[gmx-users] Gromacs Installation Error on Powerbook G$ Running OS 10.5.8

Peter C. Lai pcl at uab.edu
Mon May 23 22:01:02 CEST 2011

On 2011-05-23 02:37:54PM -0500, Matthew Bick wrote:
> Dear Gromacs community.  I am attempting to install the latest version
> of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8).  I
> have successfully installed FFTW following the instructions provided
> on the Gromacs installation page.
> "./configure --with-fft=fftw3" appears to work properly, but when I
> perform  "Make" I get the following errors:
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[4]: *** [libgmx.la] Error 1
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
> I did configure my shell (bash) environment, as per the Gromacs
> installation instructions.  "Make" runs for about 10 minutes before I
> get these errors.  I have searched the mailing list, and have seen
> people report problems similar to mine, but couldn't determine how
> those problems were resolved.  Also from the mailing list, I
> understand that the errors I've listed above aren't that informative.
> If it helps, I repeatedly get the following warnings during "Make":
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
> function ‘tMPI_Atomic_add_return’:
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:
> warning: implicit declaration of function ‘__sync_add_and_fetch’
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
> function ‘tMPI_Atomic_fetch_add’:
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:
> warning: implicit declaration of function ‘__sync_fetch_and_add’
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In
> function ‘tMPI_Atomic_cas’:
> ../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:
> warning: implicit declaration of function
> ‘__sync_bool_compare_and_swap’
> If anyone has any suggestions, they would be greatly appreciated.
> Thanks.

Some things to watch out for:
single vs. double precision (the library versions must match between
fftw and what you passed to ./configure for gromacs (--enable-float
is single precision,--disable-float is double).

Maybe you need --enable-shared and specify correct LDFLAGS...
The warnings section seems to imply this is happening in the threads/MPI
section, Justin can correct me if I'm wrong, but maybe you need to explicitly
disable mpi with --disable-mpi in the configure?

Gromacs 4.5.4 is also in MacPorts, which contains a simplified options 
framework (and will install gcc45 for you if you want as well) for all the
popular configure variations:
(I would probably go with +gcc45, +gsl, +no_x11 [avoids openmotif]
and +optimize [for gsl])

Once you do get it working, watchout for overheating on that thing :)

Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |

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