rgrass7 and snow

"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 ?crit :


  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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