[R-sig-hpc] Basic PBS question

[George Ostrouchov]

The install did not find libmpi in the usual places.
At the shell prompt, check
echo $OMPI_DIR
and if it gives you a directory, try installing pbdMPI by itself first with
R CMD INSTALL pbdMPI --configure-args="--with-mpi-type=OPENMPI 
--with-mpi=the_directory_you_got"
Quick Guide for pbdMPI (Ver. 0.2-5
George

On 11/16/14 2:26 PM, Brian Smith wrote:
> George,
>
> Unfortunately, I run into dependency issues while trying to install 
> the package:
>
> .
> .
> checking mpi.h presence... yes
> checking for mpi.h... yes
> Trying to find libmpi.so or libmpich.a ...
> checking for main in -lmpi... no
> libmpi not found. exiting...
> ERROR: configuration failed for package ‘pbdMPI’
> * removing ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1/pbdMPI’
> ERROR: dependency ‘pbdMPI’ is not available for package ‘pbdSLAP’
> * removing ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1/pbdSLAP’
> ERROR: dependencies ‘pbdMPI’, ‘pbdSLAP’ are not available for package 
> ‘pbdBASE’
> * removing ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1/pbdBASE’
> ERROR: dependencies ‘pbdMPI’, ‘pbdSLAP’, ‘pbdBASE’ are not available 
> for package ‘pbdDMAT’
> * removing ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1/pbdDMAT’
> ERROR: dependencies ‘pbdMPI’, ‘pbdSLAP’, ‘pbdBASE’, ‘pbdDMAT’ are not 
> available for package ‘pbdDEMO’
> * removing ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1/pbdDEMO’
>
> The downloaded source packages are in
>     ‘/tmp/RtmpSGvCff/downloaded_packages’
> Warning messages:
> 1: In install.packages("pbdDEMO") :
>   installation of package ‘pbdMPI’ had non-zero exit status
> 2: In install.packages("pbdDEMO") :
>   installation of package ‘pbdSLAP’ had non-zero exit status
> 3: In install.packages("pbdDEMO") :
>   installation of package ‘pbdBASE’ had non-zero exit status
> 4: In install.packages("pbdDEMO") :
>   installation of package ‘pbdDMAT’ had non-zero exit status
> 5: In install.packages("pbdDEMO") :
>   installation of package ‘pbdDEMO’ had non-zero exit status
>
> Is there a way to resolve these?
>
> thanks!
>
> On Sun, Nov 16, 2014 at 3:00 PM, George Ostrouchov 
> <georgeost at gmail.com <mailto:georgeost at gmail.com>> wrote:
>
>     Since you are running in batch on a cluster, I would recommend
>     looking at package pbdDEMO and reading its vignette.
>
>     George
>
>
>     On 11/16/14 1:48 PM, Brian Smith wrote:
>
>         Hi,
>
>         I am trying to get started on our Moab cluster. My pbs script
>         looks like:
>
>         ======= test.pbs ============
>         #!/bin/sh
>
>         #PBS -N job_name
>         #PBS -l nodes=1:ppn=3
>         #PBS -q debugq
>
>         module load R
>         cd $PBS_O_WORKDIR
>
>         mpirun -rmk pbs R --slave CMD BATCH ./test.r
>
>         ======== test.r ============
>
>         print('hello world')
>
>
>         To submit my job, I use:
>
>         msub test.pbs
>
>         When I execute this, the .Rout file contains 'hello world' and
>         everything
>         looks ok. However, how can I get each processor to write out
>         something like:
>
>         'hello world from 1'
>         'hello world from 2'
>         'hello world from 3'
>
>         How can I get the processor number as an input to the r script?
>
>         many thanks!
>
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>
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