mixPainter issue

[Mishura]

Hello,
I tried to repeat steps of badMIXTURE example and I got this error:

Error in mixPainter() : 
  You don't have mixPainter. Try downloading it from https://people.maths.bris.ac.uk/~madjl/finestructure/mixPainter.zip and putting the contents into

An annotation to this error doesn't specify where should I put the contents. I downloaded MixPainter.zip, decompressed it. I tried to execute a script mixPainter.linux and received the following error:
./mixPainter.linux: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
I have already installed gsl-bin libgsl0-dev.
I have bionic Ubuntu 18.04.2 LTS on my computer. I will be happy if you can advise anything to resolve this problem.

Thanks in advance!

[danjlawson]

As you diagnosed, this issue is to do with linking to the gsl library.

Is "libgsl0-dev" the correct package? I found "libgsl-dev" referenced here https://launchpad.net/ubuntu/bionic/+source/gsl

The output of "gsl-config --libs" and "gsl-config --version" may help.

Would you mind trying the finestructure binary (fs4, "current binary dowload" from https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure.html)? Both are built against gsl. I expect that you will get the same problem, but I have compiled this more recently and so if there is any difference in the library versions this will find it.

[Mishura]

You are right, for finestructure binary I have the same error.
libgsl-dev is already the newest version (2.4+dfsg-6)
gsl-config --libs -L/usr/local/lib -lgsl -lgslcblas -lm
gsl-config --version 2.5

But I managed to launch it on Mac OS.

[danjlawson]

Thanks. I think that this means that the default location to look for GSL isn't working. From this thread it looks like you could try

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
export LD_LIBRARY_PATH

or perhaps

ln /usr/local/lib/libgsl.so /usr/local/lib/libgsl.so.0

depending on whether the problem is that GSL isn't in your LD_LIBRARY_PATH, or whether the naming convention for libgsl changed and my code is looking for the old name?

[Mishura]

Wow! First case works on my local Ubuntu machine, but on the server all methods failed, where finestructure v2 works, so I try to use chromopainter.
Thank you for your response!

[NoeBarthelemy]

Hello!

I had the same issue as Mishura, solved by "ln /usr/local/lib/libgsl.so /usr/local/lib/libgsl.so.0"
However, I then have a memory allocation problem:

Performing PARAMETER ESTIMATION, which is followed by CHROMOSOME PAINTING. They should take similar amounts of time using the default settings.
malloc(): memory corruption

I have really no idea of how to solve it and I really really want to use badMixture for my paper!

Thank you ! :)

Noé