Emacs hangs sometimes for no reason

Emacs hangs sometimes for no reason

[Sebastian Christ]

Hi list,

in the last couple weeks (perhaps months?) Emacs hangs for no specific
reason for me. The single constant is, that when it hangs, it hangs
while I'm in org-mode. This occurs on multiple circumstance as

- changing the outline structure by demoting and promoting headline
- when refiling
- re-schedule in agenda
- yanking
- perhaps more

The strange thing is that it happens unpredictably, e.g. I re-schedule
11 items without problems and the 12th one lets Emacs crash. Sometimes
it works for days without problems and then I promote a headline and
Emacs crashes. Very sad :(

When I kill Emacs with

  $ pkill -SIGUSR2 Emacs

this leaves me in the Emacs debugger in a flyspell function or (today)
in a avl-tree function.

My actual question is, had someone had similar issues? Or is it just me
with my configuration?

Perhaps someone can guide me on how I can find the root cause for this?
I pretty much lost here.

Thanks in advance for any hints.

Best,
Sebastian

-- 
Sebastian (Rudolfo) Christ
http://rudolfochrist.github.io
GPG Fingerprint: 306D 8FD3 DFB6 4E44 5061
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Re: Emacs hangs sometimes for no reason

[Nicolas Goaziou]

Hello,

Sebastian Christ <rudolfo.christ@gmail.com> writes:

> in the last couple weeks (perhaps months?) Emacs hangs for no specific
> reason for me. The single constant is, that when it hangs, it hangs
> while I'm in org-mode. This occurs on multiple circumstance as
>
> - changing the outline structure by demoting and promoting headline
> - when refiling
> - re-schedule in agenda
> - yanking
> - perhaps more
>
> The strange thing is that it happens unpredictably, e.g. I re-schedule
> 11 items without problems and the 12th one lets Emacs crash. Sometimes
> it works for days without problems and then I promote a headline and
> Emacs crashes. Very sad :(
>
> When I kill Emacs with
>
>   $ pkill -SIGUSR2 Emacs
>
> this leaves me in the Emacs debugger in a flyspell function or (today)
> in a avl-tree function.
>
> My actual question is, had someone had similar issues? Or is it just me
> with my configuration?
>
> Perhaps someone can guide me on how I can find the root cause for this?
> I pretty much lost here.

This could be related to Org cache. I know the cache can become
corrupted upon modifying outline structure of a document. Unfortunately,
I couldn't come with a small enough recipe to reproduce the exact
problem.

You could try to set `org-element-use-cache' to nil and see if the hangs
disappear.

Regards,

-- 
Nicolas Goaziou

Re: Emacs hangs sometimes for no reason

[Samuel Wales]

fwiw, i have had the element cache turned off since org 8 because of
intermittent bugs.  i tried it on in org 9 maint recently and it
caused similar problems.  so you might be experiencing same.

funnily enough, it doesn't seem to make any difference to agenda
creation speed, which is my bottleneck.

>> My actual question is, had someone had similar issues? Or is it just me
>> with my configuration?

Re: Emacs hangs sometimes for no reason

[Sebastian Christ]

>>>>> "NG" == Nicolas Goaziou <mail@nicolasgoaziou.fr> writes:
    NG> You could try to set `org-element-use-cache' to nil and see if
    NG> the hangs disappear.

I'll try this. Thank you very much. 

/src

-- 
Sebastian (Rudolfo) Christ
http://rudolfochrist.github.io
GPG Fingerprint: 306D 8FD3 DFB6 4E44 5061
                 CE71 6407 D6F8 2AC5 55DD

Re: Emacs hangs sometimes for no reason

[Sebastian Christ]

>>>>> "SW" == Samuel Wales <samologist@gmail.com> writes:

    SW> fwiw, i have had the element cache turned off since org 8
    SW> because of intermittent bugs.  i tried it on in org 9 maint
    SW> recently and it caused similar problems.  so you might be
    SW> experiencing same.

    SW> funnily enough, it doesn't seem to make any difference to agenda
    SW> creation speed, which is my bottleneck.

Nicolas Goaziou suggested the same thing. I'll try this an report
back. Thanks.

/src

-- 
Sebastian (Rudolfo) Christ
http://rudolfochrist.github.io
GPG Fingerprint: 306D 8FD3 DFB6 4E44 5061
                 CE71 6407 D6F8 2AC5 55DD

Re: Emacs hangs sometimes for no reason

[Eric S Fraga]

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On Saturday, 14 Jan 2017 at 18:33, Sebastian Christ wrote:
> in the last couple weeks (perhaps months?) Emacs hangs for no specific
> reason for me. The single constant is, that when it hangs, it hangs
> while I'm in org-mode. This occurs on multiple circumstance as

Just to say that I experience the same.  However, I track emacs as well
as org so I never know if the problem is emacs or org.  In my case, all
hangs are when in org mode but that could be because I'm in org mode
90% of the time... :-)

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 26.0.50.1, Org release_9.0.3-201-ga51c6f

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Re: Emacs hangs sometimes for no reason

[Stig Brautaset]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> On Saturday, 14 Jan 2017 at 18:33, Sebastian Christ wrote:
>> in the last couple weeks (perhaps months?) Emacs hangs for no specific
>> reason for me. The single constant is, that when it hangs, it hangs
>> while I'm in org-mode. This occurs on multiple circumstance as
>
> Just to say that I experience the same.  However, I track emacs as well
> as org so I never know if the problem is emacs or org.  In my case, all
> hangs are when in org mode but that could be because I'm in org mode
> 90% of the time... :-)

Just to say that I too experience the same. I'm convinced it started
happening since I upgraded to Org 9 (but I also started using Org's
Agenda more around the same time, I think). My versions:

- GNU Emacs 25.1.1 (x86_64-apple-darwin13.4.0, NS appkit-1265.21 Version 10.9.5 (Build 13F1911)) of 2016-09-21
- Org mode version 9.0.3 (9.0.3-elpaplus @ - /Users/stig/.emacs.d/elpa/org-plus-contrib-20161224/)

I can go a few days without encountering it, but then it will suddenly
hit. I have a feeling that it's triggered by refiling, or closing
TODOs towards the end of the file. My agenda file is big, but not
monstrous. (I think.) C-= reports: "Region has 2025 lines, 9592 words,
and 67513 characters." There are 333 headings, most of them
TODO/NEXT/PROJECT, and I use lots of tags. I also use a few categories
on top-level headings.

I've set the following to try to speed up agenda, but it hasn't made any
discernible difference as far as I can tell:

: (setq org-agenda-use-tag-inheritance '(todo))

I've tried to turn on debug on quit, and sent a few stack traces here in
the past but to no avail. I cannot reproduce it with =emacs -q=, but
that uses Org 8 anyway, so I would not expect it to. Nor do I have a
sure-fire way to reproduce the issue, and I am not keen on being without
my regular config for days while hoping to reproduce the hang.

I do think it's related to Emacs having run for a while, because once
the hang manifests I can just quit Emacs and restart what I was doing
and no hang will manifest (for a while). When last I managed to capture
a stack trace during one of these the stack trace started  with:

: Debugger entered--Lisp error: (quit)
:  avl-tree--do-delete(org-element--cache-compare [[[[[[nil nil
: (property-drawer (:begin 18463 :end 18529 :contents-begin 18479
: :contents-end 18519 :post-blank 1 :post-affiliated 18463 :parent nil))
: 0] [nil nil (plain-list (:type unordered :begin 18547 :end 18749
: :contents-begin 18574 :contents-end 18748 :structure ... :post-blank 1
: :post-affiliated 18574 :name "candidate-names" :parent nil)) 0]
: (paragraph (:begin 18529 :end 18547 :contents-begin 18529
: :contents-end 18546 :post-blank 1 :post-affiliated 18529 :parent nil))
: 0] [[nil nil (keyword (:key "RESULTS" :value "" :begin 18905 :end
: 18920 :post-blank 1 :post-affiliated 18905 :parent nil)) 0] [nil nil
: (paragraph (:begin 19570 :end 19586 :contents-begin 19570
: :contents-end 19585 :post-blank 1 :post-affiliated 19570 :parent nil))
: 0] (table (:begin 18920 :end 19570 :type org :tblfm nil
: :contents-begin 18920 :contents-end 19568 :value nil :post-blank 2
: :post-affiliated 18920 :parent nil)) 0] (src-block (:language "sh"
: :switches nil :parameters ":var names=candidate-names :results table"
: :begin 18749 :end 18905 :number-lines nil :preserve-indent nil
: :retain-labels t :use-labels t :label-fmt nil :value "   echo $names |
: xargs -n1 | perl  -MList::Util -e
: 'print List::Util::shuffle <>'\n" :post-blank 1 :post-affiliated
: 18749 :parent nil)) 0

Further, I do notice this stack trace is full of `:drawer-name
"LOGBOOK"' entries too, like this:

: (:begin 9624 :end 9714 :drawer-name "LOGBOOK" :contents-begin 9638
: :contents-end 9704 :post-blank 0 :post-affiliated 9624 :parent nil))
: 0] [[[[nil nil ... 0] [nil nil ... 0] ... 0] [[nil nil ... 0] [nil nil
: ... 0] ... 0] (drawer ...) 0] [[[nil nil ... 0] [nil nil ... 0] ... 0]
: [[[nil nil ... 0] nil ... -1] [[nil nil ... 0] [nil nil ... 0] ... 0]
: ... 0] (item ...) 1] (drawer (:begin 15202 :end 15582 :drawer-name
: "LOGBOOK" :contents-begin 15216 :contents-end 15572 :post-blank 0
: :post-affiliated 15202 :parent nil)) 1] (drawer (:begin 11498 :end
: 11629 :drawer-name "LOGBOOK" :contents-begin 11512 :contents-end 11619
: :post-blank 0 :post-affiliated 11498 :parent nil)) 1] (property-drawer
: (:begin 7832 :end 7900 :contents-begin 7849 :contents-end 7890
: :post-blank 0 :post-affiliated 7832 :parent nil)) 1] [[[[[[nil nil ...
: 0] [nil nil ... 0] ... 0] [[nil nil ... 0] [nil nil ... 0] ... 0]
: (src-block ...) 0] [[[nil nil ... 0] [nil nil ... 0] ... 0] [[nil nil
: ... 0] [nil nil ... 0] ... 0] (drawer ...) 0] (paragraph (:begin 19586
: :end 19669 :contents-begin 19586 :contents-end 19668 :post-blank 1
: :post-affiliated 19586 :parent nil)) 0] [[[[nil nil ... 0] [nil nil
: ... 0] ... 0] [[nil nil ... 0] [nil nil ... 0] ... 0] (drawer ...) 0]
: [[[nil nil ... 0] [nil nil ... 0] ... 0] [[nil nil ... 0] [[nil nil
: ... 0] nil ... -1] ... 1] (planning ...) 1] (drawer (:begin 25456 :end
: 25514 :drawer-name "LOGBOOK" :contents-begin 25469 :contents-end 25504
: :post-blank 1 :post-affiliated 25456 :parent nil)) 1] (planning
: (:closed nil :deadline nil :scheduled (timestamp ...) :begin 23148
: :end 23180 :post-blank 0 :post-affiliated 23148 :parent nil)) 1]

The end of the stack trace was:

: 0] nil 28373 nil nil)
:  org-element--cache-sync(#<buffer Agenda.org> 28373)
:  org-element-at-point()
:  org-eldoc-get-src-lang()
:  org-eldoc-documentation-function()
:  eldoc-print-current-symbol-info()
:  #[0 "\b\204.

I must admit, I haven't tried to simply "wait it out" and see if it
eventually finishes what it's doing and returning control to me.
Perhaps I'll try that next, but usually when these hangs occur it's
when I'm in the middle of doing something that I'd rather want to
finish :-(

If anybody has tips for how I can produce a better bug report, I'd be
very happy to hear them.


Stig

Re: Emacs hangs sometimes for no reason

[Stig Brautaset]

Stig Brautaset <stig@brautaset.org> writes:

> Eric S Fraga <e.fraga@ucl.ac.uk> writes:
>
>> On Saturday, 14 Jan 2017 at 18:33, Sebastian Christ wrote:
>>> in the last couple weeks (perhaps months?) Emacs hangs for no specific
>>> reason for me. The single constant is, that when it hangs, it hangs
>>> while I'm in org-mode. This occurs on multiple circumstance as
>>
>> Just to say that I experience the same.  However, I track emacs as well
>> as org so I never know if the problem is emacs or org.  In my case, all
>> hangs are when in org mode but that could be because I'm in org mode
>> 90% of the time... :-)
>
> Just to say that I too experience the same. I'm convinced it started
> happening since I upgraded to Org 9 (but I also started using Org's
> Agenda more around the same time, I think). My versions:

I just saw Nicolas suggesting disabling org cache, and will try that.
(My stack traces from hangs did include references to the cache.) Will
report back if the hangs disappear, though it might take a while before
I'm confident they really are...

Stig

Re: Emacs hangs sometimes for no reason

[Eric Abrahamsen]

Eric S Fraga <e.fraga@ucl.ac.uk> writes:

> On Saturday, 14 Jan 2017 at 18:33, Sebastian Christ wrote:
>> in the last couple weeks (perhaps months?) Emacs hangs for no specific
>> reason for me. The single constant is, that when it hangs, it hangs
>> while I'm in org-mode. This occurs on multiple circumstance as
>
> Just to say that I experience the same.  However, I track emacs as well
> as org so I never know if the problem is emacs or org.  In my case, all
> hangs are when in org mode but that could be because I'm in org mode
> 90% of the time... :-)

I used to get this a lot, and always due to some interaction between the
cache and flyspell. It hasn't happened to me for several months, though
(Emacs from git, org-plus-contrib from the package manager). Who knows
why...

Eric

Re: Emacs hangs sometimes for no reason

[Eric S Fraga]

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On Sunday, 15 Jan 2017 at 13:55, Stig Brautaset wrote:

[...]

> Just to say that I too experience the same. I'm convinced it started
> happening since I upgraded to Org 9 (but I also started using Org's
> Agenda more around the same time, I think). My versions:

[...]

> I can go a few days without encountering it, but then it will suddenly
> hit. I have a feeling that it's triggered by refiling, or closing
> TODOs towards the end of the file. My agenda file is big, but not

For me, it does not happen with the agenda but when editing documents
(in org).  I can find no predictability to the hangs, however.  Some
days it happens more than once but I can also go many days without it
happening.

Emacs does not get completely hung in that it attempts to respond to C-g
(visual-bell indication happens).

The cache may be involved.  I do tend to have quite long and complicated
documents (full journal papers or a whole semester's set of slides for
one of my courses) with lots of babel src blocks, tables, inline tasks,
...

Anyway, not a deal breaker!

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 26.0.50.1, Org release_9.0.3-201-ga51c6f

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Re: Emacs hangs sometimes for no reason

[Michael Welle]

Hello,

Eric Abrahamsen <eric@ericabrahamsen.net> writes:
[...]
> I used to get this a lot, and always due to some interaction between the
> cache and flyspell. It hasn't happened to me for several months, though
> (Emacs from git, org-plus-contrib from the package manager). Who knows
> why...
I have no problem (in this department ;)) with Org (Org and Emacs 25,
both, are from git), but sometimes Emacs hangs when I write an email
with wanderlust. It seems to hang for a minute or maybe longer, most
times I key in a couple of C-g and then go on. I got triggered by
flyspell, that is active in wl as well. Hmm. 

Regards
hmw

Re: Emacs hangs sometimes for no reason

[Eric Abrahamsen]

Michael Welle <mwe012008@gmx.net> writes:

> Hello,
>
> Eric Abrahamsen <eric@ericabrahamsen.net> writes:
> [...]
>> I used to get this a lot, and always due to some interaction between the
>> cache and flyspell. It hasn't happened to me for several months, though
>> (Emacs from git, org-plus-contrib from the package manager). Who knows
>> why...
> I have no problem (in this department ;)) with Org (Org and Emacs 25,
> both, are from git), but sometimes Emacs hangs when I write an email
> with wanderlust. It seems to hang for a minute or maybe longer, most
> times I key in a couple of C-g and then go on. I got triggered by
> flyspell, that is active in wl as well. Hmm. 

Flyspell apparently has a few mechanisms for avoiding this sort of
thing, see the option flyspell-delayed-commands and flyspell-delay. Org
already does some manipulation of delayed commands (maybe that's why I
don't see these hangs anymore...?), perhaps you could try that in wl as
well.

Eric

Re: Emacs hangs sometimes for no reason

[Samuel Loury]

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For what it's worth, when this happens, I generally pkill -SIGUSR2
emacs. emacs reacts to the USR2 signal by stopping everything and start
a lisp debugging session. From there, I reset all the org caches with
this command:

--8<---------------cut here---------------start------------->8---
(defun konix/org-element-cache-reset-all ()
  (interactive)
  (mapc
   (lambda (file)
	 (save-window-excursion
	   (save-excursion
		 (find-file file)
		 (org-element-cache-reset)
		 )
	   )
	 )
   (org-agenda-files)
   )
  )
--8<---------------cut here---------------end--------------->8---

Finally, I quit the debugging session and reset the debug on quit with
(toggle-debug-on-quit) and everything comes back to normal.

My two cents,
-- 
Konubinix
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Re: Emacs hangs sometimes for no reason

[Eric S Fraga]

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On Wednesday, 18 Jan 2017 at 14:12, Samuel Loury wrote:
> For what it's worth, when this happens, I generally pkill -SIGUSR2

Thanks, this is useful.  I usually try INT, USR1, KILL but never USR2.

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 26.0.50.1, Org release_9.0.3-241-gc3d67b

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Re: Emacs hangs sometimes for no reason

[Sebastian Christ]

>>>>> "SL" == Samuel Loury <konubinix@gmail.com> writes:

    SL> For what it's worth, when this happens, I generally pkill
    SL> -SIGUSR2 emacs. emacs reacts to the USR2 signal by stopping
    SL> everything and start a lisp debugging session. From there, I
    SL> reset all the org caches with this command:

    SL> (defun konix/org-element-cache-reset-all ()
    SL>   (interactive)
    SL>   (mapc
    SL>     (lambda (file)
    SL>       (save-window-excursion
    SL>         (save-excursion
    SL>           (find-file file)
    SL>           (org-element-cache-reset))))
    SL>     (org-agenda-files)))

Thanks for this snippet. I know it's a little bit early but setting
`org-element-use-cache' seems to do the trick for me.

    SL> Finally, I quit the debugging session and reset the debug on
    SL> quit with (toggle-debug-on-quit) and everything comes back to
    SL> normal.

So, aren't you restarting Emacs after pkill -SIGUSR2 emacs? 

Regards,
Sebastian 

-- 
Sebastian (Rudolfo) Christ
http://rudolfochrist.github.io
GPG Fingerprint: 306D 8FD3 DFB6 4E44 5061
                 CE71 6407 D6F8 2AC5 55DD

Re: Emacs hangs sometimes for no reason

[Samuel Loury]

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Sebastian Christ <rudolfo.christ@gmail.com> writes:

[...]

> So, aren't you restarting Emacs after pkill -SIGUSR2 emacs? 

pkill -SIGUSR2 emacs does not stop emacs. Emacs will start a debugging
session that you can stop to go back to a "normal" emacs. I found out
that it generally makes emacs responsive enough so that I can launch the
org reset cache function.

I found the USR2 signal trick in irreal¹.

¹  here: http://irreal.org/blog/?p=5218
-- 
Konubinix
GPG Key    : 7439106A
Fingerprint: 5993 BE7A DA65 E2D9 06CE  5C36 75D2 3CED 7439 106A

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Re: Emacs hangs sometimes for no reason

[Karl Voit]

* Sebastian Christ <rudolfo.christ@gmail.com> wrote:
> Hi list,
>
> in the last couple weeks (perhaps months?) Emacs hangs for no specific
> reason for me. The single constant is, that when it hangs, it hangs
> while I'm in org-mode. This occurs on multiple circumstance as
>
> - changing the outline structure by demoting and promoting headline
> - when refiling
> - re-schedule in agenda
> - yanking
> - perhaps more

Same here with 3 different Emacs versions.

> The strange thing is that it happens unpredictably, e.g. I re-schedule
> 11 items without problems and the 12th one lets Emacs crash. Sometimes
> it works for days without problems and then I promote a headline and
> Emacs crashes. Very sad :(

I did not have a crash here, though.

> My actual question is, had someone had similar issues? Or is it just me
> with my configuration?
>
> Perhaps someone can guide me on how I can find the root cause for this?
> I pretty much lost here.
>
> Thanks in advance for any hints.

In a discussion on Org/Emacs scalability issues, I got a hint[1] to use
gcmh.el which indicates garbage collecting activity. My
freeze-moments are almost entirely related to garbage collecting.

You might want to try that.

I've got no solution or workaround so far.

[1] https://www.reddit.com/r/orgmode/comments/e9p84n/scaling_org_better_to_use_more_medsize_files_or/fcm5bsc/

-- 
get mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML into Org-mode:
       > get Memacs from https://github.com/novoid/Memacs <
Personal Information Management > http://Karl-Voit.at/tags/pim/
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Re: Emacs hangs sometimes for no reason

[briangpowell .]

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Emacs periodically saves all files that you are visiting; this is called
auto-saving . Auto-saving prevents you from losing more than a limited
amount of work if the system crashes. By default, auto-saves happen every
300 keystrokes, or after around 30 seconds of idle time.

Suggest you try making your auto-save-interval variable much larger and see
if that helps

Also suggest making smaller .org files when practical

On Tue, Feb 11, 2020 at 7:33 AM Karl Voit <devnull@karl-voit.at> wrote:

> * Sebastian Christ <rudolfo.christ@gmail.com> wrote:
> > Hi list,
> >
> > in the last couple weeks (perhaps months?) Emacs hangs for no specific
> > reason for me. The single constant is, that when it hangs, it hangs
> > while I'm in org-mode. This occurs on multiple circumstance as
> >
> > - changing the outline structure by demoting and promoting headline
> > - when refiling
> > - re-schedule in agenda
> > - yanking
> > - perhaps more
>
> Same here with 3 different Emacs versions.
>
> > The strange thing is that it happens unpredictably, e.g. I re-schedule
> > 11 items without problems and the 12th one lets Emacs crash. Sometimes
> > it works for days without problems and then I promote a headline and
> > Emacs crashes. Very sad :(
>
> I did not have a crash here, though.
>
> > My actual question is, had someone had similar issues? Or is it just me
> > with my configuration?
> >
> > Perhaps someone can guide me on how I can find the root cause for this?
> > I pretty much lost here.
> >
> > Thanks in advance for any hints.
>
> In a discussion on Org/Emacs scalability issues, I got a hint[1] to use
> gcmh.el which indicates garbage collecting activity. My
> freeze-moments are almost entirely related to garbage collecting.
>
> You might want to try that.
>
> I've got no solution or workaround so far.
>
> [1]
> https://www.reddit.com/r/orgmode/comments/e9p84n/scaling_org_better_to_use_more_medsize_files_or/fcm5bsc/
>
> --
> get mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML into Org-mode:
>        > get Memacs from https://github.com/novoid/Memacs <
> Personal Information Management > http://Karl-Voit.at/tags/pim/
> Emacs-related > http://Karl-Voit.at/tags/emacs/
>
>
>

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Re: Emacs hangs sometimes for no reason

[Karl Voit]

* briangpowell . <briangpowellms@gmail.com> wrote:
>
> Emacs periodically saves all files that you are visiting; this is called
> auto-saving . Auto-saving prevents you from losing more than a limited
> amount of work if the system crashes. By default, auto-saves happen every
> 300 keystrokes, or after around 30 seconds of idle time.
>
> Suggest you try making your auto-save-interval variable much larger and see
> if that helps

I had to disable auto-save because I'm using org-crypt which would
leak sensitive information to my disk (+ git repository).

I'm using real-auto-save instead.

> Also suggest making smaller .org files when practical

Way too late for that ;-) So far, I've found no one with bigger Org
files. I plan to blog about small versus big Org files in the
upcoming weeks.


However, your suggestions are valid points for the general
situation.

-- 
get mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML into Org-mode:
       > get Memacs from https://github.com/novoid/Memacs <
Personal Information Management > http://Karl-Voit.at/tags/pim/
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