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

2016-07-11 Thread Bennet Fauber 
We have found that virtually all Rmpi jobs need to be started with

$ mpirun -np 1 R CMD BATCH 

This is, as I understand it, because the first R will initialize the
MPI environment and then when you create the cluster, it wants to be
able to start the rest of the processes.  When you intialize the rest
of the workers, it should be with one less than the total number of
processors.  Something like

mpi.spawn.Rslaves(nslaves=mpi.universe.size()-1)

We have a very trivial example at

http://arc-ts.umich.edu/software/rmpi/

I have also found that making sure to add the profile that is included
with Rmpi is also needed.  I do this by adding two lines to the R
executable script near the top to set and export the and renaming that
Rmpi.  The profile should be in the Rmpi installation directory.  In
our case, that makes the first few lines of the R startup script look
like

#!/bin/sh
# Shell wrapper for R executable.
R_PROFILE=/usr/cac/rhel6/Rmpi/R-3.2.2/0.6-5/Rmpi/Rprofile
export R_PROFILE
R_HOME_DIR=/usr/cac/rhel6/R/3.2.2/lib64/R


Things get dicier if you are using doMPI on top of Rmpi rather than Rmpi itself.

Just in case that is of any help,

-- bennet




On Mon, Jul 11, 2016 at 7:52 PM, Gilles Gouaillardet  wrote:
> Note this is just a workaround, this simply disables the mxm mtl (e.g.
> Mellanox optimized infiniband driver).
>
>
> basically, there are two ways to run a single task mpi program (a.out)
>
> - mpirun -np 1 ./a.out (this is the "standard" way)
>
> - ./a.out (aka singleton mode)
>
> the logs you posted do not specify how the test was launch (e.g. with or
> without mpirun)
>
>
> bottom line, if you hit a singleton limitation (e.g. mxm/mtl is not working
> in singleton mode), then you can simply
>
> mpirun -np  a.out
>
> your Rmpi applications, and this should be just fine.
>
>
> if not, you need to
>
> export OMPI_MCA_pml=ob1
>
> regardless you are using mpirun or not.
>
> /* and for the sake of completion, if you are using mpirun, an equivalent
> option is to
>
> mpirun --mca pml ob1 ...
>
> */
>
>
> Cheers,
>
> Gilles
>
> On 7/12/2016 1:34 AM, pan yang wrote:
>
> 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
>
>
>
>
> ___
> users mailing list
> us...@open-mpi.org
> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
> Link to this post:
> http://www.open-mpi.org/community/lists/users/2016/07/29640.php
>
>
>
> ___
> users mailing list
> us...@open-mpi.org
> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
> Link to this post:
> http://www.open-mpi.org/community/lists/users/2016/07/29643.php

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

2016-07-11 Thread Gilles Gouaillardet 
Note this is just a workaround, this simply disables the mxm mtl (e.g. 
Mellanox optimized infiniband driver).



basically, there are two ways to run a single task mpi program (a.out)

- mpirun -np 1 ./a.out (this is the "standard" way)

- ./a.out (aka singleton mode)

the logs you posted do not specify how the test was launch (e.g. with or 
without mpirun)



bottom line, if you hit a singleton limitation (e.g. mxm/mtl is not 
working in singleton mode), then you can simply


mpirun -np  a.out

your Rmpi applications, and this should be just fine.


if not, you need to

export OMPI_MCA_pml=ob1

regardless you are using mpirun or not.

/* and for the sake of completion, if you are using mpirun, an 
equivalent option is to


mpirun --mca pml ob1 ...

*/


Cheers,

Gilles

On 7/12/2016 1:34 AM, pan yang wrote:

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




___
users mailing list
us...@open-mpi.org
Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users
Link to this post: 
http://www.open-mpi.org/community/lists/users/2016/07/29640.php

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

2016-07-11 Thread 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

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

2016-07-11 Thread Gilles Gouaillardet 
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  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
> 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
>

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

2016-07-11 Thread 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