FastTree on Mac - Segmentation Fault 11

Question

[celine.petitjean]

Hello all,

I am trying to run FastTree 2.1.10 on my mac and constantly have a Segmentation Fault 11. I reinstalled it several time, including previous versions, without any success.

I tried to run FastTree 2.1.10 with exactly the same alignement on a linux cluster and it runs without any problem, so I think the problem comes from my system.

Anyone would have an idea?

Thanks! Celine

[GenoMax]

Seg fault 11 on macOS appears to be related to memory.

Did you download and compile FastTree from source code on your mac? Looks like there is no native binary available for mac. You can't use the linux binary on mac, in case you were trying it as is.

[Joe]

How big is your input file? What are the servers resources like compared with your laptops?

Answer 1

[Kian Faizi]

Hi Celine,

From the installation instructions on the FastTree website:

If you use a Mac or other platform not included above, download FastTree.c and run

gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm

(gcc is installed on many Mac OS X and Unix machines. If you use a Mac, you may need to install it from xcode. gcc is also available for virtually every platform.) Note that FastTree will try to use SSE2/SSE3 instructions to speed up some inner loops. This will not work on many Windows or Mac machines. If FastTree will not run, then try compiling it with this command instead:

gcc -DNO_SSE -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm

We have also heard that the -finline-functions option can cause an error. You can omit this option.

Using the first variation, I reproduce your segfault 11 error; using the second, FastTree works :) Let me know if this helps!