Hi -
I'm trying to set up a parallelized batch job that is run under rmpi and
managed by sge, using qsub, but it reports that it can't load RMySQL because
it can't find the libmysqlclient.so.15 file.
Note, when I run R interactively, and manually load the RMySQL library, it
works without a hitch, however, when I have qsub launch R, it reports the
following error:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library
'/home/install/usr/apps/R-2.8.0/lib64/RMySQL/libs/RMySQL.so':
libmysqlclient.so.15: cannot open shared object file: No such file or
directory
On the web, I found this posting to this list:
http://tolstoy.newcastle.edu.au/R/e2/help/07/03/12876.html, which recommends
setting the LD_LIBRARY_PATH env var to the location of the
libmysqlclient.so.15 file.
I've set that in my .bashrc, and use the '-V' switch to qsub to make
sure
I'm exporting my environment variables to qsub, but still get the error.
I've also double checked the qsub job's status, with qstat -j
<jobid> and
the LD_LIBRARY_PATH is set to what I've set it to.
Since it only happens when under qsub, I think it's got to be something with
either how I'm calling qsub or how sge is configured, but I can't figure
out
what or what the problem is.
Can anyone suggest a workaround, or make a suggestion? I'm really stuck
here.
Thanks!
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