Re: [OMPI users] Problem when installing Rmpi package in HPC cluster

[pan yang]

Dear Gilles,

I tried export OMPI_MCA_pml=ob1, and it worked! Thank you very much for
your brilliant suggestion.

By the way, I don't really understand what do you mean by '*can you also
extract the command tha launch the test ?*'...

Cheers,
Pan

[OMPI users] Problem when installing Rmpi package in HPC cluster

[pan yang]

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
internalhtml
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.gethtml
mpi.cart.rank   html
mpi.cart.shift  html
mpi.cartdim.get html
mpi.commhtml
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.exithtml
mpi.finalizehtml
mpi.gather  html
mpi.gather.Robj html
mpi.get.count   html
mpi.get.processor.name  html
mpi.get.sourcetag   html
mpi.iapply  html
mpi.infohtml
mpi.intercomm.merge html
mpi.parSim  html
mpi.parapplyhtml
mpi.probe   html
mpi.realloc html
mpi.reduce  html
mpi.remote.exec html
mpi.scatter html
mpi.scatter.Robjhtml
mpi.sendhtml
mpi.send.Robj   html
mpi.sendrecvhtml
mpi.setup.rng   html
mpi.spawn.Rslaves   html
mpi.universe.size   html
mpi.waithtml
** building package indices
** testing if installed package can be loaded
--
Error obtaining unique transport key from ORTE
(orte_precondition_transports not present in
the