2008-12
On the otherwise-idle flubber:
$ git clone git://sources.redhat.com/git/glibc.git
Initialized empty Git repository in /media/data/home/tschwinge/tmp/glibc/glibc/.git/
remote: Generating pack...
remote: Done counting 380933 objects.
remote: Deltifying 380933 objects...
remote: 100% (380933/380933) done
remote: Total 380933 (delta 294166), reused 380686 (delta 294002)
Receiving objects: 100% (380933/380933), 70.31 MiB | 27 KiB/s, done.
Resolving deltas: 100% (294166/294166), done.
error: git-checkout-index: unable to create file iconvdata/ibm1122.c (Interrupted system call)
error: git-checkout-index: unable to create file localedata/charmaps/IBM862 (Interrupted system call)
Checking out files: 100% (10676/10676), done.
$ git status
# On branch master
# Changed but not updated:
# (use "git add <file>..." to update what will be committed)
#
# modified: iconvdata/ibm1122.c
# modified: localedata/charmaps/IBM862
#
no changes added to commit (use "git add" and/or "git commit -a")
$ ls -l iconvdata/ibm1122.c localedata/charmaps/IBM862
-rw-r--r-- 1 tschwinge tschwinge 0 2008-12-15 15:49 iconvdata/ibm1122.c
-rw-r--r-- 1 tschwinge tschwinge 0 2008-12-15 15:49 localedata/charmaps/IBM862
So these files are indeed of zero-length in the checked-out tree. Is this Git's fault or something else's?
Fixing this situation is easy enough:
$ git checkout -- iconvdata/ibm1122.c localedata/charmaps/IBM862
$ git status
# On branch master
nothing to commit (working directory clean)
2010-03-16
Still seen.
IRC, freenode, #hurd, 2013-10-10
<sea`> Huh? I've cloned the 'hurd' repository and I'm attempting to compile
it, but the 'rtnetlink.h' header in
'hurd/pfinet/linux-src/include/linux/' is just blank. (Which leads to an
error later down when a macro that's supposed to be defined in there is
first used)
<sea`> So I'm just wondering, is that file really blank? Or is this some
unexpected error of decompression?
<braunr> clone again and see
<braunr> the file is definitely not empty
<sea`> I cloned it twice, both have that file blank. BUT, I want to point
out that both clones do have some decompression errors. (Some files are
missing chunks in /both/ cloned repositories).
<braunr> where did you clone it from ?
<sea`> git.sv.gnu.org/hurd/hurd.git
<braunr> hum decompression errors ?
<braunr> can you paste them please ?
<sea`> Hmm, I can clone again and show you an example if I find one
<sea`> This was on the hurd. When I run: git clone $repo;, it seems to fail
almost randomly with "incorrect header check", but when it does succeed,
occasionally some files are missing chunks
<sea`> and apparently entire files can be blank
<braunr> http or git ?
<sea`> git.
<braunr> that's really weird
<braunr> actually i don't even have problems with http any more nowadays ..
<sea`> This is using the hurd image from sthibault
<sea`> So once I get it recompiled and shuffle in the new binaries, the
problem should probably go away
<braunr> no
<braunr> well maybe but
<braunr> don't recompile
<braunr> upgrade packages instead
<sea`> Alright, I'll do an upgrade instead. Why that path specifically?
<braunr> rebuilding is long
<braunr> i wonder if the image you got is corrupted
<braunr> compute the checksum
<braunr> we've had weird reports in the past about the images he provides
<braunr> well not the images themselves, but differences after dowloading
..
<braunr> downloading*
<sea`> The MD5SUMS file on his site isn't including the values for the most
recent images.
<sea`> It stops at 2012-12-28
<braunr> hummm
<sea`> Anyway, let's see. git clone failed again:
<sea`> Receiving objects: 100% (50955/50955), 15.48 MiB | 42 KiB/s, done.
<sea`> error: inflate: date stream error (incorrect header check) <- This
is the interesting part
<sea`> fatal: serious inflate inconsistency
<sea`> fatal: index-pack failed
<braunr> not intereseting enough unfortunately
<braunr> but it might come from savannah too
<sea`> Ehm. The whole thing locked up badly. I'll reboot it and try again.
<braunr> are you sure it locked oO ?
<braunr> the hurd can easily become unresponsive when performing io
operations
<braunr> but you need more than such a git repository to reach that state
<sea`> Yeah, that happens occasionally. It's not related to git, but rather
it happens when I cancel some command.
<braunr> your image must be corrupted
<braunr> have you enabled host io caching btw ?
<sea`> By now it's corrupted for sure..everytime it crashes the filesystem
gets into a weird state.
<sea`> I'll unpack a fresh image, then update the packages, and then try
cloning this git repository.
<braunr> i'll get the image too so we can compare sums
<sea`> 957bb0768c9558564f0c3e0adb9b317e ./debian-hurd.img.tar.gz
<sea`> Which unpacks to: debian-hurd-20130504.img
<azeem_> the NSA might backdoor the Hurd, in anticipation of our scheduled
world-dominance
<braunr> for now they're doing it passively :
<braunr> :p
<braunr> sea`: same thing here
<braunr> sea`: if you still have problems, the image itself might be wrong
<braunr> in which case you should try with the debian network installer
<sea`> Ah, so if problems persist, try with the network installer. Okay
<sea`> Is there some recipe for constructing a hurd/mach minimal
environment?
<sea`> A system with only just enough tools and libraries to compile and
poke at things.
<braunr> not currently
<braunr> we all work in debian environments
<braunr> the reason being that a lot of patches are queued for integration
upstream
2010-11-17
A very similar issue. The working tree had a lot of differences to HEAD.
tschwinge@grubber:~/tmp/gcc/hurd $ git reset --hard HEAD
error: unable to unlink old 'gcc/config/darwin.h' (Interrupted system call)
Checking out files: 100% (1149/1149), done.
fatal: Could not reset index file to revision 'HEAD'.
tschwinge@grubber:~/tmp/gcc/hurd $ git reset --hard HEAD
error: unable to unlink old 'gcc/config/iq2000/iq2000.md' (Interrupted system call)
error: git checkout-index: unable to create file gcc/config/lm32/lm32.c (File exists)
Checking out files: 100% (1149/1149), done.
fatal: Could not reset index file to revision 'HEAD'.
tschwinge@grubber:~/tmp/gcc/hurd $ ls -l gcc/config/iq2000/iq2000.md gcc/config/lm32/lm32.c
ls: cannot access gcc/config/iq2000/iq2000.md: No such file or directory
-rw-r--r-- 1 tschwinge tschwinge 32159 Nov 17 19:09 gcc/config/lm32/lm32.c
tschwinge@grubber:~/tmp/gcc/hurd $ git reset --hard HEAD
error: git checkout-index: unable to create file gcc/fortran/expr.c (Interrupted system call)
Checking out files: 100% (1149/1149), done.
fatal: Could not reset index file to revision 'HEAD'.
tschwinge@grubber:~/tmp/gcc/hurd $ git reset --hard HEAD
error: git checkout-index: unable to create file gcc/config/sol2.h (Interrupted system call)
Checking out files: 100% (1149/1149), done.
fatal: Could not reset index file to revision 'HEAD'.
tschwinge@grubber:~/tmp/gcc/hurd $ git reset --hard HEAD
error: unable to unlink old 'gcc/config/i386/i386.c' (Interrupted system call)
Checking out files: 100% (1149/1149), done.
fatal: Could not reset index file to revision 'HEAD'.
tschwinge@grubber:~/tmp/gcc/hurd $ git reset --hard HEAD
Checking out files: 100% (1149/1149), done.
HEAD is now at fe3e43c Merge commit 'refs/top-bases/hurd/master' into hurd/master
2010-12-22
grubber:
$ git remote update
Fetching savannah
remote: Counting objects: 582331, done.
remote: Compressing objects: 100% (124133/124133), done.
remote: Total 582331 (delta 460856), reused 578352 (delta 457598)
Receiving objects: 100% (582331/582331), 525.15 MiB | 204 KiB/s, done.
fatal: cannot pread pack file: Interrupted system call
fatal: index-pack failed
error: Could not fetch savannah
2011-06-10
coulomb.SCHWINGE, checking out binutils' master branch,
starting from an empty working directory (after an external git push):
$ git checkout -f
fatal: cannot create directory at 'gas/testsuite/gas/bfin': Interrupted system call
$ git checkout -f
error: unable to create file gas/testsuite/gas/i386/ilp32/x86-64-sse4_1-intel.d (File exists)
warning: unable to unlink gas/testsuite/gas/m68k-coff: Operation not permitted
fatal: cannot create directory at 'gas/testsuite/gas/m68k-coff': Operation not permitted
$ git checkout -f
error: unable to create file gas/testsuite/gas/h8300/h8300.exp (File exists)
error: unable to create file gas/testsuite/gas/i386/x86-64-addr32-intel.d (File exists)
error: unable to create file gas/testsuite/gas/ia64/secname.d (File exists)
error: unable to create file gas/testsuite/gas/m68k/pr11676.s (File exists)
Checking out files: 100% (12315/12315), done.
$ git status
# On branch master
# Changes not staged for commit:
# (use "git add <file>..." to update what will be committed)
# (use "git checkout -- <file>..." to discard changes in working directory)
#
# modified: gas/testsuite/gas/h8300/h8300.exp
# modified: gas/testsuite/gas/i386/x86-64-addr32-intel.d
# modified: gas/testsuite/gas/ia64/secname.d
# modified: gas/testsuite/gas/m68k/pr11676.s
#
no changes added to commit (use "git add" and/or "git commit -a")
$ rm gas/testsuite/gas/h8300/h8300.exp gas/testsuite/gas/i386/x86-64-addr32-intel.d gas/testsuite/gas/ia64/secname.d gas/testsuite/gas/m68k/pr11676.s
$ git checkout -f
$ git status
# On branch master
nothing to commit (working directory clean)
Analysis
2011-06-13
Running git checkout -f under GDB:
error: git checkout-index: unable to create file gas/testsuite/gas/cris/string-1.s (File exists)
error: git checkout-index: unable to create file gas/testsuite/gas/i386/x86-64-sse-check.d (File exists)
error: git checkout-index: unable to create file gas/testsuite/gas/i386/x86-64-sse4_1.d (File exists)
error: git checkout-index: unable to create file gas/testsuite/gas/ppc/astest.d (File exists)
error: git checkout-index: unable to create file gas/testsuite/gas/tic6x/reloc-bad-4.s (File exists)
warning: unable to unlink include/cgen: Operation not permitted
fatal: cannot create directory at 'include/cgen': Operation not permitted
Again:
error: git checkout-index: unable to create file gas/config/te-vxworks.h (File exists)
error: git checkout-index: unable to create file gas/testsuite/gas/cris/string-1.s (File exists)
error: git checkout-index: unable to create file gas/testsuite/gas/d10v/warning-019.s (File exists)
error: git checkout-index: unable to create file gas/testsuite/gas/i860/dual03.s (File exists)
error: git checkout-index: unable to create file ld/testsuite/ld-mmix/sec-7a.s (File exists)
warning: unable to unlink ld/testsuite/ld-powerpc: Operation not permitted
fatal: cannot create directory at 'ld/testsuite/ld-powerpc': Operation not permitted
And: git duplicated content.
All these (very likely) have the same root cause: SA_RESTART restarting too
much.
With git checkout, Git uses in progress.c a SIGALRM handler (SA_RESTART;
invoked every second via setitimer(ITIMER_REAL)) to display status messages:
x % already checked out.
To avoid the status update signals every second, in
[git]/progress.c:start_progress_delay we can just return NULL (manually in
GDB, for example), then both the error: git checkout-index and the
duplicated content issues go away.
I'm guessing that when returning from a SA_RESTART signal handler, too much
of the ``syscall''s is being restarted. For example, if a file has already
been created, the restarted creation attempt would fail: File exists. If
data has been written, it might get written again (duplication issue). Then,
there are cases where unlink apparently returns EINTR, which is not kosher
either. Etc.
Do we have problems with SA_RESTART vs. the atomicity of our syscall-alikes?
IRC, freenode, #hurd, 2013-01-30
<braunr> hm, let's try to clone a huge repository
<braunr> hm, cloning a whole linux repo, and still no problem :)
<pinotree> weren't most/all the issues at unpack time?
<braunr> i don't remember
<braunr> we'll see when it gets there
<braunr> the longest part is "resolving deltas", for which ext2fs is
clearly the big bottleneck (no I/O, page-cache only, but still)
<braunr> pinotree: well, slow, but no error
IRC, freenode, #hurd, 2013-01-31
<braunr> fyi, i've tried several checkouts of big repositories, and never
got a single error
<braunr> youpi: looks like the recent fixes also solved some git issues we
had
<braunr> i could clone big repositories without any problem
<youpi> cool :)