[R-sig-hpc] (R)mpi and '<U+FEFF>'

[Stefan Lüdtke]

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On 10/15/2014 11:21 PM, Jonathan Olmsted wrote:
> Hi, Stefan.
> 
> I can't replicate the BOM showing up that way even when I'm using a
> file which I'm deliberately inserting a BOM into, so this is all
> speculation...
> 
> But ​wouldn't​ ​ just strip ​ping​ leading "<U+FEFF>" from the ​ ​
> first element of the vector do the trick? This doesn't resolve the 
> reason for the mysterious BOM; that might require more info about
> platforms and versions.
> 
> -Jonathan
> 
> On Wed, Oct 15, 2014 at 3:29 PM, Stefan Lüdtke
> <sluedtke at gfz-potsdam.de> wrote:
> 
> Dear friends,
> 
> I got kind of weird problem and no idea how to approach it. First, 
> what I do.
> 
> Again, on a HPC with Rmpi we run a script that does, at very
> first, fetches some data from a PostGreSQL DB. The SQL query is
> read from a file via 'readLines()'.
> 
> What does work.
> 
> 1) the query itself from psql or pgadmin. 2) the query within the R
> -script on my local machine and on the cluster
> 
> but (and that is the part why I am writing to the list), as soon
> as the number of requested cores is that large, that batch system
> (lsf in this case) spread the tasks over 2 host, the script fails.
> 
> I tried with pure Rmpi, doMPI and foreach and RODBCext and
> RPostGreSQL and always encountered the same problem.
> 
> Comming back to my subject stated above, the error is:
> 
> ERROR:  syntax error at or near "<U+FEFF>WITH"
> 
> where my actual query starts with 'WITH'.
> 
> Those guys ...
> 
> http://postgresql.1045698.n5.nabble.com/BUG-6271-psql-f-reporting-unexpected-syntax-errors-on-first-command-td4940320.html
>
>  .... talk about a BOM at the beginning of the line, but somehow
> this BOM must be introduced to my file by MPI or Rmpi or whatever
> .. I have no idea.
> 
> So, any hint is very welcome.
> 
> Stefan
> 
> 
>> 
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> 
> 
> 

- -- 
Stefan Lüdtke

Section 5.4-  Hydrology
Tel.: +49 331 288 2821
Fax: +49 331 288 1570
Email: sluedtke at gfz-potsdam.de

Helmholtz-Zentrum Potsdam
Deutsches GeoForschungsZentrum GFZ
(GFZ German Research Centre for Geoscience)
Stiftung des öff. Rechts Land Brandenburg
Telegrafenberg, 14473 Potsdam
- -------------------

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