Merge pull request #5 from rocanale/master

Updating package, compatible with Elemental

.travis.yml

@@ -13,7 +13,7 @@ before_install:
  - curl https://cmake.org/files/v3.3/cmake-3.3.2-Linux-x86_64.tar.gz | sudo tar -x -z --strip-components 1 -C /usr
  - git clone git://github.com/elemental/Elemental.git
  - cd Elemental
- - git checkout 8a1a42c
+ - git checkout v0.87.6
  - mkdir build && cd build
  - cmake .. -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=gcc-5 -DCMAKE_Fortran_COMPILER=gfortran-5 -DCMAKE_INSTALL_PREFIX=~/local/El;
  - make -j2 && sudo make install

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: RElem
 Type: Package
 Title: Distributed Parallel Linear Algebra Through Elemental (Libelemental.org)
-Version: 0.2.874
+Version: 0.2.876
 Date: 2016-11-25
 Depends: R (>= 3.1.0)
 Author: Rodrigo Canales
 Maintainer: Rodrigo Canales <rodrigo.canales@rwth-aachen.de>
-Description: Wrappers to use Elemental library (0.87.4), allowing distributed parallel computations using native R syntax.
+Description: Wrappers to use Elemental library (0.87.6), allowing distributed parallel computations using native R syntax.
 License: MIT | file LICENSE
 URL: https://github.com/HPAC/RElem
 Collate:

R/Operators.R

@@ -464,7 +464,7 @@ setMethod("t",
 setMethod("t",
           signature(x = "ElDistMatrix"),
           function (x){
-            y <- Matrix(x@datatype)
+            y <- DistMatrix(x@datatype)
             Transpose(x,y)
             y
           })

README.md

@@ -1,6 +1,6 @@
 #RElem
 
-[![Build Status](https://travis-ci.org/rocanale/RElem.svg?branch=master)](https://travis-ci.org/rocanale/RElem) using Elemental v0.87.6 (8a1a42c)
+[![Build Status](https://travis-ci.org/rocanale/RElem.svg?branch=master)](https://travis-ci.org/rocanale/RElem) using Elemental v0.87.6
 
 This R package links R and the dense linear algebra library
 [Elemental](http://www.libelemental.org), providing distributed parallel
@@ -25,12 +25,11 @@ package:
     * Matrix Factorizations
     * Spectral Decomposition
     * Solvers
+    * Optimization Models
 * Matrix Generators
 * LibFLAME-like
     * Partition
     * Merge
-    * Repartition (_Not yet active in El headers_)
-    * Slide Partition (_Not yet active in El headers_)
 * I/O routines
 
 
@@ -40,12 +39,31 @@ package:
 The installation of the RElem requires two steps:
 
 #### 1. Install Elemental
-- [Install Elemental](http://libelemental.org/documentation/dev/build.html) as a shared library
-- Ideally, Elemental is installed in one of the default paths `/usr/local`, `$HOME/local`, `$HOME/.local`
+- [Install Elemental latest release](https://github.com/elemental/Elemental/releases/tag/v0.87.6) 0.87.6
+    - Elemental requires a C/C++ compiler, a fortran compiler and an MPI distribution like mpich. 
+- Ideally, Elemental is installed in one of these paths `/usr/local`, `$HOME/local`, `$HOME/.local`
+
+
+##### Unix Installation example
+
+```
+mkdir build
+cd build
+cmake \
+    -D EL_DISABLE_SCALAPACK=ON \
+    -D CMAKE_INSTALL_PREFIX=$HOME/local \
+    -D EL_DISABLE_PARMETIS=ON \
+    ..
+make -j4
+make install
+```
+
+*If you installed Elemental in a non default path, please be sure that libEl.so can be loaded*:
+
+`export LD_LIBRARY_PATH=$HOME/local:$LD_LIBRARY_PATH`
 
 #### 2. Install RElem
-We have plans to make R-El available in R's package manager CRAN in the future.  So far, **a
-superuser** can install the interface from R as follows:
+We have plans to make R-El available in R's package manager CRAN in the future. Nevertheless it is possible to install it manually.
 
 A zip file from the package can be downloaded from our [releases](https://github.com/rocanale/RElem/releases) and then installed using the following command:
 
@@ -117,21 +135,17 @@ For distributed computations, R needs to be invoked by MPI as follows:
 
 `mpiexec -n 4 R --no-readline --slave --quiet --vanilla -f SimpleDist.R`
 
-Note: The openmpi library (or the one installed in the system) must be preloaded using the `LD_PRELOAD` environment variable:
-
-`export LD_PRELOAD=/usr/lib/libmpi.so:$LD_PRELOAD`
+### Simple Script
 
-### Source
-
-The following example invokes `GEMM` with distributed matrices
+The following example invokes a matrix multiplication `GEMM` using distributed matrices
 
 ```s
 # Load the library
 library(RElem)
 
 # Create the Matrices
-A <- DistMatrix(g)
-B <- DistMatrix(g)
+A <- DistMatrix()
+B <- DistMatrix()
 
 #Initialize the Matrices
 Uniform(A,6,4)
@@ -143,3 +157,35 @@ C <- A%*%B
 print(C)
 
 ```
+
+## Appendix: Full installation script using mac OS X
+
+This script assumes that the computer has gfortran and mpich from macports.
+
+```
+git clone git@github.com:elemental/Elemental.git
+git checkout  v0.87.6
+
+mkdir build
+cd build
+
+cmake \
+    -D CMAKE_BUILD_TYPE=Release \
+    -D CMAKE_INSTALL_PREFIX=${HOME}/local/El \
+    -D EL_DISABLE_PARMETIS=ON \
+    -D CMAKE_Fortran_COMPILER=gfortran-mp-5 \
+    -D MPI_C_COMPILER=mpicc-mpich-mp \
+    -D MPI_CXX_COMPILER=mpic++-mpich-mp \
+    -D MPI_FORTRAN_COMPILER=mpifort-mpich-mp \
+    -D MPI_F77_COMPILER=mpif77-mpich-mp \
+    -D EL_DISABLE_SCALAPACK=ON \
+    ..
+
+make -j4
+make install
+
+export LD_LIBRARY_PATH=${HOME}/local/El/lib:$LD_LIBRARY_PATH
+
+R CMD INSTALL RElem.tar.gz
+
+```

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for configRElem v0.01.085.
+# Generated by GNU Autoconf 2.69 for configRElem v0.2.876.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -576,8 +576,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='configRElem'
 PACKAGE_TARNAME='configrelem'
-PACKAGE_VERSION='v0.01.085'
-PACKAGE_STRING='configRElem v0.01.085'
+PACKAGE_VERSION='v0.2.876'
+PACKAGE_STRING='configRElem v0.2.876'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -603,7 +603,6 @@ infodir
 docdir
 oldincludedir
 includedir
-runstatedir
 localstatedir
 sharedstatedir
 sysconfdir
@@ -669,7 +668,6 @@ datadir='${datarootdir}'
 sysconfdir='${prefix}/etc'
 sharedstatedir='${prefix}/com'
 localstatedir='${prefix}/var'
-runstatedir='${localstatedir}/run'
 includedir='${prefix}/include'
 oldincludedir='/usr/include'
 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
@@ -922,15 +920,6 @@ do
   | -silent | --silent | --silen | --sile | --sil)
     silent=yes ;;
 
-  -runstatedir | --runstatedir | --runstatedi | --runstated \
-  | --runstate | --runstat | --runsta | --runst | --runs \
-  | --run | --ru | --r)
-    ac_prev=runstatedir ;;
-  -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
-  | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
-  | --run=* | --ru=* | --r=*)
-    runstatedir=$ac_optarg ;;
-
   -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
     ac_prev=sbindir ;;
   -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1068,7 +1057,7 @@ fi
 for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
 		datadir sysconfdir sharedstatedir localstatedir includedir \
 		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
-		libdir localedir mandir runstatedir
+		libdir localedir mandir
 do
   eval ac_val=\$$ac_var
   # Remove trailing slashes.
@@ -1181,7 +1170,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures configRElem v0.01.085 to adapt to many kinds of systems.
+\`configure' configures configRElem v0.2.876 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1221,7 +1210,6 @@ Fine tuning of the installation directories:
   --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
   --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
   --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
-  --runstatedir=DIR       modifiable per-process data [LOCALSTATEDIR/run]
   --libdir=DIR            object code libraries [EPREFIX/lib]
   --includedir=DIR        C header files [PREFIX/include]
   --oldincludedir=DIR     C header files for non-gcc [/usr/include]
@@ -1243,7 +1231,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of configRElem v0.01.085:";;
+     short | recursive ) echo "Configuration of configRElem v0.2.876:";;
    esac
   cat <<\_ACEOF
 
@@ -1316,7 +1304,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-configRElem configure v0.01.085
+configRElem configure v0.2.876
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1333,7 +1321,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by configRElem $as_me v0.01.085, which was
+It was created by configRElem $as_me v0.2.876, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -1699,7 +1687,7 @@ if test -n "${UsrPrefix}"; then
 else
   #Checking the common folders
   HIDLOC="/.local"
-  for pr in /usr/local /usr/local/El /usr/local/opt/Elemental /opt/El "$HOME/local" "$HOME/local/El" "$HOME$HIDLOC"; do
+  for pr in /usr/local /usr/local/El /usr/local/Elemental /usr/share /usr/local/share /opt/El "$HOME/local" "$HOME/local/El" "$HOME$HIDLOC" /usr/local/Cellar/elemental /usr/opt/Cellar/elemental; do
     if test -f "${pr}/conf/ElVars"; then
       EL_PREFIX="${pr}"
       echo "Found Elemental in ${pr}"
@@ -1709,7 +1697,7 @@ else
 fi
 
 if test ! -n "${EL_PREFIX}" ; then
-   as_fn_error $? "Elemental not found, please specify the prefix of its installation using the flag --with-ElPrefix=/THE/PREFIX" "$LINENO" 5
+   as_fn_error $? "Elemental not found, please specify the prefix of its installation using the flag --configure-args=--with-ElPrefix=/THE/PREFIX" "$LINENO" 5
 fi
 
 
@@ -2257,7 +2245,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by configRElem $as_me v0.01.085, which was
+This file was extended by configRElem $as_me v0.2.876, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2310,7 +2298,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-configRElem config.status v0.01.085
+configRElem config.status v0.2.876
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT(configRElem, v0.01.085)
+AC_INIT(configRElem, v0.2.876)
 AC_ARG_WITH(ElPrefix,
     AC_HELP_STRING(--with-ElPrefix=EL_PREFIX,
         The elemental prefix at the installation),
@@ -15,7 +15,7 @@ if test -n "${UsrPrefix}"; then
 else
   #Checking the common folders
   HIDLOC="/.local"
-  for pr in /usr/local /usr/local/El /usr/local/opt/Elemental /opt/El "$HOME/local" "$HOME/local/El" "$HOME$HIDLOC"; do
+  for pr in /usr/local /usr/local/El /usr/local/Elemental /usr/share /usr/local/share /opt/El "$HOME/local" "$HOME/local/El" "$HOME$HIDLOC" /usr/local/Cellar/elemental /usr/opt/Cellar/elemental; do
     if test -f "${pr}/conf/ElVars"; then
       EL_PREFIX="${pr}"
       echo "Found Elemental in ${pr}"
@@ -25,7 +25,7 @@ else
 fi
 
 if test ! -n "${EL_PREFIX}" ; then
-   AC_MSG_ERROR([Elemental not found, please specify the prefix of its installation using the flag --with-ElPrefix=/THE/PREFIX])
+   AC_MSG_ERROR([Elemental not found, please specify the prefix of its installation using the flag --configure-args=--with-ElPrefix=/THE/PREFIX])
 fi
 
 AC_SUBST(EL_PREFIX)

src/Makevars.in

@@ -1,7 +1,20 @@
 include @EL_PREFIX@/conf/ElVars
 
+#To check if ElVars has the right location
+
+ifneq (,$(wildcard $(EL_LIB)/libEl* ))
+	EL_LIBR=$(EL_LIB)
+else
+	ifneq (,$(wildcard $(EL_LIB)64/libEl* ))
+	  EL_LIBR=$(EL_LIB)64
+  else
+#Go back to the original
+  EL_LIBR=$(EL_LIB)
+  endif
+endif
+
 CC_FLAGS = -std=c99 -O3
-EL_PATH=-L$(EL_LIB) -L$(EL_LIB)/external/pmrrr
+EL_PATH=-L$(EL_LIBR) -L$(EL_LIBR)/external/pmrrr
 LINK_FLAGS = $(EL_LINK_FLAGS)
 
 PKG_CFLAGS = $(CC_FLAGS)  $(R_INC) $(ALL_MPI_FLAGS) $(ALL_MATH_INC)