Merge pull request #27 from snoweye/master

0.2-3 on CRAN

.Rbuildignore

@@ -0,0 +1 @@
+^\.travis\.yml$

.gitignore

@@ -5,6 +5,9 @@
 *.co
 *.oo
 
+*~
+*.swp
+
 src/Makeconf
 src/Makevars
 src/SLmake.inc

.travis.yml

@@ -0,0 +1,31 @@
+language: r
+
+r:
+  # - devel
+  - release
+
+os:
+  - linux
+
+before_install:
+  - sudo apt-get update -q
+  - sudo apt-get install -y -q libopenmpi-dev openmpi-bin
+  - LD_PRELOAD=/usr/lib/openmpi/lib/libmpi.so
+  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
+  - chmod 755 ./travis-tool.sh
+  - ./travis-tool.sh bootstrap
+  - ./travis-tool.sh install_github snoweye/pbdMPI
+
+r_packages:
+  - rlecuyer
+
+install:
+  - ./travis-tool.sh install_deps
+
+sudo: required
+dist: trusty
+
+notifications:
+  email:
+    on_success: never
+    on_failure: never

ChangeLog

@@ -1,3 +1,7 @@
+2018-01-03: Ver. 0.2-3
+  * Fix a few warnings from CRAN R CMD check (char truncations).
+  * Move SAFE_FFLAGS inside ScaLapack.
+
 2016-09-24: Ver. 0.2-1
   * Fix "-w" problem.
   * Fix BLACS problems.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pbdSLAP
 Version: 0.2-3
-Date: 2017-04-22
+Date: 2018-01-03
 Title: Programming with Big Data -- Scalable Linear Algebra Packages
 Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
         "[email protected]"), person("Drew", "Schmidt", role = "aut"),

README.md

@@ -2,6 +2,8 @@
 
 * **Version:** 0.2-1
 * **License:** [![License](http://img.shields.io/badge/license-MPL%202-orange.svg?style=flat)](https://www.mozilla.org/MPL/2.0/)
+* **Download:** [![Download](http://cranlogs.r-pkg.org/badges/pbdSLAP)](https://cran.r-project.org/package=pbdSLAP)
+* **Status:** [![Build Status](https://travis-ci.org/snoweye/pbdSLAP.png)](https://travis-ci.org/snoweye/pbdSLAP)
 * **Author:** See section below.
 
 

src/Makevars.in

@@ -25,9 +25,10 @@ MkInclude = ${R_HOME}/etc${R_ARCH}/Makeconf
 ### Setup R package flags and substitute by configure for ${MPI_...}.
 PKG_CPPFLAGS = $(SPMD_CPPFLAGS)
 PKG_CFLAGS = 
-PKG_FFLAGS = $(SAFE_FFLAGS)
+PKG_FFLAGS = 
 ### Order is matter.
 PKG_LIBS = $(EXT_LDFLAGS) $(FLIBS) $(SPMD_LDFLAGS)
+SLAP_FFLAGS = $(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FFLAGS)
 
 ### Setup R source code and objects.
 R_OBJS = slap_blacs.o zzz.o
@@ -57,10 +58,14 @@ Makeconf:
 	echo "PKG_CFLAGS = $(PKG_CFLAGS)" >> $(USER_CONF)
 	echo "PKG_FFLAGS = $(PKG_FFLAGS)" >> $(USER_CONF)
 	echo "PKG_LIBS = $(PKG_LIBS)" >> $(USER_CONF)
+	echo "SLAP_FFLAGS = $(SLAP_FFLAGS)" >> $(USER_CONF)
 	echo "R_SLAP = lib${R_ARCH}/$(R_SLAP)" >> $(USER_CONF)
 
 $(SHLIB): $(OBJECTS)
 
+slap_blacs.o: slap_blacs.f
+	$(F77) $(SLAP_FFLAGS) -c -o slap_blacs.o slap_blacs.f
+
 ### Do not delete this coming from "../configure.in".
 userLibrary: $(R_SLAP)
 

src/Makevars.win

@@ -18,6 +18,7 @@ PKG_CFLAGS =
 PKG_FFLAGS =
 ### Order is matter.
 PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) "$(MPI_LIB)"
+SLAP_FFLAGS = $(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FFLAGS)
 
 ### Setup R source code and objects.
 R_SRCS_C = $(wildcard *.c)
@@ -42,10 +43,14 @@ Makeconf:
 	$(ECHO) 'PKG_CFLAGS = $(PKG_CFLAGS)' >> $(USER_CONF)
 	$(ECHO) 'PKG_FFLAGS = $(PKG_FFLAGS)' >> $(USER_CONF)
 	$(ECHO) 'PKG_LIBS = $(PKG_LIBS)' >> $(USER_CONF)
+	$(ECHO) 'SLAP_FFLAGS = $(SLAP_FFLAGS)' >> $(USER_CONF)
 	$(ECHO) 'R_SLAP = lib${R_ARCH}/$(R_SLAP)' >> $(USER_CONF)
 
 $(SHLIB): $(OBJECTS)
 
+slap_blacs.o: slap_blacs.f
+	$(F77) $(SLAP_FFLAGS) -c -o slap_blacs.o slap_blacs.f
+
 userLibrary: $(SHLIB) $(R_SLAP)
 
 $(R_OBJS): $(R_SLAP)

src/SLmake.inc.org

@@ -1,5 +1,5 @@
 CCFLAGS = $(ALL_CPPFLAGS) $(ALL_CFLAGS) -O3
-FCFLAGS = $(ALL_CPPFLAGS) $(ALL_FFLAGS) -O3
+FCFLAGS = $(ALL_CPPFLAGS) $(ALL_FFLAGS) $(SAFE_FFLAGS) -O3
 ARCH = $(AR)
 ARCHFLAGS = cr
 # ARCHFLAGS = -rucs

src/SLmake.inc.win

@@ -1,5 +1,5 @@
 CCFLAGS = $(ALL_CPPFLAGS) $(ALL_CFLAGS) -O3
-FCFLAGS = $(ALL_CPPFLAGS) $(ALL_FFLAGS) -O3
+FCFLAGS = $(ALL_CPPFLAGS) $(ALL_FFLAGS) $(SAFE_FFLAGS) -O3
 ARCH = $(AR)
 ARCHFLAGS = cr
 # ARCHFLAGS = -rucs

src/ScaLAPACK/pdlaqr5.f

@@ -629,13 +629,17 @@ SUBROUTINE PDLAQR5( WANTT, WANTZ, KACC22, N, KTOP, KBOT, NSHFTS,
 *                 possibly be exploited or not.
 *
                   IF( LKTOP.EQ.KTOP .AND. LKBOT.EQ.KBOT ) THEN
-                     JOB = 'All steps'
+                     !JOB = 'All steps'
+                     JOB = 'A'
                   ELSEIF( LKTOP.EQ.KTOP ) THEN
-                     JOB = 'Introduce and chase'
+                     !JOB = 'Introduce and chase'
+                     JOB = 'I'
                   ELSEIF( LKBOT.EQ.KBOT ) THEN
-                     JOB = 'Off-chase bulges'
+                     !JOB = 'Off-chase bulges'
+                     JOB = 'O'
                   ELSE
-                     JOB = 'Chase bulges'
+                     !JOB = 'Chase bulges'
+                     JOB = 'C'
                   END IF
                END IF
 *
@@ -1224,16 +1228,20 @@ SUBROUTINE PDLAQR5( WANTT, WANTZ, KACC22, N, KTOP, KBOT, NSHFTS,
      $                 (MYROW.EQ.RSRC4 .AND. MYCOL.EQ.CSRC4) ) THEN
                      IF( LKTOP.EQ.KTOP .AND. LKBOT.EQ.KBOT .AND.
      $                    (DIM1.LE.LCHAIN .OR. DIM1.LE.NTINY ) ) THEN
-                        JOB = 'All steps'
+                        !JOB = 'All steps'
+                        JOB = 'A'
                         ICHOFF = 1
                      ELSEIF( LKTOP.EQ.KTOP .AND.
      $                    ( DIM1.LE.LCHAIN .OR. DIM1.LE.NTINY ) ) THEN
-                        JOB = 'Introduce and chase'
+                        !JOB = 'Introduce and chase'
+                        JOB = 'I'
                      ELSEIF( LKBOT.EQ.KBOT ) THEN
-                        JOB = 'Off-chase bulges'
+                        !JOB = 'Off-chase bulges'
+                        JOB = 'O'
                         ICHOFF = 1
                      ELSE
-                        JOB = 'Chase bulges'
+                        !JOB = 'Chase bulges'
+                        JOB = 'C'
                      END IF
                      KU = LNWIN - KDU + 1
                      KWH = KDU + 1
@@ -1782,15 +1790,19 @@ SUBROUTINE PDLAQR5( WANTT, WANTZ, KACC22, N, KTOP, KBOT, NSHFTS,
 *                    could possibly be exploited.
 *
                      IF( LKTOP.EQ.KTOP .AND. LKBOT.EQ.KBOT ) THEN
-                        JOB = 'All steps'
+                        !JOB = 'All steps'
+                        JOB = 'A'
                      ELSEIF( LKTOP.EQ.KTOP .AND.
      $                    ( DIM1.LT.LCHAIN+1 .OR. DIM1.LE.NTINY ) )
      $                    THEN
-                        JOB = 'Introduce and chase'
+                        !JOB = 'Introduce and chase'
+                        JOB = 'I'
                      ELSEIF( LKBOT.EQ.KBOT ) THEN
-                        JOB = 'Off-chase bulges'
+                        !JOB = 'Off-chase bulges'
+                        JOB = 'O'
                      ELSE
-                        JOB = 'Chase bulges'
+                        !JOB = 'Chase bulges'
+                        JOB = 'C'
                      END IF
                   END IF
 *

src/TOOLS/Makefile

@@ -12,8 +12,8 @@ ITOOLS = picol2row.o  pirow2col.o  pilaprnt.o   pitreecomb.o  pifillpad.o  \
 
 DTOOLS = dddot.o      dlatcpy.o    dmatadd.o    pdmatadd.o    pdcol2row.o \
          pdrow2col.o  pdlaprnt.o   pdtreecomb.o pdfillpad.o   pdchekpad.o \
-         pdelset.o    pdelset2.o   pdelget.o \
-         pdlaread.o   pdlawrite.o
+         pdelset.o    pdelset2.o   pdelget.o #\
+#         pdlaread.o   pdlawrite.o
 
 PKG_ATOOLS = $(ATOOLS:.o=.fo)
 PKG_ATOOLS_C = $(ATOOLS_C:.o=.co)