[Rd] Running R embedded in an mpiexec spawned process - Fatal error: you must specify '--save', '--no-save' or '--vanilla'
Jean-Michel.Perraud at csiro.au
Jean-Michel.Perraud at csiro.au
Thu Nov 21 07:39:34 CET 2013
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
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