Hello R-help!
I am a systems administrator for the University of Southern California. I take
care of it's general-purpose research cluster, and have recently been asked to
provide access to a parallelized R platform. I do not have any previous
experience using R, and have only ever had to do anything more then 'yum -y
install R'.
We have a myrinet MPI network, and use mpich1 as our standard compiling
environment which will link programs with libmyriexpress.so as well as
libmpich.so
Our myrinet driver package is Myrinet Express (MX) 1.2.12big. (I believe it was
custom-built for us by myricom)
The R package that my predecessor built was version 2.6.1. I have since
installed 2.13.0 in an NFS exported shared software directory, and intend for
the Rmpi package to be installed there as well.
The compiler is gcc 4.3.3, the mpich version is 1.2.7..7
The install command and its output are:
[brianm@hpc-string R]$ /usr/usc/R/2.13.0/bin/R CMD INSTALL Rmpi_0.5-9.tar.gz
--configure-args="--prefix=/usr/usc/R/2.13.0 --with-Rmpi-type=MPICH
--with-Rmpi-include=/usr/usc/mpich/default/default/include
--with-Rmpi-libpath=/usr/usc/mpich/default/default/lib64
--with-mpi=/usr/usc/mpich/default/default"
* installing to library ‘/auto/usc/R/2.13.0/lib64/R/library’
* installing *source* package ‘Rmpi’ ...
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include -DMPICH
-I/usr/local/include -fpic -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include -DMPICH
-I/usr/local/include -fpic -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include -DMPICH
-I/usr/local/include -fpic -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/usr/usc/R/2.13.0/lib64/R/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/usc/mpich/default/default/include -DMPICH
-I/usr/local/include -fpic -g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o
conversion.o internal.o -L/usr/usc/mpich/default/default/lib64 -lmpich
installing to /auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so':
/auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so: undefined symbol:
MX_ERRORS_ARE_FATAL
Error: loading failed
In addition: Warning message:
.Last.lib failed in detach() for 'Rmpi', details:
call: dyn.unload(file.path(libpath, "libs", paste("Rmpi",
.Platform$dynlib.ext,
error: shared object '/auto/usc/R/2.13.0/lib64/R/library/Rmpi/libs/Rmpi.so'
was not loaded
Execution halted
ERROR: loading failed
* removing ‘/auto/usc/R/2.13.0/lib64/R/library/Rmpi’
I've tried google, but didn't get very far. The only information I found was
relative to mpich2... Is it that I need to move towards mpich2? All of the
testing done by my predecessor indicated that mpich2 was much slower then
mpich1, so we never put much time into installing it.
If I knew more about R, I might know how to keep that Rmpi.so file around so
that I could see if it is linked to a library that is missing from my
LD_LIBRARY_PATH or something. How do you stop R from deleting the files that
didn't load properly?
Any help would be greatly appreciated.
Regards,
-----
Brian Mendenhall
Linux/HPCC Administrator
University of Southern California
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