Re: attempt to build 64 bit on Solaris fails
- From: "James D. White" <jdw@xxxxxx>
- Date: Fri, 7 Oct 2005 19:20:26 +0000 (UTC)
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/tiger@{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
### (rlippan@xxxxxxxxxxxxxxx). 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)
>
> [herrick@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 majordomo@xxxxxxxxxxxxxxxxxx
--
James D. White (jdw@xxxxxx)
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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