link error on ubuntu 13.10 with apt-get installed libadolc2/libadolc-dev

[rhr]

g++ -O3 -g3 -o treePL ./main.o ./node.o ./pl_calc_parallel.o ./tnc.o ./tree.o ./tree_reader.o ./tree_utils.o ./optimize_tnc.o ./optimize_nlopt.o ./myradops.o ./siman_calc_par.o ./optim_options.o ./utils.o -lm -fopenmp -ladolc -L/usr/lib64 -lnlopt
./main.o: In function `ADOLC_OpenMP_NC':
/usr/include/adolc/adolc_openmp.h:46: undefined reference to `ADOLC_parallel_doCopy'
/usr/include/adolc/adolc_openmp.h:47: undefined reference to `beginParallel()'
./main.o: In function `~ADOLC_OpenMP_NC':
/usr/include/adolc/adolc_openmp.h:50: undefined reference to `endParallel()'
collect2: error: ld returned 1 exit status
make: *** [treePL] Error 1

[wrightaprilm]

I was also having this issue. Double check your Makefule. Mine had usr/lib64 and was therefore looking in the wrong place. When I edited this to usr/lib, I was off to the races!

[blackrim]

Thanks, yes that could be it. I may need to change that to discover it. Installed 14.04 to start debuging

On Sun, May 11, 2014 at 3:40 PM, April Wright [email protected]:

I'm was also having this issue. Double check your Makefule. Mine had usr/lib64 and was therefore looking in the wrong place. When I edited this to usr/lib, I was off to the races!

— Reply to this email directly or view it on GitHubhttps://github.com/blackrim/treePL/issues/7#issuecomment-42780645 .

[rhr]

Actually I think the issue is that libadolc from the repos isn't compiled with mpi. Also, recent versions of adolc don't compile against openmpi on linux - I had to use an older version (2.1 I think) and install it manually. So I guess this can be closed.

[wrightaprilm]

Hmm. I might have to try this solution, Rick. I've got treePL compiled and functional, but I'm running into an issue. I'm replicating a published analysis (4.1k taxa, 13k sites) with 6 calibrations. I'm running into my init vlaues == LARGE. As far as I can see, this could be 1) an issue related to my wonky compile or 2) some sort of number of taxa-by-sites-by-constraints problem that actually is resulting in the initial values being what they are.

Do you have a gut feeling about for what's up there, Stephen?