bug#44760: Closure copy in ‘guix system init’ is inefficient

["Ludovic Courtès" <ludo@gnu.org>]

‘guix system init’ ends by copying the system’s closure from the “host”
store to the target store; it also initializes the database of that
target store.

That copy is inefficient for several reasons.  Let’s pick one file,
shred.1.gz, that ends up being copied, and let’s look at its occurrences
in the strace log of ‘guix system init config.scm /tmp/os’:

--8<---------------cut here---------------start------------->8---
$ grep -A2 '/shred.1.gz' ,,s
lstat("/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", {st_mode=S_IFREG|0444, st_size=1490, ...}) = 0
openat(AT_FDCWD, "/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", O_RDONLY) = 15
fstat(15, {st_mode=S_IFREG|0444, st_size=1490, ...}) = 0
openat(AT_FDCWD, "/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", O_WRONLY|O_CREAT|O_TRUNC, 0444) = 16
read(15, "\37\213\10\0\0\0\0\0\2\3\215VMs\3336\20\275\363Wluh\354\251L%vg\322:M"..., 8192) = 1490
write(16, "\37\213\10\0\0\0\0\0\2\3\215VMs\3336\20\275\363Wluh\354\251L%vg\322:M"..., 1490) = 1490
--
utimensat(AT_FDCWD, "/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", [{tv_sec=1605721025, tv_nsec=616985411} /* 2020-11-18T18:37:05.616985411+0100 */, {tv_sec=1, tv_nsec=0} /* 1970-01-01T01:00:01+0100 */], 0) = 0
lstat("/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/sleep.1.gz", {st_mode=S_IFREG|0444, st_size=813, ...}) = 0
openat(AT_FDCWD, "/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/sleep.1.gz", O_RDONLY) = 15
--
lstat("/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", {st_mode=S_IFREG|0444, st_size=1490, ...}) = 0
lstat("/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shuf.1.gz", {st_mode=S_IFREG|0444, st_size=972, ...}) = 0
lstat("/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/sleep.1.gz", {st_mode=S_IFREG|0444, st_size=813, ...}) = 0
--
lstat("/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", {st_mode=S_IFREG|0444, st_size=1490, ...}) = 0
openat(AT_FDCWD, "/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", O_RDONLY) = 17
lseek(17, 0, SEEK_CUR)                  = 0
read(17, "\37\213\10\0\0\0\0\0\2\3\215VMs\3336\20\275\363Wluh\354\251L%vg\322:M"..., 1490) = 1490
--
lstat("/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", {st_mode=S_IFREG|0444, st_size=1490, ...}) = 0
openat(AT_FDCWD, "/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", O_RDONLY) = 17
lseek(17, 0, SEEK_CUR)                  = 0
read(17, "\37\213\10\0\0\0\0\0\2\3\215VMs\3336\20\275\363Wluh\354\251L%vg\322:M"..., 1490) = 1490
--
link("/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shred.1.gz", "/tmp/os/gnu/store/.links/0w0qcs5lp36i89yry91r2ixlghihzf0vc56bpd9yylj342gv82xl") = 0
lstat("/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shuf.1.gz", {st_mode=S_IFREG|0444, st_size=972, ...}) = 0
openat(AT_FDCWD, "/tmp/os/gnu/store/57xj5gcy1jbl9ai2lnrqnpr0dald9i65-coreutils-8.32/share/man/man1/shuf.1.gz", O_RDONLY) = 17
--8<---------------cut here---------------end--------------->8---

First, /tmp/os/…/shred.1.gz is read entirely twice: once in
‘register-items’ (in the ‘nar-sha256’ call) to compute its hash, and a
second time for deduplication (the ‘deduplicate’ call in there.)

The ‘nar-sha256’ call could be avoided because the database of
/gnu/store contains that value.  As for deduplication, we could perhaps
create those ‘.links’ entries as we copy files instead of re-traversing
the whole thing afterwards.

Second, all of /tmp/os is traversed to reset timestamps, although we
could have cleared those timestamps when we created those files in the
first place (<https://issues.guix.gnu.org/44741> prevents that though,
unless we keep a bug-fixed copy of ‘copy-recursively’ in there.)

Third, in the case of the installer, we’re really copying from
/mnt/guix-inst/store to /mnt/gnu/store, which is likely the same
device.  In this case we could create hard links instead of actually
copying files.

Fourth, we’re adding items one by one in the target store database, but
it may be more efficient to more or less dump the subset of the source
database in bulk.

Surely we can do better.

Ludo’.