[R] Problem when installing Rmpi package in HPC cluster

[pan yang]

Dear R community,

I faced this problem when I am installing the Rmpi in our university's
linux86-64 cluster:

> install.packages('Rmpi',repos='http://cran.r-project.org
',configure.args=c(
+ '--with-Rmpi-include=/usr/mpi/gcc/openmpi-1.8.2/include/',
+ '--with-Rmpi-libpath=/usr/mpi/gcc/openmpi-1.8.2/lib64/',
+ '--with-Rmpi-type=OPENMPI'))
Installing package into ?d1/pyangac/R_lilbs?
(as 滎ib?is unspecified)
trying URL 'http://cran.r-project.org/src/contrib/Rmpi_0.6-6.tar.gz'
Content type 'application/x-gzip' length 105181 bytes (102 Kb)
opened URL
==================================================
downloaded 102 Kb

* installing *source* package 槔mpi?...
** package 槔mpi?successfully unpacked and MD5 sums checked
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\"
-I/usr/mpi/gcc/openmpi-1.8.2/include/  -DMPI2 -DOPENMPI
-I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic  -c Rmpi.c -o Rmpi.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\"
-I/usr/mpi/gcc/openmpi-1.8.2/include/  -DMPI2 -DOPENMPI
-I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic  -c conversion.c -o conversion.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\"
-I/usr/mpi/gcc/openmpi-1.8.2/include/  -DMPI2 -DOPENMPI
-I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic  -c internal.c -o internal.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so Rmpi.o
conversion.o internal.o -L/usr/mpi/gcc/openmpi-1.8.2/lib64/ -lmpi
-L/usr/lib64/R/lib -lR
installing to /d1/pyangac/R_lilbs/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 槔mpi?
    finding HTML links ... done
    hosts                                   html
    internal                                html
    mpi.abort                               html
    mpi.apply                               html
    mpi.barrier                             html
    mpi.bcast                               html
    mpi.bcast.Robj                          html
    mpi.bcast.cmd                           html
    mpi.cart.coords                         html
    mpi.cart.create                         html
    mpi.cart.get                            html
    mpi.cart.rank                           html
    mpi.cart.shift                          html
    mpi.cartdim.get                         html
    mpi.comm                                html
    mpi.comm.disconnect                     html
    mpi.comm.free                           html
    mpi.comm.inter                          html
    mpi.comm.set.errhandler                 html
    mpi.comm.spawn                          html
    mpi.const                               html
    mpi.dims.create                         html
    mpi.exit                                html
    mpi.finalize                            html
    mpi.gather                              html
    mpi.gather.Robj                         html
    mpi.get.count                           html
    mpi.get.processor.name                  html
    mpi.get.sourcetag                       html
    mpi.iapply                              html
    mpi.info                                html
    mpi.intercomm.merge                     html
    mpi.parSim                              html
    mpi.parapply                            html
    mpi.probe                               html
    mpi.realloc                             html
    mpi.reduce                              html
    mpi.remote.exec                         html
    mpi.scatter                             html
    mpi.scatter.Robj                        html
    mpi.send                                html
    mpi.send.Robj                           html
    mpi.sendrecv                            html
    mpi.setup.rng                           html
    mpi.spawn.Rslaves                       html
    mpi.universe.size                       html
    mpi.wait                                html
** building package indices
** testing if installed package can be loaded
--------------------------------------------------------------------------
Error obtaining unique transport key from ORTE
(orte_precondition_transports not present in
the environment).

  Local host: login-0

--------------------------------------------------------------------------
[login-0.local:18260] Error: mtl_mxm.c:287 - ompi_mtl_mxm_module_init()
Failed to generate jobid
* DONE (Rmpi)

The downloaded source packages are in
        ?tmp/RtmpKdDI0H/downloaded_packages?
(Please forgive me about the unreadable codes, they just came out with no
reason...)

Before that I have set export
LD_LIBRARY_PATH=/usr/mpi/gcc/openmpi-1.8.2/lib64
and                             export LD_PRELOAD=/usr/lib64/libutil.so

Somehow the Rmpi cannot be loaded even though it has been installed
successfully. Can
anyone kindly give me some hint on what should be done?

Thanks a lot.
Pan

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