Re: csplit reports No space left on device

[Rodolfo Aramayo]

All right, this is what I did:

First, I am running:

Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal

Second, I have:
Size  Used Avail Use% Mounted on
58G   11G   48G  19% /
9.7T  4.7T  4.6T  51% /media/volume/sdb

Third, I have re-run the process using the following command:
strace -o zzSTRACE_Error.log csplit --keep-files --quiet
--elide-empty-files --digits=12 --prefix=zz_ uniref50.xml /"<entry id="/
{*}

Fourth, the file I am trying to split (uniref50.xml ) is 201G in size

Fifth, the resulting directory, after the job failed, is 162G in size

Sixth, the name of the last file written before Exit 1 was : zz_000017876562

Last, the tail of the zzSTRACE_Error.log is printed below (the log is 8GB
in size...)

Thanks

Rodolfo

###########################################################################
...
...
...
read(0, "rty type=\"member count\" value=\"1"..., 8185) = 8185
write(3, "<entry id=\"UniRef50_UPI000463094"..., 1119) = 1119
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876551", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_A0A1I4ZT53\" "..., 4096) = 4096
write(3, "I5ICB9\"/>\n<property type=\"protei"..., 1578) = 1578
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876552", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_UPI000463911"..., 1157) = 1157
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876553", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
read(0, "e=\"UniRef100 ID\" value=\"UniRef10"..., 8178) = 8178
write(3, "<entry id=\"UniRef50_UPI0004640C4"..., 1559) = 1559
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876554", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_UPI00046496E"..., 1185) = 1185
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876555", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_A0A087DTV5\" "..., 1608) = 1608
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876556", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_UPI00046542F"..., 1115) = 1115
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876557", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_UPI000465496"..., 1099) = 1099
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876558", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_A0A1V4SRE2\" "..., 1677) = 1677
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876559", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
read(0, "Member>\n<dbReference type=\"UniPr"..., 8176) = 8176
write(3, "<entry id=\"UniRef50_A0A1Y4NIX0\" "..., 3026) = 3026
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876560", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_UPI000466DBA"..., 1589) = 1589
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876561", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_A0A1C2HXQ8\" "..., 2085) = 2085
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876562", O_WRONLY|O_CREAT|O_TRUNC, 0666) = 3
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
fstat(3, {st_mode=S_IFREG|0664, st_size=0, ...}) = 0
write(3, "<entry id=\"UniRef50_UPI000467299"..., 1131) = 1131
close(3)                                = 0
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
openat(AT_FDCWD, "zz_000017876563", O_WRONLY|O_CREAT|O_TRUNC, 0666) = -1
ENOSPC (No space left on device)
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
write(2, "csplit: ", 8)                 = 8
write(2, "zz_000017876563", 15)         = 15
openat(AT_FDCWD, "/usr/share/locale/C.UTF-8/LC_MESSAGES/libc.mo", O_RDONLY)
= -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale/C.utf8/LC_MESSAGES/libc.mo", O_RDONLY)
= -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale/C/LC_MESSAGES/libc.mo", O_RDONLY) = -1
ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale-langpack/C.UTF-8/LC_MESSAGES/libc.mo",
O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale-langpack/C.utf8/LC_MESSAGES/libc.mo",
O_RDONLY) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/share/locale-langpack/C/LC_MESSAGES/libc.mo",
O_RDONLY) = -1 ENOENT (No such file or directory)
write(2, ": No space left on device", 25) = 25
write(2, "\n", 1)                       = 1
rt_sigprocmask(SIG_BLOCK, [HUP INT QUIT PIPE ALRM TERM XCPU XFSZ VTALRM
PROF IO], [], 8) = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
close(1)                                = 0
close(2)                                = 0
exit_group(1)                           = ?
+++ exited with 1 +++

###########################################################################


On Wed, Aug 17, 2022 at 5:23 PM Kaz Kylheku <kaz@kylheku.com> wrote:

> On 2022-08-17 14: 19, Pádraig Brady wrote: > system you use, or how much
> space is free. > > I would run csplit with --keep-files, to see how many
> files were created, > how much space is free, and whether one can create
> any more files
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> On 2022-08-17 14:19, Pádraig Brady wrote:
> > system you use, or how much space is free.
> >
> > I would run csplit with --keep-files, to see how many files were created,
> > how much space is free, and whether one can create any more files
> > in the directory using other means.
>
> I'd also try to capture at least part of the strace log where it shows
> which system call hits that error, on what file descriptor, and how
> that was opened, etc.
>
>

-- 
Dr. Rodolfo Aramayo, PhD
Faculty of Biology and Genetics
Department of Biology, Texas A&M University
PeerJ
PeerJ - the Journal of Life & Environmental Sciences
<https://peerj.com/> Academic
Editor peerj.com/RodolfoAramayo