3dDespike error

AFNI Message Board
1

Hello experts,

I’m getting a strange error from a script I haven’t used in a few years.

dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/mbmc/abin/3dDespike
Reason: image not found

I’ve echoed the 3dDespike command from the script, and I can run it just fine separately, but the script keeps failing. Other commands run fine. I’m pretty lost at this point. :slight_smile:

Thanks,
-Marina

2

I can tell you WHAT this error is, but not how to fix it :frowning:

3dDespike is written to use the OpenMP parallelizing system for speed – that is, it runs in multiple threads. The binary version of AFNI you have installed must be compiled to use OpenMP using gcc. “libgomp” is “library gcc OpenMP” – but that is not installed on your computer.

Fixing this requires either (a) using a version of Linux that supports OpenMP, or (b) installing AFNI binaries that do not use OpenMP – which will be slower. I guess that you are using one of the “linux_openmp” binaries – to check, type the command ‘afni --ver’. You could try installing one of the “linux_xorg7” binaries instead. However, using OpenMP will make various AFNI programs run faster (that’s the point of OpenMP), so it would be better to use a Linux version/gcc installation that supports OpenMP. But I can’t tell you how to do that.

3

Along the lines of what Bob said, you should be
able to update your binaries to use a package
that comes with such libraries. Then the error
should go away. Consider:

@update.afni.binaries -defaults -package macosx_10.7_local

  • rick