"deleting unused links" GC phase is too slow

OpenSubmitted by Ludovic Courtès.
Details
6 participants
  • John Kehayias
  • Ludovic Courtès
  • Maxim Cournoyer
  • Mark H Weaver
  • Ricardo Wurmus
  • Ricardo Wurmus
Owner
unassigned
Severity
important
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Ludovic Courtès wrote on 13 Nov 2016 18:41
(address . bug-guix@gnu.org)
87wpg7ffbm.fsf@gnu.org
‘LocalStore::removeUnusedLinks’ traverses all the entries in/gnu/store/.links and calls lstat(2) on each one of them and checks‘st_nlink’ to determine whether they can be deleted.
There are two problems: lstat(2) can be slow on spinning disks as foundon hydra.gnu.org, and the algorithm is proportional in the number ofentries in /gnu/store/.links, which is a lot on hydra.gnu.org.
Ludo’.
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Ludovic Courtès wrote on 9 Dec 2016 23:43
(address . 24937@debbugs.gnu.org)(name . Mark H Weaver)(address . mhw@netris.org)
87wpf867v6.fsf@gnu.org
ludo@gnu.org (Ludovic Courtès) skribis:
Toggle quote (8 lines)> ‘LocalStore::removeUnusedLinks’ traverses all the entries in> /gnu/store/.links and calls lstat(2) on each one of them and checks> ‘st_nlink’ to determine whether they can be deleted.>> There are two problems: lstat(2) can be slow on spinning disks as found> on hydra.gnu.org, and the algorithm is proportional in the number of> entries in /gnu/store/.links, which is a lot on hydra.gnu.org.
On Dec. 2 on guix-sysadmin@gnu.org, Mark described an improvement thatnoticeably improved performance:
The idea is to read the entire /gnu/store/.links directory, sort the entries by inode number, and then iterate over the entries by inode number, calling 'lstat' on each one and deleting the ones with a link count of 1.
The reason this is so much faster is because the inodes are stored on disk in order of inode number, so this leads to a sequential access pattern on disk instead of a random access pattern.
The difficulty is that the directory is too large to comfortably store all of the entries in virtual memory. Instead, the entries should be written to temporary files on disk, and then sorted using merge sort to ensure sequential access patterns during sorting. Fortunately, this is exactly what 'sort' does from GNU coreutils.
So, for now, I've implemented this as a pair of small C programs that is used in a pipeline with GNU sort. The first program simply reads a directory and writes lines of the form "<inode> <name>" to stdout. (Unfortunately, "ls -i" calls stat on each entry, so it can't be used). This is piped through 'sort -n' and then into another small C program that reads these lines, calls 'lstat' on each one, and deletes the non-directories with link count 1.
Regarding memory usage, I replied:
Really?
For each entry, we have to store roughly 70 bytes for the file name (or 52 if we consider only the basename), plus 8 bytes for the inode number; let’s say 64 bytes.
If we have 10 M entries, that’s 700 MB (or 520 MB), which is a lot, but maybe acceptable?
At worst, we may still see an improvement if we proceed by batches: we read 10000 directory entries (7 MB), sort them, and stat them, then read the next 10000 entries. WDYT?
Ludo’.
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Ludovic Courtès wrote on 9 Dec 2016 23:44
control message for bug #24937
(address . control@debbugs.gnu.org)
87vaus67uc.fsf@gnu.org
severity 24937 important
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Ludovic Courtès wrote on 11 Dec 2016 14:46
Re: bug#24937: "deleting unused links" GC phase is too slow
(address . 24937@debbugs.gnu.org)(name . Mark H Weaver)(address . mhw@netris.org)
87lgvm4lzu.fsf@gnu.org
Hello!
Here’s a proposed patch that follows your suggestion, Mark, but placesan upper bound on the number of directory entries loaded in memory.
On my laptop, which has ~500k entries in /gnu/store/.links, the resultis something like this (notice the inode numbers in ‘lstat’ calls):
Toggle snippet (22 lines)13738 write(4, "gmlo\0\0\0\0\31\0\0\0\0\0\0\0deleting unused "..., 48) = 4813738 open("/gnu/store/.links", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 813738 fstat(8, {st_dev=makedev(8, 2), st_ino=4014083, st_mode=S_IFDIR|0755, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=119224, st_size=60977152, st_atime=2016/12/11-12:01:59, st_mtime=2016/12/11-09:39:45, st_ctime=2016/12/11-09:39:45}) = 013738 getdents(8, {{d_ino=4014083, d_off=4294967296, d_reclen=24, d_name="."}[...]13738 lstat("/gnu/store/.links/1f2f3g8waxwymp9sl2slcfyara164i8w1y2sz3h9js2fcviv2rnc", {st_dev=makedev(8, 2), st_ino=47, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=88, st_size=41482, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 013738 lstat("/gnu/store/.links/1p25kpyfw354in4kykmgh5sy9h925hnil1jdzgxhz7n6abbws8px", {st_dev=makedev(8, 2), st_ino=65, st_mode=S_IFREG|0444, st_nlink=9, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2313, st_atime=2016/12/08-21:02:26, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/11-01:44:49}) = 013738 lstat("/gnu/store/.links/163187g637br9ys5pmshb01wjav53bs1g1a83m7c2alpdyx3yqz2", {st_dev=makedev(8, 2), st_ino=68, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=32, st_size=13561, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 0[...]13738 getdents(8, {{d_ino=4257114, d_off=1734093409898198492,[...]13738 lstat("/gnu/store/.links/1m6g06i01ybbkhjjbirjnj7fckw1b772cwygkvbd6v6zgkln7f7m", {st_dev=makedev(8, 2), st_ino=19, st_mode=S_IFREG|0444, st_nlink=4, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2553, st_atime=2016/12/08-21:02:54, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/07-00:05:19}) = 013738 lstat("/gnu/store/.links/1ml8n3q55ikn8h60sn67jq1y7z7mvdp5kwr33pqrid2r6kk1d4kb", {st_dev=makedev(8, 2), st_ino=30, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2090, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:21}) = 013738 lstat("/gnu/store/.links/1c8cvwlqyyqby3k13cwm40g26pwca5iiz5dcj43xrgn9y91lfvc2", {st_dev=makedev(8, 2), st_ino=33, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=16, st_size=7958, st_atime=2015/11/04-18:55:32, st_mtime=1970/01/01-01:00:01, st_ctime=2016/01/05-11:35:49}) = 0[...]13738 getdents(8, {{d_ino=328672,[...]13738 lstat("/gnu/store/.links/1l55l59dxb74himmkfzx5v63cv7287i6rjhdns1fdlwajqd73lnz", {st_dev=makedev(8, 2), st_ino=21, st_mode=S_IFREG|0444, st_nlink=31, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=615, st_atime=2016/12/08-21:02:30, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/11-01:44:47}) = 013738 lstat("/gnu/store/.links/1c7mm5amw743mb45f1zg4d4r3g549ch35wks9izkcgkx0jirpxsg", {st_dev=makedev(8, 2), st_ino=48, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=360, st_size=176750, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 013738 lstat("/gnu/store/.links/0z5s7b0yk8mfn1np6gk3cdbmpnjgxg1g0l8vfq1aa01zwp06d3f0", {st_dev=makedev(8, 2), st_ino=61, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=1440, st_atime=2016/11/03-20:37:50, st_mtime=1970/01/01-01:00:01, st_ctime=2016/11/07-00:01:57}) = 0
I can’t tell exactly how this affects performance because my machine hasan SSD where this operation takes ~3 seconds on a cold cache. I suspectit has performance comparable to that of doing all the ‘readdir’ at oncefollowed by all the ‘lstat’.
Mark, how does that sound?
I’d like to commit it soon if there are no objections.
Thanks,Ludo’.
Toggle diff (96 lines)diff --git a/nix/libstore/gc.cc b/nix/libstore/gc.ccindex 72eff52..db58603 100644--- a/nix/libstore/gc.cc+++ b/nix/libstore/gc.cc@@ -545,6 +545,9 @@ void LocalStore::tryToDelete(GCState & state, const Path & path) } +/* Like 'dirent', but with just what we need. */+typedef std::pair<Path, ino_t> MiniDirEntry;+ /* Unlink all files in /nix/store/.links that have a link count of 1, which indicates that there are no other links and so they can be safely deleted. FIXME: race condition with optimisePath(): we@@ -555,32 +558,57 @@ void LocalStore::removeUnusedLinks(const GCState & state) AutoCloseDir dir = opendir(linksDir.c_str()); if (!dir) throw SysError(format("opening directory `%1%'") % linksDir); + /* Maximum number of entries stored in memory; each 'MiniDirEntry' takes+ ~80 bytes. */+ const size_t maxEntries = 100000;+ long long actualSize = 0, unsharedSize = 0; - struct dirent * dirent;- while (errno = 0, dirent = readdir(dir)) {- checkInterrupt();- string name = dirent->d_name;- if (name == "." || name == "..") continue;- Path path = linksDir + "/" + name;-- struct stat st;- if (lstat(path.c_str(), &st) == -1)- throw SysError(format("statting `%1%'") % path);-- if (st.st_nlink != 1) {- unsigned long long size = st.st_blocks * 512ULL;- actualSize += size;- unsharedSize += (st.st_nlink - 1) * size;- continue;- }-- printMsg(lvlTalkative, format("deleting unused link `%1%'") % path);-- if (unlink(path.c_str()) == -1)- throw SysError(format("deleting `%1%'") % path);-- state.results.bytesFreed += st.st_blocks * 512;+ bool endOfDir = false;++ while (!endOfDir) {+ /* Read as many entries as possible at once, up to 'maxEntries'. */+ std::list<MiniDirEntry> entries;+ struct dirent * dirent;+ while (errno = 0,+ (entries.size() < maxEntries) && (dirent = readdir(dir))) {+ checkInterrupt();+ string name = dirent->d_name;+ if (name == "." || name == "..") continue;+ entries.emplace_back(MiniDirEntry(name, dirent->d_ino));+ }++ endOfDir = (dirent == NULL);++ /* Sort entries by inode number to minimize disk seeks induced by the+ following 'lstat' calls. */+ entries.sort([] (const MiniDirEntry& e1, const MiniDirEntry& e2) {+ return e1.second < e2.second;+ });++ for (auto && item: entries) {+ checkInterrupt();++ Path path = linksDir + "/" + item.first;++ struct stat st;+ if (lstat(path.c_str(), &st) == -1)+ throw SysError(format("statting `%1%'") % path);++ if (st.st_nlink != 1) {+ unsigned long long size = st.st_blocks * 512ULL;+ actualSize += size;+ unsharedSize += (st.st_nlink - 1) * size;+ continue;+ }+x+ printMsg(lvlTalkative, format("deleting unused link `%1%'") % path);++ if (unlink(path.c_str()) == -1)+ throw SysError(format("deleting `%1%'") % path);++ state.results.bytesFreed += st.st_blocks * 512;+ } } struct stat st;
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Mark H Weaver wrote on 11 Dec 2016 15:23
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
87twaaa6j9.fsf@netris.org
ludo@gnu.org (Ludovic Courtès) writes:
Toggle quote (34 lines)> Here’s a proposed patch that follows your suggestion, Mark, but places> an upper bound on the number of directory entries loaded in memory.>> On my laptop, which has ~500k entries in /gnu/store/.links, the result> is something like this (notice the inode numbers in ‘lstat’ calls):>> 13738 write(4, "gmlo\0\0\0\0\31\0\0\0\0\0\0\0deleting unused "..., 48) = 48> 13738 open("/gnu/store/.links", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 8> 13738 fstat(8, {st_dev=makedev(8, 2), st_ino=4014083, st_mode=S_IFDIR|0755, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=119224, st_size=60977152, st_atime=2016/12/11-12:01:59, st_mtime=2016/12/11-09:39:45, st_ctime=2016/12/11-09:39:45}) = 0> 13738 getdents(8, {{d_ino=4014083, d_off=4294967296, d_reclen=24, d_name="."}> [...]> 13738 lstat("/gnu/store/.links/1f2f3g8waxwymp9sl2slcfyara164i8w1y2sz3h9js2fcviv2rnc", {st_dev=makedev(8, 2), st_ino=47, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=88, st_size=41482, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 0> 13738 lstat("/gnu/store/.links/1p25kpyfw354in4kykmgh5sy9h925hnil1jdzgxhz7n6abbws8px", {st_dev=makedev(8, 2), st_ino=65, st_mode=S_IFREG|0444, st_nlink=9, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2313, st_atime=2016/12/08-21:02:26, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/11-01:44:49}) = 0> 13738 lstat("/gnu/store/.links/163187g637br9ys5pmshb01wjav53bs1g1a83m7c2alpdyx3yqz2", {st_dev=makedev(8, 2), st_ino=68, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=32, st_size=13561, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 0> [...]> 13738 getdents(8, {{d_ino=4257114, d_off=1734093409898198492,> [...]> 13738 lstat("/gnu/store/.links/1m6g06i01ybbkhjjbirjnj7fckw1b772cwygkvbd6v6zgkln7f7m", {st_dev=makedev(8, 2), st_ino=19, st_mode=S_IFREG|0444, st_nlink=4, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2553, st_atime=2016/12/08-21:02:54, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/07-00:05:19}) = 0> 13738 lstat("/gnu/store/.links/1ml8n3q55ikn8h60sn67jq1y7z7mvdp5kwr33pqrid2r6kk1d4kb", {st_dev=makedev(8, 2), st_ino=30, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2090, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:21}) = 0> 13738 lstat("/gnu/store/.links/1c8cvwlqyyqby3k13cwm40g26pwca5iiz5dcj43xrgn9y91lfvc2", {st_dev=makedev(8, 2), st_ino=33, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=16, st_size=7958, st_atime=2015/11/04-18:55:32, st_mtime=1970/01/01-01:00:01, st_ctime=2016/01/05-11:35:49}) = 0> [...]> 13738 getdents(8, {{d_ino=328672,> [...]> 13738 lstat("/gnu/store/.links/1l55l59dxb74himmkfzx5v63cv7287i6rjhdns1fdlwajqd73lnz", {st_dev=makedev(8, 2), st_ino=21, st_mode=S_IFREG|0444, st_nlink=31, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=615, st_atime=2016/12/08-21:02:30, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/11-01:44:47}) = 0> 13738 lstat("/gnu/store/.links/1c7mm5amw743mb45f1zg4d4r3g549ch35wks9izkcgkx0jirpxsg", {st_dev=makedev(8, 2), st_ino=48, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=360, st_size=176750, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 0> 13738 lstat("/gnu/store/.links/0z5s7b0yk8mfn1np6gk3cdbmpnjgxg1g0l8vfq1aa01zwp06d3f0", {st_dev=makedev(8, 2), st_ino=61, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=1440, st_atime=2016/11/03-20:37:50, st_mtime=1970/01/01-01:00:01, st_ctime=2016/11/07-00:01:57}) = 0>> I can’t tell exactly how this affects performance because my machine has> an SSD where this operation takes ~3 seconds on a cold cache. I suspect> it has performance comparable to that of doing all the ‘readdir’ at once> followed by all the ‘lstat’.>> Mark, how does that sound?
I think we should sort the entire directory using merge sort backed todisk files. If we load chunks of the directory, sort them and processthem individually, I expect that this will increase the amount of I/Orequired by a non-trivial factor. In each pass, we would load blocks ofinodes from disk, almost all of which are likely to be present in thestore and thus linked from the directory, but in this scheme we willprocess only a small number of them and drop the rest on the floor to beread again in the next pass. Given that even my fairly optimalimplementation takes about 35 minutes to run on Hydra, I'd prefer toavoid multiplying that by a non-trivial factor.
Why not just use GNU sort? It already exists, and does exactly what weneed.
If you object to using an external program for some reason, I wouldprefer to re-implement a similar algorithm in the daemon.
Thanks, Mark
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Ludovic Courtès wrote on 11 Dec 2016 19:02
(name . Mark H Weaver)(address . mhw@netris.org)(address . 24937@debbugs.gnu.org)
87twaa2vjx.fsf@gnu.org
Mark H Weaver <mhw@netris.org> skribis:
Toggle quote (47 lines)> ludo@gnu.org (Ludovic Courtès) writes:>>> Here’s a proposed patch that follows your suggestion, Mark, but places>> an upper bound on the number of directory entries loaded in memory.>>>> On my laptop, which has ~500k entries in /gnu/store/.links, the result>> is something like this (notice the inode numbers in ‘lstat’ calls):>>>> 13738 write(4, "gmlo\0\0\0\0\31\0\0\0\0\0\0\0deleting unused "..., 48) = 48>> 13738 open("/gnu/store/.links", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 8>> 13738 fstat(8, {st_dev=makedev(8, 2), st_ino=4014083, st_mode=S_IFDIR|0755, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=119224, st_size=60977152, st_atime=2016/12/11-12:01:59, st_mtime=2016/12/11-09:39:45, st_ctime=2016/12/11-09:39:45}) = 0>> 13738 getdents(8, {{d_ino=4014083, d_off=4294967296, d_reclen=24, d_name="."}>> [...]>> 13738 lstat("/gnu/store/.links/1f2f3g8waxwymp9sl2slcfyara164i8w1y2sz3h9js2fcviv2rnc", {st_dev=makedev(8, 2), st_ino=47, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=88, st_size=41482, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 0>> 13738 lstat("/gnu/store/.links/1p25kpyfw354in4kykmgh5sy9h925hnil1jdzgxhz7n6abbws8px", {st_dev=makedev(8, 2), st_ino=65, st_mode=S_IFREG|0444, st_nlink=9, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2313, st_atime=2016/12/08-21:02:26, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/11-01:44:49}) = 0>> 13738 lstat("/gnu/store/.links/163187g637br9ys5pmshb01wjav53bs1g1a83m7c2alpdyx3yqz2", {st_dev=makedev(8, 2), st_ino=68, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=32, st_size=13561, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 0>> [...]>> 13738 getdents(8, {{d_ino=4257114, d_off=1734093409898198492,>> [...]>> 13738 lstat("/gnu/store/.links/1m6g06i01ybbkhjjbirjnj7fckw1b772cwygkvbd6v6zgkln7f7m", {st_dev=makedev(8, 2), st_ino=19, st_mode=S_IFREG|0444, st_nlink=4, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2553, st_atime=2016/12/08-21:02:54, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/07-00:05:19}) = 0>> 13738 lstat("/gnu/store/.links/1ml8n3q55ikn8h60sn67jq1y7z7mvdp5kwr33pqrid2r6kk1d4kb", {st_dev=makedev(8, 2), st_ino=30, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=2090, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:21}) = 0>> 13738 lstat("/gnu/store/.links/1c8cvwlqyyqby3k13cwm40g26pwca5iiz5dcj43xrgn9y91lfvc2", {st_dev=makedev(8, 2), st_ino=33, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=16, st_size=7958, st_atime=2015/11/04-18:55:32, st_mtime=1970/01/01-01:00:01, st_ctime=2016/01/05-11:35:49}) = 0>> [...]>> 13738 getdents(8, {{d_ino=328672,>> [...]>> 13738 lstat("/gnu/store/.links/1l55l59dxb74himmkfzx5v63cv7287i6rjhdns1fdlwajqd73lnz", {st_dev=makedev(8, 2), st_ino=21, st_mode=S_IFREG|0444, st_nlink=31, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=615, st_atime=2016/12/08-21:02:30, st_mtime=1970/01/01-01:00:01, st_ctime=2016/12/11-01:44:47}) = 0>> 13738 lstat("/gnu/store/.links/1c7mm5amw743mb45f1zg4d4r3g549ch35wks9izkcgkx0jirpxsg", {st_dev=makedev(8, 2), st_ino=48, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=360, st_size=176750, st_atime=2015/03/10-11:29:06, st_mtime=1970/01/01-01:00:01, st_ctime=2015/11/25-11:29:20}) = 0>> 13738 lstat("/gnu/store/.links/0z5s7b0yk8mfn1np6gk3cdbmpnjgxg1g0l8vfq1aa01zwp06d3f0", {st_dev=makedev(8, 2), st_ino=61, st_mode=S_IFREG|0444, st_nlink=2, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=8, st_size=1440, st_atime=2016/11/03-20:37:50, st_mtime=1970/01/01-01:00:01, st_ctime=2016/11/07-00:01:57}) = 0>>>> I can’t tell exactly how this affects performance because my machine has>> an SSD where this operation takes ~3 seconds on a cold cache. I suspect>> it has performance comparable to that of doing all the ‘readdir’ at once>> followed by all the ‘lstat’.>>>> Mark, how does that sound?>> I think we should sort the entire directory using merge sort backed to> disk files. If we load chunks of the directory, sort them and process> them individually, I expect that this will increase the amount of I/O> required by a non-trivial factor. In each pass, we would load blocks of> inodes from disk, almost all of which are likely to be present in the> store and thus linked from the directory, but in this scheme we will> process only a small number of them and drop the rest on the floor to be> read again in the next pass. Given that even my fairly optimal> implementation takes about 35 minutes to run on Hydra, I'd prefer to> avoid multiplying that by a non-trivial factor.
Sure, though it’s not obvious to me how much of a difference it makes;my guess is that processing in large chunks is already a win, but we’dhave to measure.
Toggle quote (3 lines)> Why not just use GNU sort? It already exists, and does exactly what we> need.
Does ‘sort’ manage to avoid reading whole files in memory? If not, Ithink it wouldn’t buy us anything to use it.
Toggle quote (3 lines)> If you object to using an external program for some reason, I would> prefer to re-implement a similar algorithm in the daemon.
Yeah, I’d rather avoid serializing the list of file names/inode numberpairs just to invoke ‘sort’ on that.
Also, what algorithm are you referring to?
Thanks for the quick feedback!
Ludo’.
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Mark H Weaver wrote on 11 Dec 2016 20:27
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
87lgvm9sgq.fsf@netris.org
ludo@gnu.org (Ludovic Courtès) writes:
Toggle quote (17 lines)> Mark H Weaver <mhw@netris.org> skribis:>>> I think we should sort the entire directory using merge sort backed to>> disk files. If we load chunks of the directory, sort them and process>> them individually, I expect that this will increase the amount of I/O>> required by a non-trivial factor. In each pass, we would load blocks of>> inodes from disk, almost all of which are likely to be present in the>> store and thus linked from the directory, but in this scheme we will>> process only a small number of them and drop the rest on the floor to be>> read again in the next pass. Given that even my fairly optimal>> implementation takes about 35 minutes to run on Hydra, I'd prefer to>> avoid multiplying that by a non-trivial factor.>> Sure, though it’s not obvious to me how much of a difference it makes;> my guess is that processing in large chunks is already a win, but we’d> have to measure.
I agree, it would surely be a win. Given that it currently takes on theorder of a day to run this phase on Hydra, if your proposed method takes2 hours, that would be a huge win, but still not good, IMO. Even 35minutes is slower than I'd like.
Toggle quote (5 lines)>> Why not just use GNU sort? It already exists, and does exactly what we>> need.>> Does ‘sort’ manage to avoid reading whole files in memory?
Yes, it does. I monitored the 'sort' process when I first ran myoptimized pipeline. It created about 10 files in /tmp, approximately 70megabytes each as I recall, and then read them all concurrently whilewriting the sorted output.
My guess is that it reads a manageable chunk of the input, sorts it inmemory, and writes it to a temporary file. I guess it repeats thisprocess, writing multiple temporary files, until the entire input isconsumed, and then reads all of those temporary files, merging themtogether into the output stream.
Toggle quote (6 lines)>> If you object to using an external program for some reason, I would>> prefer to re-implement a similar algorithm in the daemon.>> Yeah, I’d rather avoid serializing the list of file names/inode number> pairs just to invoke ‘sort’ on that.
Sure, I agree that it would be better to avoid that, but IMO not at thecost of using O(N) memory instead of O(1) memory, nor at the cost ofmultiplying the amount of disk I/O by a non-trivial factor.
Toggle quote (2 lines)> Also, what algorithm are you referring to?
The algorithm I described above, which I guess is close to what GNU sortdoes.
Thanks, Mark
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Ludovic Courtès wrote on 13 Dec 2016 01:00
(name . Mark H Weaver)(address . mhw@netris.org)(address . 24937@debbugs.gnu.org)
87d1gwvgu0.fsf@gnu.org
Mark H Weaver <mhw@netris.org> skribis:
Toggle quote (24 lines)> ludo@gnu.org (Ludovic Courtès) writes:>>> Mark H Weaver <mhw@netris.org> skribis:>>>>> I think we should sort the entire directory using merge sort backed to>>> disk files. If we load chunks of the directory, sort them and process>>> them individually, I expect that this will increase the amount of I/O>>> required by a non-trivial factor. In each pass, we would load blocks of>>> inodes from disk, almost all of which are likely to be present in the>>> store and thus linked from the directory, but in this scheme we will>>> process only a small number of them and drop the rest on the floor to be>>> read again in the next pass. Given that even my fairly optimal>>> implementation takes about 35 minutes to run on Hydra, I'd prefer to>>> avoid multiplying that by a non-trivial factor.>>>> Sure, though it’s not obvious to me how much of a difference it makes;>> my guess is that processing in large chunks is already a win, but we’d>> have to measure.>> I agree, it would surely be a win. Given that it currently takes on the> order of a day to run this phase on Hydra, if your proposed method takes> 2 hours, that would be a huge win, but still not good, IMO. Even 35> minutes is slower than I'd like.
Of course.
I did some measurements with the attached program on chapters, which isa Xen VM with spinning disks underneath, similar to hydra.gnu.org. Ithas 600k entries in /gnu/store/.links.
Here’s a comparison of the “optimal” mode (bulk stats after we’vefetched all the dirents) vs. the “semi-interleaved” mode (doing bulkstats every 100,000 dirents):
Toggle snippet (19 lines)ludo@guix:~$ gcc -std=gnu99 -Wall links-traversal.c -DMODE=3ludo@guix:~$ sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'ludo@guix:~$ time ./a.out603858 dir_entries, 157 secondsstat took 1 seconds
real 2m38.508suser 0m0.324ssys 0m1.824sludo@guix:~$ gcc -std=gnu99 -Wall links-traversal.c -DMODE=2ludo@guix:~$ sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'ludo@guix:~$ time ./a.out 3852 dir_entries, 172 seconds (including stat)
real 2m51.827suser 0m0.312ssys 0m1.808s
Semi-interleaved is ~12% slower here (not sure how reproducible that isthough).
Toggle quote (16 lines)>>> Why not just use GNU sort? It already exists, and does exactly what we>>> need.>>>> Does ‘sort’ manage to avoid reading whole files in memory?>> Yes, it does. I monitored the 'sort' process when I first ran my> optimized pipeline. It created about 10 files in /tmp, approximately 70> megabytes each as I recall, and then read them all concurrently while> writing the sorted output.>> My guess is that it reads a manageable chunk of the input, sorts it in> memory, and writes it to a temporary file. I guess it repeats this> process, writing multiple temporary files, until the entire input is> consumed, and then reads all of those temporary files, merging them> together into the output stream.
OK. That seems to be that the comment above ‘sortlines’ in sort.cdescribes.
Toggle quote (10 lines)>>> If you object to using an external program for some reason, I would>>> prefer to re-implement a similar algorithm in the daemon.>>>> Yeah, I’d rather avoid serializing the list of file names/inode number>> pairs just to invoke ‘sort’ on that.>> Sure, I agree that it would be better to avoid that, but IMO not at the> cost of using O(N) memory instead of O(1) memory, nor at the cost of> multiplying the amount of disk I/O by a non-trivial factor.
Understood.
sort.c in Coreutils is very big, and we surely don’t want to duplicateall that. Yet, I’d rather not shell out to ‘sort’.
Do you know how many entries are in .links on hydra.gnu.org? If itperforms comparably to chapters, the timings suggests it should havearound 10.5M entries.
Thanks!
Ludo’.
#include <unistd.h>#include <dirent.h>#include <sys/types.h>#include <stdlib.h>#include <stdio.h>#include <sys/time.h>#include <string.h>#include <sys/stat.h>#include <assert.h>
#define STAT_INTERLEAVED 1#define STAT_SEMI_INTERLEAVED 2#define STAT_OPTIMAL 3
struct entry{ char *name; ino_t inode;};
#define MAX_ENTRIES 1000000static struct entry dir_entries[MAX_ENTRIES];
intmain (){ struct timeval start, end;
/* For useful timings, do: sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches' */ gettimeofday (&start, NULL); DIR *links = opendir ("/gnu/store/.links");
size_t count = 0;
#if MODE != STAT_INTERLEAVED void sort_entries (void) { int entry_lower (const void *a, const void *b) { return ((struct entry *)a)->inode < ((struct entry *)b)->inode; }
qsort (dir_entries, count, sizeof (struct entry), entry_lower); }#endif
void stat_entries (void) { for (size_t i = 0; i < count; i++) { struct stat st; lstat (dir_entries[i].name, &st); } }
for (struct dirent *entry = readdir (links); entry != NULL; entry = readdir (links)) { assert (count < MAX_ENTRIES); dir_entries[count].name = strdup (entry->d_name); dir_entries[count].inode = entry->d_ino;#if MODE == STAT_INTERLEAVED struct stat st; lstat (entry->d_name, &st);#endif
#if MODE == STAT_SEMI_INTERLEAVED if (count++ >= 100000) { sort_entries (); stat_entries (); count = 0; }#else count++;#endif }
#if MODE == STAT_SEMI_INTERLEAVED sort_entries (); stat_entries ();#endif
gettimeofday (&end, NULL); printf ("%zi dir_entries, %zi seconds"#if MODE != STAT_OPTIMAL " (including stat)"#endif "\n", count, end.tv_sec - start.tv_sec);
#if MODE == STAT_OPTIMAL sort_entries (); gettimeofday (&start, NULL); stat_entries (); gettimeofday (&end, NULL);
printf ("stat took %zi seconds\n", end.tv_sec - start.tv_sec);#endif
return EXIT_SUCCESS;}
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Mark H Weaver wrote on 13 Dec 2016 05:09
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
8737hs1nd1.fsf@netris.org
Do as you wish. I don't have time to continue discussing this.
Mark
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Mark H Weaver wrote on 13 Dec 2016 13:48
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
87wpf4yoz0.fsf@netris.org
ludo@gnu.org (Ludovic Courtès) writes:
Toggle quote (4 lines)> I did some measurements with the attached program on chapters, which is> a Xen VM with spinning disks underneath, similar to hydra.gnu.org. It> has 600k entries in /gnu/store/.links.
I just want to point out that 600k inodes use 150 megabytes of diskspace on ext4, which is small enough to fit in the cache, so the diskI/O will not be multiplied for such a small test case.
Toggle quote (25 lines)> Here’s a comparison of the “optimal” mode (bulk stats after we’ve> fetched all the dirents) vs. the “semi-interleaved” mode (doing bulk> stats every 100,000 dirents):>> ludo@guix:~$ gcc -std=gnu99 -Wall links-traversal.c -DMODE=3> ludo@guix:~$ sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'> ludo@guix:~$ time ./a.out> 603858 dir_entries, 157 seconds> stat took 1 seconds>> real 2m38.508s> user 0m0.324s> sys 0m1.824s> ludo@guix:~$ gcc -std=gnu99 -Wall links-traversal.c -DMODE=2> ludo@guix:~$ sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'> ludo@guix:~$ time ./a.out > 3852 dir_entries, 172 seconds (including stat)>> real 2m51.827s> user 0m0.312s> sys 0m1.808s>> Semi-interleaved is ~12% slower here (not sure how reproducible that is> though).
This directory you're testing on is more than an order of magnitudesmaller than Hydra's when it's full. Unlike in your test above, all ofthe inodes in Hydra's store won't fit in the cache.
In my opinion, the reason Hydra performs so poorly is because efficiencyand scalability are apparently very low priorities in the design of thesoftware running on it. Unfortunately, I feel that my advice in thisarea is discarded more often than not.
Toggle quote (19 lines)>>>> Why not just use GNU sort? It already exists, and does exactly what we>>>> need.>>>>>> Does ‘sort’ manage to avoid reading whole files in memory?>>>> Yes, it does. I monitored the 'sort' process when I first ran my>> optimized pipeline. It created about 10 files in /tmp, approximately 70>> megabytes each as I recall, and then read them all concurrently while>> writing the sorted output.>>>> My guess is that it reads a manageable chunk of the input, sorts it in>> memory, and writes it to a temporary file. I guess it repeats this>> process, writing multiple temporary files, until the entire input is>> consumed, and then reads all of those temporary files, merging them>> together into the output stream.>> OK. That seems to be that the comment above ‘sortlines’ in sort.c> describes.
Also, see https://en.wikipedia.org/wiki/External_sorting. This is awell-studied problem with a long history.
Toggle quote (6 lines)>>>> If you object to using an external program for some reason, I would>>>> prefer to re-implement a similar algorithm in the daemon.>>>>>> Yeah, I’d rather avoid serializing the list of file names/inode number>>> pairs just to invoke ‘sort’ on that.
I'm fairly sure that the overhead of serializing the file names andinode numbers is *far* less than the overhead you would add by iteratingover the inodes in multiple passes.
Toggle quote (9 lines)>> Sure, I agree that it would be better to avoid that, but IMO not at the>> cost of using O(N) memory instead of O(1) memory, nor at the cost of>> multiplying the amount of disk I/O by a non-trivial factor.>> Understood.>> sort.c in Coreutils is very big, and we surely don’t want to duplicate> all that. Yet, I’d rather not shell out to ‘sort’.
The "shell" would not be involved here at all, just the "sort" program.I guess you dislike launching external processes? Can you explain why?
Guix-daemon launches external processes for building derivations, so whyis using one for garbage collection a problem? Emacs, a program thatyou cite in your talks as having many qualities that we seek to emulate,does not shy away from using external programs.
Toggle quote (2 lines)> Do you know how many entries are in .links on hydra.gnu.org?
"df -i /gnu" indicates that it currently has about 5.5M inodes, butthat's with only 29% of the disk in use. A few days ago, when the diskwas full, assuming that the average file size is the same, it may havehad closer to 5.5M / 0.29 ~= 19M inodes, which is over 30 times as manyas used in your measurements above. On ext4, which uses 256-byteinodes, that's about 5 gigabytes of inodes.
Mark
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Ludovic Courtès wrote on 13 Dec 2016 18:02
(name . Mark H Weaver)(address . mhw@netris.org)
87fulrsqxx.fsf@gnu.org
Hello Mark,
Mark H Weaver <mhw@netris.org> skribis:
Toggle quote (10 lines)> ludo@gnu.org (Ludovic Courtès) writes:>>> I did some measurements with the attached program on chapters, which is>> a Xen VM with spinning disks underneath, similar to hydra.gnu.org. It>> has 600k entries in /gnu/store/.links.>> I just want to point out that 600k inodes use 150 megabytes of disk> space on ext4, which is small enough to fit in the cache, so the disk> I/O will not be multiplied for such a small test case.
Right. That’s the only spinning-disk machine I could access withoutproblem. :-/
Ricardo, Roel: would you be able to run that links-traversal.c fromhttps://debbugs.gnu.org/cgi/bugreport.cgi?filename=links-traversal.c;bug=24937;msg=25;att=1on a machine with a big store, as described athttps://debbugs.gnu.org/cgi/bugreport.cgi?bug=24937#25?
Toggle quote (7 lines)>> Semi-interleaved is ~12% slower here (not sure how reproducible that is>> though).>> This directory you're testing on is more than an order of magnitude> smaller than Hydra's when it's full. Unlike in your test above, all of> the inodes in Hydra's store won't fit in the cache.
Good point. I’m trying my best to get performance figures, there’s nodoubt we could do better!
Toggle quote (5 lines)> In my opinion, the reason Hydra performs so poorly is because efficiency> and scalability are apparently very low priorities in the design of the> software running on it. Unfortunately, I feel that my advice in this> area is discarded more often than not.
Well, as you know, I’m currently traveling, yet I take the time toanswer your email at night; I think this should suggest that far fromdiscarding your advice, I very much value it.
I’m a maintainer though, so I’m trying to understand the problem better.It’s not just about finding the “optimal” solution, but also aboutfinding a tradeoff between the benefits and the maintainability costs.
Toggle quote (6 lines)>> sort.c in Coreutils is very big, and we surely don’t want to duplicate>> all that. Yet, I’d rather not shell out to ‘sort’.>> The "shell" would not be involved here at all, just the "sort" program.> I guess you dislike launching external processes? Can you explain why?
I find that passing strings around among programs is inelegant(subjective), but I don’t think you’re really looking to argue aboutthat, are you? :-)
It remains that, if invoking ‘sort’ appears to be preferable *both* fromperformance and maintenance viewpoints, then it’s a good choice. Thatmay be the case, but again, I prefer to have figures to back that.
Toggle quote (7 lines)>> Do you know how many entries are in .links on hydra.gnu.org?>> "df -i /gnu" indicates that it currently has about 5.5M inodes, but> that's with only 29% of the disk in use. A few days ago, when the disk> was full, assuming that the average file size is the same, it may have> had closer to 5.5M / 0.29 ~= 19M inodes,
OK, good to know.
Thanks!
Ludo’.
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Ricardo Wurmus wrote on 13 Dec 2016 18:18
(name . Ludovic Courtès)(address . ludo@gnu.org)
87vaunbvcu.fsf@mdc-berlin.de
Ludovic Courtès <ludo@gnu.org> writes:
Toggle quote (5 lines)> Ricardo, Roel: would you be able to run that links-traversal.c from> <https://debbugs.gnu.org/cgi/bugreport.cgi?filename=links-traversal.c;bug=24937;msg=25;att=1>> on a machine with a big store, as described at> <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=24937#25>?
I just ran this on my workstation in the office where I regularly buildpackages. Here’s the output of “df -i /gnu”
Filesystem Inodes IUsed IFree IUse% Mounted on /dev/mapper/fedora-root 3301376 1098852 2202524 34% /
Probably not large enough to derive conclusions about hydra’s behaviour.
[I can’t run it on the shared store at the MDC because NFS performance istoo poor. I recently ran “guix gc --optimize” to dedupe the sharedstore (post-build deduplication is disabled since a few weeks) and it’sat 3,197,489 used inodes.]
Here are the results of running the link-traversal code on myworkstation:
Toggle snippet (21 lines)rwurmus in ~: gcc -std=gnu99 -Wall links-traversal.c -DMODE=3rwurmus in ~: sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'rwurmus in ~: time ./a.out 412825 dir_entries, 107 secondsstat took 0 seconds
real 1m47.264suser 0m0.214ssys 0m1.314s
rwurmus in ~: gcc -std=gnu99 -Wall links-traversal.c -DMODE=2rwurmus in ~: sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'rwurmus in ~: time ./a.out 12821 dir_entries, 107 seconds (including stat)
real 1m46.475suser 0m0.201ssys 0m1.309s

-- Ricardo
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Mark H Weaver wrote on 15 Dec 2016 02:19
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
87h9663s6e.fsf@netris.org
I apologize for losing my patience earlier.
Mark
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Ricardo Wurmus wrote on 16 Apr 2020 15:26
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
87ftd3muhp.fsf@elephly.net
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
Toggle quote (44 lines)> Ludovic Courtès <ludo@gnu.org> writes:>>> Ricardo, Roel: would you be able to run that links-traversal.c from>> <https://debbugs.gnu.org/cgi/bugreport.cgi?filename=links-traversal.c;bug=24937;msg=25;att=1>>> on a machine with a big store, as described at>> <https://debbugs.gnu.org/cgi/bugreport.cgi?bug=24937#25>?>> I just ran this on my workstation in the office where I regularly build> packages. Here’s the output of “df -i /gnu”>> Filesystem Inodes IUsed IFree IUse% Mounted on> /dev/mapper/fedora-root 3301376 1098852 2202524 34% />> Probably not large enough to derive conclusions about hydra’s behaviour.>> [I can’t run it on the shared store at the MDC because NFS performance is> too poor. I recently ran “guix gc --optimize” to dedupe the shared> store (post-build deduplication is disabled since a few weeks) and it’s> at 3,197,489 used inodes.]>> Here are the results of running the link-traversal code on my> workstation:>> --8<---------------cut here---------------start------------->8---> rwurmus in ~: gcc -std=gnu99 -Wall links-traversal.c -DMODE=3> rwurmus in ~: sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'> rwurmus in ~: time ./a.out> 412825 dir_entries, 107 seconds> stat took 0 seconds>> real 1m47.264s> user 0m0.214s> sys 0m1.314s>> rwurmus in ~: gcc -std=gnu99 -Wall links-traversal.c -DMODE=2> rwurmus in ~: sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'> rwurmus in ~: time ./a.out> 12821 dir_entries, 107 seconds (including stat)>> real 1m46.475s> user 0m0.201s> sys 0m1.309s> --8<---------------cut here---------------end--------------->8---
I ran this for the first time on ci.guix.gnu.org, which has a very bigstore (currently at around 29TB).
df -i /gnu:
Filesystem Inodes IUsed IFree IUse% Mounted on /dev/sdb1 610021376 132350406 477670970 22% /gnu
I had to increase the number of MAX_ENTRIES to 135000000.
I forgot to drop caches initially. This is the first run:
Toggle snippet (10 lines)root@berlin ~ [env]# gcc links-traversal.c -DMODE=3 -o links-traversalroot@berlin ~ [env]# time ./links-traversal57079502 dir_entries, 3906 secondsstat took 136 seconds
real 67m48.145suser 0m59.575ssys 2m30.065s
I aborted the run after I dropped caches after 67 minutes.
I’m going to continue testing on one of the build nodes, and I’ll tryusing statx.
--Ricardo
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Ricardo Wurmus wrote on 16 Apr 2020 16:27
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
87eesnmrow.fsf@elephly.net
Here are more benchmarks on one of the build nodes. It doesn’t nearlyhave as many used inodes as ci.guix.gnu.org, but I could fill it up ifnecessary.
root@hydra-guix-127 ~# df -i /gnu/ Filesystem Inodes IUsed IFree IUse% Mounted on /dev/sda3 28950528 2796829 26153699 10% /
root@hydra-guix-127 ~# ls -1 /gnu/store/.links | wc -l 2017395
I tested all three modes with statx and with lstat. Thelinks-traversal-statx.c is attached below.
* mode 1 + statx
Toggle snippet (27 lines)root@hydra-guix-127 ~ [env]# gcc -Wall -std=c99 links-traversal-statx.c -DMODE=1 -D_GNU_SOURCE=1 -o links-traversallinks-traversal-statx.c:53:8: warning: �stat_entries� defined but not used [-Wunused-function] 53 | void stat_entries (void) | ^~~~~~~~~~~~root@hydra-guix-127 ~ [env]# echo 3 > /proc/sys/vm/drop_cachesroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 9 seconds (including stat)
real 0m9.176suser 0m0.801ssys 0m4.236sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 4 seconds (including stat)
real 0m3.556suser 0m0.708ssys 0m2.848sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 4 seconds (including stat)
real 0m3.553suser 0m0.599ssys 0m2.954sroot@hydra-guix-127 ~ [env]#

* mode 2 + statx
Toggle snippet (24 lines)root@hydra-guix-127 ~ [env]# gcc -Wall -std=c99 links-traversal-statx.c -DMODE=2 -D_GNU_SOURCE=1 -o links-traversalroot@hydra-guix-127 ~ [env]# echo 3 > /proc/sys/vm/drop_cachesroot@hydra-guix-127 ~ [env]# time ./links-traversal 17377 dir_entries, 10 seconds (including stat)
real 0m9.598suser 0m1.210ssys 0m4.257sroot@hydra-guix-127 ~ [env]# time ./links-traversal 17377 dir_entries, 4 seconds (including stat)
real 0m4.094suser 0m0.988ssys 0m3.107sroot@hydra-guix-127 ~ [env]# time ./links-traversal 17377 dir_entries, 4 seconds (including stat)
real 0m4.095suser 0m0.933ssys 0m3.162sroot@hydra-guix-127 ~ [env]#

* mode 3 + statx
Toggle snippet (26 lines)root@hydra-guix-127 ~ [env]# gcc -Wall -std=c99 links-traversal-statx.c -DMODE=3 -D_GNU_SOURCE=1 -o links-traversal^Croot@hydra-guix-127 ~ [env]# echo 3 > /proc/sys/vm/drop_cachesroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 7 secondsstat took 3 seconds
real 0m9.992suser 0m1.411ssys 0m4.221sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 1 secondsstat took 2 seconds
real 0m4.265suser 0m1.120ssys 0m3.145sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 2 secondsstat took 2 seconds
real 0m4.267suser 0m1.072ssys 0m3.195sroot@hydra-guix-127 ~ [env]#
Now with just lstat:
* mode 1 + lstat
Toggle snippet (26 lines)root@hydra-guix-127 ~ [env]# gcc -Wall -std=c99 links-traversal.c -DMODE=1 -D_GNU_SOURCE=1 -o links-traversallinks-traversal.c:49:8: warning: �stat_entries� defined but not used [-Wunused-function] 49 | void stat_entries (void) | ^~~~~~~~~~~~root@hydra-guix-127 ~ [env]# echo 3 > /proc/sys/vm/drop_cachesroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 9 seconds (including stat)
real 0m9.303suser 0m0.748ssys 0m4.397sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 4 seconds (including stat)
real 0m3.526suser 0m0.540ssys 0m2.987sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 3 seconds (including stat)
real 0m3.519suser 0m0.600ssys 0m2.919sroot@hydra-guix-127 ~ [env]#
* mode 2 + lstat
Toggle snippet (23 lines)root@hydra-guix-127 ~ [env]# gcc -Wall -std=c99 links-traversal.c -DMODE=2 -D_GNU_SOURCE=1 -o links-traversalroot@hydra-guix-127 ~ [env]# echo 3 > /proc/sys/vm/drop_cachesroot@hydra-guix-127 ~ [env]# time ./links-traversal 17377 dir_entries, 9 seconds (including stat)
real 0m9.614suser 0m1.205ssys 0m4.250sroot@hydra-guix-127 ~ [env]# time ./links-traversal 17377 dir_entries, 4 seconds (including stat)
real 0m4.060suser 0m1.052ssys 0m3.008sroot@hydra-guix-127 ~ [env]# time ./links-traversal 17377 dir_entries, 4 seconds (including stat)
real 0m4.057suser 0m0.984ssys 0m3.073sroot@hydra-guix-127 ~ [env]#
* mode 3 + lstat
Toggle snippet (26 lines)root@hydra-guix-127 ~ [env]# gcc -Wall -std=c99 links-traversal.c -DMODE=3 -D_GNU_SOURCE=1 -o links-traversalroot@hydra-guix-127 ~ [env]# echo 3 > /proc/sys/vm/drop_cachesroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 6 secondsstat took 3 seconds
real 0m9.767suser 0m1.270ssys 0m4.339sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 2 secondsstat took 2 seconds
real 0m4.234suser 0m1.136ssys 0m3.097sroot@hydra-guix-127 ~ [env]# time ./links-traversal 2017397 dir_entries, 1 secondsstat took 2 seconds
real 0m4.222suser 0m1.052ssys 0m3.170sroot@hydra-guix-127 ~ [env]#
They are all very close, so I think I need to work with a bigger storeto see a difference.
Or perhaps I did something silly because I don’t know C… If so pleaselet me know.
--Ricardo
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Ludovic Courtès wrote on 17 Apr 2020 10:16
(name . Ricardo Wurmus)(address . rekado@elephly.net)(address . 24937@debbugs.gnu.org)
874ktieddi.fsf@gnu.org
Hi Ricardo,
Thanks for running this benchmark!
Ricardo Wurmus <rekado@elephly.net> skribis:
Toggle quote (3 lines)> root@hydra-guix-127 ~# ls -1 /gnu/store/.links | wc -l> 2017395
That’s not a lot, my laptop has 2.8M links.
It’s interesting to see that system time remains at ~4.2s in all modes.So the only thing that modes 2 and 3 achieve is increasing CPU time.It’s as if the order in which files are stat’d had no impact on I/Operformance.
Ludo’.
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Ricardo Wurmus wrote on 17 Apr 2020 10:28
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
874ktims89.fsf@elephly.net
Ludovic Courtès <ludo@gnu.org> writes:
Toggle quote (5 lines)>> root@hydra-guix-127 ~# ls -1 /gnu/store/.links | wc -l>> 2017395>> That’s not a lot, my laptop has 2.8M links.
Let me rerun this after copying a few thousand store items fromci.guix.gnu.org over. Maybe we’ll see the different times diverge then.
--Ricardo
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Ludovic Courtès wrote on 9 Nov 15:44 +0100
(address . 24937@debbugs.gnu.org)(name . Maxim Cournoyer)(address . maxim.cournoyer@gmail.com)
87pmr9l76m.fsf@gnu.org
Hi!
ludo@gnu.org (Ludovic Courtès) skribis:
Toggle quote (8 lines)> ‘LocalStore::removeUnusedLinks’ traverses all the entries in> /gnu/store/.links and calls lstat(2) on each one of them and checks> ‘st_nlink’ to determine whether they can be deleted.>> There are two problems: lstat(2) can be slow on spinning disks as found> on hydra.gnu.org, and the algorithm is proportional in the number of> entries in /gnu/store/.links, which is a lot on hydra.gnu.org.
Taking a step back, we could perhaps mitigate this with heuristics toreduce the number of entries in .links:
1. Do not deduplicate files with a size lower than some threshold;
2. Delete links with st_nlink <= 3 (instead of <= 2); that would prevent *further* deduplication of those files, but they’d already have two instances sharing the same inode;
3. Stop deduplicating once the number of entries in .links has reached a certain threshold.
For #1, a key insight is that about 30% of the files actuallydeduplicated (in my store, where /gnu/store/.links has 2.2M entries) aresmaller than 1 KiB:
… but 85% of them have at most 4 links (thus, saving up to 2 KiB bydeduplicating):
Attachment: nlink-small.png
On my laptop, we’re talking about space savings of 325 MiB, a tinyfraction of my store:
Toggle snippet (6 lines)scheme@(guile-user)> (saved-space (filter (lambda (file) (< (deduplicated-file-size file) 1024)) l))$40 = 325914739
Files smaller than 1 KiB represent 35% of the entries in .links:
Attachment: size.png
By not deduplicating files smaller than 1 KiB, we’d reduce the number ofentries by 35%, which should already have a tangible impact onperformance. It’d be a “mitigation” more than a “fix”, but it has agood work/reward ratio.
We could conduct a similar analysis for #2.
#3 is more difficult to implement because you cannot know the number ofentries in .links until you’ve traversed it (note that currentlydeduplication stops when link(2) returns ENOSPC in .links).
I’m attaching the script I’ve used for that, derived from an earlierexperiment¹. You’re welcome to give it a spin!
Thoughts?
Ludo’.
¹ https://lists.gnu.org/archive/html/guix-devel/2014-09/msg00422.html
(use-modules (charting) ((guix store) #:select (%store-prefix)) (ice-9 ftw) (ice-9 match) (srfi srfi-1) (srfi srfi-9)) (define-record-type <deduplicated-file> (deduplicated-file name size links) deduplicated-file? (name deduplicated-file-name) (size deduplicated-file-size) (links deduplicated-file-link-count)) (define %links-directory (string-append (%store-prefix) "/.links")) (define (links) "Return a list of <deduplicated-file>." (file-system-fold (const #t) (lambda (file stat result) ;leaf (cons (deduplicated-file file (stat:size stat) (stat:nlink stat)) result)) (lambda (directory stat result) ;down result) (lambda (directory stat result) ;up result) (const #f) ;skip (lambda (file stat errno result) (error "i/o error" file errno)) '() %links-directory lstat)) (define KiB (expt 2 10)) (define MiB (* KiB KiB)) (define GiB (* KiB MiB)) (define (saved-space files) "Return the total amount of saved space given FILES, a list of <deduplicated-file>." (fold (lambda (df result) (match df (($ <deduplicated-file> name size links) (when (< links 2) (error "too few links" name links)) (+ result (* size (- links 2)))))) 0 files)) (define (cumulative-distribution files property) "Return a list of (VALUE . COUNT) pairs representing the number of FILES whose PROPERTY is VALUE or less." (define (file<? df1 df2) (< (property df1) (property df2))) (fold (lambda (df result) (match result (((value . count) . rest) (let ((current (property df))) (if (= value current) (alist-cons value (+ count 1) rest) (alist-cons current (+ count 1) result)))) (_ (alist-cons (property df) 1 result)))) '() (sort files file<?))) (define* (plot-distribution distribution output #:key (subtitle "SUBTITLE") max-x (group-name "GROUP") x-axis-label) "Plot DISTRIBUTION, and produce file OUTPUT." (define (log2 n) (let loop ((result 1)) (if (zero? (ash n (- result))) (- result 1) (loop (+ 1 result))))) (define (format-log2-tick tick) ;; (string-append "2^" ;; (number->string (log2 (inexact->exact tick)))) (number->string (inexact->exact tick))) (define (adjust-items total) (lambda (x) (match x ;; XXX: Filter out the two cases that would give us a numerical ;; overflow. ((0 . _) #f) ((1 . _) #f) ((value . count) (and (or (not max-x) (< value max-x)) (cons value (* 100. (/ count total)))))))) (match distribution (((_ . total) . rest) (let ((percent (filter-map (adjust-items total) distribution))) (make-scatter-plot #:title (string-append "Cumulative distribution by " subtitle) #:data `((,group-name ,@percent)) #:x-axis-label x-axis-label #:y-axis-label "%" #:tick-label-formatter format-log2-tick #:log-x-base 2 #:min-x 1 #:max-y 101 #:write-to-png output))))) #! Examples (define l (links)) ;this is the expensive part (plot-distribution (cumulative-distribution l deduplicated-file-link-count) "/tmp/nlink.png" #:x-axis-label "number of hard links" #:subtitle "hard link count" #:max-x 2048 #:group-name "nlinks") (plot-distribution (cumulative-distribution (filter (lambda (file) (< (deduplicated-file-size file) 1024)) l) deduplicated-file-link-count) "/tmp/nlink-small.png" #:x-axis-label "number of hard links" #:subtitle "hard link count for files < 1KiB" #:max-x 2048 #:group-name "nlinks") (plot-distribution (cumulative-distribution l deduplicated-file-size) "/tmp/size.png" #:x-axis-label "file size" #:subtitle "file size" #:max-x 32768 #:group-name "size (B)") (plot-distribution (cumulative-distribution (filter (lambda (f) (> (deduplicated-file-link-count f) 2)) l) deduplicated-file-size) "/tmp/size-deduplicated.png" #:x-axis-label "file size" #:subtitle "size for files actually deduplicated" #:max-x 32768 #:group-name "size (B)") (plot-distribution (cumulative-distribution (filter (lambda (file) (< (deduplicated-file-size file) 1024)) l) (lambda (file) (* (deduplicated-file-size file) (- (deduplicated-file-link-count file) 2)))) "/tmp/size-savings.png" #:x-axis-label "savings" #:subtitle "savings for files < 1KiB" #:max-x 32768 #:group-name "savings (B)") !#
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Ludovic Courtès wrote on 9 Nov 16:00 +0100
(address . 24937@debbugs.gnu.org)(name . Maxim Cournoyer)(address . maxim.cournoyer@gmail.com)
87fss5l6gm.fsf@gnu.org
Ludovic Courtès <ludo@gnu.org> skribis:
Toggle quote (8 lines)> On my laptop, we’re talking about space savings of 325 MiB, a tiny> fraction of my store:>> scheme@(guile-user)> (saved-space (filter (lambda (file)> (< (deduplicated-file-size file) 1024))> l))> $40 = 325914739
For files < 4 KiB, the savings are ~2 GiB, roughly 1% of my store.
Ludo’.
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Maxim Cournoyer wrote on 11 Nov 21:59 +0100
(name . Ludovic Courtès)(address . ludo@gnu.org)(address . 24937@debbugs.gnu.org)
87v90ys911.fsf@gmail.com
Hi Ludovic,
I haven't done any analysis, just grabbed the result, but here it whatit looks for me:
Attachment: nlink.png
Attachment: nlink-small.png
Attachment: size.png
Attachment: size-savings.png
That's for 3631356 links.
Thank you!
Maxim
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Ludovic Courtès wrote on 13 Nov 17:56 +0100
(name . Maxim Cournoyer)(address . maxim.cournoyer@gmail.com)(address . 24937@debbugs.gnu.org)
87v90wat9n.fsf@gnu.org
Hi,
Maxim Cournoyer <maxim.cournoyer@gmail.com> skribis:
Toggle quote (3 lines)> I haven't done any analysis, just grabbed the result, but here it what> it looks for me:
There’s a bit more than 35% of deduplicated files that are < 1KiB, andnot much to be gained by deduplicating them.
On IRC several people shared the results on their machine; several hadsimilar results, and one person had a lot more of those small files (50%of deduplicated files were < 1KiB).
The chart (with a kinda bogus layout) below is perhaps more interesting:it shows the contribution of files below a certain size to the overallspace savings.
In a nutshell:
• Files < 1KiB contribute to 0.3% of the space savings;
• Files < 4KiB contribute to 2.5% of the space savings;
• Files < 256KiB contribute to 42% of the space savings.
You can create this plot with:
Toggle snippet (22 lines)(make-scatter-plot #:title "Contribution to space savings" #:write-to-png "/tmp/space-saving-contribution.png" #:chart-width 1000 #:y-axis-label "contribution (%)" #:x-axis-label "size (B)" #:log-x-base 2 #:min-x 513 #:data (let ((total (saved-space l))) `(("contribution" ,@(map (lambda (size) (cons size (/ (saved-space (filter (lambda (file) (< (deduplicated-file-size file) size)) l)) total .01))) (map (cut expt 2 <>) (iota 12 10 1)))))))
You can also compute individual points like this:
Toggle snippet (17 lines)scheme@(guile-user)> (/ (saved-space (filter (lambda (file) (< (deduplicated-file-size file) 1024)) l)) (saved-space l) 1.)$60 = 0.0034284626558736746scheme@(guile-user)> (/ (saved-space (filter (lambda (file) (< (deduplicated-file-size file) 4096)) l)) (saved-space l) 1.)$62 = 0.025190871178467848scheme@(guile-user)> (/ (saved-space (filter (lambda (file) (< (deduplicated-file-size file) (expt 2 18))) l)) (saved-space l) 1.)$65 = 0.42411104869782185
Choosing a deduplication threshold of 2KiB or 4KiB would have anegligible impact on disk usage on my machine.
Thanks,Ludo’.
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Ludovic Courtès wrote on 13 Nov 22:37 +0100
[PATCH 1/2] =?UTF-8?q?tests:=20Factorize=20'file=3D=3F'.?=
(address . 24937@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludo@gnu.org)
20211113213745.2601-1-ludo@gnu.org
* guix/tests.scm (file=?): Add optional 'stat' parameter. Add fastpatch comparing inode numbers.* tests/gexp.scm ("imported-files with file-like objects"): Remove'file=?' procedure and use the one from (guix tests).--- guix/tests.scm | 30 +++++++++++++++++------------- tests/gexp.scm | 11 +++-------- 2 files changed, 20 insertions(+), 21 deletions(-)
Toggle diff (81 lines)diff --git a/guix/tests.scm b/guix/tests.scmindex fc3d521163..e1c194340c 100644--- a/guix/tests.scm+++ b/guix/tests.scm@@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU-;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>+;;; Copyright © 2013-2021 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;;@@ -182,18 +182,22 @@ (define (random-bytevector n) (loop (1+ i))) bv)))) -(define (file=? a b)- "Return true if files A and B have the same type and same content."- (and (eq? (stat:type (lstat a)) (stat:type (lstat b)))- (case (stat:type (lstat a))- ((regular)- (equal?- (call-with-input-file a get-bytevector-all)- (call-with-input-file b get-bytevector-all)))- ((symlink)- (string=? (readlink a) (readlink b)))- (else- (error "what?" (lstat a))))))+(define* (file=? a b #:optional (stat lstat))+ "Return true if files A and B have the same type and same content. Call+STAT to obtain file metadata."+ (let ((sta (stat a)) (stb (stat b)))+ (and (eq? (stat:type sta) (stat:type stb))+ (case (stat:type sta)+ ((regular)+ (or (and (= (stat:ino sta) (stat:ino stb))+ (= (stat:dev sta) (stat:dev stb)))+ (equal?+ (call-with-input-file a get-bytevector-all)+ (call-with-input-file b get-bytevector-all))))+ ((symlink)+ (string=? (readlink a) (readlink b)))+ (else+ (error "what?" (stat a))))))) (define (canonical-file? file) "Return #t if FILE is in the store, is read-only, and its mtime is 1."diff --git a/tests/gexp.scm b/tests/gexp.scmindex 39a47d4e8c..0758a49f5f 100644--- a/tests/gexp.scm+++ b/tests/gexp.scm@@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>+;;; Copyright © 2014-2021 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be> ;;; ;;; This file is part of GNU Guix.@@ -827,19 +827,14 @@ (define (canonical-file? file) (files -> `(("a/b/c" . ,q-scm) ("p/q" . ,plain))) (drv (imported-files files)))- (define (file=? file1 file2)- ;; Assume deduplication is in place.- (= (stat:ino (stat file1))- (stat:ino (stat file2))))- (mbegin %store-monad (built-derivations (list (pk 'drv drv))) (mlet %store-monad ((dir -> (derivation->output-path drv)) (plain* (text-file "foo" "bar!")) (q-scm* (interned-file q-scm "c"))) (return- (and (file=? (string-append dir "/a/b/c") q-scm*)- (file=? (string-append dir "/p/q") plain*)))))))+ (and (file=? (string-append dir "/a/b/c") q-scm* stat)+ (file=? (string-append dir "/p/q") plain* stat))))))) (test-equal "gexp-modules & ungexp" '((bar) (foo))-- 2.33.0
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Ludovic Courtès wrote on 13 Nov 22:37 +0100
[PATCH 2/2] daemon: Do not deduplicate files smaller than 4 KiB.
(address . 24937@debbugs.gnu.org)(name . Ludovic Courtès)(address . ludo@gnu.org)
20211113213745.2601-2-ludo@gnu.org
Files smaller than 4 KiB typically represent ~60% of the entries in/gnu/store/.links but only contribute to ~2.5% of the space savingsafforded by deduplication.
Not considering these files for deduplication speeds up file insertionin the store and, more importantly, leaves 'removeUnusedLinks' withfewer entries to traverse, thereby speeding it up proportionally.
Partly fixes https://issues.guix.gnu.org/24937.
* config-daemon.ac: Remove symlink hard link check and CAN_LINK_SYMLINKdefinition.* guix/store/deduplication.scm (%deduplication-minimum-size): Newvariable.(deduplicate)[loop]: Do not recurse when FILE's size is below%DEDUPLICATION-MINIMUM-SIZE.(dump-port): New procedure.(dump-file/deduplicate)[hash]: Turn into...[dump-and-compute-hash]: ... this thunk.Call 'deduplicate' only when SIZE is greater than%DEDUPLICATION-MINIMUM-SIZE; otherwise call 'dump-port'.* nix/libstore/gc.cc (LocalStore::removeUnusedLinks): Drop files wherest.st_size < deduplicationMinSize.* nix/libstore/local-store.hh (deduplicationMinSize): New declaration.* nix/libstore/optimise-store.cc (deduplicationMinSize): New variable.(LocalStore::optimisePath_): Return when PATH is a symlink or smallerthan 'deduplicationMinSize'.* tests/derivations.scm ("identical files are deduplicated"): Producefiles bigger than %DEDUPLICATION-MINIMUM-SIZE.* tests/nar.scm ("restore-file-set with directories (signed, valid)"):Likewise.* tests/store-deduplication.scm ("deduplicate, below %deduplication-minimum-size"):New test.("deduplicate", "deduplicate, ENOSPC"): Produce files bigger than%DEDUPLICATION-MINIMUM-SIZE.* tests/store.scm ("substitute, deduplication"): Likewise.--- config-daemon.ac | 11 ------- guix/store/deduplication.scm | 57 ++++++++++++++++++++++++++++------ nix/libstore/gc.cc | 4 ++- nix/libstore/local-store.hh | 3 ++ nix/libstore/optimise-store.cc | 15 +++++---- tests/derivations.scm | 14 ++++++--- tests/nar.scm | 7 +++-- tests/store-deduplication.scm | 41 ++++++++++++++++++++---- tests/store.scm | 4 ++- 9 files changed, 114 insertions(+), 42 deletions(-)
Toggle diff (363 lines)diff --git a/config-daemon.ac b/config-daemon.acindex 5ddc740600..86306effe1 100644--- a/config-daemon.ac+++ b/config-daemon.ac@@ -94,17 +94,6 @@ if test "x$guix_build_daemon" = "xyes"; then AC_CHECK_FUNCS([lutimes lchown posix_fallocate sched_setaffinity \ statvfs nanosleep strsignal statx]) - dnl Check whether the store optimiser can optimise symlinks.- AC_MSG_CHECKING([whether it is possible to create a link to a symlink])- ln -s bla tmp_link- if ln tmp_link tmp_link2 2> /dev/null; then- AC_MSG_RESULT(yes)- AC_DEFINE(CAN_LINK_SYMLINK, 1, [Whether link() works on symlinks.])- else- AC_MSG_RESULT(no)- fi- rm -f tmp_link tmp_link2- dnl Check for <locale>. AC_LANG_PUSH(C++) AC_CHECK_HEADERS([locale])diff --git a/guix/store/deduplication.scm b/guix/store/deduplication.scmindex cd9660174c..8a59adad39 100644--- a/guix/store/deduplication.scm+++ b/guix/store/deduplication.scm@@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2017 Caleb Ristvedt <caleb.ristvedt@cune.org>-;;; Copyright © 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>+;;; Copyright © 2018-2021 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;;@@ -22,12 +22,13 @@ (define-module (guix store deduplication) #:use-module (gcrypt hash)- #:use-module (guix build utils)+ #:use-module ((guix build utils) #:hide (dump-port)) #:use-module (guix build syscalls) #:use-module (guix base32) #:use-module (srfi srfi-11) #:use-module (srfi srfi-34) #:use-module (srfi srfi-35)+ #:use-module (rnrs bytevectors) #:use-module (rnrs io ports) #:use-module (ice-9 ftw) #:use-module (ice-9 match)@@ -37,6 +38,31 @@ (define-module (guix store deduplication) dump-file/deduplicate copy-file/deduplicate)) +;; TODO: Remove once 'dump-port' in (guix build utils) has an optional 'len'+;; parameter.+(define* (dump-port in out+ #:optional len+ #:key (buffer-size 16384))+ "Read LEN bytes from IN (or as much as possible if LEN is #f) and write it+to OUT, using chunks of BUFFER-SIZE bytes."+ (define buffer+ (make-bytevector buffer-size))++ (let loop ((total 0)+ (bytes (get-bytevector-n! in buffer 0+ (if len+ (min len buffer-size)+ buffer-size))))+ (or (eof-object? bytes)+ (and len (= total len))+ (let ((total (+ total bytes)))+ (put-bytevector out buffer 0 bytes)+ (loop total+ (get-bytevector-n! in buffer 0+ (if len+ (min (- len total) buffer-size)+ buffer-size)))))))+ (define (nar-sha256 file) "Gives the sha256 hash of a file and the size of the file in nar form." (let-values (((port get-hash) (open-sha256-port)))@@ -127,6 +153,12 @@ (define temp-link (unless (= EMLINK (system-error-errno args)) (apply throw args))))))) +(define %deduplication-minimum-size+ ;; Size below which files are not deduplicated. This avoids adding too many+ ;; entries to '.links', which would slow down 'removeUnusedLinks' while+ ;; saving little space. Keep in sync with optimize-store.cc.+ 4096)+ (define* (deduplicate path hash #:key (store (%store-directory))) "Check if a store item with sha256 hash HASH already exists. If so, replace PATH with a hardlink to the already-existing one. If not, register@@ -144,13 +176,16 @@ (define links-directory ((file . properties) (unless (member file '("." "..")) (let* ((file (string-append path "/" file))+ (st (lstat file)) (type (match (assoc-ref properties 'type) ((or 'unknown #f)- (stat:type (lstat file)))+ (stat:type st)) (type type))))- (loop file type- (and (not (eq? 'directory type))- (nar-sha256 file)))))))+ (unless (< (stat:size st)+ %deduplication-minimum-size)+ (loop file type+ (and (not (eq? 'directory type))+ (nar-sha256 file)))))))) (scandir* path)) (let ((link-file (string-append links-directory "/" (bytevector->nix-base32-string hash))))@@ -222,9 +257,9 @@ (define* (dump-file/deduplicate file input size type This procedure is suitable as a #:dump-file argument to 'restore-file'. When used that way, it deduplicates files on the fly as they are restored, thereby-removing the need to a deduplication pass that would re-read all the files+removing the need for a deduplication pass that would re-read all the files down the road."- (define hash+ (define (dump-and-compute-hash) (call-with-output-file file (lambda (output) (let-values (((hash-port get-hash)@@ -236,7 +271,11 @@ (define hash (close-port hash-port) (get-hash))))) - (deduplicate file hash #:store store))+ (if (>= size %deduplication-minimum-size)+ (deduplicate file (dump-and-compute-hash) #:store store)+ (call-with-output-file file+ (lambda (output)+ (dump-port input output size))))) (define* (copy-file/deduplicate source target #:key (store (%store-directory)))diff --git a/nix/libstore/gc.cc b/nix/libstore/gc.ccindex e1d0765154..16519116e4 100644--- a/nix/libstore/gc.cc+++ b/nix/libstore/gc.cc@@ -606,7 +606,9 @@ void LocalStore::removeUnusedLinks(const GCState & state) throw SysError(format("statting `%1%'") % path); #endif - if (st.st_nlink != 1) {+ /* Drop links for files smaller than 'deduplicationMinSize', even if+ they have more than one hard link. */+ if (st.st_nlink != 1 && st.st_size >= deduplicationMinSize) { actualSize += st.st_size; unsharedSize += (st.st_nlink - 1) * st.st_size; continue;diff --git a/nix/libstore/local-store.hh b/nix/libstore/local-store.hhindex 9ba37219da..20d3c3c893 100644--- a/nix/libstore/local-store.hh+++ b/nix/libstore/local-store.hh@@ -292,4 +292,7 @@ void canonicaliseTimestampAndPermissions(const Path & path); MakeError(PathInUse, Error); +/* Size below which a file is not considered for deduplication. */+extern const size_t deduplicationMinSize;+ }diff --git a/nix/libstore/optimise-store.cc b/nix/libstore/optimise-store.ccindex eb303ab4c3..baca1a4890 100644--- a/nix/libstore/optimise-store.cc+++ b/nix/libstore/optimise-store.cc@@ -15,6 +15,9 @@ namespace nix { +/* Any file smaller than this is not considered for deduplication.+ Keep in sync with (guix store deduplication). */+const size_t deduplicationMinSize = 4096; static void makeWritable(const Path & path) {@@ -105,12 +108,12 @@ void LocalStore::optimisePath_(OptimiseStats & stats, const Path & path, InodeHa return; } - /* We can hard link regular files and maybe symlinks. */- if (!S_ISREG(st.st_mode)-#if CAN_LINK_SYMLINK- && !S_ISLNK(st.st_mode)-#endif- ) return;+ /* We can hard link regular files (and maybe symlinks), but do that only+ for files larger than some threshold. This avoids adding too many+ entries to '.links', which would slow down 'removeUnusedLinks' while+ saving little space. */+ if (!S_ISREG(st.st_mode) || ((size_t) st.st_size) < deduplicationMinSize)+ return; /* Sometimes SNAFUs can cause files in the store to be modified, in particular when running programs as root underdiff --git a/tests/derivations.scm b/tests/derivations.scmindex cd165d1be6..4621098df3 100644--- a/tests/derivations.scm+++ b/tests/derivations.scm@@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>+;;; Copyright © 2012-2021 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;;@@ -170,11 +170,15 @@ (define prefix-len (string-length dir)) #f)))) (test-assert "identical files are deduplicated"- (let* ((build1 (add-text-to-store %store "one.sh"- "echo hello, world > \"$out\"\n"+ ;; Note: DATA must be longer than %DEDUPLICATION-MINIMUM-SIZE.+ (let* ((data (make-string 4500 #\a))+ (build1 (add-text-to-store %store "one.sh"+ (string-append "echo -n " data+ " > \"$out\"\n") '())) (build2 (add-text-to-store %store "two.sh"- "# Hey!\necho hello, world > \"$out\"\n"+ (string-append "# Hey!\necho -n "+ data " > \"$out\"\n") '())) (drv1 (derivation %store "foo" %bash `(,build1)@@ -187,7 +191,7 @@ (define prefix-len (string-length dir)) (file2 (derivation->output-path drv2))) (and (valid-path? %store file1) (valid-path? %store file2) (string=? (call-with-input-file file1 get-string-all)- "hello, world\n")+ data) (= (stat:ino (lstat file1)) (stat:ino (lstat file2)))))))) diff --git a/tests/nar.scm b/tests/nar.scmindex ba4881caaa..bd2bf6e6e0 100644--- a/tests/nar.scm+++ b/tests/nar.scm@@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU-;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org>+;;; Copyright © 2012-2021 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;;@@ -486,8 +486,9 @@ (define-values (port get-bytevector) ;; their mtime and permissions were not reset. Ensure that this bug is ;; gone. (with-store store- (let* ((text1 (random-text))- (text2 (random-text))+ ;; Note: TEXT1 and TEXT2 must be longer than %DEDUPLICATION-MINIMUM-SIZE.+ (let* ((text1 (string-concatenate (make-list 100 (random-text))))+ (text2 (string-concatenate (make-list 100 (random-text)))) (tree `("tree" directory ("a" regular (data ,text1)) ("b" directorydiff --git a/tests/store-deduplication.scm b/tests/store-deduplication.scmindex b1c2d93bbd..b2b7c36622 100644--- a/tests/store-deduplication.scm+++ b/tests/store-deduplication.scm@@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU-;;; Copyright © 2018, 2020 Ludovic Courtès <ludo@gnu.org>+;;; Copyright © 2018, 2020-2021 Ludovic Courtès <ludo@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;;@@ -30,13 +30,40 @@ (define-module (test-store-deduplication) (test-begin "store-deduplication") +(test-equal "deduplicate, below %deduplication-minimum-size"+ (list #t (make-list 5 1))++ (call-with-temporary-directory+ (lambda (store)+ ;; Note: DATA must be longer than %DEDUPLICATION-MINIMUM-SIZE.+ (let ((data "Hello, world!")+ (identical (map (lambda (n)+ (string-append store "/" (number->string n)+ "/a/b/c"))+ (iota 5))))+ (for-each (lambda (file)+ (mkdir-p (dirname file))+ (call-with-output-file file+ (lambda (port)+ (put-bytevector port (string->utf8 data)))))+ identical)++ (deduplicate store (nar-sha256 store) #:store store)++ ;; (system (string-append "ls -lRia " store))+ (list (= (length (delete-duplicates+ (map (compose stat:ino stat) identical)))+ (length identical))+ (map (compose stat:nlink stat) identical))))))+ (test-equal "deduplicate" (cons* #t #f ;inode comparisons 2 (make-list 5 6)) ;'nlink' values (call-with-temporary-directory (lambda (store)- (let ((data (string->utf8 "Hello, world!"))+ ;; Note: DATA must be longer than %DEDUPLICATION-MINIMUM-SIZE.+ (let ((data (string-concatenate (make-list 500 "Hello, world!"))) (identical (map (lambda (n) (string-append store "/" (number->string n) "/a/b/c"))@@ -46,7 +73,7 @@ (define-module (test-store-deduplication) (mkdir-p (dirname file)) (call-with-output-file file (lambda (port)- (put-bytevector port data))))+ (put-bytevector port (string->utf8 data))))) identical) ;; Make the parent of IDENTICAL read-only. This should not prevent ;; deduplication from inserting its hard link.@@ -54,7 +81,7 @@ (define-module (test-store-deduplication) (call-with-output-file unique (lambda (port)- (put-bytevector port (string->utf8 "This is unique."))))+ (put-bytevector port (string->utf8 (string-reverse data))))) (deduplicate store (nar-sha256 store) #:store store) @@ -77,8 +104,10 @@ (define-module (test-store-deduplication) (lambda (store) (let ((true-link link) (links 0)- (data1 (string->utf8 "Hello, world!"))- (data2 (string->utf8 "Hi, world!"))+ (data1 (string->utf8+ (string-concatenate (make-list 500 "Hello, world!"))))+ (data2 (string->utf8+ (string-concatenate (make-list 500 "Hi, world!")))) (identical (map (lambda (n) (string-append store "/" (number->string n) "/a/b/c"))diff --git a/tests/store.scm b/tests/store.scmindex 2150a0048c..5089909362 100644--- a/tests/store.scm+++ b/tests/store.scm@@ -759,7 +759,9 @@ (define lst (test-assert "substitute, deduplication" (with-store s- (let* ((c (random-text)) ; contents of the output+ ;; Note: C must be longer than %DEDUPLICATION-MINIMUM-SIZE.+ (let* ((c (string-concatenate+ (make-list 100 (random-text)))) ; contents of the output (g (package-derivation s %bootstrap-guile)) (d1 (build-expression->derivation s "substitute-me" `(begin ,c (exit 1))-- 2.33.0
L
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Ludovic Courtès wrote on 13 Nov 22:45 +0100
Re: bug#24937: "deleting unused links" GC phase is too slow
(name . Maxim Cournoyer)(address . maxim.cournoyer@gmail.com)(address . 24937@debbugs.gnu.org)
87czn3buhg.fsf@gnu.org
Ludovic Courtès <ludo@gnu.org> skribis:
Toggle quote (6 lines)> In a nutshell:>> • Files < 1KiB contribute to 0.3% of the space savings;>> • Files < 4KiB contribute to 2.5% of the space savings;
I get similar results on bayfront.guix.gnu.org (with 3.2M entries):
Attachment: bayfront-size.png
… and on guix.bordeaux.inria.fr (2.0M entries):
Attachment: guix-hpc4-size.png
Files < 4KiB represent between 60% and 75% of the /gnu/store/.linksentries here.
I’ve sent patches that implement a cutoff threshold at 4 KiB.
Thanks,Ludo’.
L
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Ludovic Courtès wrote on 16 Nov 14:54 +0100
(address . 24937@debbugs.gnu.org)
87h7cc2ol6.fsf_-_@gnu.org
Hi,
Ludovic Courtès <ludo@gnu.org> skribis:
Toggle quote (10 lines)> Files smaller than 4 KiB typically represent ~60% of the entries in> /gnu/store/.links but only contribute to ~2.5% of the space savings> afforded by deduplication.>> Not considering these files for deduplication speeds up file insertion> in the store and, more importantly, leaves 'removeUnusedLinks' with> fewer entries to traverse, thereby speeding it up proportionally.>> Partly fixes <https://issues.guix.gnu.org/24937>.
Pushed a variant of this as commit472a0e82a52a3d5d841e1dfad6b13e26082a5750, with a threshold of 8 KiB.
Concretely, the number of .links entries shrinks by ~70%, from2M to 700K on my laptop, and (presumably) from 64M to 19M on berlin.
I’ll deploy it within a few days on berlin. I hope the speedup willreduce pressure there, though obviously it’ll still be an expensiveoperation (but fundamentally I think it’ll always be linear in the sizeof the store.)
I’m preparing an update of the ‘guix’ package to make this readilyavailable. When you deploy the new daemon, .links will be trimmed ofentries for files smaller than 8 KiB the first time you run ‘guix gc’.
Ludo’.
J
J
John Kehayias wrote on 22 Nov 03:30 +0100
Re: "deleting unused links" GC phase is too slow
(name . 24937@debbugs.gnu.org)(address . 24937@debbugs.gnu.org)
QAT6Oklv6MJDMioc_c1DjSQKV_v-3AWmaSFX9mnO5dqeHMJ-v9W43_z4orvQ0cp5awD2GfvFlO8rBIh5jwnHyj1ZxXGMBUsTUsOf5nYq_l8=@protonmail.com
Hello,
A little late, but wanted to add my results here, from before the commit was made. I had reported some of this on IRC before and had some outlying results. Since then I finally did some generation deleting and gc-ing, though perhaps still have a bit of cruft. I've been on core-updates-frozen for a while, so keeping a lot from before making the branch switch, as well as lots of stuff piling up in trying to fix things or trying out changes in core-updates-frozen.
Anyway, attached are the plots from the above code. Running
ls -1A /gnu/store/.links | wc -l
showed 15776256 links at the time. Still quite a bit I think, but I've had 1.5-2x as much in the past, easily. (This had caused some earlier warnings on ext4 and enabling large_dir, which will make a system unbootable due to Grub not being up to speed on this old feature. I'm now on btrfs.)
John
Attachment: nlink.png
Attachment: nlink-small.png
Attachment: size-savings.png
Attachment: size.png
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