[Bioperl-l] Options for Compiling Perl 5.8.5 Running on an UltraSparc with Solaris 2.9?

James D. White jdw at ou.edu
Tue Sep 14 12:49:16 EDT 2004

I am looking at upgrading my present Perl compiler from version
5.6.1 to version 5.8.5.  The new version will be built with GCC
3.3 into a shared /usr/local running on a cluster of various
UltraSparc models running Solaris 9.  I am looking for advice on
options for building the new Perl to ensure that it is compatible
with the modules I will be adding to the base Perl 5.8.5,
including BioPerl.

For the new 5.8.5, I am considering enabling use64bitall and
thread support (but which type of threads?).  One of the systems
has 32GB RAM, so use64bitall would enable the running of
applications needing a lot of memory.  Neither of these options
is a requirement for the production applications I am getting
ready to deploy, but I would like to build a stable Perl
environment that will last quite a while without having to
reinstall Perl and all of the modules again.  If either
use64bitall or threads will cause a problem in building and
installing my add-on modules, then I probably need to avoid
enabling these options.  If Perl and all of the modules I wish to
install can be built, tested, and installed with these options
turned on, but problems arise only when using multiple threads or
a large amount of memory with BioPerl, then I just need to avoid
using these features with BioPerl.

I am hoping someone has some experience using Perl and BioPerl
in this type of environment.  If someone can tell me that things
will work, then that is great, and I can proceed.  If someone can
tell me that these features are not yet compatible, then I will
build the new Perl without the extras and I won't waste time
trying something that is not going to work.

The major Perl modules I presently have installed and plan to run
with the new compiler include:  Apache with mod_perl, BioPerl,
CGI, DBI, DBD::Mysql, DBD::Oracle, Tk, and all of their
prerequisites and subcomponents.

The existing Perl 5.6.1 was built with the following (Perl -V
output listed at end of message):

-compiled with GCC 2.95.2
-thread support disabled
-large file support enabled

James D. White   (jdw at ou.edu)
Director of Bioinformatics
Department of Chemistry and Biochemistry/ACGT
University of Oklahoma
101 David L. Boren Blvd., SRTC 2100
Norman, OK 73019
Phone: (405) 325-4912, FAX: (405) 325-7762

================ perl -V output for old 5.6.1 compiler ===============

Summary of my perl5 (revision 5.0 version 6 subversion 1) configuration:
    osname=solaris, osvers=2.8, archname=sun4-solaris
    uname='sunos dna2.chem.ou.edu 5.8 generic_108528-08 sun4u sparc
sunw,ultra-5_10 '
    hint=previous, useposix=true, d_sigaction=define
    usethreads=undef use5005threads=undef useithreads=undef
    useperlio=undef d_sfio=undef uselargefiles=define usesocks=undef
    use64bitint=undef use64bitall=undef uselongdouble=undef
    cc='gcc', ccflags ='-fno-strict-aliasing -I/usr/local/include
    cppflags='-fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE
    ccversion='', gccversion='2.95.2 19991024 (release)',
    intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=4321
    d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
    ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
    alignbytes=8, usemymalloc=n, prototype=define
  Linker and Libraries:
    ld='gcc', ldflags =' -L/usr/local/lib '
    libpth=/usr/local/lib /usr/lib /usr/ccs/lib
    libs=-lsocket -lnsl -ldl -lm -lc
    perllibs=-lsocket -lnsl -ldl -lm -lc
    libc=/lib/libc.so, so=so, useshrplib=false, libperl=libperl.a
  Dynamic Linking:
    dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
    cccdlflags='-fPIC', lddlflags='-G -L/usr/local/lib'

Characteristics of this binary (from libperl):
  Compile-time options: USE_LARGE_FILES
  Built under solaris
  Compiled at Sep 24 2003 13:52:02

============ end of perl -V output for old 5.6.1 compiler ===========

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