[R-sig-hpc] Basic PBS question

[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:

> 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!
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>>
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