Unable to install CDO
Added by Greta Carrete over 7 years ago
I am trying to install CDO to use the software described in this paper: http://www.sciencedirect.com/science/article/pii/S1364815216302456?np=y&npKey=77c798cb64bf8e3ebe16f40ff1c04fd497af6aefb8a97fbb80ff46e9870c18db
I am using windows 7 and I have downloaded cygwin, which I had no idea it existed. I am following this instructions:
These are the instructions that I am following:
Compilation is done by performing the following steps:
- 1. Unpack the archive, if you haven’t done that yet:
gunzip cdo-$VERSION.tar.gz # uncompress the archive tar xf cdo-$VERSION.tar # unpack it cd cdo-$VERSION
- 2. Run the configure script:
./configure
• Optionaly with NetCDF [NetCDF] support:./configure --with-netcdf=<NetCDF root directory>
• and with GRIB_API:./configure --with-grib_api=<GRIB_API root directory>
For an overview of other configuration options use./configure --help
- 3. Compile the program by running make:
make
The program should compile without problems and the binary (cdo) should be available in the src directory
of the distribution.
1.1.2. Installation
After the compilation of the source code do a make install, possibly as root if the destination permissions
require that.
make install
When I run ./configure I get the following error: multithreaded settings NOT found.
I have also tried by downloading: cdo-1.8.0-cygwin64.zip. I realized I didn’t have the cyggomp-1.dll file but I managed to get it from the internet. When I double click on cdo.exe I get the error cyggcc_s-she-1.dll is missing. I am not able to find this file in the internet.
I have tried to execute cdo.exe from Cygwin and what it says is: No operator given!
I have also downloaded the packages netcdf, udunits and libproj following the instructions here: https://code.zmaw.de/projects/cdo/wiki/Win32
I have run out of ideas... Any help would be very much appreciated.
Thank you very much,
Greta
PS: This is the full info I get when I run ./configure:
$ ./configure --with-netcdf --with-hdf5 checking build system type... x86_64-unknown-cygwin checking host system type... x86_64-unknown-cygwin checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... no checking whether to enable maintainer-specific portions of Makefiles... no checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.exe checking for suffix of executables... .exe checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for ar... ar checking the archiver (ar) interface... ar configure: setting up libtool checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... c:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe ) is GNU ld... noinker (c:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe checking for BSD- or MS-compatible name lister (nm)... /cygdrive/c/Rtools/gcc-4.6.3/bin/nm -B checking the name lister (/cygdrive/c/Rtools/gcc-4.6.3/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 8192 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-cygwin file names to x86_64-unknown-cygwin format... func_convert_fil e_noop checking how to convert x86_64-unknown-cygwin file names to toolchain format... func_convert_file_noop option to reload object files... -r6-w64-mingw32/bin/ld.exe checking for objdump... objdump checking how to recognize dependent libraries... file_magic ^x86 archive import|^x86 DLL checking for dlltool... dlltool checking how to associate runtime and link libraries... func_cygming_dll_for_implib checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /cygdrive/c/Rtools/gcc-4.6.3/bin/nm -B output from gcc object... failed checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... no checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -DDLL_EXPORT -DPIC checking if gcc PIC flag -DDLL_EXPORT -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes ) supports shared libraries... yes:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe checking dynamic linker characteristics... Win32 ld.exe checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking for g++... g++ checking for gcc option to accept ISO C99... -std=gnu99 checking for C/C++ restrict keyword... __restrict checking for gcc -std=gnu99 option to support OpenMP... -fopenmp checking for ar... (cached) ar checking for ld... c:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe checking for nm... /cygdrive/c/Rtools/gcc-4.6.3/bin/nm -B checking for ar... (cached) ar checking for as... as checking for dlltool... (cached) dlltool checking for objdump... (cached) objdump checking for strip... (cached) strip checking for ranlib... (cached) ranlib checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... c:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe ) is GNU ld... noinker (c:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe ) supports shared libraries... noc:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe checking for g++ option to produce PIC... -DDLL_EXPORT -DPIC checking if g++ PIC flag -DDLL_EXPORT -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes ) supports shared libraries... noc:/rtools/gcc-4.6.3/i686-w64-mingw32/bin/ld.exe checking dynamic linker characteristics... Win32 ld.exe checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... no checking for malloc in -lmalloc... no checking for struct stat.st_blksize... no checking sys/resource.h usability... no checking sys/resource.h presence... no checking for sys/resource.h... no checking sys/times.h usability... no checking sys/times.h presence... no checking for sys/times.h... no checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking glob.h usability... no checking glob.h presence... no checking for glob.h... no checking fnmatch.h usability... no checking fnmatch.h presence... no checking for fnmatch.h... no checking wordexp.h usability... no checking wordexp.h presence... no checking for wordexp.h... no checking execinfo.h usability... no checking execinfo.h presence... no checking for execinfo.h... no checking for mallinfo... no checking for backtrace... no checking for getrlimit... no checking for gethostname... no checking for floor in -lm... no checking whether isnan is declared... no checking for sqrtl... no checking for feenableexcept... no checking for fenv_t.__control... no checking for fenv_t.__mxcsr... no checking for DATA support... checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... no checking whether pthreads work with -pthreads... no checking whether pthreads work with -mthreads... no checking for the pthreads library -lpthread... no checking whether pthreads work with --thread-safe... no checking whether pthreads work with -mt... no checking for pthread-config... no configure: error: multithreaded settings NOT found
Replies (5)
RE: Unable to install CDO - Added by Uwe Schulzweida over 7 years ago
I have tried to execute cdo.exe from Cygwin and what it says is: No operator given!That seems to be a correct working cdo version!
RE: Unable to install CDO - Added by Greta Carrete over 7 years ago
Good to know I have a working version 
But how do I install it? I have also tried to copy paste cdo.exe in C:/
I feel like I am useless at this...
Many thanks
RE: Unable to install CDO - Added by Uwe Schulzweida over 7 years ago
Hmm I'm not a window user, sorry. Maybe the docu of your software can help:
MERRA Spatial Downscaling for Hydrology (MSDH) 1.1. Installing CDO Obtain latest win32 version of CDO from https://code.zmaw.de/projects/cdo/files. Installing CDO is also very simple and similar to the installing netCDF DLL. To install CDO.exe, you just have to leave it in some directory in your computer, and tell your compiler in which directory to look for it. If you place the CDO.exe in Windows\System32 folder, you will be able to use this without further work. But if you put it in some other place, add the folder address that contains CDO.exe (Right click Computer→Properties→Advanced System Settings→Advanced→Environment variables).
RE: Unable to install CDO - Added by Greta Carrete over 7 years ago
thanks for looking at it. It has been in that folder since the begining... I am starting to think that i am having problems with another program. Many thanks!!
RE: Unable to install CDO - Added by Greta Carrete over 7 years ago
I have managed to run the programme I am interested in but I get the error: cyggcc_s-seh-1.dll is missing. Any thoughts of where I could get it? thx