[R-sig-hpc] Loading rgdal as PBS script in R
Roger.Bivand at nhh.no
Tue May 10 10:13:36 CEST 2016
Hariom Singh <hariom.cs1 at ...> writes:
> Hey all,
> I thought I'd share this since we spent quite some time with it and it
> might be relevant to some of you. Or at least amusing, possibly.
> It is stated that, I am getting difficulty in loading rgdal R library while
> using PBS script for parallel computing environment....
> + library("rgdal")
> + } ########error...*.it always loaded without pbs scipt like
> library(rgdal) but here it is not loaded.....so what is the problem in
> loading.......Plz help me out.*
> *Loading required package: spError in dyn.load(file, DLLpath = DLLpath,
> ...) : unable to load shared object
> '/SOFT/R320/lib64/R/library/rgdal/libs/rgdal.so': libgdal.so.20: cannot
> open shared object file: No such file or directory*
> Error: package or namespace load failed for ‘rgdal’
The cause seems to be very obvious:
unable to load shared object
'/SOFT/R320/lib64/R/library/rgdal/libs/rgdal.so': libgdal.so.20: cannot
open shared object file: No such file or directory
On a single core/node, the answer would be to (re)-run ldconfig and/or make
sure the underlying shared object to which rgdal links dynamically is
visible to your R process. If rgdal runs correctly on one node and not
others, then your setup is the problem, if nowhere, rgdal may have been
installed against a different GDAL installation than the one seen in the
search path. libgdal.so.20 (if that was the one rgdal.so was built against)
needs to be visible everywhere.
> Thanks in anticipation.
> Hariom Singh
> Ph.D research scholar , IIT Roorkee.
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