Re: Emacs/ESS/org freezes/hangs on big data/ RAM(~256GB) processes when run in org/babel

[Xebar Saram <zeltakc@gmail.com>]

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Thx Chuck

this sounds great. could you perhaps point us to some documentation on
this, or perhpas consider sharing a detailed overview of your workflow?
this seems it could really fit my needs.

thx so much in advance

Z


On Thu, Jun 18, 2015 at 6:17 AM, Charles C. Berry <ccberry@ucsd.edu> wrote:

> On Wed, 17 Jun 2015, William Denton wrote:
>
>  On 17 June 2015, Xebar Saram wrote:
>>
>>  I do alot of modeling work that involves using huge datasets and run
>>> process intensive R processes (such as complex mixed models, Gamms etc).
>>> in
>>> R studio all works well yet when i use the orgmode eval on R code blocks
>>> it
>>> works well for small simple process but 90% of the time when dealing with
>>> complex models and bug data (up to 256GB) it will just freeze emacs/ess.
>>> sometimes i can C-c or C-g it and other times i need to physically kill
>>> emacs.
>>>
>>
>> I've been having the same problem for a while, but wasn't able to isolate
>> it any more than large data sets, lack of memory, and heavy CPU usage.
>> Sometimes everything hangs and I need to power cycle the computer. :(
>>
>>
> And you (both) have `ess-eval-visibly' set to nil, right?
>
> I do statistical genomics, which can be compute intensive. Sometimes
> processes need to run for a while, and I get impatient having to wait.
>
> I wrote (and use) ox-ravel[1] to speed up my write-run-revise cycle in
> org-mode.
>
> Basically, ravel will export Org mode to a format that knitr (and the
> like) can run - turning src blocks into `code chunks'. That allows me to
> set the cache=TRUE chunk option, etc. I run knitr on the exported document
> to initialize objects for long running computations or to produce a
> finished report.
>
> When I start a session, I run knitr in the R session, then all the cached
> objects are loaded in and ready to use.
>
> If I write a src block I know will take a long time to export, I export
> from org mode to update the knitr document and re-knit it to refresh the
> cache.
>
> Mostly, I work in org-mode adding src blocks, revising existing ones, or
> editing text and graphics.
>
> If you decide to try ravel I recommend the `ravel-lang' branch[2] as that
> will soon replace master.
>
> HTH,
>
> Chuck
>
>
> [1] https://github.com/chasberry/orgmode-accessories
> [2] https://github.com/chasberry/orgmode-accessories/tree/ravel-lang
>

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