v 1.5.0-1

ChangeLog

@@ -2,6 +2,14 @@
 magma R package changes
 --------------------------------------------------------------------------------
 
+2014-10-06  Serguei Sokol <sokol@insa-toulouse.fr>
+
+   * magma_1.5.0-1.tar.gz: Package upgrade release.
+
+   * src/*.c:  Updated to magma 1.5.0 and cublas 6.0 (4.0+ is required) libraries
+
+   * fixed few bugs in magQRSolve()
+
 2013-04-02  Brian Smith <brian-j-smith@uiowa.edu>
 
    * magma_1.3.0-1.tar.gz: Package upgrade release.

DESCRIPTION

@@ -1,19 +1,24 @@
 Package: magma
 Title: Matrix Algebra on GPU and Multicore Architectures
-Version: 1.3.0-2
-Date: 2013-04-03
-Author: Brian J Smith <brian-j-smith@uiowa.edu>
-Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
+Version: 1.5.0-1
+Date: 2014-10-07
+Authors@R: c(person("Brian", "Smith", middle="J.", role = c("aut", "cre"),
+		email = "brian-j-smith@uiowa.edu"),
+	person("Serguei", "Sokol", role = c("com", "ctb"),
+		email="sokol@insa-toulouse.fr"))
 Depends: R (>= 2.11.0), methods
-SystemRequirements: MAGMA shared libraries (== release 1.3.0), LAPACK shared
-   library, NVIDIA CUDA Toolkit (>= release 4.0)
-Description: Magma matrix classes and methods for parallel processing of matrix
-   algebra operations.  Operations are performed with algorithms developed by
-   the MAGMA research project.  MAGMA aims to achieve the fastest possible
-   linear algebra libraries on hybrid multicore CPU and GPU architectures by
-   exploiting their massive parallelism and minimizing communication latencies.
+SystemRequirements: MAGMA software (== release 1.5.0), LAPACK
+        shared library, NVIDIA CUDA Toolkit (>= release 4.0)
+Description: Magma matrix classes and methods for parallel processing
+        of matrix algebra operations.  Operations are performed with
+        algorithms developed by the MAGMA research project.  MAGMA aims
+        to achieve the fastest possible linear algebra libraries on
+        hybrid multicore CPU and GPU architectures by exploiting their
+        massive parallelism and minimizing communication latencies.
 License: GPL-3
 URL: http://icl.cs.utk.edu/magma
 OS_type: unix
-
-
+Packaged: 
+NeedsCompilation: yes
+Repository: CRAN
+Date/Publication: 

INSTALL

@@ -1,8 +1,10 @@
 --------------------------------------------------------------------------------
 --------------------------------------------------------------------------------
-magma R Package Version 1.3.0
-Installation and Release Notes (4/2/2013)
+magma R Package Version 1.5.0
+Installation and Release Notes (2014-10-07)
+Package Author: Brian J. Smith <brian-j-smith@uiowa.edu>
 Package Maintainer: Brian J. Smith <brian-j-smith@uiowa.edu>
+Package Contributor: Serguei Sokol <sokol@insa-toulouse.fr>
 --------------------------------------------------------------------------------
 --------------------------------------------------------------------------------
 
@@ -60,14 +62,14 @@ I. (b) Hardware requirements
 I. (c) Supported operating systems
 --------------------------------------------------------------------------------
 
-* Development and testing of the package is performed on 64-bit Ubuntu Linux
-  10.04 with.  Other 64-bit Linux distributions should work as well.
-  Development is conducted with release 4.3 of the GCC tools; release 4.4 is
-  not supported and may cause errors.
+* Development and testing of the package is performed on 64-bit Mageia Linux
+  4.0.  Other 64-bit Linux distributions should work as well.
+  Development is conducted with release 4.8.2 of the GCC tools and 6.0
+  of the cuda tools.
 
 * At this time, the package has not been tried on OS X, although input from any
-  attempts to do so are welcome.  Windows is not supported currently due to a
-  lack of shared MAGMA libraries for that platform.
+  attempts to do so are welcome. Windows should be supported too as the
+  library magma is reported to copile on this platform.
 
 
 --------------------------------------------------------------------------------
@@ -137,11 +139,7 @@ Next, the MAGMA software (http://icl.cs.utk.edu/magma) must be installed.  To do
 so,
 
 * Extract the source code to a local directory, and follow the instructions
-  supplied with the code to make shared libraries 'libmagmablas.so' and
-  'libmagma.so'.  Additional help on making the shared magma libraries can be
-  found at http://www.hiplar.org/hiplar-M-installation.html#MAGMA.  After making
-  the shared libraries, refer to the previous section for instructions on
-  installing the libraries.
+  supplied with the code to make shared library 'libmagma.so'.
 
 
 --------------------------------------------------------------------------------
@@ -165,7 +163,7 @@ where <option> are optional configuration arguments that can be supplied to
 change default files and locations, and include
 
   --with-r-home=DIR       full path to R installation []
-  --with-magma-lib=DIR    full path to MAGMA shared libraries []
+  --with-magma-home=DIR   full path to MAGMA installation directory []
   --with-lapack=LIBS      LAPACK shared library [-llapack]
   --with-cuda-home=DIR    full path to CUDA installation [/usr/local/cuda]
 
@@ -182,34 +180,32 @@ the particular LAPACK implementation being used.
 
 Example:
 
-The following illustrate installation of magma package release 0.2.2-1 on a
-system in which CUDA is installed in '/opt/cuda', MAGMA shared libraries in
-'/opt/magma/lib', and with a ldconfig-registered LAPACK library named
-'liblapack.so' (the default for --with-lapack):
+The following illustrate installation of magma package release 1.5.0-1 on a
+system in which CUDA is installed in '/usr/local/cuda' (default), MAGMA home directory in
+'/usr/local/src/magma-1.5.0', and LAPACK library compiled by ATLAS project and named
+/usr/local/atlas/lib64/libsatlas.so
 
   Terminal command prompt
   -----------------------
-  R CMD INSTALL \
-    --configure-args="
-       --with-cuda-home=/opt/cuda \
-       --with-magma-lib=/opt/magma/lib" \
-    magma_0.2.2-1.tar.gz
+  R CMD INSTALL --configure-args="\
+       --with-lapack=/usr/local/atlas/lib64/libsatlas.so \
+       --with-magma-home=/usr/local/src/magma-1.5.0 \
+       --with-r-home=/usr/local/src/R-3.1.1" \
+    magma_1.5.0-1.tar.gz
 
   R command prompt
   ----------------
   install.packages("magma",
-    configure.args = "--with-cuda-home=/opt/cuda
-      --with-magma-lib=/opt/magma/lib"
+    configure.args = "--with-lapack=/usr/local/atlas/lib64/libsatlas.so \
+       --with-magma-home=/usr/local/src/magma-1.5.0 \
+       --with-r-home=/usr/local/src/R-3.1.1"
   )
 
 
 --------------------------------------------------------------------------------
 III. Known Issues
 --------------------------------------------------------------------------------
 
-* Performance (speed) of the QR solver may be suboptimal due to workarounds for
-  a bug in version 1.3.0 of the magma_dgeqrs_gpu routine.
-
 
 --------------------------------------------------------------------------------
 IV. Troubleshooting
@@ -248,11 +244,11 @@ cannot find -llapack
 - If an alternative, installed LAPACK library is desired, then specify it using
   the configuration option '--with-lapack'.  See Section II(d).
 
-cannot find -lmagmablas or -lmagma
-- Check that the shared MAGMA libraries 'libmagmablas.so' and 'libmagma.so' are
+cannot find -lmagma
+- Check that the shared MAGMA sources are
   installed on your system.  Install them, if not.  Refer to Section II(c).
 - If they are installed, try supplying their directory path using the
-  configuration option '--with-magma-lib'.  See Section II(d).
+  configuration option '--with-magma-home'.  See Section II(d).
 
 
 R Run-time Errors

MD5

@@ -0,0 +1,67 @@
+8f0e2cd40e05189ec81232da84bd6e1a *COPYING
+73ab637c95c8ac53586ad63383f31cdd *ChangeLog
+41354a359a950d8b01fd7015da692c9c *DESCRIPTION
+32407b0000dca1262d5ae79eb6b2efe3 *INSTALL
+2280c65898c35e3cc4406de62d5591cc *NAMESPACE
+7ae7c3651a63677b5d19f0f79b5c2ac4 *R/AllGenerics.r
+0fd7bd1e34a61517905b0ac7648edadb *R/Classes.r
+83db8b129155879edd5394abe0c5dbcf *R/magAriths.r
+26c0a2607d6070cf27c18dd537c87e36 *R/magFactors.r
+b3542f41432a2b897de3292401665399 *R/magSolvers.r
+1d81b96b1ee67a180921872426beaafd *R/magUtils.r
+148260b02ac4fb6f5282dac388f04df5 *cleanup
+3dec06adf97f1edf973b0172bc32db86 *configure
+378499169b30549fea419e41b0a90fb5 *configure.ac
+dc328f38f8241e9b06baa73dc0a4cffc *inst/CITATION
+653f8fb438453be3e2abf132cf2d3db3 *man/backsolve.Rd
+62299a88fde6682670012392fc09cba9 *man/gpu.Rd
+5d5d438c4b47d8e5362af1474e4b0ad4 *man/lu.Rd
+2ab45972f6f7a5021dd6f7c4d1cd9fbf *man/magma-class.Rd
+fa1c83d80ce326f1e03fe1762dbf8650 *man/magma.Rd
+522aa9e97a32ce0c110aa075496b2fe5 *man/magmaLU-class.Rd
+e56bf7401e61d779303af3354f85054a *man/magmaQR-class.Rd
+9d9736f21d2a4ad3616165e3ad08a9f0 *src/Makefile.in
+7d5fb6df5d668708ae0adc3063073920 *src/include/cblas.h
+b7a6db7b7113f0fada181c6551ed7628 *src/include/gnu/stubs-32.h
+583f7b4ad3da81a6abd04eb0bedda2da *src/include/magma.h
+634e9149c1a9a561e45d8a1bbe4899e5 *src/include/magma_bulge.h
+3acd63edfe6c7b07dd2e7f0f63ea3f78 *src/include/magma_c.h
+b0a28f624ee0a44c93d54cc60df8f405 *src/include/magma_cbulge.h
+77c9ffe11af54fbb8cedbb1cd7b50a94 *src/include/magma_cbulgeinc.h
+5e03b80ca7395d39c9d341d2c4d8ab7e *src/include/magma_clapack.h
+926bbe7507c0d675c59fbf7acc855c14 *src/include/magma_d.h
+f58ec1510fa2fc29a915813b2ab885c2 *src/include/magma_dbulge.h
+55a551bb76ec432bd1a5f190701ba898 *src/include/magma_dbulgeinc.h
+4196ba980162736f10641930cf8ddca2 *src/include/magma_dlapack.h
+ed7021241404fb0fe6df2b3d99cddc86 *src/include/magma_ds.h
+925fd142dad8503fd1ec4d36c655208d *src/include/magma_lapack.h
+d587d1f3cb23db4c72dbd0a9e7307a93 *src/include/magma_s.h
+3224f475fc75a0248030ce6993ebaf20 *src/include/magma_sbulge.h
+d915a843903b8d713d46b4966cd76a95 *src/include/magma_sbulgeinc.h
+3d5560d8ee310d7328a2b9ab3014d6d6 *src/include/magma_slapack.h
+65b1d335a4f22e641ab44dc6184f7322 *src/include/magma_z.h
+07b558b924b08b26568e5685179420ed *src/include/magma_zbulge.h
+a1b4f0be8c8257ef66e53c38b4b98685 *src/include/magma_zbulgeinc.h
+8128878591d7e4058ff7818b5817e527 *src/include/magma_zc.h
+47c2b0df91b0e7e49c06f52e21f4d81f *src/include/magma_zlapack.h
+7fc5789de32e359e8711b0b0dd9b6b12 *src/include/magmablas.h
+35b8347b6671eb5ee9a31cfba958e4c7 *src/include/magmablas_c.h
+dfda4612b57e30da40515d43385ab51b *src/include/magmablas_d.h
+f9ac54a3d30ef1265bf38b5bde74e7ab *src/include/magmablas_ds.h
+97b832fef3ba6f487ab928965a120c55 *src/include/magmablas_s.h
+ada11fe61165197b33ecd2a110baca08 *src/include/magmablas_z.h
+456c856a727c5403d14b6b3ec6f564b3 *src/include/magmablas_zc.h
+94eb0f34cf187bcebab8f7a92887bf2e *src/magAriths.c
+579bdb18c98658bd8ec131dc9e88b0e8 *src/magAriths.h
+1a2287e375f765e59db9643a9a0f7071 *src/magFactors.c
+5971e4b06c2ad948878cca54324793c7 *src/magFactors.h
+1133c23184c3bad1701e7d19c4465dc5 *src/magSolvers.c
+47d396d5bdd3353ae0f7bc847bc3a980 *src/magSolvers.h
+4b6b4b4be94df1a3c1acb0c0fe828e0e *src/magUtils.c
+02a2617f6d7a1144a7b80da991361956 *src/magUtils.h
+eb1af5b1366c148007a2aada94f6f905 *tests/testing.r
+cc4680349521e99e797af60e980642c6 *tools/config.guess
+6adca7f3405b57aeecc1df1704f27ba1 *tools/config.sub
+5cc51dc6eb45a90231a4e31efbc3f220 *tools/install-sh
+b65c3f66a47925985fbf5ffecb22c48c *tools/mdate-sh
+c7645c248f924f07869059b76300fea9 *tools/missing

NAMESPACE

@@ -1,31 +1,30 @@
-useDynLib(magma)
-
-export(
-   "forwardsolve",
-   "magma"
-)
-
-exportClasses(
-   "magma",
-   "magmaLU",
-   "magmaQR"
-)
-
-exportMethods(
-   "Arith",
-   "%*%",
-
-   "backsolve",
-   "chol",
-   "chol2inv",
-   "crossprod",
-   "gpu",
-   "gpu<-",
-   "lu",
-   "qr",
-   "show",
-   "solve",
-   "tcrossprod"
-)
-
-
+useDynLib(magma)
+
+export(
+   "forwardsolve",
+   "magma"
+)
+
+exportClasses(
+   "magma",
+   "magmaLU",
+   "magmaQR"
+)
+
+exportMethods(
+   "Arith",
+   "%*%",
+
+   "backsolve",
+   "chol",
+   "chol2inv",
+   "crossprod",
+   "gpu",
+   "gpu<-",
+   "lu",
+   "qr",
+   "show",
+   "solve",
+   "tcrossprod"
+)
+

R/magAriths.r

@@ -50,26 +50,28 @@ setMethod("Arith", signature(e1 = "numeric", e2 = "magma"),
 #################### Multiplication Operators ####################
 
 setMethod("%*%", signature(x = "magma", y = "magma"),
-   function(x, y) .Call("magMultmm", x, FALSE, y, FALSE)
+   function(x, y) { .Call("magMultmm", x, FALSE, y, FALSE) }
 )
 
 setMethod("%*%", signature(x = "magma", y = "matrix"),
-   function(x, y) .Call("magMultmm", x, FALSE, y, FALSE)
+   function(x, y) { .Call("magMultmm", x, FALSE, y, FALSE) }
 )
 
 setMethod("%*%", signature(x = "magma", y = "numeric"),
    function(x, y) {
+      #cat("mmn\n")
       if(ncol(x) == 1) .Call("magMultmm", x, FALSE, as.matrix(y), TRUE)
       else .Call("magMultmv", x, FALSE, y, TRUE)
    }
 )
 
 setMethod("%*%", signature(x = "matrix", y = "magma"),
-   function(x, y) .Call("magMultmm", x, FALSE, y, FALSE)
+   function(x, y) { .Call("magMultmm", x, FALSE, y, FALSE) }
 )
 
 setMethod("%*%", signature(x = "numeric", y = "magma"),
    function(x, y) {
+      #cat("nmm\n"); 
       if(nrow(y) == 1) .Call("magMultmm", as.matrix(x), FALSE, y, FALSE)
       else .Call("magMultmv", y, FALSE, x, FALSE)
    }
@@ -131,4 +133,3 @@ setMethod("tcrossprod", signature(x = "numeric", y = "magma"),
       else .Call("magMultmv", y, TRUE, x, FALSE)
    }
 )
-

R/magSolvers.r

@@ -56,12 +56,12 @@ setMethod("solve", signature(a = "magmaQR", b = "missing"),
       n <- nrow(a$qr)
       if(n != ncol(a$qr))
          stop("only square matrices can be inverted in 'solve'", call.=FALSE)
-      callGeneric(a, diag(n))
+      .Call("magQRSolve", a, diag(n))
    }
 )
 
 setMethod("solve", signature(a = "magmaQR", b = "numeric"),
-   function(a, b) as.numeric(callGeneric(a, as.matrix(b)))
+   function(a, b) as.numeric(.Call("magQRSolve", a, as.matrix(b)))
 )
 
 
@@ -92,6 +92,7 @@ setMethod("solve", signature(a = "matrix", b = "magma"),
 
 setMethod("backsolve", signature(r = "magma", x = "magma"),
    function(r, x, k, upper.tri, transpose) {
+      #cat("utri=", upper.tri, "trans=", transpose, "\n", sep="")
       .Call("magTriSolve", r, x, k, upper.tri, transpose)
    }
 )
@@ -115,4 +116,3 @@ forwardsolve <- function(l, x, k = ncol(l), upper.tri=FALSE, transpose=FALSE)
 {
    backsolve(l, x, k, upper.tri, transpose)
 }
-

R/magUtils.r

@@ -29,6 +29,3 @@
 .onUnload <- function(libname) {
    .C("magUnload", PACKAGE="magma")
 }
-
-
-

cleanup

@@ -5,13 +5,11 @@
 #
 echo "Cleaning up after installing the magma package"
 
-for f in config.log config.status config.cache ; do
+for f in config.log config.status config.cache *.bck */*.bck; do
   if test -w $f ; then
     rm -f $f
   fi
 done
 
 cd src
-make clean
-rm -f Makefile
-
+if test -e Makefile; then make clean; rm -f Makefile; fi