[R-sig-hpc] Fwd: Basic PBS question

[Brian Smith]

Thanks Sean. I run into trouble when installing the packages. After
invoking R, I try to install the packages - with mixed success:

> install.packages("parallel")
Installing package into ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
Warning message:
package ‘parallel’ is not available (for R version 3.1.0)

> install.packages("Rmpi")
Installing package into ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/Rmpi_0.6-5.tar.gz'
Content type 'application/x-gzip' length 102182 bytes (99 Kb)
opened URL
==================================================
downloaded 99 Kb

* installing *source* package ‘Rmpi’ ...
** package ‘Rmpi’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
.
.
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 ‘Rmpi’
* removing ‘/nv/dom/R/x86_64-unknown-linux-gnu-library/3.1/Rmpi’

The downloaded source packages are in
    ‘/tmp/RtmpSGvCff/downloaded_packages’
Warning message:
In install.packages("Rmpi") :
  installation of package ‘Rmpi’ had non-zero exit status



The packages ‘foreach’ and ‘snow’ installed ok, although i’m not sure how
well snow will do, given that I get errors on trying to install Rmpi.

Any suggestions for these? Or where I should go from here?

thanks!

On Sun, Nov 16, 2014 at 2:54 PM, Sean Davis <seandavi at gmail.com> wrote:

>
>
> On Sun, Nov 16, 2014 at 2:48 PM, Brian Smith <bsmith030465 at gmail.com>
> 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')
>>
>
> You'll need to change "test.R" to use something like the parallel,
> foreach, BiocParallel, or other parallel processing package. Just running
> using MPI will not help you here.
>
> Sean
>
>
>
>
>>
>>
>> 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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>>
>
>

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