cannot install ncdf4_1.6.1 in R-3.0.0 on Cray XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 4)
Dear Pragnesh, I turned out I had to use the newest versions of the available netcdf libraries to compile ncdf (netcdf-hdf5parallel/4.2.0). With netcdf-4.1.1.0 compilation is never successful. Now I have a problem compiling pbdMPI, which I descripe in a separate thread. Many thanks for Your support. Best regards, Martin
On 05/08/2013 09:23 PM, Pragnesh Patel wrote:
---------- Forwarded message ----------
From: Pragnesh Patel <pragnesh777 at gmail.com>
Date: Wed, 8 May 2013 09:25:13 -0400
Subject: Re: [R-sig-hpc] cannot install ncdf4_1.6.1 in R-3.0.0 on Cray
XE6 HERMIT (R-sig-hpc Digest, Vol 56, Issue 4)
To: George Ostrouchov <ostrouchovg at ornl.gov>
Cc: Martin Ivanov <martin.ivanov at ifg.uni-tuebingen.de>, Drew Schmidt
<schmidt at math.utk.edu>
Hi Martin,
Please follow below steps for HDF5 installation.
============================================
make distclean
./configure --prefix=your home directory \
--with-zlib=/usr \
--with-szlib=$SZIP_DIR \
--enable-fortran \
--enable-cxx \
--enable-parallel \
--enable-shared
=======================
make all
# after failing to run newly compiled H5make_libsettings
interactively with aprun. It works fine on backend.
# retry by compiling for frontend and then restart make
cd src
gcc -o H5make_libsettings H5make_libsettings.c
cd ..
make all
# after failing to run newly compiled H5detect interactively with
aprun. It works fine on backend.
# retry by compiling for frontend and then restart make
cd src
gcc -o H5detect H5detect.c
./H5detect > H5Tinit.c
cd ..
make all
=======================
make install
============================================
Thanks
Pragnesh
On 5/7/13, George Ostrouchov <ostrouchovg at ornl.gov> wrote:
Hi Martin, Glad that we can help with your configuration. Pragnesh is our CS expert on the pbdR project. Let me do a little advertising ... If you will be at the UseR! conference this July in Albacete, Spain, Drew and I are running a pbdR tutorial the day before the conference. Please consider signing up. We have the most scalable infrastructure in R. Cheers, George On 5/7/13 1:04 PM, Martin Ivanov wrote:
Hello, Pragnesh, Thank You very much for Your responsiveness. Now I am trying to compile hdf5, but unsuccessfully. Here is my setting: -- Dr. Martin Ivanov Eberhard-Karls-Universit?t T?bingen Mathematisch-Naturwissenschaftliche Fakult?t Fachbereich Geowissenschaften Water & Earth System Science (WESS) H?lderlinstra?e 12, 72074 T?bingen, Deutschland Tel. +4970712974213
_______________________________________________ R-sig-hpc mailing list R-sig-hpc at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
-- George Ostrouchov, Ph.D. Scientific Data Group Computer Science and Mathematics Division Oak Ridge National Laboratory (865) 574-3137 http://www.csm.ornl.gov/~ost
Dr. Martin Ivanov Eberhard-Karls-Universit?t T?bingen Mathematisch-Naturwissenschaftliche Fakult?t Fachbereich Geowissenschaften Water & Earth System Science (WESS) H?lderlinstra?e 12, 72074 T?bingen, Deutschland Tel. +4970712974213