netcdf4 chaining test fails

Added by Ian Harris over 6 years ago

Hi,

I'm trying to install CDO (1.9.5rc1) on OSX 10.12.6

I'm getting the error described here: https://code.mpimet.mpg.de/boards/2/topics/4398

ie, 'FAIL: tsformat.test 8 - chaining set 1 with netCDF4'

I followed the advice given there and reinstalled HDF5 1.8.20 in threadsafe mode:

./configure --enable-threadsafe --prefix=/usr/local/hdf5 --enable-fortran --enable-cxx --enable-unsupported

That appeared to install properly, but I still get the error when installing CDO.

Any advice would be most welcome.

Replies (6)

RE: netcdf4 chaining test fails - Added by Ian Harris over 6 years ago

HI,

This needs to be deleted - a similar post just got answered and it solved my problem as well.

RE: netcdf4 chaining test fails - Added by Ralf Mueller over 6 years ago

Hi Ian!

could you please upload the output of

cdo -V

one option is: Since you installed hdf5 into a non-standard path (/usr/local/hdf5) it could be, that another hdf5 library is taken at runtime. After installation, could you run

otool -L

on that cdo binary?

Finally: Why do you want to use an un-released version of CDO? mac-ports is up-to-date and its hdf5 package has a thread-safe variant. Hence it should be possible to build cdo against this thread-safe hdf5. cdo-1.9.4 is just released, there isn't much difference to 1.9.5rc1.

cheers
ralf

RE: netcdf4 chaining test fails - Added by Ian Harris over 6 years ago

Hi Ralf,

I should start by reiterating that my problem is solved. I hadn't appreciated the need to run cdo as 'cdo -L' whenever I used it; that worked fine.

Anyway, in case you're interested..

ianharris% cdo -V
Climate Data Operators version 1.9.5rc1 (http://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin16.7.0
CXX Compiler: g++ -std=gnu++11 -g -O2 -fopenmp -D_THREAD_SAFE -pthread
CXX version : g++ (GCC) 5.0.0 20141005 (experimental)
C Compiler: gcc -std=gnu99 -m64 -fopenmp -D_THREAD_SAFE -pthread -D_THREAD_SAFE -D_THREAD_SAFE -pthread
C version : gcc (GCC) 5.0.0 20141005 (experimental)
F77 Compiler: g77 -m64
F77 version : g77: `-V' option must have argument
Features: 16GB C++11 DATA PTHREADS OpenMP4 NC4/HDF5 OPeNDAP SSE3
Libraries:
Filetypes: srv ext ieg grb1 nc1 nc2 nc4 nc4c
CDI library version : 1.9.5rc1
CGRIBEX library version : 1.9.1
NetCDF library version : 4.3.3.1 of Apr 23 2015 15:17:13 $
HDF5 library version : 1.8.13
EXSE library version : 1.4.0
FILE library version : 1.8.3

ianharris% otool -L /sw/bin/cdo
/sw/bin/cdo:
/usr/local/lib/libnetcdf.7.dylib (compatibility version 10.0.0, current version 10.0.0)
/usr/local/lib/libhdf5_hl.8.dylib (compatibility version 9.0.0, current version 9.2.0)
/usr/local/lib/libhdf5.8.dylib (compatibility version 9.0.0, current version 9.2.0)
/usr/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
/usr/local/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.21.0)
/usr/local/lib/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2)
/usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

I use fink and have always had issues with macports. Hence I just downloaded the CDO described as the 'current release':

https://code.mpimet.mpg.de/projects/cdo/files

Cheers

Harry