Re: attempt to build 64 bit on Solaris fails

Thank-you, James. (Great sigs of relief!)

I'll report later on how it went.

dan

On Fri, 7 Oct 2005, James D. White wrote:

> Daniel,>> The following is some notes I wrote to myself in case I had to do this> all over again.  It includes the things I had to do to install Perl 5.8.5> with Tk, GD, DBI, DBD::MySQL, DBD::Oracle, and at least part> of BioPerl.  The Tk source distribution includes zlib compression,> libpng, andf libjpeg, but these libraries are not built as 64-bit> libraries needed to link with a 64-bit Tk.  These notes have more> information than you need, so just ignore the rest.>> Jim White>> --------->> This is a summary of my process for installing a 64-bit gcc-compiled> version of Perl 5.8.5 running under Solaris 9 (or Solaris 8).  I have> not yet tried Solaris 10.  We were running a 32-bit version of Perl> 5.6.1, but with the change to 64-bits, I did not try to reuse any> modules that were already installed for Perl 5.6.1.  In addition Perl> 5.6.1 was installed a few years ago, and I wanted current versions of> the modules.>> Perl 5.8.5 seems to work well in 64-bit mode under Solaris 9 running> on Sun Ultra processors.  The problem is primarily in getting 64-bit> versions of the external C libraries installed into the right location> and getting Perl 5.8.5 to look in the right place.  You need to build> 64-bit versions of many of the C libraries, because Sun did not build> them for you.>> Solaris 8 and 9 can run in mixed 32-bit and 64-bit mode, but any> particular process runs in one mode or the other.  Object files and> libraries must be compiled and linked in either 32-bit or 64-bit mode.> A linked binary is either all 32-bit or all 64-bit, and dynamically> loaded libraries must match the mode of the caller.  You will know you> are trying to mix 32-bit and 64-bit objects when you get messages> about something being the wrong ELFCLASS.  If the complaint is about> ELFCLASS32, then you are linking or dynamically loading into a 64-bit> object file or program, but the linker or dynamic loader is pointing> to the 32-bit libraries.  If the complaint is about ELFCLASS64, then> you are linking or dynamically into a 32-bit object or program, but> the linker or dynamic loader is pointing to the 64-bit libraries.>> In order to keep both 32-bit and 64-bit libraries separate, Sun keeps> the C header files (common to both 32-bit and 64-bit versions) in> /usr/include, /usr/local/include, etc. (I'll abbreviate this as> "*/include".)  The 32-bit object files/libraries are kept in "*/lib".> In some directories "*/lib/32" may be a link to "*/lib" for the> 32-bit libraries, but this is not always present.  The 64-bit object> files/libraries are kept in "*/lib/sparcv9".  Again in some> directories "*/lib/64" may be a link to "*/lib/sparcv9" for the> 64-bit libraries, but you can't depend upon this either.>> To keep things straight, the Sun linker will use LD_LIBRARY_PATH_32> in preference to LD_LIBRARY_PATH when linking 32-bit programs and> LD_LIBRARY_PATH_64 in preference to LD_LIBRARY_PATH when linking> 64-bit programs.  Judicious use of LD_LIBRARY_PATH_32 and> LD_LIBRARY_PATH_64, instead of LD_LIBRARY_PATH might avoid a lot> of problems, but some of the make files and "configure" scripts> have LD_LIBRARY_PATH and "*/lib" hardwired into them.>> I have moved my usual LD_LIBRARY_PATH to LD_LIBRARY_PATH_32 and> created LD_LIBRARY_PATH_64 by adding "/sparcv9" to each directory> in LD_LIBRARY_PATH_32.  I do not use LD_LIBRARY_PATH, except when> installing a library whose "configure" script explicitly looks for> LD_LIBRARY_PATH.  Then LD_LIBRARY_PATH should be set the same as> LD_LIBRARY_PATH_32 or LD_LIBRARY_PATH_64, as appropriate.>> For the libraries that use "configure" scripts, you need to tell the> configure script to use gcc, with the right compile time and link> time options for 64-bits.  The --libdir option is usually needed to> specify /usr/local/lib/sparcv9 as the target directory for 64-bit> object libraries.>>> ####################>>> The environment in which Perl was installed:>> We are running a cluster of Sun Ultras of various models with shared> NFS mounted RAID5 arrays.  Perl 5.8.5 and all of the external libraries> were installed into a shared /usr/local.>> Everything was compiled with gcc version 3.3.  Linking was done using> the Solaris Link Editors version 5.9-1.385 that come with Solaris 9.>> Each section below is a summary of the commands used to install it.> There can be some reordering of sections, and some sections can be> omitted if particular Perl modules are not needed.  I have tried to> indicate prerequisites.>> These summaries were written after the fact to give a minimal set of> commands for installation.  In some cases it took several attempts to> discover what tricks to use to successfully install a particular> package.  I tried to leave out the mistakes and summarize the process> to get an optimal set of commands, but in doing so I may have missed a> step that was inadvertently left over from a previous try, so I cannot> guarantee that each of these sections is correct, but I hope that I> can save someone else a lot of frustration.>> I normally use csh, and su to root normally uses the sh shell.  The> Perl CPAN module gets each Perl module and stores it into a separate> directory in ~/.cpan/build.  We store the source directories for the> external C libraries in another directory.  The command summaries> below are written with these assumptions.  You may have to change> some commands for your use.  Have fun!>>> ####################>>> "Getting" source for an external C library>> In the sections below, when you see a line like>> {get xxx source <.tar.gz_file> ...}>> it may involve some or all of the following set of commands:>> $ cd <your_directory_of_source_directories>> {use a web download, ftp, or other means to get a <.tar.gz_file> file}> ### Use next command to determine where output goes, hopefully to new> ### directory> $ gunzip -c <.tar.gz_file> | tar -tf -> ### If tar does not show a new directory as the target, then you> ### need to create one and cd into it before the next command> $ gunzip -c <.tar.gz_file> | tar -xovf -  # extract to dir structure> ### now is a good time to either save or remove the <.tar.gz_file>.> $ mv <.tar.gz_file> <your_source_archive_of_.tar.gz_files>/> $ cd <the_new_source_directory>  # if you aren't already here>> Then your current directory is the directory containing the source> files.  For the external C libraries, that is where each of the> following sections usually continues.>>> ####################>>> ### "Getting" source for a Perl module or package>> ### In the sections below, when a new Perl modules is to be installed,> ### the CPAN shell is used, which downloads the module/package and untars> ### it into a new directory, "~/.cpan/build/<new_module_source_directory>".> ### You can cd into it directly, or within the CPAN shell, the "look"> ### command opens up a new shell inside the source directory for you.> ### Then your current directory is the directory containing the source> ### files.  If you need to do anything special, that is usually where the> ### non-CPAN shell commands need to be run.>>> ####################>>> ### Installing gdb (gdbm-1.8.3) - GNU database manager, used by Perl> ### GDBM_File module>> {get gdbm source <.tar.gz_file> from www.gnu.org}> ### use gcc, 64bitall, ultrasparc> $ ./configure CC=gcc CFLAGS='-mcpu=v9 -m64' LDFLAGS='-m64' \>     -libdir=/usr/local/lib/sparcv9> $ make> $ make check> $ su> # /usr/local/bin/make install> # ^D>>> ####################>>> ### Installing Berkeley db (db-4.2.52), used by Perl BerkeleyDB and> ### DB_File modules>> {get Berkeley db source <.tar.gz_file> from www.sleepycat.com}> ### Build into /usr/local/BerkeleyDB or later change Perl BerkeleyDB> ### config.in to point to /usr/local/BerkeleyDB.<version>> ### If you want both 32-bit and 64-bit libraries, then you should add a> ### -libdir flag to the configure command below to put the 64-bit library> ### into /usr/local/BerkeleyDB.<version>/lib/sparcv9.  I was lazy and> ### didn't bother to build a 32-bit version for this library, so I left> ### the 64-bit version in /usr/local/BerkeleyDB.<version>/lib> $ cd build_unix> ### use gcc, 64bitall, ultrasparc> $ ../dist/configure CC=gcc CFLAGS='-mcpu=v9 -m64' LDFLAGS='-m64'> ###       -libdir /usr/local/BerkeleyDB.<version>/lib/sparcv9 # ???> $ make> $ make check> $ su> # make install> # ^D>>> ####################>>> ### Installing zlib (zlib-1.2.1) - Zlib Data Compression Library, used> ### by libpng, Perl Compress::Zlib module, and Perl IO::Zlib module>> {get zlib source <.tar.gz_file> from www.gzip.org/zlib}> $ make clean> $ sh   # if necessary> ### use gcc, 64bitall, ultrasparc> $ CC=gcc CFLAGS='-mcpu=v9 -m64 -O' LDFLAGS='-m64' \>     LDSHARED='gcc -G -mcpu=v9 -m64' ./configure --shared \>     --libdir=/usr/local/lib/sparcv9> $ make> $ LD_LIBRARY_PATH_64=.:$LD_LIBRARY_PATH_64 make test> $ su> # /usr/local/bin/make install> # ^D>>> ####################>>> ### Installing libpng (libpng-1.2.8-config) - PNG Graphics Library, used> ### by libgd and Perl Tk module>> {get libpng source <.tar.gz_file> from www.libpng.org}> $ make clean> ### use gcc, 64bitall, ultrasparc> $ ./configure -libdir=/usr/local/lib/sparcv9 CC=gcc \>     CFLAGS='-mcpu=v9 -m64 -O' LDFLAGS='-m64 -L/usr/local/lib/sparcv9'> $ make> $ make check> $ su> # /usr/local/bin/make install> ### After the install, I had to modify /usr/local/bin/libpng-config and> ### /usr/local/bin/libpng12-config. This was needed to help the 64-bit> ### build for the libgd library work properly.  To build a 32-bit app> ### you would need to put the files back the way they were.> {edit /usr/local/bin/libpng-config and /usr/local/bin/libpng12-config>   (They have the same contents.).  diff output is below.}>   27a28,32>   > # following line needed for Solaris ld with gcc on Ultra 64-bit>   > R_opts="-Wl,-R,/usr/local/lib/sparcv9">   > # following line needed for Solaris Ultra 64-bit>   > libdir="/usr/local/lib/sparcv9">   >> # ^D>>> ####################>>> ### Installing FreeType 2 (freetype-2.1.9) - A Free Type Engine, used> ### by libgd, which is used by Bioperl>> {get freetype2 source <.tar.gz_file> from sourceforge.net}> ### Note: ./builds/unix/configure needs an egrep that can read "long"> ###   lines, such as GNU grep.  I dropped a copy of GNU grep into> ###   ./builds/unix/> ### Note: LD_LIBRARY_PATH was set to point to the libraries in> ###   LD_LIBRARY_PATH_64 before ./configure was run> ### ./configure --help       # get help for configure> ### Note: CFLAGS='"..."' is needed below because ./configure runs> ###   ./builds/unix/configure, causing the outside quotes to be lost> $ ./configure CC=gcc CFLAGS='"-mcpu=v9 -m64"' LDFLAGS='-m64' \>      -libdir=/usr/local/lib/sparcv9> $ make> $ su> # /usr/local/bin/make install> # ^D>>> ####################>>> ### Installing XPM - XPixMap, used by libgd>> ### This comes with Solaris 9 in /usr/openwin/lib, so I used the one> ### that was already available.  XPixMap does not come preinstalled> ### with Solaris 8.>>> ####################>>> ### Installing fontconfig, used by libgd>> ### This comes with Solaris 9 in /usr/lib, so I used the one that was> ### already available.  fontconfig does not come preinstalled with> ### Solaris 8.>>> ####################>>> ### Installing expat (expat-1.95.8), which is used by XML-Parser, which> ### is part of Bioperl>> {get expat source <.tar.gz_file> from http://sourceforge.net/projects/expat/}> $ ./configure --help       # get help for configure> $ ./configure --libdir=/usr/local/lib/sparcv9 \>     CC=gcc CFLAGS='-mcpu=v9 -m64 -O' \>     LDFLAGS='-m64 -L/usr/local/lib/sparcv9'> $ make> $ make check # this fails because the sharable library is not>   # installed yet, so it cannot be loaded at runtime> $ su> ### /usr/local/bin and /usr/ccs/bin needed to find make, ar, and ranlib> # PATH=/usr/local/bin:/usr/sbin:/usr/bin:/usr/ccs/bin> # export PATH> # make install> ### The following fix is needed because "On solaris at least, it appears> ### that install-sh does not handle installing multiple files. As a> ### consequence the expat_external.h is not installed.  A manual workaround> ### to this problem is to install the expat_external.h file by hand."> # cp lib/expat_external.h /usr/local/include/> # ^D> $ make check # make check works now>>> ####################>>> ### Install Oracle client library, which is used by Perl DBD::Oracle.>> ### I installed an Oracle client library separately into /usr/local,> ### because the copy of Perl we use is in a shared /usr/local, and the> ### Oracle server does not share its volumes with the rest of the cluster.> $ su - oracle> ### Used "Oracle 9i Enterprise Edition" CD and used the Oracle Universal> ###   Installer> # cd /cdrom/oracle9i> # ./runInstaller> ### Installed the "Oracle Client" in /usr/local/Oracle/OracleHome9i.> ### Used the "Custom" install to include the programmer tools/libs.>> ### The following is needed to use the just installed client.> setenv ORACLE_HOME /usr/local/Oracle/OraHome9i>>> ####################>>> ### Install Mysql client library, which is used by Perl DBD::Mysql module>> ### I downloaded mysql-standard-4.0.24-sun-solaris2.9-sparc-64bit.tar.gz> ### from www.mysqp.com, gunzipped and untarred into /usr/local with> ### "gunzip -c <.tar.gz_file> | tar -xovf -".  I did not set up the> ### database.  I am only using the client portion to connect to another> ### host.  The mysql_config provided options for a 64-bit Sun ForteC> ### compiler.  I had to provide my own CFLAGS when building DBD::Oracle.>>> ####################>>> ### Installing openssl (openssl-0.9.7g), which is used by Net::SSLeay> ### and Crypt::SSLeay, which is used by Bioperl for HTTPS support>> {get openssl source <.tar.gz_file> from http://www.openssl.org}> $ ./Configure -h       # get help for configure> ### We had a 32-bit SSL library in /usr/local/ssl.  I am putting the> ### 64-bit openssl library in /usr/local/openssl.> $ ./Configure --openssldir=/usr/local/openssl solaris64-sparcv9-gcc> { To work around gcc optimization bugs, modify CFLAG in Makefile to>   contain -O1 instead of -O3.  (That's change to dash-oh-one from>   dash-oh-three.) }> $ make> $ make check> $ su> # /usr/local/bin/make install> # ^D>>> ####################>>> ### Installing Perl 5.8.5:>> {get Perl source <.tar.gz_file>}> $ sh  # if necessary> ### To build a 64-bit Solaris Ultra version of Perl, LD_LIBRARY_PATH should> ### point to the 64-bit libraries in "*/lib/sparcv9", instead of the usual> ### "*/lib" before configuring Perl.  If any non-"sparcv9" libraries are> ### configured into Perl, then you can edit> ### /usr/local/lib/perl5/5.8.5/sun4-solaris-thread-multi-64/Config.pm> ### to fix libpth, lddlflags, ldflags, libsdirs, libsfound, libspath, and> ### loclibpth.  I did this after after Perl is built, but it would be better> ### to catch it early.> $ LD_LIBRARY_PATH=/usr/local/lib/sparcv9:/usr/lib/sparcv9:/usr/openwin/lib/sparcv9:/usr/dt/lib/sparcv9> $ export LD_LIBRARY_PATH> $ sh Configure -Dcc=gcc -Dusethreads -Duse64bitall> ### To configure, just answer the questions. I used the defaults,> ### except to not use modules from previous versions by answering> ### 'none' to the following question:> ###   List of earlier versions to include in @INC? [5.6.1 5.005] none> ### I think that's all I changed.> ### (Configure includes 'make depend', unless you tell it not to)> $ make> $ make test> $ su> ### The following, except for make install, is needed to preserve perl> ### 5.6.1 as the default perl, until everything is installed> # cp perldoc perldoc5.6.1 # save older version of perldoc> # /usr/local/bin/make install> # cd /usr/local/bin> # mv perl perlnew  # to keep /usr/local/bin/perl pointing> # cp perl5.6.1 perl  #   to older version of Perl until all>     #   modules are updated> # mv perldoc perldocnew  # to keep /usr/local/bin/perldoc pointing> # cp perldoc perldoc5.8.5 #   to older version of Perl until all> # cp perldoc5.6.1 perldoc #   modules are updated> # ^D>>> ####################>>> ### next update the Perl CPAN module>> $ su> # PATH=/usr/local/bin:/usr/sbin:/usr/bin:/usr/ccs/bin> # export PATH> # perlnew -MCPAN -e shell # use temporary perlnew while> #    #   installing modules> cpan> install Bundle::CPAN # reply yes to dependencies> cpan> reload cpan> cpan> exit> # ^D>>> ####################>>> ### next install HTTP::Date, which also installs HTML::Parser and libwww>> ### I seem to remember the CPAN shell checking for a new HTTP:Date each> ### time it started, until I installed this.> $ su> # PATH=/usr/local/bin:/usr/sbin:/usr/bin:/usr/ccs/bin> # export PATH> # perlnew -MCPAN -e shell> cpan> install HTTP::Date> ### I took all of the defaults> cpan> exit> # ^D>>> ####################>>> ### install BerkeleyDB>> $ perlnew -MCPAN -e shell # run CPAN module with extra features> cpan> get BerkeleyDB  # get BerkeleyDB (needs config)> cpan> look BerkeleyDB  # bring up new shell inside build directory> ### You may need to edit config.in to point to the BerkeleyDB libs at:> ### /usr/local/BerkeleyDB.../include and /usr/local/BerkeleyDB.../lib> ### (or usr/local/BerkeleyDB.../lib/sparcv9)> $ perlnew Makefile.PL> $ make> ### The Berkeley DB library does not work on NFS mounted drives.> ### If you try it, you get error messages about mmap resources being> ### temporarily unavailable> $ ssh <your_file_server>> your_file_server% cd ~/.cpan/build/BerkeleyDB-...> your_file_server% make test> your_file_server% ^D> $ su    # must be root to install> # make install> # ^D    # exit to non-root shell> $ ^D    # exit to CPAN shell> cpan> q    # exit to original shell>>> ####################>>> ### install DB_File>> $ perlnew -MCPAN -e shell # run CPAN module with extra features> cpan> get DB_File  # get DB_File (needs config)> cpan> look DB_File> ### You may need to edit config.in to point to the BerkeleyDB libs at:> ### /usr/local/BerkeleyDB.../include and /usr/local/BerkeleyDB.../lib> $ perlnew Makefile.PL> $ make> ### The Berkeley DB library does not work on NFS mounted drives.> ### If you try it, you may get error messages about mmap resources being> ### temporarily unavailable> $ ssh <your_file_server>> your_file_server% cd ~/.cpan/build/DB_File-...> your_file_server% make test> your_file_server% ^D> $ su    # must be root to install> # make install> # ^D    # exit to non-root shell> $ ^D    # exit to CPAN shell> cpan> q    # exit to original shell>>> ####################>>> ### Prepare to install Perl/Tk and GD.>> ### Perl/Tk needs zlib, jpeg and png.  All but jpeg already installed.> ### GD needs libgd, which needs zlib, jpeg, png, freetype-2, and XPM.> ### All but jpeg and libgd already installed.  libjpeg seems pretty> ### stable -- the version of libjpeg that comes with Perl-Tk can be> ### made to work.> $ perlnew -MCPAN -e shell # use temporary perlnew> cpan> get Tk> cpan> exit> $>> ####################>>> ### Installing libjpeg (version 6b), which was includes with Tk>> ### { after CPAN get Tk }> $ cd ~/.cpan/build/Tk-804.027/JPEG/jpeg> $ cp Makefile.maybe Makefile.PL2 # create our own modified version> $ chmod 644 Makefile.PL2  #   of Makefile.PL (renamed)> $ edit Makefile.PL2   # diff output follows> 36c36,37> <   system(sh => "./configure");> ---> >   system(sh => "./configure",> >     qw(--enable-shared --enable-static --libdir=/usr/local/lib/sparcv9);> $ perlnew Makefile.PL2> ### For some reason the --libdir parameter seems to have been ignored.> ### The following edit fixes it.> $ edit Makefile  # diff output follows> 15c15> < libdir = $(exec_prefix)/lib> ---> > libdir = $(exec_prefix)/lib/sparcv9> $ make> $ make test # fails, because libjpeg needed to be installed first,>   # because libtool links the test programs to dynamically>   # load libjpeg from the installed location, not the build>   # location> $ su> # /usr/local/bin/make install> # ^D  # drop back to user shell> $ make test # works now>>> ####################>>> ### install Perl/Tk>> ### Perl/Tk was difficult to install, because the included zlib, libjpeg,> ### and libpng libraries were not configured to run in 64-bit mode.  I> ### downloaded a new zlib, because some bugs were fixed in the new> ### version.  A new libpng was used, because some bugs were fixed in the> ### new version.  I used the Perl/Tk version of libjpeg, because it seems> ### to be stable.  All three of these libraries were separately installed> ### before installing Perl/Tk.  The other problem to overcome was telling> ### Perl/Tk where to find the X11 library.> ###> ### Remember that we already got the Perl/Tk module from CPAN> $ cd ~/.cpan/build/Tk-804.027...> {edit myConfig to point to Solaris 64-bit X11 library.  This change lets>  configure find the right X11 library for the build.  diff output follows}> 154a155,163> >      # Because of the mixed 32-bit and 64-bit nature of UltraSparc> >      # Solaris, 64-bit Solaris libs usually reside in ".../lib/sparcv9",> >      # instead of ".../lib".  The ".../lib/sparcv9" directory sometimes> >      # is aliased by a soft link, ".../lib/64".> >      if ($Config{'osname'} eq 'solaris' &&> >          $Config{'archname'} =~ /^sun4-solaris.*-64/)> >        {> >        $_ .= '/sparcv9' if (-d "$_/sparcv9");> >        }> {edit Tk.pm to point to Solaris 64-bit X11 library.  This change tells Tk>  where to preload the right X11 library at runtime.  A better patch would>  check for 64-bit Solaris at runtime.  diff output follows.}> 89,90c89,90> < Preload(DynaLoader::dl_findfile('-L/usr/openwin/lib','-lX11'))> <   if (NeedPreload() && -d '/usr/openwin/lib');> ---> > Preload(DynaLoader::dl_findfile('-L/usr/openwin/lib/sparcv9','-lX11'))> >   if (NeedPreload() && -d '/usr/openwin/lib/sparcv9');> $ perlnew Makefile.PL> $ make> $ make test> $ su    # must be root to install> # make install> # ^D>>> ####################>>> ### Installing libgd (gd-2.0.33) - GD Graphics Library, used by Perl GD> ### module>> ### libgd wants to use /usr/openwin/lib/libXpm.so and> ### /usr/lib/libfonconfig.so, both of which are present with Solaris 9,> ### but not Solaris 8.  If you have a mixed 8/9 environment, then building> ### on Solaris 8 causes these features to be unavailable for both 8 and 9.> ### Building on 9 and copying these files (and appropriate symlinks) from> ### a 9 system to an 8 system seems to work.>> {get libgd source <.tar.gz_file> from www.boutell.com}> $ make clean> $ sh   # if necessary>    # use gcc, 64bitall, ultrasparc> $ ./configure --libdir=/usr/local/lib/sparcv9 \>     CC=gcc CFLAGS='-mcpu=v9 -m64 -O' \>     LDFLAGS='-m64 -L/usr/local/lib/sparcv9'> ### The version of libtool used by this install quits if ranlib if not> ### found, even though on Solaris it is not needed.  During the make install> ### the PATH for root doesn't have /usr/ccs/bin, so ranlib is not found.> ###> { Edit libtool to make ranlib definition path explicit.  Change line 175>   to be:>   RANLIB="/usr/ccs/bin/ranlib">   Another solution is to add /usr/ccs/bin to the PATH before running>   "make install".> }> $ make> $ make check> $ su> # /usr/local/bin/make install> # ^D>>> ####################>>> ### Install Perl GD module>> $ su> # perlnew -MCPAN -e shell # run CPAN module interactively> cpan> install GD  # GD graphics module> cpan> q> # ^D>>> ####################>>> ### Install Perl DBI module>> $ su> # perlnew -MCPAN -e shell # run CPAN module interactively> cpan> install Bundle::DBI # generic DBI module for SQL access> ### cpan> install Bundle::DBI # install this if you need DBD::Proxy> ###    #   and/or DBI::ProxyServer> cpan> q> # ^D>>> ####################>>> ### Install Perl DBD::Oracle-1.16 module (DBD::Oracle needs Oracle> ### client library installed first)>> $ setenv ORACLE_HOME /usr/local/Oracle/OraHome9i> $ setenv ORACLE_SID host={hostname};sid={database}> $ setenv ORACLE_USER scott/tig...@{database} # for testing DBD::Oracle> $ perlnew -MCPAN -e shell  # run CPAN module interactively> ### We can't just install DBD::Oracle directly from CPAN, because> ### DBD::Oracle's Makefile.PL defaults to using the Oracle 9+ make> ### build32 rule, which tries to link with 32-bit options and the> ### 32-bit Oracle libraries.  It can be fixed by editing Makefile.PL> ### as shown below, or by using "perlnew Makefile.PL -r=build" to force> ### usage of the "build" rule to find the 64-bit libraries.  (This> ### patch was emailed to Tim Bunce, so it may already be there in> ### future versions of DBD::Oracle.)> cpan> get DBD::Oracle> cpan> look DBD::Oracle> { edit Makefile.PL to fix 32/64-bit library problem }> 331c331> <       $build_target = "build32" if $mk_target_rules{build32};> ---> >       $build_target = "build32" if $mk_target_rules{build32} && ! perl_is_64bit();> $ perlnew Makefile.PL> $ make> $ make test> $ su> # make install> # ^D    # exit to non-root shell> $ ^D    # exit to CPAN shell> cpan> q    # exit to original shell>>> ####################>>> ### Install Perl DBD::mysql module (DBD::mysql needs mysql client> ### library installed first)>> # /usr/local/bin/perlnew -MCPAN -e shell # run CPAN module interactively> cpan> get DBD::mysql> cpan> look DBD::mysql> ### The two setenv commands and the two edits below let you provide> ### the test username and test password as environment variables,> ### instead of passing them on the "perl Makefile.PL ..." command,> ### which writes the username and password to the file t/mysql.mtest.> ### The two edit were sent as a suggested patch to Rudy Lippan> ### (rlip...@remotelinux.com).  If these edits are already present> ### in a newer version, then only two setenv commands are needed here.> ### Without the edits, the file t/mysql.mtest contains the values you> ### passed (or the defaults) and overwrites the values obtained from> ### DBI_USER and DBI_PASS.> $ setenv DBI_USER your_test_username> $ setenv DBI_PASS your_test_password> $ edit t/lib.pl  # diff output follows> 47c47> <     $::test_password = $::test_passowrd || $ENV{'DBI_PASS'}  ||  '';> ---> >     $::test_password = $::test_password || $ENV{'DBI_PASS'}  ||  '';> $ edit Makefile.PL # diff output follows> 129c129> <             "\$::test_user = \$opt->{'testuser'};\n" .> ---> >             "\$::test_user = \$opt->{'testuser'} if \$opt->{'testuser'};\n" .> 131c131> <             "\$::test_password = \$opt->{'testpassword'};\n" .> ---> >             "\$::test_password = \$opt->{'testpassword'} if \$opt->{'testpassword'};\n" .> 133,135c133,135> <             "\$::test_dsn = \"DBI:mysql:\$::test_db\";\n" .> <             "\$::test_dsn .= \":\$::test_host\" if \$::test_host;\n" .> <             "\$::test_dsn .= \":\$::test_port\" if \$::test_port;\n" .> ---> >             "\$::test_dsn = \"DBI:mysql:\$::test_db\" if \$::test_db;\n" .> >             "\$::test_dsn .= \":\$::test_host\" if \$::test_host && \$::test_db;\n" .> >             "\$::test_dsn .= \":\$::test_port\" if \$::test_port && \$::test_db;\n" .> ### If the edits were not done above, then the alternative is to add> ### the following two options to the "perl Makefile.PL ..." command.> ###    --testuser=your_test_username --testpassword=your_test_password> ### If you provide them on the Makefile.PL command line, then they> ### are placed in "t/mysql.mtest" for use during "make test".  You> ### should delete the file or edit the file to remove your username> ### and password after testing;  otherwise, your username and password> ### are lying around where they might be discovered.  I prefer the> ### patch, so they are never in the file.> $ tcsh  # sh and csh cannot handle the long command line below> > perlnew Makefile.PL --help  # display options for Makefile.PL> ### "--mysql_config=..." is required for me, because this is not the> ### production version of mysql pointed to by /usr/local/mysql.  This> ### copy of mysql is used for the client libraries only.> ### "--testhost=..." is needed because I was using a mysql server on a> ### different system, not localhost.> ### "--cflags=..." is needed because mysql_config provides the compile> ### options for the Sun Forte C compiler, not the gcc compiler.  I got> ### most of the values here from "perl -V".> > perlnew Makefile.PL \>     --mysql_config=/usr/local/mysql-standard-4.0.24-sun-solaris2.9-sparc-64bit/bin/mysql_config \>     --testhost=your_test_hostname \>     --cflags="-D_REENTRANT -mcpu=v9 -m64 -Wa,-xarch=v9 -I/usr/local/include \>       -I/usr/local/mysql-standard-4.0.24-sun-solaris2.9-sparc-64bit/include"> > make> > make test> > ^D    # exit to CPAN shell> $ su> # make install> # ^D    # exit to non-root shell> $ ^D    # exit to CPAN shell> cpan> q    # exit to original shell>>> ####################>>> ### Install BioPerl packages and modules>> # perlnew -MCPAN -e shell # run CPAN module interactively> cpan> get Bundle::Bioperl> cpan> install Bundle::BioPerl> ### install Bundle::BioPerl, which is a bundle of just the prerequisite> ### modules for BioPerl itself.  Replied yes to dependencies.> ### XML::DOM got errors testing utf8 support.  The problem is in mixing> ### euc-jp and utf8 encodings.  To get the tests to work, edit the> ### following test programs: t/dom_jp_attr.t, t/dom_jp_ cdata.t,> ### t/dom_jp_minus.t, t/dom_jp_modify.t, and t/dom_jp_print by> ### changing the line with "use utf8;" to "use encoding utf8;".> ### ("use encoding utf8;" already does "use utf8;".)> cpan> look XML::DOM> $ edit t/dom_jp_attr.t> ...> $ edit t/dom_jp_print.t> $ make test> $ su> # make install> # ^D> $ ^D>>> installed Perl Crypt::SSLeay, Mail::Address, MIME::Types, MIME::Parser,> MIME::Lite>>> ####################>>> ### Install Perl Net::SSLeay module (Net::SSLeay needs openssl> ### client library installed first)>> $ perlnew -MCPAN -e shell  # run CPAN module interactively> ### We can't just install Net::SSLeay directly from CPAN, because> ### test.pl runs perl, not perlnew and TCP case was wrong?)> cpan> get Net::SSLeay> cpan> look Net::SSLeay> $ perlnew Makefile.PL> $ make> $ edit test.pl # diff output follows> 47a48> > $perl = "/usr/local/bin/perlnew $inc"; # force selection of perlnew> 95c96> < print &test('5tcp', ($res =~ /SSLEAY-TCP-TEST/));> ---> > print &test('5tcp', ($res =~ /SSLEAY-TCP-TEST/i)); # make case insensitive> $ make test> $ su> # /usr/local/bin/make install> # ^D    # exit to non-root shell> $ ^D    # exit to CPAN shell> cpan> q    # exit to original shell>>> ####################>>> cpan> install IO::Socket::SSL # needs Net::SSLeay first>>> cpan> install Bundle::BioPerl  # install BioPerl again to finish>      #   the rest> cpan> i /BioPerl/  # get the full name and version of BioPerl> cpan> install B/BI/BIRNEY/bioperl-0.7.1.tar.gz   # now really install BioPerl> cpan> install B/BI/BIRNEY/bioperl-ext-0.6.tar.gz #   and extras> cpan> install B/BI/BIRNEY/bioperl-gui-0.7.tar.gz #   *> cpan> q>>> ####################>>> ### Make Perl 5.8.5 the new default version of perl.  Don't do this step> ### until you have tested everything and are ready to make the new Perl> ### the production one.>> $ su> # cd /usr/local/bin> # mv perldoc perldocold  # save older version of perldoc> # mv perldocnew perldoc  # use new perldoc> # cp perl perlold  # save older version of perl> # cp perl5.8.5 perl  # use new perl> # ^D>> ### Now it is done.>>> daniel lance herrick wrote:>> > The perl we are using was compiled 64 bit. I'm> > trying to get TK running with it:> >> > make[2]: Entering directory `/work/appl4/gm/gme/TK/Tk-804.027/PNG/libpng'> > gcc -fPIC -I../zlib -Wall -O2   -c -o pngtest.o pngtest.c> > gcc -fPIC -o pngtest pngtest.o -L. -L../zlib -lpng -lz -lm -s> > ld: warning: file ../zlib/libz.a(crc32.o): wrong ELF class: ELFCLASS64> >> > Then there is a list of 9 undefined symbols that> > libpng.a presumably expected to access from libz.a> >> > There were many gcc commands with an "-m64" on the> > command line before this point, but not in> > directory PNG/libpng.> >> > The command line used to bring us to this point:> >> > /epo/app/martin/gme/epc3/thirdPartyLinks/perl Makefile.PL ; make> >> > Scrolling back a bit, PNG/zlib is compiled with> > the "-m64" switch as it needs to be, as, for> > example:> >> > gcc -fPIC -mcpu=v9 -m64 -Wa,-xarch=v9 -mcpu=v9 \> > -m64 -fno-strict-aliasing -I/usr/local/include \> > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC \> > -DHAVE_UNISTD_H -DUSE_MMAP   -c -o inffast.o \> > inffast.c> >> > But in PNG/libpng, the compile commands are much> > shorter:> >> > make[2]: Entering directory `/work/appl4/gm/gme/TK/Tk-804.027/PNG/libpng'> > gcc -fPIC -I../zlib -Wall -O2   -c -o png.o png.c> > gcc -fPIC -I../zlib -Wall -O2   -c -o pngerror.o pngerror.c> >> > I suspect the problem is that Makefile.PL is> > choosing scripts/makefile.gcc when it needs to> > choose scripts/makefile.64sunu, except I don't see> > the string "-m64" in the 64sunu makefile.> >> > So, I hand-edited the CFLAGS variable in> > PNG/libpng/Makefile, did a make clean in> > PNG/libpng and repeated the make in the build> > directory. This time it compiled all the library> > components 64 bit, but still compiled> > PNG/libpng/pngtest without the -m64.> >> > Where is the proper place to make such a> > configuration change so it affects the whole> > build?> >> > dan> > (perl -V below)> >> > [herr...@rfautopub:Tk-804.027]$/epo/app/martin/gme/epc3/thirdPartyLinks/perl -V> > Summary of my perl5 (revision 5.0 version 8 subversion 1) configuration:> >   Platform:> >     osname=solaris, osvers=2.9, archname=sun4-solaris-64> >     uname='sunos build9 5.9 generic_112233-08 sun4u sparc sunw,ultra-4 '> >     config_args='-Dprefix=/opt/perl/5.8.1 -Dcc=gcc -Accflags=-mcpu=v9 -m64 -Aldflags=-mcpu=v9 -m64 -Alddlflags=-mcpu=v9 -m64 -Duse64bitall'> >     hint=recommended, useposix=true, d_sigaction=define> >     usethreads=undef use5005threads=undef useithreads=undef usemultiplicity=undef> >     useperlio=define d_sfio=undef uselargefiles=define usesocks=undef> >     use64bitint=define use64bitall=define uselongdouble=undef> >     usemymalloc=n, bincompat5005=undef> >   Compiler:> >     cc='gcc', ccflags ='-mcpu=v9 -m64 -Wa,-xarch=v9 -mcpu=v9 -m64 -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',> >     optimize='-O',> >     cppflags='-mcpu=v9 -m64 -Wa,-xarch=v9 -mcpu=v9 -m64 -fno-strict-aliasing -I/usr/local/include'> >     ccversion='', gccversion='3.3.2', gccosandvers='solaris2.9'> >     intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=87654321> >     d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16> >     ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8> >     alignbytes=8, prototype=define> >   Linker and Libraries:> >     ld='gcc', ldflags =' -mcpu=v9 -m64 -L/usr/lib/sparcv9 -L/usr/local/lib '> >     libpth=/usr/lib/sparcv9 /usr/local/lib /usr/lib /usr/ccs/lib> >     libs=-lsocket -lnsl -ldl -lm -lc> >     perllibs=-lsocket -lnsl -ldl -lm -lc> >     libc=/usr/lib/sparcv9/libc.so, so=so, useshrplib=false, libperl=libperl.a> >     gnulibc_version=''> >   Dynamic Linking:> >     dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='  -z ignore -z lazyload -z combreloc'> >     cccdlflags='-fPIC', lddlflags=' -mcpu=v9 -m64 -G  -z ignore -z lazyload -z combreloc -L/usr/lib/sparcv9 -L/usr/local/lib'> >> > Characteristics of this binary (from libperl):> >   Compile-time options: USE_64_BIT_INT USE_64_BIT_ALL USE_LARGE_FILES> >   Built under solaris> >   Compiled at Oct 27 2003 16:50:15> >   @INC:> >     /opt/perl/5.8.1/lib/5.8.1/sun4-solaris-64> >     /opt/perl/5.8.1/lib/5.8.1> >     /opt/perl/5.8.1/lib/site_perl/5.8.1/sun4-solaris-64> >     /opt/perl/5.8.1/lib/site_perl/5.8.1> >     /opt/perl/5.8.1/lib/site_perl> >     .> >> > -++**==--++**==--++**==--++**==--++**==--++**==--++**==> > This message was posted through the Stanford campus mailing list> > server.  If you wish to unsubscribe from this mailing list, send the> > message body of "unsubscribe ptk" to majo...@lists.stanford.edu>> --> James D. White   (j...@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>>>>

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