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Basic PBS question

4 messages · Brian Smith, George Ostrouchov

Original
Brian Smith
# 
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!
George Ostrouchov
# 
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:
Brian Smith
# 
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>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      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: