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 ?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 ?mpi?...
** package ?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 ?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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