Re: [AMBER-Developers] sander arpack undefined reference to second_

From: Gustavo Seabra <>
Date: Mon, 1 Mar 2010 15:29:18 -0300

I see exactly the same thing here, compiling with gcc/gfortran:

$ gfortran --version
GNU Fortran (GCC) 4.3.4 20090804 (release) 1
Copyright (C) 2008 Free Software Foundation, Inc.

lib]$ uname -a
CYGWIN_NT-6.0 Home-Desktop 1.7.0(0.218/5/3) 2009-12-04 17:08 i686 Cygwin

lib]$ nm libnab.a | grep second
         U _seconds
         U _seconds
         U _seconds
         U _arsecond_
0000d740 T _seconds

Compilation works fine, though, and now only stops at mm_pbsa. (see
separate thread.)

Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7450 Ext. 5021

On Mon, Mar 1, 2010 at 3:04 PM, Ben Roberts <> wrote:
> Hi Dave,
> On 1/03/2010, at 10:38 AM, case wrote:
>> On Mon, Mar 01, 2010, Ben Roberts wrote:
>>> This morning when I rebuilt and tested AT, some of the nab tests
>>> failed with the following:
>>> ld: duplicate symbol _second in /opt/intel/Compiler/11.1/076/
>>> Frameworks/mkl/lib/em64t/libmkl_intel_lp64.a(_time_mkl_second.o) and /
>>> Applications/Amber11/lib/libnab.a(time.o)
>> Do you have any notion of why this is showing up now and not earlier?
>> Do you think it is specific to Frameworks?  I don't see any problem with
>> MKL
>> under Linux.  My code is also searching libmkl_intel_lp64.a.
>> Aha:  on linux (icc) if I do this:
>>  cd amber11/lib;  nm libnab.a | grep second
>> I see that libnab.a is defining "second";  however, if I do the same
>> on a Mac (with gcc), libnab is exporting "_second".  And MKL is also
>> exporting "_second".  What compiler are you using??  And what do you get
>> on your system with the above nm command?
>> Don't do anything right now to the code; I think we can eliminate all
>> references to second() pretty easily.  But it would be nice to track down
>> exactly what combination is failing.
> First, as to why now and not earlier: I hadn't done a full cvs checkout for
> several days, during which time a lot changed. Partly, I was waiting for
> things to settle down. I knew people had changed something to do with
> second, and figured that the chances were good that this breakage was
> related to that.
> Secondly, the nm command reports this:
> [roberts.qtpclnt070 lib]$ nm libnab.a | grep second
>                 U _seconds
>                 U _seconds
>                 U _seconds
>                 U _second
> 0000000000000000 T _seconds
> 00000000000000d0 T _second
> I'm not entirely sure what all that means. "man nm" tells me that U means
> "undefined" and T means "in the text section". But that doesn't illuminate
> me greatly, since I'm not yet familiar with such programming technical
> terms.
> I've been using the Intel compiler, icc 11.1.076, and its associated MKL
> libraries.
> - Ben
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Received on Mon Mar 01 2010 - 10:30:07 PST
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