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Gentoo Live 32 to 64 migration as clean as possible:

This is my method - letting portage track every file and package except glibc and ld-linux.so.2 loader. System and all services can remain running. If this is done correctly only 2 reboots will be required.

make sure system is completely up to date and has been depcleaned, preserved-rebuilt and revdep-rebuild - to clean up old 32bit libraries else lots of work later
a full up to date backup of the system is a good idea and has saved me in the past.
make sure you have an *identically* up to date 64bit multilib profile VM to create binary packages on. Ensure CFLAGS is going to be identical, or compatible (“-mtune=generic -O2 -pipe” is safe). Make sure USE flags are the same between the systems as this makes live easier when doing emerge -k binarypackage on the other side. If changes are required to CFLAGS then emerge -e world.

Steps

mkdir /migration-backup
cp /etc/portage/make.conf /migration-backup/

see previous versions of this page which built a cross compiler for compiling a 64bit kernel. This is not needed if building the kernel and initramfs on the 64bit VM.

ON THE 64bit VM (which will build ia32 emulation by default):

genkernel all

copy the resulting kernel, initramfs, system.map, and lib/modules/x.x directory over
reboot test into the 64bit kernel
Change CHOST to x86_64-pc-linux-gnu
copy lib and /usr/lib and /bin and /usr/bin and /sbin and /usr/sbin to /migration-backup
make /etc/env.d/99migration with LDPATH=/migration-backup/lib:/lib32:/lib64:/migration-backup/usr/lib:/usr/lib32:/usr/lib64

env-update
source /etc/profile
ldconfig

mkdir /lib32
mkdir /lib64
mkdir /usr/lib32
mkdir /usr/lib64

If applicable, dont use distcc till its remerged:

rm -Rf /usr/lib/distcc

back up these 32bit crossdev versions, they may be useful if something goes wrong (experience says it may!)

cp -ar /usr/x86_64-pc-linux-gnu /migration-backup/usr/

cp -ar /usr/include /migration-backup/usr

put -sandbox -usersandbox in features
add */* abi_x86_32 to package.use
most 32bit doesnt get built on stable unless u do this:

# cat /etc/portage/profile/use.mask
-abi_x86_32

change make.profile symlink to point to a multilib amd64 profile

on donor pc or VM:

quickpkg glibc gcc zlib ncurses gmp mpfr util-linux acl attr sandbox coreutils procps binutils libcap mpc cracklib flex =db-5* glib pam pambase =python-3.8* bash readline findutils install-xattr bzip2 tar xz-utils make grep patch gawk sed libpcre dev-libs/libffi gettext libxml2

on source VM, scp -r /var/cache/binpkgs to target PC

for this lib / lib64 link ↔ switcheroo
* make sure busybox is functional. run this from busybox
* have a few shells open, in case you break the one you're working from

mv /lib oldlib
ln -s lib64 lib
cd /usr
mv lib to oldlib
ln -s lib64 lib

this will get overwritten by emerge at the appropriate time, but lets the 32bit loader continue to work for now

cp migration-backup/lib/ld-linux.so.2 /lib
ldconfig

/usr/lib symlink creation will break python. The following will not create orphans as the files are in exactly the same location from portage's point of view.

cd /usr/oldlib
mv python-exec python3.6 libpython* portage gcc ../lib64
cp -r /oldlib/gentoo /lib

disable collision detection and emerge gcc AND binutils using this method:

LD_PRELOAD="/usr/lib/gcc/i686-pc-linux-gnu/10.3.0/libgcc_s.so.1" PATH="/migration-backup/bin:/migration-backup/usr/bin:/migration-backup/sbin:/migration-backup/usr/sbin:${PATH}"   FEATURES="-collision-detect -protect-owned" emerge -1kav sys-devel/gcc

check /usr/libexec/gcc/x86_64-pc-linux-gnu/ for any links pointing at i686 versions. remove.
continue to deploy initial binary packages using this method (except with collision detection) donated from prebuilt VM from /usr/portage/packages or /var/cache/binpkgs. Of these, mpc, zlib, glibc needs to come first, then everything else will come good. In the process of deploying glibc, /lib needs to be a symlink to /lib64 which will break 32bit programs. see ld-linux.so.2 trick above. ldconfig is your friend here with the above 99migration env file.

If you get into trouble getting 64bit loader working, do this (only if needed):
* backup these: /etc/env.d/99glibc /etc/gai.conf /etc/host.conf /etc/locale.gen /etc/nsswitch.conf /etc/rpc
* extract glibc tbz2 binary package directly into root of filesystem. subsequent remerge will track the files correctly later.
* restore etc files from above backup

This might not be needed. Fix 32bit toolchain and python in wrong directory by running:

PKGDIR=/var/cache/binpkgs emerge -1kav sys-devel/gcc mpfr mpc binutils 
  gcc-config 1
  binutils-config 1
  . /etc/profile

Finally now that theres a working coreutils etc, If you manually extracted glibc in previous step, overwrite it with package copy.

PKGDIR=/var/cache/binpkgs emerge -1kav glibc

Double check /etc/nsswitch.conf and other files backed up above, this may have overwritten them again.

mv /migration-backup/lib/modules /lib64

Emerging gcc needs to be done now, but also acts as a sanity check to see what we've missed. Repeat the quickpkg / emerge -1k steps for missing things

emerge gcc -1av

leave /etc/env.d/99migration in place at least until libraries in /lib32 are populated

@system rebuild - adjust USE as needed

FEATURES="-sandbox -usersandbox" USE="-X -gtk -qt5 -introspection -cairo -gpm -consolekit -policykit -net -ipv6 -spell -sqlite -nls -berkdb -gdbm -openssl" emerge -1eav @system

work through any problems caused by emerge ordering above. If a dependancy problem proves too hard to solve, cheat by grabbing a binary package from the donor VM prepared earier. The subsequent @world emerge will take over the package later.
/etc/env.d/99migration can now be removed. env-update, source /etc/profile, ldconfig

remove -sandbox and -usersandbox from features
check for i686 compiler orphans with: qfile -o /usr/bin/i686-pc-linux-gnu-*

emerge -eav –keep-going @world

take note of failed, packages - these are usually caused by ordering/dependancy so a subsequent emerge run of the failed list will work. If not, work through the issues.

Things to do later

uncomment LINGUAS from make.conf
take out /etc/env.d/99migration
remove /migration-backup
erase /usr/portage/packages (whole dir)
remove abi_x86_32 from package.use and profiles/use.mask, then emerge –newuse
clean up /lib.old and /usr/lib.old

check for orphans in /usr/lib and all the other places. (bin sbin /usr/bin /usr/sbin). For finding orphan files after migration in /lib32, /usr/lib32, /usr/lib64

cd /lib32 ; find  -xdev -type f -exec qfile -o {} + |less