Possible bug in make

Mitch Day

unread,

Jan 25, 2012, 2:38:02 PM1/25/12

to Stacks

Hi, Julian.

I'm Mitch Day, a new scientific aide in Paul H's lab. I'm just
starting to get
my head around Stacks and have found what may be a bug. I hope I can
help
you squish it.

I'm trying to install Stacks on a 64-bit Mac with 2 x 2.66 GHz 6-Core
Intel Xeon processors.

configure proceeds without any error messages. I used no flags for
configure.

make seems to proceed fine until the end.
I get the error:
====================

Undefined symbols for architecture x86_64:
"_gomp_thread_attr", referenced from:
_initialize_env in libgomp.a(env.o)
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[1]: *** [genotypes] Error 1
make: *** [all] Error 2

==========================

The individual pipeline components seemed to build alright. They are
at least available in the make directory and they respond properly to
a help request.

On issuing make install as root, I get the very similar error:
=============================================

g++ -fopenmp -g -O2 -fopenmp -o genotypes src/genotypes-genotypes.o
src/genotypes-DNASeq.o src/genotypes-stacks.o src/genotypes-input.o
Undefined symbols for architecture x86_64:
"_gomp_thread_attr", referenced from:
_initialize_env in libgomp.a(env.o)
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make: *** [genotypes] Error 1
===========================================

and, of course, the install doesn't work.

Have I given you enough information to chase this apparent bug? Let
me
know if I haven't provided enough context. I can also provide complete
logs if needed.

I'm glad to be aboard. Thanks for such a well-documented software.

Mitch

Kelly O'Quin

unread,

Jan 26, 2012, 8:50:38 AM1/26/12

to Stacks

Does it work if you try "./configure --disable-openmp" before you run
make?

Mitch Day

unread,

Jan 27, 2012, 12:27:32 PM1/27/12

to Stacks

I'll give it a try and report back.

Thanks for the suggestion.

Mitch

Elisa Zhang

unread,

Jan 31, 2012, 3:13:18 PM1/31/12

to Stacks

Hi all,

I had the same problem, and doing as Kelly suggested allowed me to
successfully install Stacks.

Thank you so much, Kelly!

Elisa

Julian Catchen

unread,

Jan 31, 2012, 5:42:09 PM1/31/12

to stacks...@googlegroups.com

Hi all,

Yes, Mac OS X has broken the OpenMP installation on its systems (OpenMP provides
for parallelization in the pipeline). Although it is supposed to be built into
the GCC compiler, OS X does not include the library. To install Stacks anyway,
you have to disable parallelism (which Kelly described correctly how to do).

I wonder if this is also the case on Mac OSX Server, does anyone have
experience? I could see them disabling the OpenMP library on their 'less
powerful' operating system installation.

Cheers,

julian

--
Julian M Catchen, Ph.D.
Institute of Ecology and Evolution
University of Oregon
--
jcat...@uoregon.edu
http://www.uoregon.edu/~jcatchen/

Matthew Conte

unread,

Jan 31, 2012, 5:54:56 PM1/31/12

to stacks...@googlegroups.com

Hi Julian,

I thought I'd chime in quick to say that I too get the same error on OSX Server 10.6.8 and gcc version 4.2.1 (Apple Inc. build 5666) (dot 3). I'm not sure how to fix it though. Perhaps one could install gcc through Fink and try using that version instead of what Apple provides. I haven't tried this, but it might be worth a shot.

-Matt

--
For more options or to unsubscribe: http://groups.google.com/group/stacks-users
Stacks website: http://creskolab.uoregon.edu/stacks/

Mitch Day

unread,

Feb 1, 2012, 6:08:12 PM2/1/12

to Stacks

Kelly, this worked and the make/install went off without a hitch. I am
embarrassed to admit that I completely ignored this bit of advice that
is prominently displayed on the "Requirements" page of the website.

RTFM, indeed.

Thanks,

Mitch

On Jan 26, 5:50 am, "Kelly O'Quin" <kellyoq...@gmail.com> wrote:

Reply all

Reply to author

Forward