Delphine > I finally solve my problem by installing hdf5 1.8.5 patch1 and netcdf 4.1.1 > many thanks for your support, I'm glad you get that combination working, thanks for letting us know. --Russ > On 16 Mar 2011, at 23:52, Delphine Deryng wrote: > > > Dear Ruth, > > > > I've re-installed all the libraries trying to have them better organized. > > > > However, I'm encountering a different problem. > > > > I've installed hdf5 1.8.6 and netcdf 4.1.2-beta2. > > > > I got 3 errors when I performed make check (results from make check is > > attached to this email). > > > > Then, I have the following output when I run nc-config --all: > > > > This netCDF 4.1.2-beta2 has been built with the following features: > > > > --cc -> icc > > --cflags -> -I/opt/local/include -I/opt/local/include > > -I/opt/local/include -I/opt/local/include > > --libs -> -L/opt/local/lib -lnetcdf -L/opt/local/lib -lhdf5_hl -lhdf5 > > -L/opt/local/lib -lz -L/opt/local/lib -lcurl -L/opt/local/lib > > -L/opt/local/lib -L/opt/local/lib -lidn -lssl -lcrypto -lssl -lcrypto -lz > > -lz -lz > > > > --cxx -> icpc > > --has-c++ -> yes > > > > --fc -> ifort > > --fflags -> -g -I/opt/local/include > > --flibs -> -L/opt/local/lib -lnetcdff -lnetcdf > > --has-f77 -> yes > > --has-f90 -> yes > > > > --has-dap -> yes > > --has-nc2 -> yes > > --has-nc4 -> yes > > --has-hdf5 -> yes > > --has-hdf4 -> no > > --has-pnetcdf-> no > > --has-szlib -> no > > > > --prefix -> /opt/local > > --includedir-> /opt/local/include > > --version -> netCDF 4.1.2-beta2 > > > > I can now compile my fortran program. However, when I run it I got this > > error message: > > > > dyld: Symbol not found: _H5P_CLS_DATASET_ACCESS_g > > Referenced from: /opt/local/lib/libnetcdf.0.dylib > > Expected in: flat namespace > > in /opt/local/lib/libnetcdf.0.dylib > > Trace/BPT trap > > > > Please, let me know if you could find out how to solve my problem. > > > > I'm using ifort version 12.0 > > > > Thanks in advance. > > Delphine > > > > <make_check> > > > > On 16 Mar 2011, at 00:31, Delphine Deryng wrote: > > > >> Dear Ruth, > >> many thanks for your help. I've made sure to build the library for a > >> 64-bit. > >> > >> I also corrected the links regarding the // > >> > >> However, I've perform a make check and got one error. > >> I'm attaching the result of this command. > >> > >> Could this be the cause of the problem? > >> > >> Please, let me know. > >> Thank you, > >> Delphine > >> > >> <make-check> > >> On 15 Mar 2011, at 21:19, Unidata netCDF Support wrote: > >> > >>> Hi Delphine , > >>> > >>>> I'm trying to compile a fortran code but it seems my netcdf library is > >>>> not referenced correctly. However, I can't find the reason why. I hope > >>>> you could help me finding the source of the problem. > >>>> > >>>> My environment is Mac OS X 10.6.6. > >>>> Fortran compiler is ifort 12.0.0 > >>>> > >>>> I have installed the netcdf 4.1.1 library. See below the results of the > >>>> command 'nc-config --all' > >>>> > >>>> I'm trying to compile a simple code requiring netcdf library. However, > >>>> I'm getting this error message: > >>>> > >>>> Undefined symbols: > >>>> "_nf_open_", referenced from: > >>>> _wr4dnc_ in netcdf4d.o > >>>> ld: symbol(s) not found > >>>> make: *** [main] Error 1 > >>> > >>> First, please check that the library was compiled for the same > >>> architecture > >>> as your application program. A common error on Mac's is to build a > >>> library > >>> for a 64-bit x86_64 architecture and try to link a program compiled for a > >>> 32-bit i386 architecture with that library (or vice versa). The result is > >>> that netCDF library functions won't be found. You can check what > >>> architectures your program and library are compiled for with the "file" > >>> command, as in > >>> > >>> $ file /opt/local/lib/netcdff.dylib > >>> /opt/local/lib/netcdff.dylib: Mach-O 64-bit dynamically linked shared > >>> library x86_64 > >>> > >>> If your Fortran and C compilers have different defaults for arcitectures, > >>> you may have to use -m64 or -m32 CFLAGS or FCFLAGS explicitly to make sure > >>> they match. > >>> > >>> That may not be the problem, because I see another possible symptom of > >>> a problem in the nc-config output you sent: > >>> > >>>> --libs -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl -lhdf5 > >>>> -L/opt/local//lib -lz -lm -L/opt/local//lib -lsz -L/opt/local/lib -lcurl > >>>> -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib -lidn -lssl -lcrypto > >>>> -lssl -lcrypto -lz -lz > >>> ... > >>>> --flibs -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl -lhdf5 > >>>> -L/opt/local//lib -lz -lm -L/opt/local//lib -lsz -L/opt/local/lib -lcurl > >>>> -L/opt/local/lib -L/opt/local/lib -L/opt/local/lib -lidn -lssl -lcrypto > >>>> -lssl -lcrypto -lz -lz > >>> > >>> Both of these have a double slash "//" in some -L options, as in > >>> "-L/opt/local//lib". That seems wrong, and may be the result of a typo > >>> when the library was configured and built, or may be a bug in nc-config, > >>> but I don't see such a double slash in the --libs or --flibs output of > >>> the 4.1.1 nc-config here. > >>> > >>> Can you check if things work if you change this "//" to "/" in your link > >>> command? > >>> > >>> --Russ > >>> > >>>> nc-config --all > >>>> > >>>> This netCDF 4.1.1 has been built with the following features: > >>>> > >>>> --cc -> icc > >>>> --cflags -> -I/opt/local/include > >>>> --libs -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl > >>>> -lhdf5 -L/opt/local//lib -lz -lm -L/opt/local//lib -lsz > >>>> -L/opt/local/lib -lcurl -L/opt/local/lib -L/opt/local/lib > >>>> -L/opt/local/lib -lidn -lssl -lcrypto -lssl -lcrypto -lz -lz > >>>> > >>>> --cxx -> icpc > >>>> --has-c++ -> yes > >>>> > >>>> --fc -> ifort > >>>> --fflags -> -g -I/opt/local/include > >>>> --flibs -> -L/opt/local/lib -lnetcdf -L/opt/local//lib -lhdf5_hl > >>>> -lhdf5 -L/opt/local//lib -lz -lm -L/opt/local//lib -lsz > >>>> -L/opt/local/lib -lcurl -L/opt/local/lib -L/opt/local/lib > >>>> -L/opt/local/lib -lidn -lssl -lcrypto -lssl -lcrypto -lz -lz > >>>> --has-f77 -> yes > >>>> --has-f90 -> yes > >>>> > >>>> --has-dap -> yes > >>>> --has-nc2 -> yes > >>>> --has-nc4 -> yes > >>>> --has-hdf5 -> yes > >>>> --has-hdf4 -> no > >>>> --has-szlib -> yes > >>>> > >>>> --prefix -> /opt/local > >>>> --includedir-> /opt/local/include > >>>> --version -> netCDF 4.1.1 > >>>> > >>>> > >>> > >>> Russ Rew UCAR Unidata Program > >>> address@hidden http://www.unidata.ucar.edu > >>> > >>> > >>> > >>> Ticket Details > >>> =================== > >>> Ticket ID: QGV-335526 > >>> Department: Support netCDF > >>> Priority: Normal > >>> Status: Closed > >>> > >> > > > > Russ Rew UCAR Unidata Program address@hidden http://www.unidata.ucar.edu Ticket Details =================== Ticket ID: QGV-335526 Department: Support netCDF Priority: Normal Status: Closed
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