[R-sig-hpc] (R)mpi and '<U+FEFF>'
jpolmsted at gmail.com
Wed Oct 15 23:21:06 CEST 2014
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...
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
On Wed, Oct 15, 2014 at 3:29 PM, Stefan Lüdtke <sluedtke at gfz-potsdam.de>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 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 ...
> .... 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 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
> Helmholtz-Zentrum Potsdam
> Deutsches GeoForschungsZentrum GFZ
> (GFZ German Research Centre for Geoscience)
> Stiftung des öff. Rechts Land Brandenburg
> Telegrafenberg, 14473 Potsdam
> - -------------------
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.11 (GNU/Linux)
> -----END PGP SIGNATURE-----
> R-sig-hpc mailing list
> R-sig-hpc at r-project.org
j.p.olmsted at gmail.com
[[alternative HTML version deleted]]
More information about the R-sig-hpc