Release 0.1.0

.gitattributes

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+* linguist-vendored
+*.R linguist-vendored=false

.gitmodules

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+[submodule "src"]
+	path = src
+	url = https://github.com/ecrc/exageostat.git

DESCRIPTION

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+Package: exageostat
+SystemRequirements: GNU make, libstarpu, libnlopt, libgsl, libstarpu-1.2, libchameleon, libchameleon_starpu, libmkl_intel_lp64, libmkl_sequential, libmkl_core, libpthread, libm
+Version: 0.1.0
+Date: 2017-11-14
+Title: R package demonstrates the R / C Language interface for ExaGeoStat
+Author: Sameh Abdulah <[email protected]>
+Maintainer: Sameh Abdulah <[email protected]>
+Depends: R (>= 2.0.1), RhpcBLASctl
+Description: ExaGeoStat-R is an R-wrapper for ExaGeoStat: a parallel
+             high performance unified framework for geostatistics on
+             manycore systems. Its abbreviation stands for Exascale
+             Geostatistics. The framework aims at optimizing the 
+             likelihood function for a given spatial data to provide
+             an efficient way to predict missing observations. The 
+	     framework targets many-core systems: clusters of CPUs
+             and GPUs.
+License: GPL (version 2 or later)
+Packaged: Tuesday Nov. 14 13:01:38 2017; sameh
+

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2017, King Abdullah University of Science and Technology
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NAMESPACE

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+useDynLib(exageostat)
+export(TestWrapper)
+export(exageostat_gen_zR)
+export(exageostat_likelihoodR)
+export(exageostat_initR)
+export(exageostat_finalizeR)
+

NEWS

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+2017-11-14 version 0.1.0
+* The first release of ExaGeoStat-R
+

R/exageostat_test_wrapper.R

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+ #
+ #
+ # Copyright (c) 2017, King Abdullah University of Science and Technology
+ # All rights reserved.
+ #
+ # ExaGeoStat-R is a software package provided by KAUST
+ #
+ #
+ #
+ # @file exageostat_test_wrapper.R
+ # ExaGeoStat R wrapper functions
+ #
+ # @version 0.1.0
+ #
+ # @author Sameh Abdulah
+ # @date 2017-11-14
+
+
+TestWrapper <- function()
+{
+	library("exageostat")                                   #Load ExaGeoStat-R lib.
+	theta1          = 1                                     #Initial variance.
+	theta2          = 0.1                                   #Initial smoothness.
+	theta3          = 0.5                                   #Initial range.
+	computation     = 0                                     #0 --> exact computation, 1--> LR approx. computation.
+	dmetric         = 0                                     #0 --> Euclidean distance, 1--> great circle distance.
+	n               = 1600                                  #n*n locations grid.
+	ncores          = 2                                     #Number of underlying CPUs.
+	gpus            = 0                                     #Number of underlying GPUs.
+	ts              = 320                                   #Tile_size:  changing it can improve the performance. No fixed value can be given.
+	p_grid          = 1                                     #More than 1 in the case of distributed systems
+	q_grid          = 1                                     #More than 1 in the case of distributed systems ( usually equals to p_grid)
+	clb             = vector(mode="numeric",length = 3)     #Optimization function lower bounds values.
+	cub             = vector(mode="numeric",length = 3)     #Optimization function upper bounds values.
+	theta_out       = vector(mode="numeric",length = 3)     #Parameter vector output.
+	globalveclen    = 3*n
+	vecs_out        = vector(mode="numeric",length = globalveclen)     #Z measurements of n locations
+	clb             = as.numeric(c("0.01", "0.01", "0.01"))
+	cub             = as.numeric(c("5.00", "5.00", "5.00"))
+	vecs_out[1:globalveclen]        = -1.99
+	theta_out[1:3]                  = -1.99
+	#Initiate exageostat instance
+	rexageostat_initR(ncores, gpus, ts)
+	#Generate Z observation vector
+	vecs_out        = rexageostat_gen_zR(n, ncores, gpus, ts, p_grid, q_grid, theta1, theta2, theta3, computation, dmetric, globalveclen)
+	#Estimate MLE parameters
+	theta_out       = rexageostat_likelihoodR(n, ncores, gpus, ts, p_grid, q_grid,  vecs_out[1:n],  vecs_out[n+1:(2*n)],  vecs_out[(2*n+1):(3*n)], clb, cub, computation, dmetric)
+	#finalize exageostat instance
+	rexageostat_finalizeR()
+	print("Back from exageostat_gen_z! hit key...")
+	browser()
+}
+
+exageostat_gen_zR <- function(n, ncores, gpus, ts, p_grid, q_grid, theta1, theta2, theta3, computation, dmetric, globalveclen)
+{
+	globalvec= vector (mode="numeric", length = globalveclen)
+	globalvec2 = .C("rexageostat_gen_z",
+			as.integer(n),
+                	as.integer(ncores),
+	                as.integer(gpus),
+        	        as.integer(ts),
+                	as.integer(p_grid),
+	                as.integer(q_grid),
+        	        as.numeric(theta1),
+			as.numeric(theta2),
+			as.numeric(theta3),
+        	        as.integer(computation),		
+                	as.integer(dmetric),
+	                as.integer(globalveclen),		
+			globalvec = numeric(globalveclen))$globalvec
+
+	globalvec[1:globalveclen] <- globalvec2[1:globalveclen]
+	print("back from exageostat_gen_z C function call. Hit key....")
+	return(globalvec)
+}
+
+
+exageostat_likelihoodR <- function(n, ncores, gpus, ts, p_grid, q_grid, x, y, z, clb, cub, computation, dmetric)
+{
+	theta_out2= .C("rexageostat_likelihood",
+	                as.integer(n),
+	                as.integer(ncores),
+	                as.integer(gpus),
+	                as.integer(ts),
+	                as.integer(p_grid),
+	                as.integer(q_grid),
+			as.numeric(x),
+			as.integer((n)),
+			as.numeric(y),
+			as.integer((n)),
+			as.numeric(z),
+	                as.integer((n))	,	
+	                as.numeric(clb),
+	                as.integer((3)),	
+			as.numeric(cub),
+	                as.integer((3)),
+			as.integer(computation),
+	                as.integer(dmetric),
+			theta_out=numeric(3))$theta_out		
+	theta_out[1:3] <- theta_out2[1:3]
+	print("back from exageostat_likelihood C function call. Hit key....")
+	return(theta_out)
+}
+
+exageostat_initR <- function(ncores, gpus, ts)
+{
+	#install.packages(repos="https://cran.r-project.org", "RhpcBLASctl")
+        library(RhpcBLASctl)
+	blas_get_num_procs()
+	blas_set_num_threads(1)
+	omp_set_num_threads(1)
+	.C("rexageostat_init",
+            as.integer(ncores),
+            as.integer(gpus),
+            as.integer(ts))
+	print("back from exageostat_init C function call. Hit key....")
+}
+
+exageostat_finalizeR <- function()
+{
+	.C("rexageostat_finalize")
+	print("back from exageostat_finalize C function call. Hit key....")
+}
+
+

README.md

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-# exageostat-rwrapper-dev
+ExaGeoStat-R
+============
+
+`ExaGeoStat-R` is an R-Wrapper for [ExaGeoStat framework]((https://github.com/ecrc/exageostat)), a parallel high performance unified framework for geostatistics on manycore systems.
+
+Getting Started
+===============
+
+### Installation
+
+#### Software dependencies
+1. [Portable Hardware Locality (hwloc)](https://www.open-mpi.org/projects/hwloc/).
+2. [NLopt](https://nlopt.readthedocs.io/en/latest/).
+3. [GNU Scientific Library (GSL)](https://www.gnu.org/software/gsl/doc/html/index.html).
+4. [StarPU](http://starpu.gforge.inria.fr/).
+5. [Chameleon](https://project.inria.fr/chameleon/).
+
+An easy installation of the above packages is available by using [build-deps.sh](https://github.com/ecrc/exageostatR/blob/master/build_deps.sh)
+
+
+#### Install latest ExaGeoStat-R version hosted on GitHub
+```r
+install.packages("devtools")
+library(devtools)
+install_git(url="https://github.com/ecrc/exageostatR")
+library(exageostat)
+```
+
+
+#### Get the latest ExaGeoStat-R release  hosted on GitHub
+
+1. Download exageostat_0.1.0.tar.gz from release
+2. Use R to install exageostat_0.1.0.tar.gz
+```r
+install.packages(repos=NULL, "exageostat_0.1.0.tar.gz")
+library(exageostat)
+```
+
+
+Features of ExaGeoStat-R
+========================
+Operations:
+
+1. Generate synthetic spatial datasets (i.e., locations & environmental measurements).
+2. Maximum likelihood evaluation using dense matrices.
+
+
+More information
+================
+
+A more detailed description of the underlying ExaGeoStat software package can be found. [here](https://github.com/ecrc/exageostat)
+
+R Example
+================
+```r
+library("exageostat")					#Load ExaGeoStat-R lib.
+theta1		= 1					#Initial variance.
+theta2 		= 0.1					#Initial smoothness.
+theta3 		= 0.5   				#Initial range.
+computation 	= 0					#0 --> exact computation, 1--> LR approx. computation.
+dmetric 	= 0					#0 --> Euclidean distance, 1--> great circle distance.
+n		= 1600         				#n*n locations grid.
+ncores          = 2                                     #Number of underlying CPUs.
+gpus		= 0    					#Number of underlying GPUs.
+ts		= 320					#Tile_size:  changing it can improve the performance. No fixed value can be given.
+p_grid		= 1					#More than 1 in the case of distributed systems 
+q_grid		= 1					#More than 1 in the case of distributed systems ( usually equals to p_grid)
+clb 		= vector(mode="numeric",length = 3)  	#Optimization function lower bounds values.
+cub		= vector(mode="numeric",length = 3)	#Optimization function upper bounds values.
+theta_out 	= vector(mode="numeric",length = 3)   	#Parameter vector output.
+globalveclen 	= 3*n
+vecs_out 	= vector(mode="numeric",length = globalveclen)     #Z measurements of n locations
+clb		= as.numeric(c("0.01", "0.01", "0.01"))
+cub		= as.numeric(c("5.00", "5.00", "5.00"))
+vecs_out[1:globalveclen]	= -1.99
+theta_out[1:3]			= -1.99
+#Initiate ExaGeoStat instance
+exageostat_initR(ncores, gpus, ts)
+#Generate Z observation vector
+vecs_out	= exageostat_gen_zR(n, ncores, gpus, ts, p_grid, q_grid, theta1, theta2, theta3, computation, dmetric, globalveclen)
+#Estimate MLE parameters
+theta_out	= exageostat_likelihoodR(n, ncores, gpus, ts, p_grid, q_grid,  vecs_out[1:n],  vecs_out[n+1:(2*n)],  vecs_out[(2*n+1):(3*n)], clb, cub, computation, dmetric)
+#Finalize ExaGeoStat instance
+exageostat_finalizeR()
+```