From: Richard Owczarzy <>
Date: Mon, 20 Dec 2010 20:58:11 +0000

(1) What is in

(2) You may have run in the same problem that I had with 4.1.2 compiler ( I solved it by creating soft symbolic links in /GNU44 directory

g++ -> /usr/bin/g++44
gcc -> /usr/bin/gcc44
gcov -> /usr/bin/gcov44
gfortran -> /usr/bin/gfortran44

and placing the directory at the top of PATH in the bash shell when I run NAB or I compile AmberTools and Amber11. I execute

export PATH=/GNU44:$PATH

This changes my compilers to version 4.4.0. AmberTools and Amber compiles fine and passes all test with no errors. You do not have to modify the AmberTools installation script, because gcc will point to new version.

NAB works as a compiler, so it seems to demand the same default version of gcc that it was compiled with. If the bash shell has different default gcc, nab fails on my machine in runtime.

When I want to get back to standard RHEL 5.5 GNU compilers, I logon again or start a new shell. This removes /GNU44 from the top of the path.

Richard Owczarzy

From: Mark Foster []
Sent: Monday, December 20, 2010 1:53 PM
Subject: [AMBER]


I (finally) succeeded in installing AmberTools 1.4 on my OSX 10.6 mac using fink-installed gcc-4.4. To do so, I replaced instances of gcc and g++ in the configure script with gcc-4 and g++4. Most tests PASSED.

However, I am not able to run NAB independently:

[kex:AmberTools/examples/suppose] foster% nab --v
Using built-in specs.
Target: i386-apple-darwin9.8.0
Configured with: ../gcc-4.4.4/configure --prefix=/sw --prefix=/sw/lib/gcc4.4 --mandir=/sw/share/man --infodir=/sw/lib/gcc4.4/info --enable-languages=c,c++,fortran,objc,obj-c++,java --with-gmp=/sw --with-libiconv-prefix=/sw --with-ppl=/sw --with-cloog=/sw --with-mpc=/sw --with-system-zlib --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --program-suffix=-fsf-4.4
Thread model: posix
gcc version 4.4.4 (GCC)
COLLECT_GCC_OPTIONS='-mmacosx-version-min=10.6.5' '-I/usr/local/amber11/include' '-v' '-mtune=generic'
 /sw/lib/gcc4.4/libexec/gcc/i386-apple-darwin9.8.0/4.4.4/collect2 -dynamic -arch i386 -macosx_version_min 10.6.5 -weak_reference_mismatches non-weak -o a.out -lcrt1.10.5.o -L/sw/lib/gcc4.4/lib/gcc/i386-apple-darwin9.8.0/4.4.4 -L/sw/lib/gcc4.4/lib/gcc/i386-apple-darwin9.8.0/4.4.4/../../.. /usr/local/amber11/lib/libnab.a /usr/local/amber11/lib/arpack.a -lgfortran -framework Accelerate -lm -lgcc_s.10.5 -lgcc -lSystem
Undefined symbols:
  "_main", referenced from:
      start in crt1.10.5.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
cc failed!


[kex:AmberTools/examples/suppose] foster% nab
Undefined symbols:
  "_MAT_istrue", referenced from:
      _main in ccFNRvC6.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
cc failed!

Any help would be appreciated.



Mark P. Foster, Ph.D.
Professor, Interim Chair Department of Biochemistry
(614) 292-1377 The Ohio State University
FAX 292-6773 484 West 12th Ave. Columbus, OH 43210-1214

AMBER mailing list
AMBER mailing list
Received on Mon Dec 20 2010 - 13:30:02 PST
Custom Search