I solved the problem of the missing Eigen (eigen3 @3.2.5 is installed), but
still cannot compile openbabel with OpenMP on Mac OS.
This is my cmake results showing that Eigen3 is found.
-- The C compiler identification is GNU 4.8.3
-- The CXX compiler identification is GNU 4.8.3
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /opt/local/bin/gcc-mp-4.8
-- Check for working C compiler: /opt/local/bin/gcc-mp-4.8 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /opt/local/bin/g++-mp-4.8
-- Check for working CXX compiler: /opt/local/bin/g++-mp-4.8 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Using included inchi library.
-- Found LibXml2: /opt/local/lib/libxml2.dylib (found version "2.9.2")
-- Found ZLIB: /opt/local/lib/libz.dylib (found version "1.2.8")
-- Found wxWidgets: TRUE
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - not found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Found Eigen3: /opt/local/include/eigen3 (Required is at least version
"2.91.0")
-- Found PkgConfig: /opt/local/bin/pkg-config (found version "0.28")
-- checking for module 'cairo'
-- found cairo, version 1.14.2
-- Found Cairo: /opt/local/lib/libcairo.dylib
-- Cairo found. PNG output will be supported.
-- Optimizing code for this machine's architecture. Use -DOPTIMIZE_NATIVE=OFF
if cross-compiling.
-- Looking for getopt
-- Looking for getopt - found
-- GUI will not be built
-- Found PythonInterp: /opt/local/bin/python (found version "2.7.10")
-- Configuring done
-- Generating done
-- Build files have been written to:
/Users/ghahremanpour/GG/openbabel-dev/openbabel/build
Then, when I run make I face these errors immediately.
Scanning dependencies of target inchi
Scanning dependencies of target openbabel
[ 0%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_io.o
[ 0%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.o
[ 1%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichican2.o
[ 1%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichicano.o
[ 1%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
[ 1%] Building CXX object src/CMakeFiles/openbabel.dir/atom.o
[ 1%] Building CXX object src/CMakeFiles/openbabel.dir/base.o
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:265:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:275:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:446:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:456:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:761:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:1087:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:2611:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:2621:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:2877:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:2887:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:3190:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:3200:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:3467:no such
instruction: `vzeroupper'
/var/folders/fc/hrcbkx7s57q10l8py793cfpw0000gx/T//cckpTYL3.s:3477:no such
instruction: `vzeroupper'
make[2]: *** [src/CMakeFiles/openbabel.dir/base.o] Error 1
make[2]: *** Waiting for unfinished jobs….
.
.
.
[ 2%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichimake.o
make[2]: *** [src/CMakeFiles/openbabel.dir/atom.o] Error 1
make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs...
I appreciate if you give me some hints.
Cheers,
Mohammad
> On Feb 8, 2016, at 5:25 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
>
> Missing Eigen.
>
> On 8 February 2016 at 13:28, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
>> Hi,
>>
>> if I compiled OB with -DCMAKE_BUILD_TYPE=Debug on my mac (OSX Mavericks,
>> gcc 4.9) many tests fail with
>> 4/150 Test #4: test_align_4 .....................***Exception: Other
>> 6.57 sec
>> Start 5: test_align_5
>> 5/150 Test #5: test_align_5 .....................***Exception:
>> Other 6.78 sec
>> Start 6: test_automorphism_1
>> 6/150 Test #6: test_automorphism_1 ..............***Exception:
>> Other 6.46 sec
>> Start 7: test_automorphism_2
>>
>> Using the normal Release build type all tests pass. Any idea?
>> (I compiled it like that in order to debug a particular test).
>>
>> On Linux the build_type has no influence on the tests.
>>
>> Cheers,
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se
>>
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