Comments (1)
Later, I got some libomp errors:
/Users/corneliusromer/code/iqtree2/simulator/alisimulator.cpp:1755:71: error: use of undeclared identifier 'omp_get_num_threads'
1755 | if ((*it)->node->sequence->num_threads_done_simulation == omp_get_num_threads())
| ^
1 error generated.
gmake[2]: *** [simulator/CMakeFiles/simulator.dir/build.make:76: simulator/CMakeFiles/simulator.dir/alisimulator.cpp.o] Error 1
gmake[2]: *** Waiting for unfinished jobs....
gmake[1]: *** [CMakeFiles/Makefile2:997: simulator/CMakeFiles/simulator.dir/all] Error 2
gmake: *** [Makefile:156: all] Error 2
I fixed them by using this build script with the help of chatgpt:
export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
export CMAKE_CXX_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include -L/opt/homebrew/opt/libomp/lib -lomp"
export CMAKE_C_FLAGS="-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include -L/opt/homebrew/opt/libomp/lib -lomp"
cmake .. -DCMAKE_CXX_FLAGS="$CMAKE_CXX_FLAGS" -DCMAKE_C_FLAGS="$CMAKE_C_FLAGS" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
make -j
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Related Issues (20)
- problem with start the program in command HOT 12
- [BUG] Infinite loop while using BNNI under PMSF model HOT 2
- Error when estimating linked exchangeabilities (GTRpmix) HOT 4
- not an issue, would like clarification on how to use pmsf
- Crash due to assertion failure in `PhyloSuperTreePlen::computeFuncDerv` HOT 3
- Bug in writing best_model.nex file HOT 1
- Document in help string that `--nt`/`-c`/`-T`/`--threads` are synonyms, print always `-T` instead of `-nt` HOT 1
- Suggestion: Error instead of warn if `--pathogen-force` is set but cmaple not integrated
- doc: code not well formatted for macosx compilation guide
- Consider lowering minimum clang version to 16 for bioconda compatibility HOT 1
- How to reduce verbosity of build logs? HOT 1
- Paired bootstrap values in a .treefile without having specified -alrt
- `--polytomy` flag seems to be ignored when iqtree is using cmaple HOT 1
- Cmaple CLI args not appearing in help string
- Despite passing `--output-multifurcating-tree`, resulting tree is bifurcating, when run in cmaple mode HOT 1
- [Feature Request] Add support for the `--link-exchange-rates` option in the MAST model HOT 2
- Manual out of date with respect to `-t RANDOM`
- Web docs (and wiki) are different from cli help
- ERROR: ratefree.cpp:199: virtual void RateFree::initFromCatMinusOne(Checkpoint&, double): Assertion `fabs(sum_prop + getPInvar() - 1.0) < 0.01' failed. HOT 2
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