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[netCDF #USP-401162]: about install netcdf-4.1.3 by intel-2015
- Subject: [netCDF #USP-401162]: about install netcdf-4.1.3 by intel-2015
- Date: Wed, 05 Nov 2014 14:07:33 -0700
Hi Xiaojuan,
You are seeing a bug that occurred when trying to use the szip library with the
June 2011 netCDF-4.1.3 version that was a combined release for netCDF-C,
netCDF-Fortran, and netCDF-C++. I think if you don't need szlib and don't
try to build with it, that error will not occur.
The bug was fixed in later versions of the software, but those versions also
separated the netCDF-C and netCDF-Fortran libraries into different software
packages to make the software easier to build, install, and maintain. See
http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg10369.html
If you could use a later version, such as the most recent releases, you would
not encounter this bug. The latest release of netCDF C and Fortran are
available here, along with instructions for building them:
https://github.com/Unidata/netcdf-c/releases/tag/v4.3.2
https://github.com/Unidata/netcdf-fortran/releases/tag/v4.4.1
http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
--Russ
> I am sorry to trouble you .
>
> Rencently ,I install netcdf 4.1.3 by intel -2015 , the make is ok ,but when
> make check ,I always get the following error:
>
> f90tst_vars2.f90(37): error #6418: This name has already been assigned a data
> type. [CACHE_NELEMS]
> integer, parameter :: CACHE_SIZE = 8, CACHE_NELEMS = 571, CACHE_PREEMPTION =
> 66
> ----------------------------------------^
> f90tst_vars2.f90(77): error #6284: There is no matching specific function for
> this generic function reference. [NF90_DEF_VAR]
> call check(nf90_def_var(ncid, VAR5_NAME, NF90_INT, dimids, varid5, chunksizes
> = chunksizes, &
> -------------^
> f90tst_vars2.f90(85): error #6404: This name does not have a type, and must
> have an explicit type. [NF90_SET_VAR_CHUNK_CACHE]
> call check(nf90_set_var_chunk_cache(ncid, varid1, CACHE_SIZE, &
> -------------^
> compilation aborted for f90tst_vars2.f90 (code 1)
> make[2]: *** [f90tst_vars2.o] Error 1
> make[2]: *** Waiting for unfinished jobs....
> libtool: link: /pkg/intel/composerxe/bin/ifort -I../fortran -I../include
> -I../f90 -O3 -xHost -ip -no-prec-div -static-intel -o .libs/ftst_vars
> ftst_vars.o fortlib.o handle_err.o -L/pkg/zlib/1.2.8/intel-15/lib
> -L/pkg/szip/2.1/intel-15/lib
> -L/pkg/hdf5/1.8.10/intel-15/lib:/pkg/szip/2.1/intel-15/lib:/pkg/zlib/1.2.8/intel-15/lib:/pkg/intel/composerxe/ipp/lib/intel64:/pkg/intel/composerxe/mkl/lib/intel64:/pkg/intel/composerxe/tbb/lib/intel64:/pkg/intel/composerxe/debugger/lib/intel64:/pkg/intel/composerxe/lib/intel64:/pkg/intel/composer_xe_2015.0.090/compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/mpirt/lib/intel64:/pkg/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/ipp/lib/intel64:/pkg/intel/composer_xe_2015.0.090/compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/mkl/lib/intel64:/pkg/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4
> -L/pkg/hdf5/1.8.10/intel-15/lib ../fortran/.libs/libnetcdff.so
> /tmp/build/liuxj/netcdf-4.1
.3/liblib/.libs/libnetcdf.so /pkg/hdf5/1.8.10/intel-15/lib/libhdf5_hl.so
/pkg/hdf5/1.8.10/intel-15/lib/libhdf5.so /pkg/szip/2.1/intel-15/lib/libsz.so
-lz -lrt -lm -lcurl -Wl,-rpath -Wl,/tmp/build/liuxj/netcdf-install/lib
-Wl,-rpath -Wl,/pkg/hdf5/1.8.10/intel-15/lib -Wl,-rpath
-Wl,/pkg/szip/2.1/intel-15/lib
> libtool: link: /pkg/intel/composerxe/bin/ifort -I../fortran -I../include
> -I../f90 -O3 -xHost -ip -no-prec-div -static-intel -o .libs/tst_f77_v2
> tst_f77_v2.o -L/pkg/zlib/1.2.8/intel-15/lib -L/pkg/szip/2.1/intel-15/lib
> -L/pkg/hdf5/1.8.10/intel-15/lib:/pkg/szip/2.1/intel-15/lib:/pkg/zlib/1.2.8/intel-15/lib:/pkg/intel/composerxe/ipp/lib/intel64:/pkg/intel/composerxe/mkl/lib/intel64:/pkg/intel/composerxe/tbb/lib/intel64:/pkg/intel/composerxe/debugger/lib/intel64:/pkg/intel/composerxe/lib/intel64:/pkg/intel/composer_xe_2015.0.090/compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/mpirt/lib/intel64:/pkg/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/ipp/lib/intel64:/pkg/intel/composer_xe_2015.0.090/compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/mkl/lib/intel64:/pkg/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4
> -L/pkg/hdf5/1.8.10/intel-15/lib ../fortran/.libs/libnetcdff.so
> /tmp/build/liuxj/netcdf-4.1.3/liblib/.libs/libne
tcdf.so /pkg/hdf5/1.8.10/intel-15/lib/libhdf5_hl.so
/pkg/hdf5/1.8.10/intel-15/lib/libhdf5.so /pkg/szip/2.1/intel-15/lib/libsz.so
-lz -lrt -lm -lcurl -Wl,-rpath -Wl,/tmp/build/liuxj/netcdf-install/lib
-Wl,-rpath -Wl,/pkg/hdf5/1.8.10/intel-15/lib -Wl,-rpath
-Wl,/pkg/szip/2.1/intel-15/lib
> libtool: link: /pkg/intel/composerxe/bin/ifort -I../fortran -I../include
> -I../f90 -O3 -xHost -ip -no-prec-div -static-intel -o .libs/ftst_vars2
> ftst_vars2.o fortlib.o handle_err.o -L/pkg/zlib/1.2.8/intel-15/lib
> -L/pkg/szip/2.1/intel-15/lib
> -L/pkg/hdf5/1.8.10/intel-15/lib:/pkg/szip/2.1/intel-15/lib:/pkg/zlib/1.2.8/intel-15/lib:/pkg/intel/composerxe/ipp/lib/intel64:/pkg/intel/composerxe/mkl/lib/intel64:/pkg/intel/composerxe/tbb/lib/intel64:/pkg/intel/composerxe/debugger/lib/intel64:/pkg/intel/composerxe/lib/intel64:/pkg/intel/composer_xe_2015.0.090/compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/mpirt/lib/intel64:/pkg/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/ipp/lib/intel64:/pkg/intel/composer_xe_2015.0.090/compiler/lib/intel64:/pkg/intel/composer_xe_2015.0.090/mkl/lib/intel64:/pkg/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4
> -L/pkg/hdf5/1.8.10/intel-15/lib ../fortran/.libs/libnetcdff.so
> /tmp/build/liuxj/netcdf-4
.1.3/liblib/.libs/libnetcdf.so /pkg/hdf5/1.8.10/intel-15/lib/libhdf5_hl.so
/pkg/hdf5/1.8.10/intel-15/lib/libhdf5.so /pkg/szip/2.1/intel-15/lib/libsz.so
-lz -lrt -lm -lcurl -Wl,-rpath -Wl,/tmp/build/liuxj/netcdf-install/lib
-Wl,-rpath -Wl,/pkg/hdf5/1.8.10/intel-15/lib -Wl,-rpath
-Wl,/pkg/szip/2.1/intel-15/lib
> ftst_vars.o: In function `MAIN__':
> ftst_vars.F:(.text+0x371): undefined reference to `nf_set_chunk_cache_'
> ftst_vars.F:(.text+0x399): undefined reference to `nf_get_chunk_cache_'
> ftst_vars.F:(.text+0x3ed): undefined reference to `nf_create_'
> ftst_vars.F:(.text+0x420): undefined reference to `nf_def_dim_'
> ftst_vars.F:(.text+0x453): undefined reference to `nf_def_dim_'
> ftst_vars.F:(.text+0x4b1): undefined reference to `nf_def_var_'
> ftst_vars.F:(.text+0x4f6): undefined reference to `nf_def_var_chunking_'
> ftst_vars.F:(.text+0x51e): undefined reference to `nf_def_var_endian_'
> ftst_vars.F:(.text+0x551): undefined reference to `nf_def_var_deflate_'
> ftst_vars.F:(.text+0x579): undefined reference to `nf_def_var_fletcher32_'
> ftst_vars.F:(.text+0x5b4): undefined reference to `nf_inq_var_deflate_'
> ftst_vars.F:(.text+0x601): undefined reference to `nf_inq_var_fletcher32_'
> ftst_vars.F:(.text+0x65e): undefined reference to `nf_inq_var_chunking_'
> ftst_vars.F:(.text+0x6bb): undefined reference to `nf_inq_var_endian_'
> ftst_vars.F:(.text+0x703): undefined reference to `nf_enddef_'
> ftst_vars.F:(.text+0x72b): undefined reference to `nf_put_var_int_'
> ftst_vars.F:(.text+0x746): undefined reference to `nf_close_'
> ftst_vars.F:(.text+0x770): undefined reference to `nf_open_'
> ftst_vars.F:(.text+0x79d): undefined reference to `nf_inq_varid_'
> ftst_vars.F:(.text+0x805): undefined reference to `nf_inq_var_deflate_'
> ftst_vars.F:(.text+0x852): undefined reference to `nf_inq_var_fletcher32_'
> ftst_vars.F:(.text+0x8af): undefined reference to `nf_inq_var_chunking_'
> ftst_vars.F:(.text+0x90c): undefined reference to `nf_inq_var_endian_'
> ftst_vars.F:(.text+0x961): undefined reference to `nf_get_var_int_'
> ftst_vars.F:(.text+0x9dc): undefined reference to `nf_close_'
> handle_err.o: In function `handle_err_':
> handle_err.F:(.text+0x5a): undefined reference to `nf_strerror_'
> ../fortran/.libs/libnetcdff.so: undefined reference to `nf_get_varm_double_'
> ../fortran/.libs/libnetcdff.so: undefined reference to `nf_get_vara_real_'
> ../fortran/.libs/libnetcdff.so: undefined reference to
> `nf_inq_compound_fieldname_'
> ../fortran/.libs/libnetcdff.so: undefined reference to `nf_inq_typeid_'
> ..............................
>
> I use the configure command :
>
>
> export CC=icc
>
> export CXX=icpc
>
> export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
>
> export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
>
> export F77=ifort
>
> export FC=ifort
>
> export F90=ifort
>
> export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
>
> export CPP='icc -E'
>
> export CXXCPP='icpc -E'
>
> ./configure LDFLAGS='-I'${LD_LIBRARY_PATH}' -I/pkg/zlib/1.2.8/intel-15/lib
> -I/pkg/szip/2.1/intel-15/lib -I/pkg/hdf5/1.8.10/intel-15/lib'
> CPPFLAGS='-I'${INCLUDE}' -I/pkg/zlib/1.2.8/intel-15/include/
> -I/pkg/szip/2.1/intel-15/include -I/pkg/hdf5/1.8.10/intel-15/include'
> --prefix=/tmp/build/liuxj/netcdf-install --enable-shared --enable-cxx-4
> --enable-fortran --enable-cxx --enable-static --enable-netcdf-4 --disable-dap
> >& configure.log &
>
> The attachment is my configure.log ,make.log,and makecheck.log.
>
> I have try my best to solve the problem by google and other document. But I
> still cannot get the answer.
>
> Please help me to check the error ,and give me some advice.Thank you very
> much .
>
> Thanks again and looking forward to your reply.
>
> Good luck
>
>
>
> ??? Xiaojuan Liu
> ------------------------------------------------------
> Institute of Plasma Physics
> Chinese Academy of Sciences
> PO Box 1126, Hefei, Anhui, China 230031
> Email:address@hidden Tel: +86-0551-65593187
> ------------------------------------------------------
> ??????????????
> ???address@hidden ???+86-0551-65593187
>
Russ Rew UCAR Unidata Program
address@hidden http://www.unidata.ucar.edu
Ticket Details
===================
Ticket ID: USP-401162
Department: Support netCDF
Priority: Normal
Status: Closed