[Rd] Running R embedded in an mpiexec spawned process - Fatal error: you must specify '--save', '--no-save' or '--vanilla'
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Nov 21 09:58:28 CET 2013
You can test my guess by
mpiexec -n 1 R --interactive
Works for me ....
On 21/11/2013 07:17, Prof Brian Ripley wrote:
> 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
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