Failure to compile multi-thread version of FDPPDiv

[Satoshi Eguchi]

Hello all,

Although single thread version of FDPPDiv 1.3 was successfully compiled, multi-thread version failed.

I tried to make dppdiv-par on Mac OS 10.10 and following error was produced:

$ make dppdiv-par

g++ -o dppdiv-par -fopenmp dppdiv.o Alignment.o MbEigensystem.o MbMath.o MbRandom.o MbTransitionMatrix.o Mcmc.o Parameter.o Parameter_basefreq.o Parameter_exchangeability.o Parameter_rate.o Parameter_shape.o Parameter_tree.o Parameter_cphyperp.o Parameter_treescale.o Parameter_speciaton.o Parameter_expcalib.o Calibration.o Model.o Model_likelihood-par.o

ld: library not found for -lgomp

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [dppdiv-par] Error 1

I also tried on Windows 7 with MinGW but it failed.

g++ -o dppdiv-par -fopenmp dppdiv.o Alignment.o MbEigensystem.o MbMath.o MbRandom.o MbTransitionMatrix.o Mcmc.o Parameter.o Parameter_basefreq.o Parameter_exchangeability.o Parameter_rate.o Parameter_shape.o Parameter_tree.o Parameter_cphyperp.o Parameter_treescale.o Parameter_speciaton.o Parameter_expcalib.o Calibration.o Model.o Model_likelihood-par.o

c:mingw/bin/../lib/gcc/minggw32/4.8.1/../../../../ming32/bin/ld.exe: cannot find -lpthread

collect2.exe: error: ld returned 1 exit status

make : *** [dppdiv-par] Error 1

What is wrong?

Please help me to solve the problem.

Thank you,

Satoshi Eguchi

[Tomas Flouri]

Hello Satoshi,

> $ make dppdiv-par
> g++ -o dppdiv-par -fopenmp dppdiv.o Alignment.o MbEigensystem.o
> MbMath.o MbRandom.o MbTransitionMatrix.o Mcmc.o Parameter.o
> Parameter_basefreq.o Parameter_exchangeability.o Parameter_rate.o
> Parameter_shape.o Parameter_tree.o Parameter_cphyperp.o
> Parameter_treescale.o Parameter_speciaton.o Parameter_expcalib.o
> Calibration.o Model.o Model_likelihood-par.o
> ld: library not found for -lgomp
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [dppdiv-par] Error 1

You'll need to install openmp on your machine. If you use a debian-based
distro, you can run (as root):

apt-get install libgomp1

> I also tried on Windows 7 with MinGW but it failed.
>
> g++ -o dppdiv-par -fopenmp dppdiv.o Alignment.o MbEigensystem.o
> MbMath.o MbRandom.o MbTransitionMatrix.o Mcmc.o Parameter.o
> Parameter_basefreq.o Parameter_exchangeability.o Parameter_rate.o
> Parameter_shape.o Parameter_tree.o Parameter_cphyperp.o
> Parameter_treescale.o Parameter_speciaton.o Parameter_expcalib.o
> Calibration.o Model.o Model_likelihood-par.o
> c:mingw/bin/../lib/gcc/minggw32/4.8.1/../../../../ming32/bin/ld.exe:
> cannot find -lpthread
> collect2.exe: error: ld returned 1 exit status
> make : *** [dppdiv-par] Error 1

pthreads do not come on Windows by default; you'll need to install them
separately. This page might help:

https://www.sourceware.org/pthreads-win32/

However, there might be more problems when compiling on Windows that I
am not aware of.

Hope this helps,

Tomas

[Satoshi Eguchi]

Hello Tomas,

Thanks!

Your advise led me to compile without error.

However, I have another problem.

Analysing my data which has about five hundred fossils resulted in segmentation fault.

When I reduced fossils to 200, it runs well.

Is the number of fossil calibrations limited?

Satoshi

2014年11月28日金曜日 23時42分19秒 UTC+9 Tomas Flouri:

[Tracy Heath]

Hi Stoshi,

It should work with 500 fossils, I have run it with that many before. It might be that there was some interaction among the fossils that caused the tree initialization to fail. How many extant taxa are in your tree? 500 fossils is quite a lot for MCMC under the FBD model and will lead to extremely long mixing times. 

Cheers!

Tracy

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[Satoshi Eguchi]

Hi Tracy,

My data contains 120 taxa.

Thanks,
Satoshi