Merge pull request #72 from snoweye/master

0.3-8 on CRAN

.Rbuildignore

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

ChangeLog

@@ -1,3 +1,12 @@
+2018-08-03: Ver. 0.3-8
+  * Fedora28 use "module load mpi/openmpi-x86_64" to obtain mpiexec.
+  * Roll back partially to Ver. 0.3-6 because pkg-config may give linking order
+    differently that may triggle some dynamic loading problems.
+
+2018-07-29: Ver. 0.3-7
+  * Add "pkg-config" to "configure.ac".
+  * Check "OpenMPI" and "MPICH2" with "pkg-config".
+
 2018-05-18: Ver. 0.3-6
   * Move "rlecuyer" to Imports.
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pbdMPI
-Version: 0.3-6
-Date: 2018-04-30
+Version: 0.3-8
+Date: 2018-08-04
 Title: Programming with Big Data -- Interface to MPI
 Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
         "[email protected]"),
@@ -33,3 +33,14 @@ MailingList: Please send questions and comments regarding pbdR to
         [email protected]
 NeedsCompilation: yes
 Maintainer: Wei-Chen Chen <[email protected]>
+Packaged: 2018-07-30 01:19:36 UTC; snoweye
+Author: Wei-Chen Chen [aut, cre],
+  George Ostrouchov [aut],
+  Drew Schmidt [aut],
+  Pragneshkumar Patel [aut],
+  Hao Yu [aut],
+  Christian Heckendorf [ctb] (FreeBSD),
+  Brian Ripley [ctb] (Windows HPC Pack 2012),
+  R Core team [ctb] (some functions are modified from the base packages)
+Repository: CRAN
+Date/Publication: 2018-08-01 15:20:14 UTC

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/spmd_communicator.r

@@ -11,6 +11,8 @@ spmd.comm.set.errhandler <- function(comm = .pbd_env$SPMD.CT$comm){
   invisible(ret)
 } # End of spmd.comm.set.errhandler().
 
+comm.set.errhandler <- spmd.comm.set.errhandler
+
 spmd.comm.is.null <- function(comm = .pbd_env$SPMD.CT$comm){
   .Call("spmd_comm_is_null", as.integer(comm), PACKAGE = "pbdMPI")
 } # End of spmd.comm.is.null().

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