Question: Cannot run or build KING on Mac OS X
1
gravatar for gaelgarcia05
2.4 years ago by
gaelgarcia05210
UK
gaelgarcia05210 wrote:

I'm having an issue running KING on Mac OS X . It has to do with a dylib, I think. Does anybody have any suggestions on how to fix this error?

Thanks!

  > ./king -b ./ex/ex.bed

Returns:

dyld: Symbol not found: __ZdaPvm
  Referenced from: /Users/gaelgarcia/Downloads/./king (which was built for Mac OS X 10.13)
  Expected in: /usr/local/lib/libstdc++.6.dylib
 in /Users/gaelgarcia/./king
Abort trap: 6

UPDATE: Have been following valuable suggestions, but I'm still stuck in the dreadful circle of missing libraries/broken symlinks... any help is greatly appreciated.

I've tried building my own KING as suggested, and got the error:

clang: error: unsupported option '-fopenmp'. I further tried to install a new version of gcc via Homebrew, but get: gcc 8.1.0 is already installed, it's just not linked.

Then, I ran brew link --overwrite gcc, which returns: Could not symlink include/c++/8.1.0 /usr/local/include/c++ is not writable.

Also followed a suggestion somebody else gave on stackoverflow, to run clang++ -L /opt/local/lib/libomp/ -lm -lz -O2 -fopenmp -o king *.cpp , alas to no avail. Yikes... đŸ˜«


UPDATE:

Having installed llvm via Homebrew (brew install llvm), the command that got KING properly built and running on my Mac OS 10.12 was:

/usr/local/Cellar/llvm/6.0.0/bin/clang++ -I /usr/local/Cellar/llvm/6.0.0/include -L /usr/local/Cellar/llvm/6.0.0/lib -O2 -fopenmp -lm -lz -o king *.cpp

Running the newly built executable with the example .bed file provided:

> ./king -b ../ex/ex.bed

KING 2.1.3 - (c) 2010-2018 Wei-Min Chen

The following parameters are in effect:
Binary File :    ../ex/ex.bed (-bname)
ibd error plink dylib king • 1.6k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by gaelgarcia05210
1
gravatar for jbalberge
2.4 years ago by
jbalberge140
France/Nantes
jbalberge140 wrote:

KING was probably built with gcc 6.x and is looking for a gcc 6 library. Try build your own KING with the C++ source code with http://people.virginia.edu/~wc9c/KING/KINGcode.tar.gz as mentioned in http://people.virginia.edu/~wc9c/KING/Download.htm

cd Downloads/KINGcode/
c++ -lm -lz -O2 -fopenmp -o king *.cpp

PS: found more details on https://www.ncl.ucar.edu/Download/macosx.shtml#ZdaPvmNotFound

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by jbalberge140

Yup. I found it necessary to use Homebrew to install a newer version of gcc in order to build/run KING on my Mac.

ADD REPLYlink written 2.4 years ago by chrchang5237.3k

Thanks @jbalberge and @chrchang523 - I've tried building my own KING as suggested, and got the error: clang: error: unsupported option '-fopenmp'. I further tried to install a new version of gccvia Homebrew, but get gcc 8.1.0 is already installed, it's just not linked. Then, I ran brew link --overwrite, which returns: Could not symlink include/c++/8.1.0 /usr/local/include/c++ is not writable. Also followed a suggestion somebody else gave on stackoverflow, to run clang++ -L /opt/local/lib/libomp/ -lm -lz -O2 -fopenmp -o king *.cpp , alas to no avail. Yikes... đŸ˜«

ADD REPLYlink written 2.4 years ago by gaelgarcia05210
1

My bad, building c++ code with the Open MP lib on Mac OS X seems quite hard. Let's go back to the compiled version. I managed to have it work after setting the dyld library path

brew install gcc
brew link gcc
export DYLD_LIBRARY_PATH=/usr/local/lib/gcc/8/:$DYLD_LIBRARY_PATH
./king -b ex/ex.bed

Let me know if this works for you

ADD REPLYlink written 2.4 years ago by jbalberge140

Thank you, @jbalberge! I managed to get it working via the source build alternative (See Update). Thank you for all your time and help!

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by gaelgarcia05210

Great! Thanks for the updates!

ADD REPLYlink written 2.4 years ago by jbalberge140
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