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
--
========================================
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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