AMBER: Error when compiling and testing AmberTools

From: Ben Roberts <>
Date: Thu, 21 Aug 2008 17:46:43 -0400

Hi list,

I've been trying to compile AmberTools for Amber Version 10. It
apparently compiles OK, but when I run the tests, I get the following

[previous test results all OK]


Running test to compute GB Newton-Raphson and normal modes:

/scr/ra_2/roberts/amber10/lib/libnab.a(newton.o)(.text+0xb0): In
function `newton':
: undefined reference to `assert'
/scr/ra_2/roberts/amber10/lib/libnab.a(nmode.o)(.text+0x711): In
function `nmode':
: undefined reference to `assert'
cc failed!
make[1]: *** [asp_test] Error 1
make[1]: Leaving directory `/scr/ra_2/roberts/amber10/test/nab'
make: *** [] Error 2

at which point the testing script unceremoniously aborts.

As far as I can tell, this is an indication that either I'm missing an
"include" statement in e.g. nmode.c or newton.c, or I'm not linking
correctly to a library file. But I don't know in which header file or
library the function "assert" is defined and/or declared, so I'm not
sure how to remedy this. Can anyone point me in the right direction?

Information you may find helpful:

C compiler: icc version 9.1.044
C++ compiler: icpc version 9.1.044
Fortran compiler: ifort version 9.1.037
System: Linux, kernel version 2.6.18-8.1.14.el5.L-1642 (SMP build,
64-bit). Not sure what exact distribution.

Thanks in advance,

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Received on Sun Aug 24 2008 - 06:07:44 PDT
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