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Re: ccplot 1.5-rc7 build error
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From: Peter K. <pet...@wa...> - 2013-11-22 20:48:58
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Ryan, It seems like libhdfeos.0.dylib is compiled as 64-bit, but python is 32-bit (or vice-versa). Could you please try: file `which python` file /opt/local/lib/libhdfeos.0.dylib python -V python -c 'import platform; print platform.machine(); print platform.architecture()' Also if you can tell me your Mac OS X version... Hopefully, having more information will help. Cheers, Peter On 11/22/2013 08:57 PM, Ryan Scott wrote: > Hi Peter, > > Unfortunately, I'm running into new trouble. Perhaps the issue might be > specific to my machine? > > Here is output from a simple command which should work if installation > were successful. > > bash-3.2$ ccplot -V > Traceback (most recent call last): > File "/usr/local/bin/ccplot", line 56, in <module> > from ccplot.hdfeos import HDFEOS > ImportError: dlopen(/Library/Python/2.7/site-packages/ccplot/hdfeos.so, > 2): Symbol not found: _for_init > Referenced from: /opt/local/lib/libhdfeos.0.dylib > Expected in: flat namespace > in /opt/local/lib/libhdfeos.0.dylib > > Thanks, > > Ryan > > > > > > On Fri, Nov 22, 2013 at 11:40 AM, Ryan Scott <rsc...@gm... > <mailto:rsc...@gm...>> wrote: > > Hey Peter, > > I just ran the build script (using the latest setup.py file that you > sent in the last message) and didn't receive any errors like those > that have been causing a forced exit on previous attempts. I ran > sudo python setup.py install and it seems to check out alright. Is > there a way of testing the install to ensure that everything should > work correctly before I embark on learning how to use ccplot? > > Attached is the previous setup.py script that resided in ccplot-master. > > Many thanks for your patience and assistance, > > Ryan > > > On Fri, Nov 22, 2013 at 11:29 AM, Peter Kuma <pet...@wa... > <mailto:pet...@wa...>> wrote: > > Ryan, > > Yes it helped! The library_dirs option is apparently not even > applied. > Could you please send me your current setup.py - in case > anything was > wrongly applied? > > Attached is one that should have all modifications needed. > > Peter > > On 11/22/2013 08:11 PM, Ryan Scott wrote: > > Hi Peter, > > > > Here's the build output after having applied the .diff file in the > > ccplot-master directory: > > > > bash-3.2$ cd ~/Desktop/ccplot-master/ > > bash-3.2$ ls > > LICENSEccplot > > MANIFEST.inccplot-verbose-link.diff > > NEWScmap > > README.mdman > > binsetup.py > > buildtest > > bash-3.2$ patch < ccplot-verbose-link.diff > > (Stripping trailing CRs from patch.) > > patching file setup.py > > bash-3.2$ python setup.py build > > running build > > running build_py > > running build_ext > > skipping 'ccplot/hdf.c' Cython extension (up-to-date) > > building 'ccplot.hdf' extension > > clang -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe > -fno-common > > -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE > -DMACOSX > > -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG > -g -Os > > -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 > > -I/Users/ryan/Desktop/src/boost_1_53_0 -pipe -I/usr/include/hdf > > -I/usr/local/include/hdf -I/opt/local/include > > > -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include > > > -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > > -c ccplot/hdf.c -o build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o > > clang: warning: argument unused during compilation: > '-mno-fused-madd' > > In file included from ccplot/hdf.c:314: > > In file included from > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:14: > > In file included from > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:26: > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__multiarray_api.h:1532:1: > > warning: > > unused function '_import_array' [-Wunused-function] > > _import_array(void) > > ^ > > In file included from ccplot/hdf.c:315: > > In file included from > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ufuncobject.h:152: > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__ufunc_api.h:226:1: > > warning: > > unused function '_import_umath' [-Wunused-function] > > _import_umath(void) > > ^ > > 2 warnings generated. > > In file included from ccplot/hdf.c:314: > > In file included from > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:14: > > In file included from > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:26: > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__multiarray_api.h:1532:1: > > warning: > > unused function '_import_array' [-Wunused-function] > > _import_array(void) > > ^ > > In file included from ccplot/hdf.c:315: > > In file included from > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ufuncobject.h:152: > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__ufunc_api.h:226:1: > > warning: > > unused function '_import_umath' [-Wunused-function] > > _import_umath(void) > > ^ > > 2 warnings generated. > > clang -bundle -undefined dynamic_lookup -Wl,-F. -arch i386 > -arch x86_64 > > -L/Users/ryan/Desktop/src/hdf5-1.8.10/hdf5/lib > > -I/Users/ryan/Desktop/src/boost_1_53_0 > > build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o -lmfhdf -ldf > -ljpeg -lz -o > > build/lib.macosx-10.8-intel-2.7/ccplot/hdf.so -v > > Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn) > > Target: x86_64-apple-darwin12.4.0 > > Thread model: posix > > "/usr/bin/ld" -demangle -dynamic -arch i386 -bundle > -macosx_version_min > > 10.8.0 -undefined dynamic_lookup -undefined dynamic_lookup -o > > /var/folders/fx/t186xjbj1wl66fscp60wm0yw0000gp/T//i8J7H3.out > > -L/Users/ryan/Desktop/src/hdf5-1.8.10/hdf5/lib -F. > > build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o -lmfhdf -ldf > -ljpeg -lz > > -arch_multiple -final_output > > build/lib.macosx-10.8-intel-2.7/ccplot/hdf.so -lSystem > > /usr/bin/../lib/clang/4.2/lib/darwin/libclang_rt.eprintf.a > > /usr/bin/../lib/clang/4.2/lib/darwin/libclang_rt.osx.a > > ld: library not found for -lmfhdf > > clang: error: linker command failed with exit code 1 (use -v > to see > > invocation) > > error: command 'clang' failed with exit status 1 > > > > Hopefully this helps! > > > > -Ryan > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, Nov 22, 2013 at 10:58 AM, Peter Kuma > <pet...@wa... <mailto:pet...@wa...> > > <mailto:pet...@wa... > <mailto:pet...@wa...>>> wrote: > > > > Hi Ryan, > > > > dylib is the equivalent of so files on other unix systems. > The linker > > should find the library just fine if it is indeed located > under > > /opt/local/lib/libmfhdf.dylib. I don't know why it does not. > > > > The best I can think of is to add a verbose flag to the > linker to get a > > more detailed error report. A patch is attached. It can be > applied with: > > > > patch < ccplot-verbose-link.diff > > > > in the ccplot directory. If you can send me the build > output that would > > be great. > > > > Regards, > > > > Peter > > > > On 11/22/2013 06:47 PM, Ryan Scott wrote: > > > Hi Peter, > > > > > > After receiving the same error with the up-to-date > ccplot-master, I > > > checked /opt/local/lib and I have the following > libmfhdf* files > > > > > > libmfhdf.0.dylib > > > libmfhdf.a > > > libmfhdf.dylib > > > libmfhdf.la <http://libmfhdf.la> <http://libmfhdf.la> > <http://libmfhdf.la> > > > > > > The lack of the libmfhdf.so file is presumably then the > root of the > > > error. Do you know where this can be obtained? > > > > > > Best, Ryan > > > > > > > > > > > > On Thu, Nov 21, 2013 at 11:53 PM, Peter Kuma > > <pet...@wa... <mailto:pet...@wa...> > <mailto:pet...@wa... <mailto:pet...@wa...>> > > > <mailto:pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>>>> > > wrote: > > > > > > Hi Ryan, > > > > > > I think this could be a similar problem as with the > include > > path. The > > > solution depends on where the libmfhdf.so library > is, I assume > > it is > > > /opt/local/lib. Please try adding the path to > hdf_library_dirs in > > > setup.py: > > > > > > - hdf_library_dirs = [] > > > + hdf_library_dirs = ['/opt/local/lib'] > > > > > > (line 25) > > > > > > Or, if it does not work, please try locate libmfhdf.so. > > > > > > The current master incorporates both fixes for the > include > > path and > > > MAX_VAR_DIMS. > > > > > > Regards, > > > > > > Peter > > > > > > On 11/22/2013 01:38 AM, Ryan Scott wrote: > > > > Hello Peter, > > > > > > > > I have attempted to build both ccplot-master as > well as > > > ccplot-1.5-rc7, > > > > ensuring that hdf.c everywhere reads > H4_MAX_VAR_DIMS where > > necessary. > > > > However, still no luck on the build. > > > > > > > > Here is the output from my latest try: > > > > > > > > bash-3.2$ python setup.py build > > > > running build > > > > running build_py > > > > running build_ext > > > > skipping 'ccplot/hdf.c' Cython extension (up-to-date) > > > > building 'ccplot.hdf' extension > > > > clang -fno-strict-aliasing -fno-common -dynamic -g > -Os -pipe > > > -fno-common > > > > -fno-strict-aliasing -fwrapv -mno-fused-madd > -DENABLE_DTRACE > > -DMACOSX > > > > -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 > > -DNDEBUG -g -Os > > > > -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch > i386 -arch > > x86_64 > > > > -I/Users/ryan/Desktop/src/boost_1_53_0 -pipe > -I/usr/include/hdf > > > > -I/usr/local/include/hdf -I/opt/local/include > > > > > > > > > > -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include > > > > > > > > > > -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > > > > -c ccplot/hdf.c -o > build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o > > > > clang: warning: argument unused during compilation: > > '-mno-fused-madd' > > > > In file included from ccplot/hdf.c:314: > > > > In file included from > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:14: > > > > In file included from > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:26: > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__multiarray_api.h:1532:1: > > > > warning: > > > > unused function '_import_array' > [-Wunused-function] > > > > _import_array(void) > > > > ^ > > > > In file included from ccplot/hdf.c:315: > > > > In file included from > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ufuncobject.h:152: > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__ufunc_api.h:226:1: > > > > warning: > > > > unused function '_import_umath' > [-Wunused-function] > > > > _import_umath(void) > > > > ^ > > > > 2 warnings generated. > > > > In file included from ccplot/hdf.c:314: > > > > In file included from > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:14: > > > > In file included from > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:26: > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__multiarray_api.h:1532:1: > > > > warning: > > > > unused function '_import_array' > [-Wunused-function] > > > > _import_array(void) > > > > ^ > > > > In file included from ccplot/hdf.c:315: > > > > In file included from > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ufuncobject.h:152: > > > > > > > > > > /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/__ufunc_api.h:226:1: > > > > warning: > > > > unused function '_import_umath' > [-Wunused-function] > > > > _import_umath(void) > > > > ^ > > > > 2 warnings generated. > > > > clang -bundle -undefined dynamic_lookup -Wl,-F. > -arch i386 -arch > > > x86_64 > > > > -L/Users/ryan/Desktop/src/hdf5-1.8.10/hdf5/lib > > > > -I/Users/ryan/Desktop/src/boost_1_53_0 > > > > build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o > -lmfhdf -ldf > > -ljpeg > > > -lz -o > > > > build/lib.macosx-10.8-intel-2.7/ccplot/hdf.so > > > > ld: library not found for -lmfhdf > > > > clang: error: linker command failed with exit code > 1 (use -v > > to see > > > > invocation) > > > > error: command 'clang' failed with exit status 1 > > > > > > > > Hopefully this is also an easy fix. Best, > > > > > > > > Ryan > > > > > > > > > > > > On Thu, Nov 21, 2013 at 2:10 PM, Peter Kuma > > > <pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>> > > <mailto:pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>>> > > > > <mailto:pet...@wa... > <mailto:pet...@wa...> > > <mailto:pet...@wa... > <mailto:pet...@wa...>> <mailto:pet...@wa... > <mailto:pet...@wa...> > > <mailto:pet...@wa... > <mailto:pet...@wa...>>>>> > > > wrote: > > > > > > > > Hi Ryan, > > > > > > > > Thanks for the follow-up. It is nice to hear > you find ccplot > > > useful. > > > > > > > > I was afraid there may be more problems. I'm > sure other mac > > > users will > > > > be happy to see this sorted out. > > > > > > > > The reason is that MAX_VAR_DIMS is only > available when HDF4 > > > was compiled > > > > with netcdf-3 compatibility. It should be easy > to fix by > > > replacing all > > > > occurrences of MAX_VAR_DIMS with H4_MAX_VAR_DIMS. > > > > > > > > Please try an updated version from github: > > > > > > > > > https://github.com/peterkuma/ccplot/archive/master.zip > > > > > > > > Regards, > > > > > > > > Peter > > > > > > > > On 11/21/2013 09:37 PM, Ryan Scott wrote: > > > > > Hello Peter, > > > > > > > > > > I very much appreciate the timely response > and your > > > willingness to > > > > help. > > > > > I was happy to see that a new version of > ccplot was > > > available without > > > > > the PyNIO dependency, which has prevented me > from using it > > > in the > > > > past. > > > > > ccplot appears to be far superior than what is > > possible using > > > > Matlab and > > > > > NCAR Command Language! > > > > > > > > > > I have modified line 24 of setup.py to reflect > > > '/opt/local/include' as > > > > > well, and I no longer receive the error > regarding > > hntdefs.h. > > > > > > > > > > Unfortunately, though I'm presented with a > new error. To > > > give you as > > > > > much detail as possible, here's the new issue: > > > > > > > > > > "bash-3.2$ python setup.py build > > > > > running build > > > > > running build_py > > > > > running build_ext > > > > > skipping 'ccplot/hdf.c' Cython extension > (up-to-date) > > > > > building 'ccplot.hdf' extension > > > > > clang -fno-strict-aliasing -fno-common > -dynamic -g -Os > > -pipe > > > > -fno-common > > > > > -fno-strict-aliasing -fwrapv -mno-fused-madd > > -DENABLE_DTRACE > > > -DMACOSX > > > > > -DNDEBUG -Wall -Wstrict-prototypes > -Wshorten-64-to-32 > > > -DNDEBUG -g -Os > > > > > -Wall -Wstrict-prototypes -DENABLE_DTRACE > -arch i386 -arch > > > x86_64 > > > > > -I/Users/ryan/Desktop/src/boost_1_53_0 -pipe > > -I/usr/include/hdf > > > > > -I/usr/local/include/hdf -I/opt/local/include > > > > > > > > > > > > > > > -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include > > > > > > > > > > > > > > > -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > > > > > -c ccplot/hdf.c -o > > build/temp.macosx-10.8-intel-2.7/ccplot/hdf.o > > > > > clang: warning: argument unused during > compilation: > > > '-mno-fused-madd' > > > > > ccplot/hdf.c:5266:30: error: use of > undeclared identifier > > > > 'MAX_VAR_DIMS' > > > > > __pyx_t_1 = PyInt_FromLong(MAX_VAR_DIMS); if > > > (unlikely(!__pyx_t_1)) > > > > > {__pyx_filename =... > > > > > ^ > > > > > ccplot/hdf.c:7066:30: error: use of > undeclared identifier > > > > 'MAX_VAR_DIMS' > > > > > __pyx_t_1 = PyInt_FromLong(MAX_VAR_DIMS); if > > > (unlikely(!__pyx_t_1)) > > > > > {__pyx_filename =... > > > > > ^ > > > > > 2 errors generated. > > > > > error: command 'clang' failed with exit > status 1" > > > > > > > > > > Perhaps there is an easy fix? > > > > > > > > > > Best, > > > > > > > > > > -Ryan > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Nov 21, 2013 at 12:11 AM, Peter Kuma > > > > <pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>> > > <mailto:pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>>> > > > <mailto:pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>> > > <mailto:pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>>>> > > > > > <mailto:pet...@wa... > <mailto:pet...@wa...> > > <mailto:pet...@wa... > <mailto:pet...@wa...>> > > > <mailto:pet...@wa... > <mailto:pet...@wa...> > > <mailto:pet...@wa... > <mailto:pet...@wa...>>> <mailto:pet...@wa... > <mailto:pet...@wa...> > > <mailto:pet...@wa... > <mailto:pet...@wa...>> > > > <mailto:pet...@wa... > <mailto:pet...@wa...> <mailto:pet...@wa... > <mailto:pet...@wa...>>>>>> > > > > wrote: > > > > > > > > > > On 11/21/2013 02:07 AM, ryan scott wrote: > > > > > > I have installed all dependencies for > ccplot. > > However, > > > when > > > > > attempting to build ccplot before > installation, I > > > receive the > > > > > following error message: > > > > > > > > > > > > "ccplot/hdf.c:317:10: fatal error: > 'hntdefs.h' file > > > not found > > > > > > #include "hntdefs.h" > > > > > > ^ > > > > > > 1 error generated. > > > > > > error: command 'clang' failed with > exit status 1" > > > > > > > > > > > > I do, however, have the hdf4 library > installed (via > > > > MacPorts), the > > > > > following > > > > > > > > > > > > bash-3.2$ locate hntdefs.h > > > > > > /opt/local/include/hntdefs.h > > > > > > > > > > > > shows that I do have this file. Could > anyone please > > > point me in > > > > > the right direction? > > > > > > > > > > > > Any help is very much appreciated. Thanks, > > > > > > > > > > > > Ryan > > > > > > > > > > Dear Ryan, > > > > > > > > > > Sorry - I think this is a problem with > ccplot rather > > > than your > > > > > configuration. It assumes that hdf is > available > > under either > > > > > /usr/include/hdf or > /usr/local/include/hdf, which > > is a valid > > > > assumption > > > > > on linux, but not on mac. For now, could you > > please just add > > > > the path to > > > > > hdf_include_dirs in setup.py? > > > > > > > > > > - hdf_include_dirs = ['/usr/include/hdf', > > > > '/usr/local/include/hdf'] > > > > > + hdf_include_dirs = ['/usr/include/hdf', > > > > '/usr/local/include/hdf', > > > > > '/opt/local/include'] > > > > > > > > > > (line 24) > > > > > > > > > > Unfortunately, I don't have access to a > mac system for > > > testing > > > > now, so I > > > > > would not find out. Hopefully, darwin > will be good > > > enough for > > > > this. I'll > > > > > try to fix these issues soon. > > > > > > > > > > Thank you very much for reporting the > problem. > > > > > > > > > > Regards, > > > > > > > > > > Peter > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > |
