[R-sig-Geo] rgrass7 and snow

[Rainer M Krug]

Le vendredi 22 avril 2016, Dr Didier G. Leibovici <
didier.leibovici at nottingham.ac.uk> a écrit :

> Hi,
>
> we are trying to use 'grass' in parallel programming with 'snow'
>
> The code does multiple simulations of a r.viewshed resampling the points
> generating the viewshed.
> (I guess the other solution would be to have an equivalent of r.viewshed
> in an R library or script) ...
> I think the problems are to do with the gisDbase ...
>
> Testing with 2 clusters we start with:
>  >  clusterCall(cl,initGRASS,"/usr/lib/grass70",home=getwd(),
> gisDbase="GRASS_TEMP", override=TRUE )
> [[1]]
> gisdbase    GRASS_TEMP
> location    file5edb6bf06d70
> mapset      file5edb4b0cda81
> rows        1
> columns     1
> north       1
> south       0
> west        0
> east        1
> nsres       1
> ewres       1
> projection  NA
>
> [[2]]
> gisdbase    GRASS_TEMP
> location    file5edb6bf06d70
> mapset      file5edb4b0cda81
>
> then read a DEM
> clusterCall(cl,execGRASS,"r.in.gdal", flags="o",
> parameters=list(input=baseDemFilename, output="DEM"))
>    clusterCall(cl,execGRASS, "g.region", parameters=list(raster="DEM"))
>
> and then loop on the sampled points ... involving
>   execGRASS("r.viewshed", parameters = list(input = "DEM", output =
> "cumulativeViewshed", max_distance=maxDistance, coordinates =
> as.integer(coords[i,])), flags = c("overwrite" , "b","quiet"))
>
>   and cumulating the viewshed (reading the ouput using
> readRAST("cumulativeViewshed")), all this (loop over the points)within a
> function simul() called
> by a
>   parSapply(cl,1:nDsimul,simul)
>
>
> Here is the error
> Error in checkForRemoteErrors(val) :
>    2 nodes produced errors; first error: no such file:
>
> GRASS_TEMP/file5edb6bf06d70/file5edb4b0cda81/.tmp/geoprocessing/cumulativeViewshed
> Calls: parSapply ... clusterApply -> staticClusterApply ->
> checkForRemoteErrors
>
> any idea?


The problem is likely that you are working in parallel in the same map set.
I would suggest to use a separate Mauser for each parallel task to write
to, read from a different map set which no parallel task is writing to, and
finally, after all threads are finished, you can collect the results from
each thread in one map set and delete the temporary map sets.

Cheers,

Rainer

>
> thanks,
>
> DIdier
>
> --
> Dr Didier G. Leibovici
>     d-d'ye    ley-bow-v-c
> Senior Research Fellow
> Geocomputational Modelling & Geospatial Statistics
> Nottingham Geospatial Institute
> University of Nottingham, UK
> +44 (0)115 84 13924
> http://www.nottingham.ac.uk/ngi/people/didier.leibovici
> Google+ didier.leibovici at gmail.com <javascript:;>
> Skype didierleibovici
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo at r-project.org <javascript:;>
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax (F):       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug

	[[alternative HTML version deleted]]