[R-sig-Geo] rgrass7 and snow

[Dr Didier G. Leibovici]

On 22/04/2016 16:21, Rainer M Krug wrote:
>
>
> Le vendredi 22 avril 2016, Dr Didier G. Leibovici 
> <didier.leibovici at nottingham.ac.uk 
> <mailto: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
Yes all the problem is there for each cluster to work on a separate 
GRASS_TEMP
( we have verified that it was running with I cl only!)
Can we generate randomly the location or mapset so they will not 
collapse onto the same?

DIdier
>
>
>     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
>
>
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>
>
> -- 
> 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 <mailto:Rainer at krugs.de>
>
> Skype:      RMkrug
>

-- 
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
Skype didierleibovici


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