[Swift-devel] Re: R library(ncdf) [PADS Support #12231]

Tue Apr 5 11:52:48 CDT 2011

----- Forwarded Message -----
From: "Michael Wilde" <wilde at mcs.anl.gov>
To: "Neil Best" <nbest at ci.uchicago.edu>
Cc: "joshua elliott" <jelliott at ci.uchicago.edu>, "PADS Support" <pads-support at ci.uchicago.edu>
Sent: Tuesday, April 5, 2011 11:47:04 AM
Subject: Re: R library(ncdf) [PADS Support #12231]

According to this thread I found on google, the R install may be looking for HDF5 libs to load netCDF:

http://www.unidata.ucar.edu/support/help/MailArchives/netcdf-perl/msg00374.html

Does the R package doc say anything about how to ensure that the HDF5 libs are in your LD_LIBRARY_PATH?

- MIke

----- Original Message -----
> Begin forwarded message:
> 
> > From: Neil Best <nbest at ci.uchicago.edu>
> > Date: March 28, 2011 3:04:17 PM CDT
> > To: pads-support at ci.uchicago.edu
> > Subject: Re: R library(ncdf) [PADS Support #12231]
> >
> > In a fresh login shell starting a fresh R session after changing my
> > .soft I get this:
> >
> >> sessionInfo()
> > R version 2.12.0 (2010-10-15)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> > [9] LC_ADDRESS=C LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >> .libPaths()
> > [1] "/home/nbest/R/x86_64-unknown-linux-gnu-library/2.12/"
> > [2] "/soft/R-DBI-0.2-5-gcc4.1-r1/lib/R2.12/site-library"
> > [3] "/soft/R-RPostgreSQL-0.1-7-gcc4.1-r1/lib/R2.12/site-library"
> > [4] "/soft/R-sp-0.9-72-gcc4.1-r1/lib/R2.12/site-library"
> > [5] "/soft/R-rgdal-0.6-30-gcc4.1-r1/lib/R2.12/site-library"
> > [6] "/soft/R-RColorBrewer-1.0.2-gcc4.1-r1/lib/R2.12/site-library"
> > [7] "/soft/R-ncdf-1.8-gcc4.1-r1/lib/R2.12/site-library"
> > [8] "/soft/R-2.12.0-gcc4.1-r1/lib64/R/library"
> >> library(ncdf)
> > Error: package 'ncdf' was built before R 2.10.0: please re-install
> > it
> >
> >
> > You were able to load it? What would be different between our
> > sessions? It's not in my home library, so I reasonably sure that
> > it's trying to load your build.
> >
> > [nbest at login2 R]$ find ~nbest/R -type d -name ncdf
> > [nbest at login2 R]$ find /soft/R-ncdf-1.8-gcc4.1-r1/ -type d -name
> > ncdf
> > /soft/R-ncdf-1.8-gcc4.1-r1/lib/R2.12/site-library/ncdf
> >
> > I tried installing it to ~nbest/R using the args you gave me, but it
> > still fails:
> >
> > [nbest at login2 src]$ R CMD INSTALL -l ~/R
> > /software/common/src/ncdf_1.8.1.tar.gz
> > --configure-args="LDFLAGS='-L/soft/hdf5-1.8.2-gcc4.1-r1/lib -lhdf5
> > -lhdf5_hl' --with-netcdf_incdir=/soft/netcdf-4.0-gcc4.1-r1/include
> > --with-netcdf_libdir=/soft/netcdf-4.0-gcc4.1-r1/lib"
> > . . .
> >  unable to load shared object
> >  '/autonfs/home/nbest/R/ncdf/libs/ncdf.so':
> >  /soft/netcdf-4.0-gcc4.1-r1/lib/libnetcdf.so.5: undefined symbol:
> >  H5P_CLS_FILE_CREATE_g
> >
> > I think that's the same error as before. I still can't imagine
> > what's different about our environments. Can you?
> >
> >
> >

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory

----- Original Message -----
> Hi Neil,
> 
> Thanks for the heads-up. No, I have never tried building R with ncdf.
> 
> The next 4 weeks are very busy for me as well with travel, workshops
> and proposals.
> 
> I'm sending to swift-devel as well as Rob and Sheri of the MCS Climate
> group to see if they have any info on building the netCDF package for
> R.
> 
> Regards,
> 
> Mike
> 
> ----- Original Message -----
> > Hi, Mike. Have you ever tried to install the ncdf package for R? I
> > have a ticket open with Ti, but he seems to be having trouble with
> > it.
> > He thought he had it at one point (see below) but there was a
> > problem
> > -- I think he used the OS version of R. I'll send you my reply from
> > when I tried to use what he had built. If you have any spare cycles
> > for this in the interest of moving my SwiftR project forward over
> > the
> > next 2-3 weeks that would be great. I'll let you know if I hear
> > anything from Ti. I'm not bugging him about it this week because I
> > have my hands full and I think he's helping get ready for the Globus
> > meeting, but I'm just trying to keep the issue alive. Thanks, Mike.
> >
> >
> > Neil
> >
> >
> > Begin forwarded message:
> >
> > > From: "Ti Leggett" <pads-support at ci.uchicago.edu>
> > > Date: March 28, 2011 12:42:58 PM CDT
> > > To: nbest at ci.uchicago.edu
> > > Subject: R library(ncdf) [PADS Support #12231]
> > > Reply-To: pads-support at ci.uchicago.edu
> > >
> > > Bleh, accidentally hit comment instead of reply:
> > >
> > >
> > > The magic command was this:
> > > R CMD INSTALL -l /soft/R-ncdf-1.8-gcc4.1-r1/lib/R2.12/site-library
> > > /software/common/src/ncdf_1.8.1.tar.gz
> > > --configure-args="LDFLAGS='-L/soft/hdf5-1.8.2-gcc4.1-r1/lib -lhdf5
> > > -lhdf5_hl' --with-netcdf_incdir=/soft/netcdf-4.0-gcc4.1-r1/include
> > > --with-netcdf_libdir=/soft/netcdf-4.0-gcc4.1-r1/lib"
> > >
> > > Add the following to your .soft to use it:
> > >
> > > +netcdf-4.0-gcc4.1-r1
> > > +szip-2.1-gcc4.1-r1
> > > +hdf5-1.8.2-gcc4.1-r1
> > > +R-ncdf-gcc-R2.12
> 
> --
> Michael Wilde
> Computation Institute, University of Chicago
> Mathematics and Computer Science Division
> Argonne National Laboratory
> 
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> Swift-devel at ci.uchicago.edu
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-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory