bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[N. Jackson]

In the Emacs 30 pretest I have been getting the following warning
every few days:

  Warning (emacs): Emacs reader failed to read data in
  "/home/nlj/.cache/org-persist/gc-lock.eld". The error was: "End of
  file during parsing"

The `gc-lock' part suggests this might have something to do with
garbage collection, whereas `org-persist' suggests Org mode, but
I could find nothing in the Org manual about org-persist or about
gc-lock.

I don't know how to reproduce this.  The warning pops up seemingly
at random, often when the only visible window [before the *Warnings*
window appears] is NOT in Org mode.


In GNU Emacs 30.0.93 (build 1, x86_64-pc-linux-gnu, GTK+ Version
 3.24.43, cairo version 1.18.0) of 2024-12-20 built on fedora
Windowing system distributor 'The X.Org Foundation', version 11.0.12014000
System Description: Fedora Linux 40 (Xfce)

Configured features:
ACL CAIRO DBUS FREETYPE GIF GLIB GMP GNUTLS GPM GSETTINGS HARFBUZZ
JPEG LIBOTF LIBSELINUX LIBSYSTEMD LIBXML2 M17N_FLT MODULES
NATIVE_COMP NOTIFY INOTIFY PDUMPER PNG RSVG SECCOMP SOUND SQLITE3
THREADS TIFF TOOLKIT_SCROLL_BARS WEBP X11 XDBE XIM XINPUT2 XPM GTK3
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Load-path shadows:
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bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Eli Zaretskii]

> From: "N. Jackson" <njackson@posteo.net>
> Date: Mon, 30 Dec 2024 18:48:31 +0000
> 
> In the Emacs 30 pretest I have been getting the following warning
> every few days:
> 
>   Warning (emacs): Emacs reader failed to read data in
>   "/home/nlj/.cache/org-persist/gc-lock.eld". The error was: "End of
>   file during parsing"
> 
> The `gc-lock' part suggests this might have something to do with
> garbage collection, whereas `org-persist' suggests Org mode, but
> I could find nothing in the Org manual about org-persist or about
> gc-lock.

Does the file exist?  If so, what is its content (assuming you can
post it here)?

> I don't know how to reproduce this.  The warning pops up seemingly
> at random, often when the only visible window [before the *Warnings*
> window appears] is NOT in Org mode.

Ihor, any ideas or suggestions?  Should this be reported to the Org
list first?

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Eli Zaretskii]

> From: "N. Jackson" <njackson@posteo.net>
> Cc: Ihor Radchenko <yantar92@posteo.net>,  75209@debbugs.gnu.org
> Date: Mon, 30 Dec 2024 19:53:42 +0000
> 
> At 21:31 +0200 on Monday 2024-12-30, Eli Zaretskii wrote:
> 
> >> From: "N. Jackson" <njackson@posteo.net>
> >> Date: Mon, 30 Dec 2024 18:48:31 +0000
> >> 
> >>   Warning (emacs): Emacs reader failed to read data in
> >>   "/home/nlj/.cache/org-persist/gc-lock.eld". The error was: "End
> >>   of file during parsing"
> 
> > Does the file exist?  If so, what is its content (assuming you can
> > post it here)?
> 
> It exists and currently has the following contents:
> 
>   ;;   -*- mode: lisp-data; -*-
>   (((26482 57035 301257 992000) 26482 60639 74163 973000) ((26482 62694 821331 522000) 26482 62698 583212 450000))

This one seems okay.  I guess we need to wait for the warning and see
then?

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Ihor Radchenko]

Eli Zaretskii <eliz@gnu.org> writes:

>> I don't know how to reproduce this.  The warning pops up seemingly
>> at random, often when the only visible window [before the *Warnings*
>> window appears] is NOT in Org mode.
>
> Ihor, any ideas or suggestions?  Should this be reported to the Org
> list first?

Sounds like Emacs being killed by force in the middle of writing to that
file. Or, alternatively, C-g in the middle of writing.

If that's kill -9 or similar, I would not call this unexpected.

gc-lock.eld is a file used to flag that cache dir is being worked on by
multiple emacs instances. GC here refers to garbage-collecting cache data.

-- 
Ihor Radchenko // yantar92,
Org mode maintainer,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Ihor Radchenko]

"N. Jackson" <njackson@posteo.net> writes:

>> Or, alternatively, C-g in the middle of writing.
>
> I use C-g very frequently.  I type `M-x' and then realise I want to
> do `C-h f' first instead, so I do `C-g' to exit from the M-x prompt.
> Or I do an isearch and then change my mind (or find and read
> whatever I was looking for) then I do `C-g' (twice, I think) to exit
> the isearch and get back to where I started.  Usages like that.
> From my (probably naive) point of view, if that messes up Org Mode,
> then Org Mode is doing something wrong.

That should not be a problem then.
Reading/writing GC file is done using timer and, AFAIK, Emacs should not
run timers while you are running a command.

>> gc-lock.eld is a file used to flag that cache dir is being worked
>> on by multiple emacs instances. GC here refers to
>> garbage-collecting cache data.
>
> I do run multiple (two) instances of Emacs.  One is my normal
> session where I use Org quite heavily.  The other is my Gnus session
> in which I never open an Org file and never (as far as I know) use
> any Org features.

Gnus may load Org. (AFAIU, it does it when viewing gnus articles)

Another possible scenario is two Org instances writing to the same file
at the same time.
If it is what is happening in your case, your problem may be similar to 
https://list.orgmode.org/orgmode/CAMJKaZxA_VmLdFP_u1rNiF2s0X2kVivjT31jEM_r3BYCHri1PQ@mail.gmail.com/

-- 
Ihor Radchenko // yantar92,
Org mode maintainer,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Eli Zaretskii]

> From: Ihor Radchenko <yantar92@posteo.net>
> Cc: Eli Zaretskii <eliz@gnu.org>, 75209@debbugs.gnu.org
> Date: Tue, 31 Dec 2024 19:02:35 +0000
> 
> "N. Jackson" <njackson@posteo.net> writes:
> 
> >> Or, alternatively, C-g in the middle of writing.
> >
> > I use C-g very frequently.  I type `M-x' and then realise I want to
> > do `C-h f' first instead, so I do `C-g' to exit from the M-x prompt.
> > Or I do an isearch and then change my mind (or find and read
> > whatever I was looking for) then I do `C-g' (twice, I think) to exit
> > the isearch and get back to where I started.  Usages like that.
> > From my (probably naive) point of view, if that messes up Org Mode,
> > then Org Mode is doing something wrong.
> 
> That should not be a problem then.
> Reading/writing GC file is done using timer and, AFAIK, Emacs should not
> run timers while you are running a command.

If this happens while the user types some command, then timers could
fire during that typing, since people rarely type fast enough to not
let timers run.

But all this is not relevant, because Emacs binds inhibit-quit to a
non-nil value while it runs the timer function.  So, unless the timer
in question somehow forcibly resets inhibit-quit to nil, C-g should
not be able to interrupt a timer.

> >> gc-lock.eld is a file used to flag that cache dir is being worked
> >> on by multiple emacs instances. GC here refers to
> >> garbage-collecting cache data.
> >
> > I do run multiple (two) instances of Emacs.  One is my normal
> > session where I use Org quite heavily.  The other is my Gnus session
> > in which I never open an Org file and never (as far as I know) use
> > any Org features.
> 
> Gnus may load Org. (AFAIU, it does it when viewing gnus articles)
> 
> Another possible scenario is two Org instances writing to the same file
> at the same time.
> If it is what is happening in your case, your problem may be similar to 
> https://list.orgmode.org/orgmode/CAMJKaZxA_VmLdFP_u1rNiF2s0X2kVivjT31jEM_r3BYCHri1PQ@mail.gmail.com/

Can't Org prevent more than one session writing to this file?  We have
file locks which can be used here, I think.

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Ihor Radchenko]

Eli Zaretskii <eliz@gnu.org> writes:

>> Another possible scenario is two Org instances writing to the same file
>> at the same time.
>> If it is what is happening in your case, your problem may be similar to 
>> https://list.orgmode.org/orgmode/CAMJKaZxA_VmLdFP_u1rNiF2s0X2kVivjT31jEM_r3BYCHri1PQ@mail.gmail.com/
>
> Can't Org prevent more than one session writing to this file?  We have
> file locks which can be used here, I think.

That's exactly the idea I am trying in the linked thread to address the
issue.

It is not the biggest problem there though. The problem is when there is
a race between Emacs processes writing to the same file one after
another (without any locking). Contents of the file may then become
unexpected compared to other Emacs session.

-- 
Ihor Radchenko // yantar92,
Org mode maintainer,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Eli Zaretskii]

> From: Ihor Radchenko <yantar92@posteo.net>
> Cc: njackson@posteo.net, 75209@debbugs.gnu.org
> Date: Wed, 01 Jan 2025 09:42:28 +0000
> 
> Eli Zaretskii <eliz@gnu.org> writes:
> 
> >> Another possible scenario is two Org instances writing to the same file
> >> at the same time.
> >> If it is what is happening in your case, your problem may be similar to 
> >> https://list.orgmode.org/orgmode/CAMJKaZxA_VmLdFP_u1rNiF2s0X2kVivjT31jEM_r3BYCHri1PQ@mail.gmail.com/
> >
> > Can't Org prevent more than one session writing to this file?  We have
> > file locks which can be used here, I think.
> 
> That's exactly the idea I am trying in the linked thread to address the
> issue.
> 
> It is not the biggest problem there though. The problem is when there is
> a race between Emacs processes writing to the same file one after
> another (without any locking). Contents of the file may then become
> unexpected compared to other Emacs session.

Is the gc-lock.eld file supposed to be a singleton across all the
Emacs sessions?  Earlier you said:

> gc-lock.eld is a file used to flag that cache dir is being worked
> on by multiple emacs instances. GC here refers to
> garbage-collecting cache data.

Can you tell more about the purpose and use of this file?  What is
written to it, and how is it supposed to be used after being written?
And what bad things happen when the Lisp readers errors out because it
is unable to read the data for some reason?

I'm asking because I'd like to think about, and then suggest, some
suitable solutions, but I don't want to suggest nonsensical ones.

Thanks.

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[N. Jackson]

At 19:02 +0000 on Tuesday 2024-12-31, Ihor Radchenko wrote:
>
> Gnus may load Org. (AFAIU, it does it when viewing gnus articles)

Yes, I suppose it might.  [When I read an email with Org markup in
Gnus (source blocks, for example), the email gets nicely fontified.
Gnus might be using Org to do that rather than rolling its own
parser.]

> Another possible scenario is two Org instances writing to the same
> file at the same time.

I don't think that's the case here.

Certainly not the same user-owned Org Mode data file.  (I'm careful
not to open my Org mode files in my Gnus instance of Emacs [and
consequently I have to live with the inconvenience of not being able
to Capture directly from email or News].)

However now that I've learned that Org has internal files that it
writes to, it seems quite possible that two instances of Org might
write to one of those files at the same time.

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Pip Cet via Bug reports for GNU Emacs, the Swiss army knife of text editors]

"Eli Zaretskii" <eliz@gnu.org> writes:

>> From: "N. Jackson" <njackson@posteo.net>
>> Cc: Ihor Radchenko <yantar92@posteo.net>,  75209@debbugs.gnu.org
>> Date: Mon, 30 Dec 2024 19:53:42 +0000
>>
>> At 21:31 +0200 on Monday 2024-12-30, Eli Zaretskii wrote:
>>
>> >> From: "N. Jackson" <njackson@posteo.net>
>> >> Date: Mon, 30 Dec 2024 18:48:31 +0000
>> >>
>> >>   Warning (emacs): Emacs reader failed to read data in
>> >>   "/home/nlj/.cache/org-persist/gc-lock.eld". The error was: "End
>> >>   of file during parsing"
>>
>> > Does the file exist?  If so, what is its content (assuming you can
>> > post it here)?
>>
>> It exists and currently has the following contents:
>>
>>   ;;   -*- mode: lisp-data; -*-
>>   (((26482 57035 301257 992000) 26482 60639 74163 973000) ((26482 62694 821331 522000) 26482 62698 583212 450000))
>
> This one seems okay.  I guess we need to wait for the warning and see
> then?

I'm assuming that the resolution was that the file was read before we
finished writing it.  I've run into the same issue a number of times
(interrupting and resuming Emacs builds leads to build failures, "make
bootstrap" makes them go away).

Can we consider modifying the .elc format to have a footer indicating
that the file is complete?  Ideally, it would also indicate the checksum
of the file as well as the fact that it is complete, but this would have
a performance impact which might be significant in some cases (very
large .elc files; of course, we could simply modify the footer to
indicate a "too large to checksum" condition has occurred, if the file
is large).

It's tempting to put this information in the header, the way we do for
pdumps (they are first written to start with "!UMPEDGNUEMACS", then the
last thing pdumper does is to rewrite the first character to be "D"),
but using a footer is more reliable: it detects truncation (or
modification) for whatever reason, and makes fewer assumptions about
data atomicity.

While we're in there, let's indicate in the ELC header whether the
special circumstances of native compilation applied to the compilation
process of this file.  This is particularly important if we use
benchmarks defined in .elc files: using the wrong compiled version would
lead to unreliable benchmark results, and be somewhat difficult to
detect otherwise.  (I'm assuming it is still the case that
native-compiling a Lisp file leaves behind user-visible .elc artifacts.
If that has been fixed, please ignore this paragraph).

But, please, no timestamp.  Let's keep things reproducible where we can,
and not leak sensitive information by accident.

It may be necessary to bump the produced ELC version code for this.

The equivalent issues are less urgent, but ultimately identical, for
pdumper files (apparently, we don't detect truncation or modification)
and object files produced during the build (it's the job of the make
implementation and the compiler to avoid truncated .o files, but if they
don't do that, we might want to write x.o.tmp first, then rename it, in
the usual fashion of Makefiles).

Note that it is, of course, possible to usefully modify .elc (and .pdmp)
files after creation, so we shouldn't make detected modifications an
unconditional error.

Pip

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Eli Zaretskii]

> Date: Wed, 01 Jan 2025 17:41:57 +0000
> From: Pip Cet <pipcet@protonmail.com>
> Cc: "N. Jackson" <njackson@posteo.net>, yantar92@posteo.net, 75209@debbugs.gnu.org
> 
> I'm assuming that the resolution was that the file was read before we
> finished writing it.  I've run into the same issue a number of times
> (interrupting and resuming Emacs builds leads to build failures, "make
> bootstrap" makes them go away).
> 
> Can we consider modifying the .elc format to have a footer indicating
> that the file is complete?

The .elc file is supposed to be created only when the compilation is
complete and successful.  If you look at byte-compile-file, you will
see that we first compile the Lisp code, then write the produced
bytecode to a temporary file, and only after that we rename the
temporary file into the target .elc file.  Renaming a file is an
atomic operation on Posix filesystems, so it either completely
succeeds or completely fails.

We only write directly to the target file if that file's directory is
unwritable.

So I don't understand why you see incomplete .elc files when you
interrupt the build.  What happens in my case is that I see those
temporary files left around, but I don't think I've ever saw an
incomplete .elc file after interrupting the build.

Is it likely that the directory where you build Emacs is not writable
by your user?  That's the only way I could explain what you see.  Or
maybe there's some other factor at work here, in which case we should
find out what that factor is, before we consider how to fix it.

In any case, I think this is a separate issue, so I'd prefer to have a
separate bug report for it.

Thanks.

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Pip Cet via Bug reports for GNU Emacs, the Swiss army knife of text editors]

"Eli Zaretskii" <eliz@gnu.org> writes:

>> Date: Wed, 01 Jan 2025 17:41:57 +0000
>> From: Pip Cet <pipcet@protonmail.com>
>> Cc: "N. Jackson" <njackson@posteo.net>, yantar92@posteo.net, 75209@debbugs.gnu.org
>>
>> I'm assuming that the resolution was that the file was read before we
>> finished writing it.  I've run into the same issue a number of times
>> (interrupting and resuming Emacs builds leads to build failures, "make
>> bootstrap" makes them go away).
>>
>> Can we consider modifying the .elc format to have a footer indicating
>> that the file is complete?
>
> The .elc file is supposed to be created only when the compilation is
> complete and successful.  If you look at byte-compile-file, you will

You're right.  Sorry for the noise.  The most likely explanation is I
missed a "Pure Lisp storage overflowed" message which "explained" it,
because I just tried and that's what happened.

There's a bug in pin_string which assumes no purespace overflow, and
corrupts bytecode after one, so it's entirely possible that an .elc file
was truncated.  Probably not worth fixing at this point.

I'll try interrupting a few more builds when no-purespace is merged.

Pip

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[N. Jackson]

At 18:48 +0000 on Monday 2024-12-30, N. Jackson wrote:
>
> In the Emacs 30 pretest I have been getting the following warning
> every few days:
>
>   Warning (emacs): Emacs reader failed to read data in
>   "/home/nlj/.cache/org-persist/gc-lock.eld". The error was: "End of
>   file during parsing"

When I woke my system from suspend this morning and switched to the
Emacs session running Gnus, the warning had popped up in that
session -- possibly during suspend or resume.

I immediately looked at gc-lock.eld which contained this:

  ;;   -*- mode: lisp-data; -*-
  (((26485 51608 866710 15000) 26486 34929 321731 426000))

(which I guess is again unremarkable).

I checked my buffer list to be absolutely certain that I hadn't
opened any Org Mode files and the only buffers were *Group*,
*scratch*, *Messages*, .newsrc-dribble, and *Warnings*.

The session has one frame and in that frame there was just the Gnus
Group buffer open (until the *Warnings* buffer popped up below it).

With Gnus sitting idle with just it's Group buffer open, I can't see
how it would use any Org Mode features -- or even _do_ anything at
all -- and as I said, no Org Mode (user) files were open in the
session.

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Ihor Radchenko]

Eli Zaretskii <eliz@gnu.org> writes:

>> gc-lock.eld is a file used to flag that cache dir is being worked
>> on by multiple emacs instances. GC here refers to
>> garbage-collecting cache data.
>
> Can you tell more about the purpose and use of this file?  What is
> written to it, and how is it supposed to be used after being written?
> And what bad things happen when the Lisp readers errors out because it
> is unable to read the data for some reason?

Let me then describe briefly what org-persist does.

In the nutshell, it is cache manager.
The main cache data consists of:
1. index describing everything stored in the cache and its expiry
   settings
2. cache data stored in individual files. Each file in the cache is
   mentioned in the index file

From time to time (before quitting Emacs), org-persist needs to do some
"garbage collection" and remove cache files that are expired or
unreferenced from index to avoid cache growing infinitely.

The GC process works well, and helps keeping the cache directory
clean. However, there are problems when multiple Emacs processes are
running simultaneously.

Consider Emacs A loading cache index into memory and doing nothing.
Then, Emacs B also loads the cache index, but adds data to the cache.
If Emacs A is closed while Emacs B is running (and Emacs B not yet
updating cache index on disk), it also performs garbage
collection. However, Emacs A has no knowledge about cache data written
by Emacs B and may "garabge collect" this data. We do not want that.

"gc-lock.eld" keeps track of the running Emacs processes - every Emacs
process regularly write to "gc-lock.eld", putting a record in the form
of (before-init-time . <last known time that Emacs is running>). If
there are no known recently running Emacs processes (apart from
current), garbage collection process is suppressed to avoid removing
cache data from other Emacsen.

-- 
Ihor Radchenko // yantar92,
Org mode maintainer,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

bug#75209: 30.0.93; Emacs reader failed to read data in "/home/nlj/.cache/org-persist/gc-lock.eld"

[Eli Zaretskii]

> From: Ihor Radchenko <yantar92@posteo.net>
> Cc: njackson@posteo.net, 75209@debbugs.gnu.org
> Date: Thu, 02 Jan 2025 17:28:02 +0000
> 
> Eli Zaretskii <eliz@gnu.org> writes:
> 
> > Can you tell more about the purpose and use of this file?  What is
> > written to it, and how is it supposed to be used after being written?
> > And what bad things happen when the Lisp readers errors out because it
> > is unable to read the data for some reason?
> 
> Let me then describe briefly what org-persist does.
> 
> In the nutshell, it is cache manager.
> The main cache data consists of:
> 1. index describing everything stored in the cache and its expiry
>    settings
> 2. cache data stored in individual files. Each file in the cache is
>    mentioned in the index file
> 
> >From time to time (before quitting Emacs), org-persist needs to do some
> "garbage collection" and remove cache files that are expired or
> unreferenced from index to avoid cache growing infinitely.
> 
> The GC process works well, and helps keeping the cache directory
> clean. However, there are problems when multiple Emacs processes are
> running simultaneously.
> 
> Consider Emacs A loading cache index into memory and doing nothing.
> Then, Emacs B also loads the cache index, but adds data to the cache.
> If Emacs A is closed while Emacs B is running (and Emacs B not yet
> updating cache index on disk), it also performs garbage
> collection. However, Emacs A has no knowledge about cache data written
> by Emacs B and may "garabge collect" this data. We do not want that.

Thanks.  I think I still don't have a clear idea of the usage of these
caches.  Are the caches supposed to be common to all Emacs sessions?
E.g., when a cache changes by one session, are other sessions supposed
to know about the change?  If the cache is for a single session, then
why are several session allowed to write to the cache simultaneously?
And if the cache is common to all sessions, then perhaps reading the
index before writing it should avoid several sessions step on each
other's toes?

> "gc-lock.eld" keeps track of the running Emacs processes - every Emacs
> process regularly write to "gc-lock.eld", putting a record in the form
> of (before-init-time . <last known time that Emacs is running>). If
> there are no known recently running Emacs processes (apart from
> current), garbage collection process is suppressed to avoid removing
> cache data from other Emacsen.

One way of rewriting a file atomically is to write the stuff to a
temporary file, then rename it to the target name.  If Org doesn't
already do that, maybe you should try doing that (together with
reading the file before updating it)?