4.93 Release Notes for Linux
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CONTENTS
1. LINUX REQUIREMENTS
2. 64-BIT SUPPORT
3. XVIEW PROGRAMS
4. ENDIAN ISSUES
5. THORSERVER
6. CTYPE SYMBOLS IN LIBC
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1. LINUX REQUIREMENTS
The 4.93 Linux release for Daylight software needs the following:
o) An Intel x86 (or compatible) or AMD Opteron-based
machine running Linux, with networking.
o) RedHat Linux Enterprise Editions (2.1, 3, 4) on x86,
RedHat Linux Enterprise Editions (3, 4) on AMD64.
o) A networked ethernet card on the PC. This is essential,
as the card's MAC address is used for licensing.
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2. 64-BIT SUPPORT
Beginning with release 4.91, the Linux distribution contains
64-bit objects for Opteron (AMD64). The Linux release contains
two sets of lib and bin directories, as follows:
$DY_ROOT/bin - 32-bit x86 Linux binaries
$DY_ROOT/lib - 32-bit x86 Linux libraries
$DY_ROOT/binAMD64 - 64-bit x86_64 Linux binaries
$DY_ROOT/libAMD64 - 64-bit x86_64 Linux libraries
For a regular 32-bit x86-based Linux system the 64-bit
directories can be ignored. They are not needed.
For 64-bit Opteron, both the 32-bit and 64-bit
objects may be needed, depending on the users application.
Currently, the only 64-bit application provided is
merlinserver, which can take advantage of the large memory
addressing of 64-bits. The 64-bit libraries for all supported
toolkits are available for developers.
One installation/configuration note: It is recommended that
users of 64-bit Linux create symbolic links for bin64 and
lib64. In general the Daylight documentation refers to these
directories. Furthermore, code and makefiles in contrib and
the thorhome configuration refer to these directories.
cd $DY_ROOT
ln -s binAMD64 bin64
ln -s libAMD64 lib64
NOTE: This organization allows us to add IA64 support
at a future date, with binIA64 and libIA64 directories,
without a reorganization of the directories.
XView is not available in 64-bit format in this release. If you
are developing XView programs using the Daylight widgets, they
must be compiled using the 32-bit libraries.
To compile the contrib code in 32-bit format, in $DY_ROOT/contrib/src
type "make install". To compile the contrib code in 64-bit format,
in $DY_ROOT/contrib/src type "make install64".
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3. XVIEW PROGRAMS
There are a set of XView-based graphical programs included in the
Daylight 4.93 distribution. To run these, XView needs to be installed
on the client. The XView RPMs are not installed by default but can
either be installed as optional packages from Red Hat or copied
from the distribution.
To install the package from the RPM included in the release,
become root on your Linux machine, and then type:
cd $DY_ROOT/exotic/XView/linux
rpm -U xview*rpm
Furthermore, to use the 'Print Preview' option in the XV applications,
one must install the 'gv' package. The 'gv' package is included on
the Linux RedHat distribution.
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4. ENDIAN ISSUES
Intel and Intel-compatible processors, unlike the SGI MIPS or
Sun SPARC processors, are little endian. Endianness refers to how
the byte-ordering which the processor uses internally to store
numbers. A big endian processor like the Sun SPARC or SGI MIPS
processor represents a number 0x1000, as 0x1000 internally.
A little endian processor like the Intel Pentium represents this
as 0x0001 internally instead. The ordering of the individual bytes
is swapped. This is a factor when performing datatype conversion
and writing binary files.
The Daylight software has been written so that endianness is never
an issue. Hence all Daylight Database files may be used
interchangeably between Sun, SGI or Intel-Linux computers. The only
case where endianness is an issue is in the clogp binary database
files. You cannot use a fragment database binary file created on
a Sun or SGI on an Intel Linux computer. However the textual form
of the fragment files can be interchanged and used. When the clogp
program runs the first time, it checks for a binary file and
generates it, if not present, from the text file. The generated
binary file is of the correct endianness for the system.
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5. THORSERVER
Prior to version 4.91, thorserver used 32-bit file offsets and had
a database file size limit of 2GB. Beginning with 4.91 all
Thor databases can be created up to the 16GB datafile limit.
Writing data beyond the limit will cause database corruption.
As a protective measure, the thorserver will deny I/O and issue a
nonfatal error when a load of a TDT begins within 1MB of the limit.
If you want to load large (>1MB) TDT's, you are unprotected from
writing beyond the limit.
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6. CTYPE SYMBOLS in LIBC
The following information addresses a linking issue which arises
on later Red Hat versions in the following situations:
- Running ES3.0 (or later, presumably)
- Statically linking a Daylight toolkit program
One will get errors from the link step:
undefined reference to '__ctype_b'
undefined reference to '__ctype_tolower'
undefined reference to '__ctype_toupper'
Red Hat only guarantees forwards binary compatibility for
executables and shared object libraries; not for object
files or archives. The Daylight toolkit archives are
built using Red Hat ES 2.1. Red Hat removed the symbols
__ctype_b, __ctype_lower and __ctype_upper from glibc
beginning with version 2.3.
The three symbols were removed in favor of locale-aware
versions, and the older versions are no longer be
available. Red Hat has indicated that they don't consider
this a bug and have no plans to change the behavior.
There are two simple workarounds:
First, link dynamically rather than statically. So, in the
makefile or link statement, change the references to all
of the Daylight libraries as follows:
Static:
gcc -o myprogram.exe myprogram.o ... libdt_smiles.a
Dynamic (preferred):
gcc -o myprogram.exe myprogram.o ... -L $(DY_ROOT)/lib -ldt_smiles
The second workaround comes from the Red Hat bugs database
and is provided here unmodified for convenience. See
http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=111928
for the complete listing of the fix:
Customer Fix
-------------
We used a brute force approach. Make the following code into
a .c file, and include it in your program. At the start of
main(), call ctSetup().
Make sure you compile statically or else the dynamic loader will
cause problems.
I've seen others use macros, but this worked good enough for us...
#include <ctype.h>
__const unsigned short int *__ctype_b;
__const __int32_t *__ctype_tolower;
__const __int32_t *__ctype_toupper;
void ctSetup()
{
__ctype_b = *(__ctype_b_loc());
__ctype_toupper = *(__ctype_toupper_loc());
__ctype_tolower = *(__ctype_tolower_loc());
}
Also, additional information is available in the bugs
database at redhat.com. A search for the string "__ctype_b"
at http://bugzilla.redhat.com/bugzilla/ is the simplest
way to get the latest information. As of Jan, 28, 2004,
the following entries were found:
http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=76402
http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=86465
http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=90515
http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=91290
http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=111928
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