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

[Justin A. Lemkul]

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
> 

The information about the actual missing symbols should be just above this 
output, so that would be useful information.  Also pertinent would be the 
compiler versions you're using.  From what you've posted below it looks like 
GCC, but which version?

I don't think those warnings are particularly harmful, but I know that trying to 
install a new version of Gromacs on PowerPC can be a challenge.  If your 
compiler is relatively old, you may have to disable some of the newer features, 
like threading, although that should have been caught during configuration.

Is the ./configure command given above the exact command you used?  If not, 
posting that would be useful.

-Justin

> 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.
> 
> Matthew Bick
> Rockefeller University

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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