3.0.2 .

Library versions <= SL04f

Are supported via backward compatibility links through RedHat 8.0 .

Instructions for administrators

SL4.4 out of the box may not work for the STAR typical environment and usage. The following issues were identified and need attention:

Kernel parameters adjustments

The following lines need to be added to /etc/sysctl.conf
vm.dirty_ratio = 10
vm.lower_zone_protection = 150
vm.dirty_writeback_centisecs = 500
Default for the last parameter is 500 but left in for consistency as we may need to adjust later. You can always test the changes under a running kernel conditions by instead modifying the equivalent /proc/sys/vm files but the settings would likely be lost at the next reboot unless you set them in sysctl.conf.

echo 150 >/proc/sys/vm/lower_zone_protection  
echo 10  >/proc/sys/vm/dirty_ratio
echo 500 >/proc/sys/vm/dirty_writeback_centisecs
ROOT 5.12.00 and ROOT4STAR adjustments
  1. For creating backward compatibility links in the STAR libraries
    • get a recent copy of the mgr/CreateLinks script (tag SL07d or newer)
    • go to the STAR library versions between L <= SL06f
    • execute the CreateLinks scripts with argument "init"
    Note: do NOT do this in a native library i.e. in any STAR libraries L >- SL06g
  2. Issue with log4cxx and incompatible libstdc++
    An incompatibility between libstdc++ versions was found when running root4star linked under older Scientific Linux (gcc) versions under SL4.4: root4star (backward compatible compiled) loads libstdc++.so.5 and log4cxx (native) loading libstdc++.so.6 . To avoid the issue, the work around is to ensure a copy of an older version of liblog4cxx exists in all backward compatible STAR libraries supporting the logger: this include SL05f < L <= SL06f. The recipe follows
    • Keep a copy of log4cxx from Scientific Linux 3.0.5 on your system before the upgrade. This is located in $OPTSTAR.
    • For each STAR Library L mentioned above, copy your saved liblog4cxx.so in $STAR/.$STAR_HOST_SYS/lib/ and $STAR/.$STAR_HOST_SYS/LIB/
  3. ...

Scientific Linux 5.3 from 4.4

Configuration and RPM list

General configuration

Distribution 

% cat /etc/redhat-release
Scientific Linux SL release 5.3 (Boron)

Default compiler version

ATTENTION: The STAR software stack will NOT compile and/or link properly with the default SL5.3 gcc version (it has problems interpreting FORtran codes hence linking will fail in  a few places and running may crash unexpectedly). You MUST upgrade and make 4.3.2 or greater the minimal version number.

% gcc --version
gcc (GCC) 4.3.2 20081007 (Red Hat 4.3.2-7)

To make gcc 4.3.2 the default, you could use the following quick helper script (you do not want to execute this twice)

#!/bin/sh
##### comp_switch.sh #################################
#
# Make GCC 4.3 the default system compiler
# Written by Chris Hollowell @ RACF
#

# gcc
mv /usr/bin/gcc /usr/bin/gcc41
mv /usr/bin/gcov /usr/bin/gcov41
mv /usr/bin/x86_64-redhat-linux-gcc /usr/bin/x86_64-redhat-linux-gcc41
ln -sfn /usr/bin/gcc43 /usr/bin/gcc
ln -sfn /usr/bin/gcov43 /usr/bin/gcov
ln -sfn /usr/bin/x86_64-redhat-linux6E-gcc43 /usr/bin/x86_64-redhat-linux-gcc

# g++
mv /usr/bin/c++ /usr/bin/c++41
mv /usr/bin/g++ /usr/bin/g++41
mv /usr/bin/x86_64-redhat-linux-c++ /usr/bin/x86_64-redhat-linux-c++41
mv /usr/bin/x86_64-redhat-linux-g++ /usr/bin/x86_64-redhat-linux-g++41
ln -sfn /usr/bin/g++43 /usr/bin/c++
ln -sfn /usr/bin/g++43 /usr/bin/g++
ln -sfn /usr/bin/x86_64-redhat-linux6E-g++43 /usr/bin/x86_64-redhat-linux-c++
ln -sfn /usr/bin/x86_64-redhat-linux6E-g++43 /usr/bin/x86_64-redhat-linux-g++

# gfortran
mv /usr/bin/gfortran /usr/bin/gfortran41
ln -sfn /usr/bin/gfortran43 /usr/bin/gfortran

 

AFS sysname

See Setting up your computing environment for more information related to the sysname.

 

RPM list

A reminder that some of those RPMs may have been created at BNL. See Additional software components "System Wide RPMs" for more information.

kernel-headers-2.6.18-164.6.1.el5
compat-libf2c-34-3.4.6-4
sl-release-notes-5.3-1
chkconfig-1.3.30.1-2
atk-1.12.2-1.fc6
libtermcap-2.0.8-46.1
readline-5.1-1.1
gawk-3.1.5-14.el5
elfutils-libelf-0.137-3.el5
binutils-2.17.50.0.6-9.el5
libart_lgpl-2.3.17-4
slang-2.0.6-4.el5
libgpg-error-1.4-2
lcms-1.18-0.1.beta1.el5_3.2
libgfortran-4.1.2-44.el5
gzip-1.3.5-10.el5
libusb-0.1.12-5.1
dmidecode-2.7-1.28.2.el5
perl-Digest-SHA1-2.11-1.2.1
iputils-20020927-45.el5
libFS-1.0.0-3.1
numactl-0.9.8-7.el5
acl-2.2.39-3.el5
mgetty-1.1.33-9.fc6
rcs-5.7-30.1
compat-glibc-2.3.4-2.26
dos2unix-3.1-27.2.el5
libattr-2.4.32-1.1
sqlite-3.3.6-2
keyutils-libs-1.2-1.el5
libmng-1.0.9-5.1
gmp-4.1.4-10.el5
libgfortran43-4.3.2-7.el5
beecrypt-4.1.2-10.1.1
compat-readline43-4.3-3
libXrender-0.9.1-3.1
libjpeg-devel-6b-37
redhat-menus-6.7.8-3.el5
libXres-1.0.1-3.1
libIDL-devel-0.8.7-1.fc6
sqlite-devel-3.3.6-2
compat-gcc-34-3.4.6-4
perl-libwww-perl-5.805-1.1.1
anacron-2.3-45.el5
readline-devel-5.1-1.1
freetype-devel-2.2.1-21.el5_3
gmp-devel-4.1.4-10.el5
audiofile-devel-0.2.6-5
gamin-devel-0.1.7-8.el5
perl-DateManip-5.44-1.2.1
keyutils-libs-devel-1.2-1.el5
db4-devel-4.3.29-9.fc6
libX11-1.0.3-9.el5
libXfixes-4.0.1-2.1
libXTrap-1.0.0-3.1
libXfontcache-1.0.2-3.1
compat-gcc-34-c++-3.4.6-4
fontconfig-2.4.1-7.el5
openldap-2.3.43-3.el5
alsa-lib-1.0.17-1.el5
libselinux-devel-1.33.4-5.1.el5
mesa-libGLU-6.5.1-7.7.el5
libgssapi-0.10-2
mx-2.0.6-2.2.2
python-sqlite-1.1.7-1.2.1
libselinux-utils-1.33.4-5.1.el5
python-iniparse-0.2.3-4.el5
mtools-3.9.10-2.fc6
glibc-utils-2.5-34
wget-1.10.2-7.el5
xorg-x11-apps-7.1-4.0.1.el5
libtool-1.5.22-6.1
ntp-4.2.2p1-9.el5_3.2
libXft-2.1.10-1.1
gail-1.9.2-1.fc6
pam-0.99.6.2-4.el5
redhat-artwork-5.0.9-1.SL.2
screen-4.0.3-1.el5
xorg-x11-proto-devel-7.1-9.fc6
e2fsprogs-libs-1.39-20.el5
openssl-devel-0.9.8e-7.el5
portmap-4.0-65.2.2.1
libXcursor-devel-1.1.7-1.1
pycairo-devel-1.2.0-1.1
emacs-common-21.4-20.el5
openssh-server-4.3p2-29.el5
quota-3.13-1.2.5.el5
pygtk2-devel-2.10.1-12.el5
tk-devel-8.4.13-5.el5_1.1
mesa-libGLU-devel-6.5.1-7.7.el5
libXi-devel-1.0.1-3.1
libXcursor-devel-1.1.7-1.1
libXfont-devel-1.2.2-1.0.3.el5_1
dbus-glib-0.73-8.el5
mesa-libGLU-6.5.1-7.7.el5
sendmail-8.13.8-2.el5
bind-utils-9.3.4-10.P1.el5
pam_krb5-2.2.14-10
systemtap-runtime-0.7.2-3.el5_3
Xaw3d-devel-1.5E-10.1
openldap-devel-2.3.43-3.el5
dbus-libs-1.1.2-12.el5
dbus-python-0.70-7.el5
avahi-qt3-0.6.16-1.el5_2.1
rpm-build-4.4.2.3-9.el5
redhat-lsb-3.1-12.3.EL
pm-utils-0.99.3-10.el5
gimp-print-4.2.7-22.2.el5
xorg-x11-fonts-truetype-7.1-2.1.el5
hal-0.5.8.1-38.el5
ImageMagick-6.2.8.0-4.el5_1.1
openafs-kernel-1.4.10-2.6.18_164.6.1.el5_1.1
xemacs-21.4.22-1
tcsh-6.16.00-1
filesystem-2.4.0-2
desktop-backgrounds-basic-2.0-37
pygobject2-doc-2.12.1-5.el5
emacs-leim-21.4-20.el5
libstdc++-4.1.2-44.el5
libjpeg-6b-37
libxml2-2.6.26-2.1.2.7
libxml2-2.6.26-2.1.2.7
sqlite-3.3.6-2
tcl-8.4.13-3.fc6
tcp_wrappers-7.6-40.6.el5
gmp-4.1.4-10.el5
procps-3.2.7-11.1.el5
glib2-devel-2.12.3-4.el5_3.1
make-3.81-3.el5
lapack-3.0-37.el5
indent-2.2.9-14.fc6
bc-1.06-21
hesiod-3.1.0-8
crash-4.0-7.2.3.el5_3.1
ethtool-6-2.el5
libvolume_id-095-14.20.el5_3
bison-2.3-2.1
ftp-0.17-35.el5
dev86-0.16.17-2.2
ctags-5.6-1.1
hdparm-6.6-2
compat-readline43-4.3-3
elfutils-libelf-0.137-3.el5
nspr-4.7.3-2.el5
blas-3.0-37.el5
libidn-0.6.5-1.1
libXfont-1.2.2-1.0.3.el5_1
audit-libs-1.7.7-6.el5
valgrind-3.2.1-6.el5
libtermcap-2.0.8-46.1
libXext-1.0.1-2.1
libXrandr-1.1.1-3.1
libXau-devel-1.0.1-3.1
libXcomposite-0.3-5.1
libfontenc-devel-1.0.2-2.2.el5
libattr-devel-2.4.32-1.1
glibc-headers-2.5-34
libxkbfile-1.0.3-3.1
gcc43-c++-4.3.2-7.el5
perl-libxml-perl-0.08-1.2.1
libXp-devel-1.0.0-8.1.el5
xorg-x11-xtrans-devel-1.0.1-1.1.fc6
blas-devel-3.0-37.el5
libtool-ltdl-devel-1.5.22-6.1
ncurses-devel-5.5-24.20060715
bzip2-devel-1.0.3-4.el5_2
libcap-devel-1.10-26
binutils-devel-2.17.50.0.6-9.el5
libXi-1.0.1-3.1
libXinerama-1.0.1-2.1
libXcomposite-0.3-5.1
gcc-4.1.2-44.el5
shadow-utils-4.0.17-14.el5
krb5-libs-1.6.1-31.el5_3.3
mysql-5.0.45-7.el5
libxml2-devel-2.6.26-2.1.2.7
ghostscript-fonts-5.50-13.1.1
pygobject2-2.12.1-5.el5
nfs-utils-lib-1.0.8-7.2.z2
python-numeric-23.7-2.2.2
postgresql-libs-8.1.11-1.el5_1.1
e2fsprogs-devel-1.39-20.el5
elfutils-libelf-devel-static-0.137-3.el5
xterm-215-8.el5
compat-openldap-2.3.43_2.2.29-3.el5
tcpdump-3.9.4-14.el5
ksh-20080202-2.el5
automake17-1.7.9-7
kernel-devel-2.6.18-164.6.1.el5
GConf2-2.14.0-9.el5
pygtk2-2.10.1-12.el5
gtk2-engines-2.8.0-3.el5
gd-2.0.33-9.4.el5_1.1
vim-X11-7.0.109-4.el5_2.4z
pam-0.99.6.2-4.el5
openldap-2.3.43-3.el5
mesa-libGL-devel-6.5.1-7.7.el5
which-2.16-7
libXext-devel-1.0.1-2.1
kbd-1.12-21.el5
yp-tools-2.9-0.1
authconfig-5.3.21-5.el5
mc-4.6.1a-35.el5
libXv-devel-1.0.1-4.1
libSM-devel-1.0.1-3.1
mysql-devel-5.0.45-7.el5
libXTrap-devel-1.0.0-3.1
libXfixes-devel-4.0.1-2.1
libXtst-devel-1.0.1-3.1
gail-1.9.2-1.fc6
apr-util-1.2.7-7.el5_3.1
libuser-0.54.7-2.el5.5
libXmu-devel-1.0.2-5
gail-devel-1.9.2-1.fc6
mesa-libGLU-devel-6.5.1-7.7.el5
gd-devel-2.0.33-9.4.el5_1.1
policycoreutils-1.33.12-14.2.el5
cups-1.3.7-8.el5_3.6
kdbg-2.0.2-1.2.1
selinux-policy-targeted-2.4.6-203.el5
libbonoboui-2.16.0-1.fc6
xorg-x11-xfs-1.0.2-4
xorg-x11-fonts-misc-7.1-2.1.el5
libgnomeprintui22-2.12.1-6
librsvg2-2.16.1-1.el5
openafs-1.4.10-1.1.1
pgi64-workstation-8.0-4
AdobeReader_enu-9.1.0-1
setup-2.5.58-4.el5
gnome-mime-data-2.4.2-3.1
termcap-5.5-1.20060701.1
glibc-common-2.5-34
yum-conf-53-1.SL
man-pages-2.39-12.el5
mailcap-2.1.23-1.fc6
zlib-1.2.3-3
zlib-1.2.3-3
pkgconfig-0.21-2.el5
libpng-1.2.10-7.1.el5_3.2
libart_lgpl-2.3.17-4
info-4.8-14.el5
libsepol-1.15.2-1.el5
expat-1.95.8-8.2.1
freetype-2.2.1-21.el5_3
cyrus-sasl-lib-2.1.22-4
libattr-2.4.32-1.1
atk-1.12.2-1.fc6
popt-1.10.2.3-9.el5
desktop-file-utils-0.10-7
ncurses-5.5-24.20060715
audiofile-0.2.6-5
m4-1.4.5-3.el5.1
bzip2-1.0.3-4.el5_2
libfontenc-1.0.2-2.2.el5
perl-5.8.8-18.el5
aspell-0.60.3-7.1
shared-mime-info-0.19-5.el5
file-4.17-15
blas-3.0-37.el5
gdb-6.8-27.el5
ed-0.2-39.el5_2
time-1.7-27.2.2
grep-2.5.1-54.2.el5
libogg-1.1.3-3.el5
pax-3.4-1.2.2
iptables-ipv6-1.3.5-4.el5
perl-Compress-Zlib-1.42-1.fc6
groff-1.18.1.1-11.1
libdaemon-0.10-5.el5
checkpolicy-1.33.1-4.el5
libdrm-2.0.2-1.1
iptstate-1.4-1.1.2.2
psutils-1.17-26.1
ltrace-0.5-13.45svn.el5
cyrus-sasl-plain-2.1.22-4
telnet-0.17-39.el5
gperf-3.0.1-7.2.2
swig-1.3.29-2.el5
rdist-6.1.5-44
ncompress-4.2.4-47
strace-4.5.18-2.el5_3.3
flex-2.5.4a-41.fc6
zip-2.31-2.el5
libXau-1.0.1-3.1
libgcrypt-1.2.4-1.el5
db4-4.3.29-9.fc6
tcl-8.4.13-3.fc6
ORBit2-2.14.3-5.el5
libgfortran-4.1.2-44.el5
nss-3.12.2.0-4.el5
libcroco-0.6.1-2.1
libdaemon-0.10-5.el5
gnutls-1.4.1-3.el5_2.1
libogg-1.1.3-3.el5
slang-2.0.6-4.el5
elfutils-libs-0.137-3.el5
cyrus-sasl-plain-2.1.22-4
libgomp-4.3.2-7.el5
compat-glibc-2.3.4-2.26
tcp_wrappers-7.6-40.6.el5
libXt-1.0.2-3.1.fc6
libXpm-3.5.5-3
libXp-1.0.0-8.1.el5
libXfixes-4.0.1-2.1
atk-devel-1.12.2-1.fc6
libXxf86vm-1.0.1-3.1
gtk+-1.2.10-56.el5
libXxf86dga-1.0.1-3.1
tcl-devel-8.4.13-3.fc6
libidn-devel-0.6.5-1.1
nspr-devel-4.7.3-2.el5
libtermcap-devel-2.0.8-46.1
glibc-devel-2.5-34
libXxf86misc-1.0.1-3.1
perl-HTML-Tagset-3.10-2.1.1
libstdc++43-devel-4.3.2-7.el5
compat-gcc-34-g77-3.4.6-4
openmotif22-2.2.3-18
grub-0.97-13.2
nss-devel-3.12.2.0-4.el5
libmng-devel-1.0.9-5.1
xorg-x11-xtrans-devel-1.0.1-1.1.fc6
libtool-ltdl-devel-1.5.22-6.1
gamin-devel-0.1.7-8.el5
blas-devel-3.0-37.el5
db4-devel-4.3.29-9.fc6
pstack-1.2-7.2.2
atk-devel-1.12.2-1.fc6
automake15-1.5-16
ncurses-devel-5.5-24.20060715
glib-devel-1.2.10-20.el5
audiofile-devel-0.2.6-5
libtiff-devel-3.8.2-7.el5_2.2
libstdc++43-devel-4.3.2-7.el5
libjpeg-devel-6b-37
libXrender-0.9.1-3.1
libXp-1.0.0-8.1.el5
libXcursor-1.1.7-1.1
libXxf86vm-1.0.1-3.1
libXres-1.0.1-3.1
libXv-1.0.1-4.1
tix-8.4.0-11.fc6
gcc-c++-4.1.2-44.el5
giflib-devel-4.1.3-7.1.el5_3.1
findutils-4.2.27-5.el5
libXft-2.1.10-1.1
openssl-0.9.8e-7.el5
module-init-tools-3.3-0.pre3.1.42.el5
kpartx-0.4.7-23.el5_3.2
mesa-libGL-6.5.1-7.7.el5
hicolor-icon-theme-0.9-2.1
newt-0.52.2-12.el5
autoconf-2.59-12
device-mapper-multipath-0.4.7-23.el5_3.2
neon-0.25.5-10.el5
openmotif-2.3.1-2.el5
vim-minimal-7.0.109-4.el5_2.4z
openjade-1.3.2-27
libxml2-python-2.6.26-2.1.2.7
m2crypto-0.16-6.el5.3
fipscheck-1.0.3-1.el5
logrotate-3.7.4-9
hwdata-0.213.11-1.el5
python-urlgrabber-3.1.0-5.el5
docbook-dtds-1.0-30.1
subversion-1.4.2-4.el5
gnupg-1.4.5-14
perl-DBD-MySQL-3.0007-2.el5
autofs-5.0.1-0.rc2.102
rhpl-0.194.1-1
libpcap-0.9.4-14.el5
parted-1.8.1-23.el5
audit-1.7.7-6.el5
vim-enhanced-7.0.109-4.el5_2.4z
perl-IO-Socket-SSL-1.01-1.fc6
libbonobo-devel-2.16.0-1.fc6
bitmap-fonts-0.3-5.1.1
cairo-1.2.4-5.el5
gtk2-2.10.4-20.el5
gnome-keyring-0.6.0-1.fc6
pycairo-1.2.0-1.1
scrollkeeper-0.3.14-9.el5
at-3.1.8-82.fc6
libwnck-2.16.0-4.fc6
arts-1.5.4-1
libutempter-1.1.4-4.el5
cvs-1.11.22-5.el5
GConf2-devel-2.14.0-9.el5
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device-mapper-1.02.28-2.el5
dbus-libs-1.1.2-12.el5
usermode-1.88-3.el5.2
libSM-devel-1.0.1-3.1
pango-devel-1.14.9-5.el5_3
lvm2-2.02.40-6.el5
openssh-clients-4.3p2-29.el5
smartmontools-5.38-2.el5
pygtk2-devel-2.10.1-12.el5
libXext-devel-1.0.1-2.1
xorg-x11-proto-devel-7.1-9.fc6
pam-devel-0.99.6.2-4.el5
libICE-devel-1.0.1-2.1
libXfont-devel-1.2.2-1.0.3.el5_1
libglade2-2.6.0-2
apr-1.2.7-11
libwmf-0.2.8.4-10.2
mdadm-2.6.4-1.el5
krb5-devel-1.6.1-31.el5_3.3
systemtap-0.7.2-3.el5_3
Xaw3d-devel-1.5E-10.1
openldap-devel-2.3.43-3.el5
dbus-glib-0.73-8.el5
avahi-0.6.16-1.el5_2.1
kdnssd-avahi-0.1.3-0.1.20060713svn.fc6
avahi-glib-0.6.16-1.el5_2.1
chkfontpath-1.10.1-1.1
gnome-desktop-2.16.0-1.fc6
xorg-x11-fonts-ISO8859-1-75dpi-7.1-2.1.el5
xorg-x11-fonts-75dpi-7.1-2.1.el5
eog-2.16.0.1-6.el5
gimp-help-2-0.1.0.10.1.1
openafs-client-1.4.10-1.1.1
pgi-workstation-sl3-5.1-6
nfs-utils-1.0.9-40

Special instructions

General

A blog page with compiler and specificities of sharing 32 and 64 bits architecture on the same node was created and accessible at You do not have access to view this node.

Instructions for administrators 

You must save a copy of libmysqlclient.so.14 from an SL44 system and copy it under your SL5 distribution. This is due to the fact that SL5 libmysql is of version 15.0.0 but our older code hard linked to verison 14.0.0 . Hence, if you want support for your old libraries, you must preserve a copy of libmysql.

Similarly, you will need to make a copy of liblog4cxx.so.9 .

Both could be copied in $OPTSTAR/lib/ under the 32 bits deployment.

 

Supported STAR libraries

Native support

Backward compatible libraries

 

 

Scientific Linux 6.2 from 5.3

Configuration and RPM list

General configuration

Distribution 

% cat /etc/redhat-release
Scientific Linux SL release 6.1 (Carbon)

Default compiler version

The default compiler coming with SL6 was installed.

% gcc --version
gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)

Other revisions are in /opt/gcc at BNL and this location is supported by the STAR login's 'setup' script. Note that an alternative to set another compiler location is supported via an environment variable named USE_GCC_DIR. See documentation Setting up your computing environment for more information.

The secondary compiler choice is gcc 4.6.3 .

AFS sysname

See Setting up your computing environment for more information related to the sysname. The sysname can be determined by the command

% fs sysname

On sites where the sysname is set to other values than what STAR/RHIC cell expects, please note that you can always set alternate sysname for your systems by using the folowing command (from a privileged account and at boot time):

 % fs sysname -newsys ppc_darwin_80 -newsys foo

The above adds two new sysname to the existsing system's default. This example is provided by the AFS manpages as well as at the bottom of our Setting up your computing environment page.

Special instructions

General

A blog page with compiler and specificities of sharing 32 and 64 bits architecture on the same node was created and accessible at You do not have access to view this node. This page was used since the SL5 32/64 bits transition.

New in SL6 - SIMD

Support for SIMD instructions may appear under SL6 (the large amount of currebt issues still make this a "if" as wide support for our sites will be rendered more difficult). Please note this page: SIMD instruction sets. SIMD instructions support will NOT guarantee ABI compatibility across hardware. THe STAR_HOST_SYS environment variable may be alterred accordingly.

ATTENTION: the introduction of SIMD instructions will also create a secondary issue: compiler bugs related to SIMD instructions are numerous. We hope for this situation to settle as SIMD instruction support matures. Therefore, only strictly approved compilers will be allowed in STAR. Any other minor/major version than the "approved" one cannot be supported. A table of acceptable gcc versions will be maintained on this page (compatibility links will not be created as they used to).

Instructions for administrators 

(TBC)

You must save a copy of libmysqlclient.so.14 from an SL44 system and copy it under your SL5 distribution. This is due to the fact that SL5 libmysql is of version 15.0.0 but our older code hard linked to verison 14.0.0 . Hence, if you want support for your old libraries, you must preserve a copy of libmysql.

Similarly, you will need to make a copy of liblog4cxx.so.9 .

Both could be copied in $OPTSTAR/lib/ under the 32 bits deployment.

Supported STAR libraries

Native support

Backward compatible libraries

 

RPM list

 

 

Scientific Linux 6.4 from 6.2

Configuration and RPM list

General configuration

Distribution 

% cat /etc/redhat-release
Scientific Linux release 6.4 (Carbon)

Default compiler version

The default compiler coming with SL6 was installed.

% gcc --version
gcc (GCC) 4.8.2 20140120 (Red Hat 4.8.2-15)

Our gcc compiler was backward and forward compatible with gcc 4.4.6 by using the devtoolset (repackaged).

Other revisions are in /opt/gcc at BNL and this location is supported by the STAR login's 'setup' script. Note that an alternative to set another compiler location is supported via an environment variable named USE_GCC_DIR. See documentation Setting up your computing environment for more information.

The secondary compiler choice is gcc 4.6.3 and we also supported 4.4.7 for an even smoother support.

sysname


The AFS canonical sysname for SL6 is x8664_sl6.

List of RPMs


The final list of RPMs is attached to this post as a text file for historical purposes (as well as helping setting up new systems).
 

Scientific Linux 7.3 from 6.2

Configuration and RPM list

General configuration

Distribution 

% cat /etc/redhat-release
Scientific Linux release 7.3 (Nitrogen)

Default compiler version

The default compiler coming with SL6 was installed.

% gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11)


Other revisions are in /opt/gcc at BNL and this location is supported by the STAR login's 'setup' script. Note that an alternative to set another compiler location is supported via an environment variable named USE_GCC_DIR. See documentation Setting up your computing environment for more information.

The secondary compiler choice is gcc 4.8.2 (so we connect smoothly with the past 4.8.2/SL6.5 and 4.6.3/SL6.2 library releases) and we also have 4.4.7 so we can go backward as far as SL11).

Specific to our environment

sysname

The AFS fs sysname for those systems is a canonical x8664_sl7.

STAR_HOST_SYS

Since the transition begins at SL7.3, gcc 4.8.5, the new base for STAR software is sl73_gcc485 and sl73_x8664_gcc485 for the 32 and 64 bits versions respectively.
Possible support for variation of SL version / gcc version combinations (each greater than the base) would go through those directories. Possible supports of SL7.x x < 3 and/or gcc versions lower than 4.8.5 would have to be made toward the sl64_gcc482 and sl64_x8664_gcc482 paths instead (in those cases, please fix the AFS sysname to be the one indicated as used for SL6).
 

Noticeable changes from 6.2

  • In the newer perl "." is not included as part of @INC
  • SL7 has no f77 / g77 - users need to be aware of that (or a soft-link for g77 to gfortran created to facilitate the transition)
  • While in previous SL6, we had repackaged libfl (as support for 32/64 was missing) but in SL7, the support is back so there will be NO need to install the BNL RPM (in other words, install SL7 flex packages for both 32 and 64 bits and this will work)

List of RPMs


The final list of RPMs is attached to this post as a text file for historical purposes (as well as helping setting up new systems).