From: Maxime Boissonneault Date: Mon, 21 Jan 2013 16:14:35 GMT Subject: Re: GIT get corrupted on lustre Message-ID: <50FD696B.5000205@calculquebec.ca> In-Reply-To: <87a9s2o6ri.fsf@pctrast.inf.ethz.ch> Hi Thomas, Can you tell me what is the version of the lustre servers and the lustre clients ? Thanks, Maxime Boissonneault HPC specialist @ Calcul Québec. Le 2013-01-21 11:11, Thomas Rast a écrit : > Erik Faye-Lund writes: > >> On Fri, Jan 18, 2013 at 6:50 PM, Eric Chamberland >> wrote: >>> Good idea! >>> >>> I did a strace and here is the output with the error: >>> >>> http://www.giref.ulaval.ca/~ericc/strace_git_error.txt >>> >>> Hope it will be insightful! >> This trace doesn't seem to contain child-processes, but instead having >> their stderr inlined into the log. Try using "strace -f" instead... > I happen to have access to a lustre FS on the brutus cluster of ETH > Zurich, so I figured I could give it a shot. > > What's odd is that while I cannot reproduce the original problem, there > seems to be another issue/bug with utime(): > > $ strace -f -o ~/gc.trace git gc > warning: failed utime() on .git/objects/68/tmp_obj_sCAEVc: Interrupted system call > warning: failed utime() on .git/objects/a6/tmp_obj_3cdB2c: Interrupted system call > warning: failed utime() on .git/objects/69/tmp_obj_lbU3Xc: Interrupted system call > warning: failed utime() on .git/objects/c3/tmp_obj_EU97Wc: Interrupted system call > warning: failed utime() on .git/objects/3e/tmp_obj_tb2j3c: Interrupted system call > warning: failed utime() on .git/objects/15/tmp_obj_e6zMXc: Interrupted system call > warning: failed utime() on .git/objects/54/tmp_obj_ExOJVc: Interrupted system call > warning: failed utime() on .git/objects/e3/tmp_obj_GtPw4c: Interrupted system call > warning: failed utime() on .git/objects/21/tmp_obj_Xex32c: Interrupted system call > warning: failed utime() on .git/objects/1a/tmp_obj_CzwsZc: Interrupted system call > warning: failed utime() on .git/objects/18/tmp_obj_o6fp3c: Interrupted system call > warning: failed utime() on .git/objects/32/tmp_obj_Ih0G4c: Interrupted system call > warning: failed utime() on .git/objects/41/tmp_obj_1RXV1c: Interrupted system call > Counting objects: 137744, done. > Delta compression using up to 48 threads. > Compressing objects: 100% (36510/36510), done. > Writing objects: 100% (137744/137744), done. > Total 137744 (delta 101591), reused 135512 (delta 99472) > > The trace is here (2.1MB compressed): > > http://thomasrast.ch/download/gc.trace.bz2 > > For the test I used a clone of another git.git I had around. I think > the error is from sha1_file.c:2564. While that doesn't look too > important (see ca11b212 for context), it does raise the question: what > other system calls that we never expect to EINTR can do this on > sufficiently arcane system/FS combinations? > > > Peff's test ran without any apparent issue for a few minutes. I also > ran an extended version (at the end) that sets alarms, so as to actually > get interrupted. That proved more interesting. I had to fix verify() > and write_in_full() to account for EINTR in read()/write(), as those > seem likely to fail. I also got link() to fail: > > $ ~/lustre-peff-reproducer > unable to create hard link: Interrupted system call > unable to open index file: No such file or directory > > but it took a long time. Unfortunately, when running it with strace I > managed to panic the host I ran it on: > > $ strace -o ~/peff-reproducer.trace ~/lustre-peff-reproducer > > Message from syslogd@brutus1 at Jan 21 17:09:43 ... > kernel:LustreError: 37417:0:(osc_lock.c:1182:osc_lock_enqueue()) ASSERTION( ols->ols_state == OLS_NEW ) failed: Impossible state: 4 > > Message from syslogd@brutus1 at Jan 21 17:09:43 ... > kernel:LustreError: 37417:0:(osc_lock.c:1182:osc_lock_enqueue()) LBUG > > Message from syslogd@brutus1 at Jan 21 17:09:43 ... > kernel:Kernel panic - not syncing: LBUG > > Yay for now having to explain this to the cluster team. > > > I tried finding a standard that limits the syscalls to which EINTR > applies, without too much success. I'm not sure how far I should trust > my manpages, but while some of them explicitly list EINTR as a possible > error (read, write, etc.) link() does not. (And the linux manpages > agree with the POSOIX ones for once.) > > If somebody finds such a standard, we could of course use it to blame > lustre instead :-) > > In the absence of it, wouldn't we in theory have to write a simple > loop-on-EINTR wrapper for *all* syscalls? > > Of course there's the added problem that when open(O_CREAT|O_EXCL) fails > with EINTR, it's hard to tell whether a file that may now exist is > indeed yours or some other process's. > > --- 8< ---- > #include > #include > #include > #include > #include > #include > #include > #include > > struct itimerval itv; > > static int randomize(unsigned char *buf, int len) > { > int i; > len = rand() % len; > for (i = 0; i < len; i++) > buf[i] = rand() & 0xff; > return len; > } > > static int check_eof(int fd) > { > int ch; > int r = read(fd, &ch, 1); > if (r < 0) { > perror("read error after expected EOF"); > return -1; > } > if (r > 0) { > fprintf(stderr, "extra byte after expected EOF"); > return -1; > } > return 0; > } > > static int verify(int fd, const unsigned char *buf, int len) > { > while (len) { > char to_check[4096]; > int got = read(fd, to_check, > len < sizeof(to_check) ? len : sizeof(to_check)); > > if (got < 0 && errno == EINTR) > continue; > if (got < 0) { > perror("unable to read"); > return -1; > } > if (got == 0) { > fprintf(stderr, "premature EOF (%d bytes remaining)", len); > return -1; > } > if (memcmp(buf, to_check, got)) { > fprintf(stderr, "bytes differ"); > return -1; > } > > buf += got; > len -= got; > } > > return check_eof(fd); > } > > int write_in_full(int fd, const unsigned char *buf, int len) > { > while (len) { > int r = write(fd, buf, len); > if (r < 0 && errno == EINTR) > continue; > if (r < 0) > return -1; > buf += r; > len -= r; > } > return 0; > } > > int move_into_place(const char *old, const char *new) > { > if (link(old, new) < 0) { > perror("unable to create hard link"); > return 1; > } > unlink(old); > return 0; > } > > void handle_alarm(int signal) > { > } > > int main(void) > { > struct sigaction sa; > > sa.sa_handler = handle_alarm; > sa.sa_flags = SA_RESTART; > sigaction(SIGALRM, &sa, NULL); > > itv.it_interval.tv_sec = 0; > itv.it_interval.tv_usec = 10000; > itv.it_value.tv_sec = 0; > itv.it_value.tv_usec = 100000; > setitimer(ITIMER_REAL, &itv, NULL); > > while (1) { > static unsigned char junk[1024*1024]; > int len = randomize(junk, sizeof(junk)); > int fd; > > /* clean up from any previous round */ > unlink("tmpfile"); > unlink("final.idx"); > > fd = open("tmpfile", O_WRONLY|O_CREAT, 0666); > if (fd < 0) { > perror("unable to open tmpfile"); > return 1; > } > if (write_in_full(fd, junk, len) < 0 || > fsync(fd) < 0 || > close(fd) < 0) { > perror("unable to write"); > return 1; > } > > if (move_into_place("tmpfile", "final.idx") < 0) > return 1; > > fd = open("final.idx", O_RDONLY); > if (fd < 0) { > perror("unable to open index file"); > return 1; > } > if (verify(fd, junk, len) < 0) > return 1; > close(fd); > } > } -- --------------------------------- Maxime Boissonneault Analyste de calcul - Calcul Québec, Université Laval Ph. D. en physique