updates

.Rbuildignore

@@ -1 +1,2 @@
 ^\.travis\.yml$
+appveyor.yml

NAMESPACE

@@ -79,6 +79,7 @@ export(
 
   ### "R/util_*.r"
   "execmpi",
+  "runmpi",
 
   ### "R/000_pbd_opt.r"
   "pbd_opt" #,

R/get_conf.r

@@ -2,15 +2,20 @@
 ###   "pbd*/src/Makevars.in" and "pbd*/src/Makevar.win"
 ### to find the default configurations from
 ###   "pbd*/etc${R_ARCH}/Makconf".
-get.conf <- function(arg, arch = '', package = "pbdMPI"){
+get.conf <- function(arg, arch = '', package = "pbdMPI", return = FALSE){
   file.name <- paste("./etc", arch, "/Makeconf", sep = "")
   file.path <- tools::file_path_as_absolute(
                  system.file(file.name, package = package))
   ret <- scan(file.path, what = character(), sep = "\n", quiet = TRUE)
 
   id <- grep(paste("^", arg, " = ", sep = ""), ret)
   if(length(id) > 0){
-    cat(gsub(paste("^", arg, " = (.*)", sep = ""), "\\1", ret[id[1]]))
+    ret <- gsub(paste("^", arg, " = (.*)", sep = ""), "\\1", ret[id[1]])
+    if(!return){
+      cat(ret)
+    } else{
+      return(invisible(ret))
+    }
   } else{
     stop("The arg is not found.")
   }

R/util_execmpi.r

@@ -45,17 +45,20 @@ execmpi <- function(spmd.code = NULL, spmd.file = NULL,
         mpicmd <- "mpiexec"
       }
     } else{
-      mpicmd <- system("which mpiexec", intern = TRUE)
+      mpicmd <- suppressWarnings(system("which mpiexec",
+                                 ignore.stderr = TRUE, intern = TRUE))
       if(! is.null(attr(mpicmd, "status"))){
-        mpicmd <- system("which mpirun", intern = TRUE)
+        mpicmd <- suppressWarnings(system("which mpirun",
+                                   ignore.stderr = TRUE, intern = TRUE))
         if(! is.null(attr(mpicmd, "status"))){
-          mpicmd <- system("which orterun", intern = TRUE)
+          mpicmd <- suppressWarnings(system("which orterun",
+                                     ignore.stderr = TRUE, intern = TRUE))
           if(! is.null(attr(mpicmd, "status"))){
-            mpicmd <- get.conf("MPIEXEC")
+            mpicmd <- get.conf("MPIEXEC", return = TRUE)
             if(mpicmd == ""){
-              mpicmd <- get.conf("MPIRUN")
+              mpicmd <- get.conf("MPIRUN", return = TRUE)
               if(mpicmd == ""){
-                mpicmd <- get.conf("ORTERUN")
+                mpicmd <- get.conf("ORTERUN", return = TRUE)
                 if(mpicmd == ""){
                   warning("No MPI executable can be found.")
                   return(invisible(NULL))
@@ -128,3 +131,4 @@ execmpi <- function(spmd.code = NULL, spmd.file = NULL,
   invisible(ret)
 } # End of execmpi().
 
+runmpi <- execmpi

configure

@@ -674,7 +674,6 @@ infodir
 docdir
 oldincludedir
 includedir
-runstatedir
 localstatedir
 sharedstatedir
 sysconfdir
@@ -752,7 +751,6 @@ datadir='${datarootdir}'
 sysconfdir='${prefix}/etc'
 sharedstatedir='${prefix}/com'
 localstatedir='${prefix}/var'
-runstatedir='${localstatedir}/run'
 includedir='${prefix}/include'
 oldincludedir='/usr/include'
 docdir='${datarootdir}/doc/${PACKAGE}'
@@ -1005,15 +1003,6 @@ 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=$ac_optarg ;;
-
   -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
     ac_prev=sbindir ;;
   -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1151,7 +1140,7 @@ fi
 for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
 		datadir sysconfdir sharedstatedir localstatedir includedir \
 		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
-		libdir localedir mandir runstatedir
+		libdir localedir mandir
 do
   eval ac_val=\$$ac_var
   # Remove trailing slashes.
@@ -1304,7 +1293,6 @@ 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]
@@ -4458,6 +4446,40 @@ MPIRUN=`which mpirun`
 MPIEXEC=`which mpiexec`
 ORTERUN=`which orterun`
 
+if test "X$MPIRUN" = "X" -o "X$MPIEXEC" = "X" -o "X$ORTERUN" = "X" ; then
+  if test "$MPITYPE" = "OPENMPI" ; then
+    TMP_MODULE=`module avail mpi/o | grep "mpi/o" | sed -e "s/^\(mpi\/o\S*\)\(\s*.*\)$/\1/"`
+  fi
+
+  if test "$MPITYPE" = "MPICH" -o "$MPITYPE" = "MPICH2" -o "$MPITYPE" = "MPICH3" -o "$MPITYPE" = "MPICH3" ; then
+    TMP_MODULE=`module avail mpi/m | grep "mpi/m" | sed -e "s/^\(mpi\/m\S*\)\(\s*.*\)$/\1/"`
+  fi
+
+  if test $"X$TMP_MODULE" != "X" ; then
+    if test "X$MPIRUN" = "X" ; then
+      TMP_EXEC=`module load ${TMP_MODULE}; which mpirun`
+      if test "X$TMP_EXEC" != "X" ; then
+        MPIRUN="module load ${TMP_MODULE}; ${TMP_EXEC}"
+      fi
+    fi
+
+    if test "X$MPIEXEC" = "X" ; then
+      TMP_EXEC=`module load ${TMP_MODULE}; which mpiexec`
+      if test "X$TMP_EXEC" != "X" ; then
+        MPIEXEC="module load ${TMP_MODULE}; ${TMP_EXEC}"
+      fi
+    fi
+
+    if test "X$ORTERUN" = "X" ; then
+      TMP_EXEC=`module load ${TMP_MODULE}; which orterun`
+      if test "X$TMP_EXEC" != "X" ; then
+        ORTERUN="module load ${TMP_MODULE}; ${TMP_EXEC}"
+      fi
+    fi
+
+  fi
+fi
+
 
 # Check whether --enable-pbdPROF was given.
 if test "${enable_pbdPROF+set}" = set; then :
@@ -4508,6 +4530,9 @@ fi
 echo " "
 echo "******************* Results of pbdMPI package configure *****************"
 echo " "
+echo ">> MPIRUN = ${MPIRUN}"
+echo ">> MPIEXEC = ${MPIEXEC}"
+echo ">> ORTERUN = ${ORTERUN}"
 echo ">> TMP_INC = ${TMP_INC}"
 echo ">> TMP_LIB = ${TMP_LIB}"
 echo ">> TMP_LIBNAME = ${TMP_LIBNAME}"

configure.ac

@@ -775,6 +775,42 @@ MPIRUN=`which mpirun`
 MPIEXEC=`which mpiexec`
 ORTERUN=`which orterun`
 
+dnl Mainly for Fedora which has "mpi/openmpi-x86_64" and "mpi/mpich-x86_64"
+dnl Others may have "mpi/gcc/openmpi-*" or so which need more works.
+if test "X$MPIRUN" = "X" -o "X$MPIEXEC" = "X" -o "X$ORTERUN" = "X" ; then
+  if test "$MPITYPE" = "OPENMPI" ; then
+    TMP_MODULE=`module avail mpi/o | grep "mpi/o" | sed -e "s/^\(mpi\/o\S*\)\(\s*.*\)$/\1/"`
+  fi
+
+  if test "$MPITYPE" = "MPICH" -o "$MPITYPE" = "MPICH2" -o "$MPITYPE" = "MPICH3" -o "$MPITYPE" = "MPICH3" ; then
+    TMP_MODULE=`module avail mpi/m | grep "mpi/m" | sed -e "s/^\(mpi\/m\S*\)\(\s*.*\)$/\1/"`
+  fi
+
+  if test $"X$TMP_MODULE" != "X" ; then
+    if test "X$MPIRUN" = "X" ; then
+      TMP_EXEC=`module load ${TMP_MODULE}; which mpirun`
+      if test "X$TMP_EXEC" != "X" ; then
+        MPIRUN="module load ${TMP_MODULE}; ${TMP_EXEC}"
+      fi
+    fi
+
+    if test "X$MPIEXEC" = "X" ; then
+      TMP_EXEC=`module load ${TMP_MODULE}; which mpiexec`
+      if test "X$TMP_EXEC" != "X" ; then
+        MPIEXEC="module load ${TMP_MODULE}; ${TMP_EXEC}"
+      fi
+    fi
+
+    if test "X$ORTERUN" = "X" ; then
+      TMP_EXEC=`module load ${TMP_MODULE}; which orterun`
+      if test "X$TMP_EXEC" != "X" ; then
+        ORTERUN="module load ${TMP_MODULE}; ${TMP_EXEC}"
+      fi
+    fi
+
+  fi
+fi
+
 
 dnl pbdPROF
 AC_ARG_ENABLE([pbdPROF],
@@ -829,6 +865,9 @@ dnl Report
 echo " "
 echo "******************* Results of pbdMPI package configure *****************"
 echo " "
+echo ">> MPIRUN = ${MPIRUN}"
+echo ">> MPIEXEC = ${MPIEXEC}"
+echo ">> ORTERUN = ${ORTERUN}"
 echo ">> TMP_INC = ${TMP_INC}"
 echo ">> TMP_LIB = ${TMP_LIB}"
 echo ">> TMP_LIBNAME = ${TMP_LIBNAME}"

man/uu_execmpi.Rd

@@ -1,5 +1,6 @@
 \name{Utility execmpi}
 \alias{execmpi}
+\alias{runmpi}
 \title{ Execute MPI code in system }
 \description{
   This function basically saves code in a spmd.file and executes
@@ -9,6 +10,8 @@
 \usage{
 execmpi(spmd.code = NULL, spmd.file = NULL,
     mpicmd = NULL, nranks = 2L, verbose = TRUE)
+runmpi(spmd.code = NULL, spmd.file = NULL,
+    mpicmd = NULL, nranks = 2L, verbose = TRUE)
 }
 \arguments{
   \item{spmd.code}{SPMD code to be run via mpicmd and \code{Rscript}.}