That could be specific to mtl/mxm
could you
export OMPI_MCA_pml=ob1
and try again ?
can you also extract the command tha launch the test ?
I am curious whether this is via mpirun or as a singleton
Cheers,
Gilles
On Monday, July 11, 2016, pan yang <hippolionforl...@gmail.com> wrote:
> Dear OpenMPI community,
>
> I faced this problem when I am installing the Rmpi:
>
> > 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
>
