[Rd] Embedded R Fails When Run on LSF Queue System

[Nigel Delaney]

Thanks Dirk.  I'll confess I am mostly trying to follow the practices
outlined in the writing R-extensions manual and books by Chambers and
Gentleman, but  have found some conflicting advice on the internet in
various places, and am also trying to build off a previously existing code
base (that at least worked on some
operating-systems/architectures/scenarios, but seems to break when I move
the program around to any new type of environment).  Will definitely
re-write that bit.

Sincere thanks again.  Out of curiosity, can I ask one more question since I
gather you have much more expertise than myself?  The extension manual has a
somewhat obscure, to me at least, section on threading issues (8.1.5).  My
understanding is that because the R_CStackStart is a single value, if R is
called from multiple threads (even if never simultaneously), it is
essentially best to just disable the stack check rather than try to re-write
this value each time, which I gather might need to be done (and simply
increasing the stack size of the calling thread will not help).  Is this the
approach you have taken in your projects?  Or do you think this is also a
bad idea?

-----Original Message-----
From: Dirk Eddelbuettel [mailto:edd at debian.org] 
Sent: Sunday, November 10, 2013 8:50 PM
To: Nigel Delaney
Cc: r-devel at r-project.org
Subject: Re: [Rd] Embedded R Fails When Run on LSF Queue System


On 10 November 2013 at 16:32, Nigel Delaney wrote:
| I had a quick question I was hoping someone might be able to answer, as my
journey through the source code so far has not been very profitable. I have
a command line program that embeds R, and the program works just fine when
run from the command line. However, when I run the program as a job in the
LSF cluster at my institute, the following error occurs:
| 
| Fatal error: you must specify '--save', '--no-save' or '--vanilla'
| 
| This is confusing becasue I believe I have set this by changing the
startup parameters so that the no-save option is in use. I initialize R with
the following collection of function calls:
| 
| 1-Rf_initialize_R
| 2-R_SetParams
| 3-setup_Rmainloop
| 
| At step 2 I pass in a structure that specifies the no-save option (as well
as interactive=true, verbose=false), so I would expect it to be okay, but I
still receive this error. Again, not at the terminal but only when run as a
separate process.
| 
| I gathered from this thread that someone else has experienced this
(https://stat.ethz.ch/pipermail/r-help/2008-March/155935.html), but am not
sure how best to rectify it as I believe I have already changed the setting.
| 
| Does anyone know what a good solution or work around might be?

As a first approximation, when the manual tells you do something a certain
way, you are in fact better off doing it that way.

I stand behind two projects embedding R: littler (with Jeff Horner), and
RInside (with Romain Francois).  Both do this explicitly.  From littler.c:

	char *R_argv[] = {(char*)programName, "--gui=none", "--no-restore",
"--no-save", "--no-readline", "--silent", "", ""};
	char *R_argv_opt[] = {"--vanilla", "--slave"};
	int R_argc = (sizeof(R_argv) - sizeof(R_argv_opt) ) /
sizeof(R_argv[0]);

        [...]
        /* some logic to add R_argv_opt parts to R_argv omitted (/
        [...]

	Rf_initEmbeddedR(R_argc, R_argv);	/* Initialize the embedded R
interpreter */

Hope this helps,  Dirk

--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com