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

[Jonathan Olmsted]

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:

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> 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
>
>
> - --
> Stefan Lüdtke
>
> Section 5.4-  Hydrology
> Tel.: +49 331 288 2821 <https://rz-vm54.gfz-potsdam.de:443>
> Fax: +49 331 288 1570 <https://rz-vm54.gfz-potsdam.de:443>
> Email: sluedtke at gfz-potsdam.de
>
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> (GFZ German Research Centre for Geoscience)
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> Telegrafenberg, 14473 Potsdam
> - -------------------
>
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-- 

J.P. Olmsted
j.p.olmsted at gmail.com

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