Basic PBS question

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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