[Rd] Rmpi and OpenMPI ?
Ei-ji Nakama
nakama at ki.rim.or.jp
Fri Mar 30 05:48:39 CEST 2007
Prof. Nakano(ism Japan) and I wrestled in Rmpi on HP-MPI.
Do not know a method to distinguish MPI well?
It is an ad-hoc patch at that time as follows.
diff -ruN Rmpi.orig/configure Rmpi/configure
--- Rmpi.orig/configure 2006-10-12 23:47:03.000000000 +0900
+++ Rmpi/configure 2007-01-10 21:24:55.000000000 +0900
@@ -1268,7 +1268,7 @@
fi;
if test -z "$MPI_ROOT"; then
- for d in /opt/lib /usr/local/lib /usr/lib; do
+ for d in /opt /opt/lib /usr/local/lib /usr/lib; do
if test -f $d/lam/include/mpi.h && test -f $d/lam/lib/libmpi.a; then
echo "I am here $d/lam"
MPI_ROOT=$d/lam
@@ -1281,6 +1281,10 @@
echo "I am here $d/mpich"
MPI_ROOT=$d/mpich
break
+ elif test -f $d/hpmpi/include/mpi.h; then
+ echo "I am here $d/hpmpi"
+ MPI_ROOT=$d/hpmpi
+ break
fi
done
fi
@@ -2781,6 +2785,9 @@
if test -f ${MPI_ROOT}/lib/libmpi.a; then
echo "Found libmpi in ${MPI_ROOT}/lib"
MPI_LIBS="-L${MPI_ROOT}/lib -lmpi"
+elif test -f ${MPI_ROOT}/lib/linux_amd64/libmpi.a; then
+ echo "Found in ${MPI_ROOT}/lib/linux_amd64"
+ MPI_LIBS="-L${MPI_ROOT}/lib/linux_amd64 -lmpi -lmpio
-Wl,-rpath=${MPI_ROOT}/lib/linux_amd64"
elif test -f ${MPI_ROOT}/lib/libmpich.a; then
echo "Found libmpich in ${MPI_ROOT}/lib"
MPI_LIBS="-L${MPI_ROOT}/lib -lmpich"
@@ -2835,7 +2842,7 @@
echo "$as_me:$LINENO: result: $ac_cv_lib_mpi_main" >&5
echo "${ECHO_T}$ac_cv_lib_mpi_main" >&6
if test $ac_cv_lib_mpi_main = yes; then
- MPI_LIBS="-lmpi"
+ MPI_LIBS="-lmpi -lmpio"
else
echo "libmpi not found. exiting..."
exit 1
diff -ruN Rmpi.orig/R/Rcomm.R Rmpi/R/Rcomm.R
--- Rmpi.orig/R/Rcomm.R 2006-02-08 07:11:25.000000000 +0900
+++ Rmpi/R/Rcomm.R 2007-01-10 21:26:42.000000000 +0900
@@ -72,11 +72,11 @@
if (!is.character(slave))
stop("character argument (slave) expected")
- #if (nslaves > mpi.universe.size()){
- # tmp <- paste("Number of R slaves is over",
- # mpi.universe.size(),": maximum CPUs.")
- # warning(tmp)
- # }
+ if (nslaves > mpi.universe.size()){
+ tmp <- paste("Number of R slaves is over",
+ mpi.universe.size(),": maximum CPUs.")
+ warning(tmp)
+ }
else if (nslaves <= 0)
stop("Choose a positive number of slaves.")
.Call("mpi_comm_spawn",
diff -ruN Rmpi.orig/R/zzz.R Rmpi/R/zzz.R
--- Rmpi.orig/R/zzz.R 2005-11-24 04:19:26.000000000 +0900
+++ Rmpi/R/zzz.R 2007-01-10 21:18:49.000000000 +0900
@@ -7,13 +7,13 @@
# cat(vertxt)
# Check if lam-mpi is running
- if (.Platform$OS=="unix"){
- if (length(system("lamnodes",TRUE,ignore.stderr = TRUE)) == 0){
- cat("\n\tLAM/MPI runtime environment is not operating.\n")
- cat("\tStarting LAM/MPI runtime environment.\n")
- system("lamboot -H",ignore.stderr = TRUE)
- }
- }
+ #if (.Platform$OS=="unix"){
+ # if (length(system("lamnodes",TRUE,ignore.stderr = TRUE)) == 0){
+ # cat("\n\tLAM/MPI runtime environment is not operating.\n")
+ # cat("\tStarting LAM/MPI runtime environment.\n")
+ # system("lamboot -H",ignore.stderr = TRUE)
+ # }
+ #}
library.dynam("Rmpi", pkg, lib)
if (!TRUE)
diff -ruN Rmpi.orig/src/Rmpi.c Rmpi/src/Rmpi.c
--- Rmpi.orig/src/Rmpi.c 2006-09-05 23:10:59.000000000 +0900
+++ Rmpi/src/Rmpi.c 2007-01-10 21:18:49.000000000 +0900
@@ -77,7 +77,7 @@
return AsInt(LENGTH(STRING_ELT(sexp_data,0)));
}
-#ifdef MPI2
+#if defined(MPI2) || (defined(HP_MPI) && HP_MPI > 200)
SEXP mpi_universe_size(){
int *MPI_Universe_Size;
int univ_flag;
@@ -857,7 +857,7 @@
return AsInt(flag);
}
-#ifdef MPI2
+#if defined(MPI2) || (defined(HP_MPI) && HP_MPI > 200)
SEXP mpi_comm_spawn (SEXP sexp_slave,
SEXP sexp_argv,
SEXP sexp_nslave,
2007/3/28, Dirk Eddelbuettel <edd at debian.org>:
>
> Has anybody tried to use Rmpi with the OpenMPI library instead of LAM/MPI?
>
> LAM appears to be somewhat hardcoded in the Rmpi setup. Before I start to
> experiment with changing this, has anybody else tried Rmpi with non-LAM MPI
> implementations?
>
> Dirk
>
> --
> Hell, there are no rules here - we're trying to accomplish something.
> -- Thomas A. Edison
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
--
EI-JI Nakama <nakama at ki.rim.or.jp>
"\u4e2d\u9593\u6804\u6cbb" <nakama at ki.rim.or.jp>
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