Compile Error on Mac OS X 10.7 Lion

[Steven Higgins]

To whom this may concern,

I recently downloaded the tar file to install the finis genome gap closing software, but to my dismay am having some issues with getting the code to compile.

Specifically, the error I get is:

[LD]
g++ -o finis obj/CommonFunction.o obj/ConfigReader.o obj/Configure.o obj/ConnectedNode.o obj/Contig.o obj/ContigGraphAnalyzer.o obj/Gap.o obj/PathNode.o obj/QuadProgSolver.o -L/Users/shiggin8/bin/mosek/6/tools/platform/osx64x86/bin -lmosek
ld: library not found for -lmosek
collect2: ld returned 1 exit status
make: *** [finis] Error 1

In the make.sh file, MSKLIBNAME is set to "mosek". Is this correct? I have installed mosek version 6 and have set up the *.dylib files to be accessible via the DYLD_LIBRARY_PATH. Additionally, mosek is specified in my path environment and callable from the shell.

At this point, I don't feel like searching through all the object files using nm or objdump -t to figure out which functions are being called and what libraries are not accessible to them.

If you could provide any assistance on this subject I would greatly appreciate it.

Thank you,

Steve

[Dario Pavlovic]

Hi Steven,

My suggestion for now is to change MSKLIBNAME=mosek to MSKLIBNAME=mosek64. Let me know if this worked.

[Steven Higgins]

Hi Dario,

I set MSKLIBNAME equal to mosek64 but now I get this error message:

[LD]
g++ -o finis obj/CommonFunction.o obj/ConfigReader.o obj/Configure.o obj/ConnectedNode.o obj/Contig.o obj/ContigGraphAnalyzer.o obj/Gap.o obj/PathNode.o obj/QuadProgSolver.o -L/Users/shiggin8/bin/mosek/6/tools/platform/osx64x86/bin -lmosek64
Undefined symbols for architecture x86_64:
"omp_get_thread_num", referenced from:
ContigGraphAnalyzer::GenSubgraphImproved(Gap) in ContigGraphAnalyzer.o
ContigGraphAnalyzer::GenerateGapSeq(Gap) in ContigGraphAnalyzer.o
__ZN19ContigGraphAnalyzer13MixedAnalysisEPSt6vectorIP3GapSaIS2_EES5.omp_fn.0 in ContigGraphAnalyzer.o

...many more function calls...

"_omp_set_num_threads", referenced from:
ContigGraphAnalyzer::MixedAnalysis(std::vector<Gap*, std::allocator<Gap*=""> >,
ContigGraphAnalyzer::AnalyzeGaps(std::basic_string<char, std::char_traits<char="">, std::allocator<char> >, std::basic_string<char, std::char_traits<char="">, std::allocator<char> >&)in ContigGraphAnalyzer.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make: ** [finis] Error 1

Thanks for any input you have,

Steve

[Dario Pavlovic]

One of the finis dependencies right now is OpenMP so you should install it if possible. If not, I would have to modify the code and I am not sure how long that would take.

[Steven Higgins]

Thanks Dario,

Let me install OpenMP if I have not and I will get back to you.

Steve

[Dario Pavlovic]

Great. Please do let me know if that fixed it.