Build notes for optics_dbscan_mex_src

[hirschmichael]

There are no build notes or any build_mex.m in optics_dbscan_mex_src. I'm not sure how to build this without it.

[grcedw1]

%In Linux running matlab 2017b
%Idea taken from https://uk.mathworks.com/matlabcentral/answers/237411-can-i-make-use-of-openmp-in-my-matlab-mex-files#comment_562414

mex -v -largeArrayDims CFLAGS="$CFLAGS -fopenmp" -I/usr/include -cxx -c pdsdbscan.cpp utils.cpp omp_dbscan.cpp kdtree2.cpp clusters.cpp dbscan.cpp

%First command runs ok

mex -v -largeArrayDims CFLAGS="$CFLAGS -fopenmp" CLIBS="$CLIBS -fopenmp" -cxx pdsdbscan.o utils.o omp_dbscan.o kdtree2.o clusters.o dbscan.o -output pdsdbscan

%Second command fails
Error using mex
omp_dbscan.o: In function omp_dbscan(double*, double*, int, int, double, int)': omp_dbscan.cpp:(.text+0x2b): undefined reference to omp_set_num_threads'
omp_dbscan.cpp:(.text+0x2a9): undefined reference to omp_get_wtime' omp_dbscan.cpp:(.text+0x2c2): undefined reference to omp_get_wtime'
omp_dbscan.cpp:(.text+0x370): undefined reference to omp_get_wtime' omp_dbscan.cpp:(.text+0x389): undefined reference to omp_get_wtime'
dbscan.o: In function NWUClustering::run_dbscan_algo_uf(NWUClustering::ClusteringAlgo&) [clone ._omp_fn.2]': dbscan.cpp:(.text+0xfe): undefined reference to omp_get_num_threads'
dbscan.cpp:(.text+0x106): undefined reference to omp_get_thread_num' dbscan.cpp:(.text+0x23a): undefined reference to omp_set_lock'
dbscan.cpp:(.text+0x268): undefined reference to omp_unset_lock' dbscan.cpp:(.text+0x2a1): undefined reference to omp_set_lock'
dbscan.cpp:(.text+0x2cf): undefined reference to omp_unset_lock' dbscan.cpp:(.text+0x2f1): undefined reference to omp_set_lock'
dbscan.cpp:(.text+0x316): undefined reference to omp_unset_lock' dbscan.cpp:(.text+0x335): undefined reference to omp_unset_lock'
dbscan.cpp:(.text+0x347): undefined reference to omp_unset_lock' dbscan.cpp:(.text+0x358): undefined reference to omp_unset_lock'
dbscan.o: In function NWUClustering::run_dbscan_algo_uf(NWUClustering::ClusteringAlgo&) [clone ._omp_fn.1]': dbscan.cpp:(.text+0x38a): undefined reference to omp_get_num_threads'
dbscan.cpp:(.text+0x392): undefined reference to omp_get_thread_num' dbscan.cpp:(.text+0x3c3): undefined reference to omp_init_lock'
dbscan.o: In function NWUClustering::run_dbscan_algo_uf(NWUClustering::ClusteringAlgo&) [clone ._omp_fn.0]': dbscan.cpp:(.text+0x72b): undefined reference to omp_get_thread_num'
dbscan.cpp:(.text+0x9ad): undefined reference to GOMP_barrier' dbscan.cpp:(.text+0x9da): undefined reference to GOMP_barrier'
dbscan.o: In function NWUClustering::run_dbscan_algo(NWUClustering::ClusteringAlgo&)': dbscan.cpp:(.text+0x12db): undefined reference to omp_get_wtime'
dbscan.cpp:(.text+0x16ce): undefined reference to omp_get_wtime' dbscan.o: In function NWUClustering::run_dbscan_algo_uf(NWUClustering::ClusteringAlgo&)':
dbscan.cpp:(.text+0x19c0): undefined reference to omp_get_max_threads' dbscan.cpp:(.text+0x1ae1): undefined reference to omp_get_wtime'
dbscan.cpp:(.text+0x1b25): undefined reference to GOMP_parallel' dbscan.cpp:(.text+0x1b2a): undefined reference to omp_get_wtime'
dbscan.cpp:(.text+0x1bec): undefined reference to omp_get_wtime' dbscan.cpp:(.text+0x1c16): undefined reference to GOMP_parallel'
dbscan.cpp:(.text+0x1c4b): undefined reference to GOMP_parallel' dbscan.cpp:(.text+0x1c57): undefined reference to omp_get_wtime'
collect2: error: ld returned 1 exit status

Error in build_mex_pdsdbscan (line 2)
mex -v -largeArrayDims CFLAGS="$CFLAGS -fopenmp" CLIBS="$CLIBS -fopenmp" -cxx pdsdbscan.o utils.o omp_dbscan.o kdtree2.o clusters.o dbscan.o -output pdsdbscan

[yalexand]

I was advised by my HPC team to use 2017a Matlab in command line mode (that may be crucial)
The commands to compile these 2 mexa64 files then pass normally (run this when cd to corresponding directories):

mex -v -largeArrayDims CXXFLAGS="$CXXFLAGS -fPIC -fopenmp" -I/usr/include -cxx -c kdtree2.cpp utils.cpp kdtree2rnearest.cpp

mex -v -largeArrayDims CXXFLAGS="$CXXFLAGS -fPIC -fopenmp" CXXLIBS="$CXXLIBS -fopenmp" -cxx kdtree2.o utils.o kdtree2rnearest.o -output kdtree2rnearest

and

mex -v -largeArrayDims CXXFLAGS="$CXXFLAGS -fPIC -fopenmp" -I/usr/include -cxx -c kdtree2.cpp dbscan.cpp utils.cpp clusters.cpp omp_dbscan.cpp pdsdbscan.cpp

mex -v -largeArrayDims CXXFLAGS="$CXXFLAGS -fPIC -fopenmp" CXXLIBS="$CXXLIBS -fopenmp" -cxx kdtree2.o dbscan.o utils.o clusters.o omp_dbscan.o pdsdbscan.o -output pdsdbscan

don't forger to rename "pdsdbscan.mexa64 to "t_dbscan.mexa64", the latter name is used by ClusDoC.