R devel - Nov 2013 - Running R embedded in an mpiexec spawned process - Fatal error: you must specify '--save', '--no-save' or '--vanilla'

I'd like someone familiar with the R options initialization to comment on a
difference of behavior within/without mpiexec

I have a (.NET) application with embedded R that is proven to run in a single
process:

    ./Sample1.exe

on a Debian Linux with R 3.0.2

Running the same code with mpiexec, it fails at the R engine initialization:

    mpiexec -n 1 ./Sample1.exe
    Fatal error: you must specify '--save', '--no-save' or
'--vanilla'
    -------------------------------------------------------------------------

The behavior is actually reproducible with the straight R 
    mpiexec -n 1 R
    Fatal error: you must specify '--save', '--no-save' or
'--vanilla'
    -------------------------------------------------------------------------
The following is working:
    mpiexec -n 1 R --no-save

However in my Sample1 application, I do set up R init options that should be
suitable AFAIK:

            rEngine = REngine.CreateInstance("RDotNet");
            StartupParameter rStartParams = new StartupParameter
            {
                Quiet = true,
                SaveAction = StartupSaveAction.NoSave,
                Slave = false,
                Interactive = true,
                Verbose = false,
                LoadInitFile = true,
                LoadSiteFile = true,
                RestoreAction = StartupRestoreAction.NoRestore,
                NoRenviron = false
            };
            rEngine.Initialize(rStartParams); // calls the R API R_SetParams,
then setup_Rmainloop


I gather that the following is hit in src/R-3.0.2/src/unix/system.c, in the
function Rf_initialize_R:

    if (!R_Interactive && Rp->SaveAction != SA_SAVE &&
	Rp->SaveAction != SA_NOSAVE)
	R_Suicide(_("you must specify '--save', '--no-save' or
'--vanilla'"));

I don't understand why it would complain if spawned by mpiexec and fine
otherwise.

I do not have a suitable debugging environment to step through a R with debug
symbols, and no stack trace is given as console output.
As an aside, the same code (barring platform specifics) works on Windows.

Thanks

On 21/11/2013 06:39, Jean-Michel.Perraud at csiro.au
wrote:
> I'd like someone familiar with the R options initialization to comment
on a difference of behavior within/without mpiexec
> I have a (.NET) application with embedded R that is proven to run in a
single process:
>
>      ./Sample1.exe
>
> on a Debian Linux with R 3.0.2
>
> Running the same code with mpiexec, it fails at the R engine
initialization:
>
>      mpiexec -n 1 ./Sample1.exe
>      Fatal error: you must specify '--save', '--no-save' or
'--vanilla'
>     
-------------------------------------------------------------------------
>
> The behavior is actually reproducible with the straight R
>      mpiexec -n 1 R
>      Fatal error: you must specify '--save', '--no-save' or
'--vanilla'
>     
-------------------------------------------------------------------------
> The following is working:
>      mpiexec -n 1 R --no-save
>
> However in my Sample1 application, I do set up R init options that should
be suitable AFAIK:
>
>              rEngine = REngine.CreateInstance("RDotNet");
>              StartupParameter rStartParams = new StartupParameter
>              {
>                  Quiet = true,
>                  SaveAction = StartupSaveAction.NoSave,
>                  Slave = false,
>                  Interactive = true,
>                  Verbose = false,
>                  LoadInitFile = true,
>                  LoadSiteFile = true,
>                  RestoreAction = StartupRestoreAction.NoRestore,
>                  NoRenviron = false
>              };
>              rEngine.Initialize(rStartParams); // calls the R API
R_SetParams, then setup_Rmainloop
>
>
> I gather that the following is hit in src/R-3.0.2/src/unix/system.c, in the
function Rf_initialize_R:
>
>      if (!R_Interactive && Rp->SaveAction != SA_SAVE &&
> 	Rp->SaveAction != SA_NOSAVE)
> 	R_Suicide(_("you must specify '--save', '--no-save'
or '--vanilla'"));
>
> I don't understand why it would complain if spawned by mpiexec and fine
otherwise.
Most likely because the way you are running R is considered to be batch 
use, and R_Interactive is false.  You've mixed up two scenarios here: 
one an embedded use where we don't have all the code, and mpiexec.  In 
the mpiexec case, it is likely that stdin is not a ptty.
> I do not have a suitable debugging environment to step through a R with
debug symbols, and no stack trace is given as console output.
> As an aside, the same code (barring platform specifics) works on Windows.
Deciding if Rterm is interactive is clearly done differently on an OS 
without pttys.


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

I don't have any real answers for you. Perhaps someone with more experience
will.

This may be an R.NET issue though. I'm suprised that from your comment, and
a very brief glance at R.NET's sourcecode,  it is calling setup_Rmainloop.
I've successfully embedded R in C programs and the entrypoint I always used
was Rf_initEmbeddedR. My understanding is that setup_Rmainloop is for the
non-embedded case (R running itself).

Perhaps I'm wrong and using setup_Rmainloop is supported in the embedded
case as well as Rf_initEmbeddedR. If not I can't offer any insight to why
it usually works anyway other than Dr. Ripleys suggestion about stdin and
mpiexec.

Sorry I can't be of more help.
~G


On Wed, Nov 20, 2013 at 10:39 PM, <Jean-Michel.Perraud@csiro.au> wrote:
> I'd like someone familiar with the R options initialization to comment
on
> a difference of behavior within/without mpiexec
>
> I have a (.NET) application with embedded R that is proven to run in a
> single process:
>
>     ./Sample1.exe
>
> on a Debian Linux with R 3.0.2
>
> Running the same code with mpiexec, it fails at the R engine
> initialization:
>
>     mpiexec -n 1 ./Sample1.exe
>     Fatal error: you must specify '--save', '--no-save' or
'--vanilla'
>
> -------------------------------------------------------------------------
>
> The behavior is actually reproducible with the straight R
>     mpiexec -n 1 R
>     Fatal error: you must specify '--save', '--no-save' or
'--vanilla'
>
> -------------------------------------------------------------------------
> The following is working:
>     mpiexec -n 1 R --no-save
>
> However in my Sample1 application, I do set up R init options that should
> be suitable AFAIK:
>
>             rEngine = REngine.CreateInstance("RDotNet");
>             StartupParameter rStartParams = new StartupParameter
>             {
>                 Quiet = true,
>                 SaveAction = StartupSaveAction.NoSave,
>                 Slave = false,
>                 Interactive = true,
>                 Verbose = false,
>                 LoadInitFile = true,
>                 LoadSiteFile = true,
>                 RestoreAction = StartupRestoreAction.NoRestore,
>                 NoRenviron = false
>             };
>             rEngine.Initialize(rStartParams); // calls the R API
> R_SetParams, then setup_Rmainloop
>
>
> I gather that the following is hit in src/R-3.0.2/src/unix/system.c, in
> the function Rf_initialize_R:
>
>     if (!R_Interactive && Rp->SaveAction != SA_SAVE &&
>         Rp->SaveAction != SA_NOSAVE)
>         R_Suicide(_("you must specify '--save',
'--no-save' or
> '--vanilla'"));
>
> I don't understand why it would complain if spawned by mpiexec and fine
> otherwise.
>
> I do not have a suitable debugging environment to step through a R with
> debug symbols, and no stack trace is given as console output.
> As an aside, the same code (barring platform specifics) works on Windows.
>
> Thanks
>
>
>
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis

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