Find and remove large files that are open but have been deleted

Question

How does one find large files that have been deleted but are still open in an application? How can one remove such a file, even though a process has it open?

The situation is that we are running a process that is filling up a log file at a terrific rate. I know the reason, and I can fix it. Until then, I would like to rm or empty the log file without shutting down the process.

Simply doing rm output.log removes only references to the file, but it continues to occupy space on disk until the process is terminated. Worse: after rming I now have no way to find where the file is or how big it is! Is there any way to find the file, and possibly empty it, even though it is still open in another process?

I specifically refer to Linux-based operating systems such as Debian or RHEL.

If you know the pid then you can use lsof -p <pid> to list its open files and their sizes. The deleted file will have a (deleted) next to it. The deleted file will be linked at /proc/<pid>/fd/1 probably. I don't know how to make a process stop writing to its file descriptor without terminating it. I would think that would depend on the process. — donothingsuccessfully, Mar 20 '13 at 08:15
Thanks. How might one get the PIDs of all rmed files that are still open? — dotancohen, Mar 20 '13 at 08:17
@donothingsuccessfully The "deleted" tag reported by lsof is Solaris specific, in fact Solaris 10 or later only. The OP did not specify what operating system he is using. @dotancohen On Solaris you can pipe the output of lsof to search for deleted, eg lsof | grep "(deleted)". When there are no more processes holding a deleted file open, the kernel will free up the inode and disk blocks. Processes do not have "handlers" by which they can be notified that an open, essentially locked file, have been removed from disk. — Johan, Mar 20 '13 at 08:43
@Johan, the lsof | grep '(deleted)' works on Linux as well. On Linux, you can be notified of file deletion (even files that already don't have any entry in any directory other than /proc/some-pid/fd anymore) with the inotify mechanism (IN_DELETE_SELF event) — Stéphane Chazelas, Mar 20 '13 at 11:14
I created somefile and opened it in VIM, then rmed it in another bash process. I then run lsof | grep somefile and it is not in there, even though the file is open in VIM. — dotancohen, Mar 20 '13 at 11:23
@dotancohen: try using : tail -f /tmp/somefile on one terminal and rm /tmp/somefile on another terminal. tail -f will keep the fd open until you stop it. Not sure vi/vim will keep the fd open when not needed... and use : lsof -p PID to see all fd of process PID (ie, the tail). to find its pid : before deleting the file: ps -ef | grep '/tmp/[s]omefile' ([s]omething greps for "something", and thus will not show the "grep ...." line as that line contains s]omething instead) — Olivier Dulac, Mar 20 '13 at 13:45
@dotancohen vim writes a new file when told to, it doesn't modify the existing file. The new file is then moved on top of the old file. Try using ls -i to follow this. — , Jun 14 '22 at 08:33

score 206 · Accepted Answer · edited Apr 13 '17 at 12:36

206

If you can't kill your application, you can truncate instead of deleting the log file to reclaim the space. If the file was not open in append mode (with O_APPEND), then the file will appear as big as before the next time the application writes to it (though with the leading part sparse and looking as if it contained NUL bytes), but the space will have been reclaimed (that does not apply to HFS+ file systems on Apple OS/X that don't support sparse files though).

To truncate it:

: > /path/to/the/file.log

If it was already deleted, on Linux, you can still truncate it by doing:

: > "/proc/$pid/fd/$fd"

Where $pid is the process id of the process that has the file opened, and $fd one file descriptor it has it opened under (which you can check with lsof -p "$pid".

If you don't know the pid, and are looking for deleted files, you can do:

lsof -nP | grep '(deleted)'

lsof -nP +L1, as mentioned by @user75021 is an even better (more reliable and more portable) option (list files that have fewer than 1 link).

Or (on Linux):

find /proc/*/fd -ls | grep  '(deleted)'

Or to find the large ones with zsh:

ls -ld /proc/*/fd/*(-.LM+1l0)

An alternative, if the application is dynamically linked is to attach a debugger to it and make it call close(fd) followed by a new open("the-file", ....).

edited Apr 13 '17 at 12:36

Community

1

answered Mar 20 '13 at 08:42

Stéphane Chazelas

544,893

3

There's also a truncate command that does the same thing more explicitly. – Tobu Mar 20 '13 at 09:15
nope, even as root: AIX 6.1, lsof 4.82 : doesn't show the filename. instead, using procfiles -n pid instead of lsof -p pid will show the filename, UNTIL you delete it (ie, after deletion, it still shows its other informations, inode, modes, etc, but the things -n was showing (ie: its full path : name:.........) is no longer shown once the corresponding file is deleted). So please if anyone knows a solution for AIX 6.1, I'm interrested. – Olivier Dulac Mar 20 '13 at 13:40
2

@OlivierDulac, lsof is probably going to be the closest to a portable solution you can get to list open files. the debugger approach to close the fd under the application feet should be quite portable as well. – Stéphane Chazelas Mar 20 '13 at 13:50
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@StephaneChazelas: thanks. I found a way to list all PIDs which have a file open on each partitions : df -k | awk 'NR>1 { print $NF }' | xargs fuser -Vud (and then easy to send signals to the offenders to force them to release the fd) – Olivier Dulac Mar 20 '13 at 18:56
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You can also use lsof +L1. From the lsof man page: "A specification of the form +L1 will select open files that have been unlinked. A specification of the form +aL1 <file_system> will select unlinked open files on the specified file system.". That should be a bit more reliable than grepping. – Synchro Oct 23 '14 at 06:26

score 52 · Answer 2 · edited Nov 12 '23 at 15:33

Check out the quickstart here: lsof Quickstart

I'm surprised no one mentioned the lsof quickstart file (included with lsof). Section "3.a" shows how to find open, unlinked files:

lsof -a +L1 *mountpoint*

E.g.:

[root@enterprise ~]# lsof -a +L1 /tmp
COMMAND   PID   USER   FD   TYPE DEVICE    SIZE NLINK  NODE NAME
httpd    2357 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
mysqld   2588  mysql    4u   REG 253,17      52     0  1495 /tmp/ibY0cXCd (deleted)
mysqld   2588  mysql    5u   REG 253,17    1048     0  1496 /tmp/ibOrELhG (deleted)
mysqld   2588  mysql    6u   REG 253,17       0     0  1497 /tmp/ibmDFAW8 (deleted)
mysqld   2588  mysql    7u   REG 253,17       0     0 11387 /tmp/ib2CSACB (deleted)
mysqld   2588  mysql   11u   REG 253,17       0     0 11388 /tmp/ibQpoZ94 (deleted)
httpd    3457   root   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8437 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8438 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8439 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8440 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8441 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8442 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8443 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd    8444 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd   16990 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd   19595 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd   27495 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd   28142 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)
httpd   31478 apache   29u   REG 253,17 3926560     0  1499 /tmp/.NSPR-AFM-3457-9820130.0 (deleted)

peterph · Answer 3 · 2013-03-20T08:48:16.183

3

It's up to the file system driver to actually free the allocated space, and that will usually happen only once all file descriptors referring to that file are released. So you can't really reclaim the space, unless you make the application close the file. Which means either terminating it or playing with it "a bit" in a debugger (e.g. closing the file and making sure it is not opened/written to again, or opening /dev/null instead). Or you could hack the kernel, but I would advise against that.

Truncating the file as Stephane suggests might help, but the real outcome will also depend on your file system (for example pre-allocated blocks will likely be freed only after you close the file in any case).

The rationale behind this behaviour is that the kernel wouldn't know what to do with data requests (both read and write, but reading is actually more critical) targeting such a file.

edited Mar 20 '13 at 08:48

answered Mar 20 '13 at 08:42

peterph

30,838

3

As Linux supports sparse files on most file systems, the behaviour is well-defined and the disk driver can really free disk space. I have tested it for ext3 and ext4, and it works like Stephane wrote. – jofel Mar 20 '13 at 10:14
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What makes you say that truncating a file will not reclaim preallocated blocks? Truncating is meant to deallocate data, I don't thing there's any ambiguity with that. – Stéphane Chazelas Mar 20 '13 at 11:22
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The file system may keep the blocks allocated to save time later (especially if the file still remains open), especially when it was big enough before truncating. At least that's what XFS seems to be doing. – peterph Mar 20 '13 at 12:53
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Thank you Peter. I am glad that you address the "why" in this post. – dotancohen Mar 21 '13 at 06:09
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As far as I can tell, truncating open files does reclaim space on XFS as well. Tested with both normal file and file allocated with fallocate on Linux 4.9. Can you please clarify under what filesystem and condition truncating a file does not reclaim space? – Stéphane Chazelas May 03 '17 at 11:52

score -1 · Answer 4 · edited Jun 14 '22 at 09:46

-1

Instead of deleting a file held by a process that you can't kill now, you can empty that log file with echo:

echo -n > /var/log/myapp.log

You can check after that with df command - the "Used bytes" column will be decreased.

edited Jun 14 '22 at 09:46

AdminBee

22,803

answered Jun 14 '22 at 05:30

Shnbook

1

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Many echo implementations output -n<newline> upon echo -n. The UNIX compliant ones do at least. For a POSIX command that outputs nothing see : (like in the accepted answer) or true or eval or printf '' – Stéphane Chazelas Jun 14 '22 at 05:42

Find and remove large files that are open but have been deleted

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