[R-sig-Geo] rgrass7 and snow

[Dr Didier G. Leibovici]

can you paste the call to create n mapsets. thanks


On 22/04/2016 17:37, Rainer M Krug wrote:
> "Dr Didier G. Leibovici" <didier.leibovici at nottingham.ac.uk> writes:
>
>> 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> 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?
> I used a setup for parallel processing (simulating spread under
> different scenarios), where I had
>
> 1) one locaction in which everything happened, which contained:
> 2) one mapset which was read-only for each parallel task
> 3) one mapset for each task in which the results were written; this was
> a folder, which was created for each parallel task
> 4) one mapset into which the individual simulation tasks were analysed into.
>
> So finally, I had a mapset for each simulation, and one in which the
> analysis was.
>
> So yes, why shouldn't you be able to create a mapset per task? You can
> do it during the initialization by using GRASS.
>
> Hope this helps,
>
> Rainer
>
>
>
>> 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
>>   Skype didierleibovici
>>
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>>
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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
>>
>>   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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