[gmx-users] Re: Re: Re: Gromacs Installation Error on Powerbook G4 Running OS 10.5.8

[Szilárd Páll]

Hi Matt,

Just wanted to warn you that AFAIK Gromacs 4.5.x was not tested with
gcc 4.0.1, we've done testing only with 4.1 and later. This doesn't
mean that it shouldn't work, but if you encounter anything strange,
the first thing you should do is to get a newer gcc.

Also, your tMPI errors might be related to gcc 4.0.1, but as the
Powerbook G4 has a single core that's irrelevant.

--
Szilárd



On Thu, May 26, 2011 at 1:31 AM, Matthew Bick
<bickm at mail.rockefeller.edu> wrote:
> Justin.  Thank you very much.  using --disable-threads fixed the problem.
>  Installation completed without error.  And by the way, my gcc version is
> 4.0.1.
> Matt
>
>
> On May 24, 2011, at 8:22 PM, gmx-users-request at gromacs.org wrote:
>
> 1. Re: Re: Gromacs Installation Error on Powerbook G4 Running        OS
>      10.5.8
>
> Matthew Bick wrote:
>
> On May 23, 2011, at 4:24 PM, gmx-users-request at gromacs.org
>
> <mailto:gmx-users-request at gromacs.org> wrote:
>
> Re: Gromacs Installation Error on Powerbook G$ Running    OS
>
>     10.5.8
>
>
> Hi Justin.  Thanks for you response.  See my responses below, embedded
>
> in the original message:
>
> 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 am using the latest Developer's tools for Leopard 10.5.8.  So that
>
> comes with gcc 4.0 and 4.2.  I
>
>        can't say for certain which version was used during
>
> configuration.  I do know that when 'configuration'
>
>        looks for gcc it finds it.
>
>
> If you're not specifying a custom PATH, then your default gcc is being
> detected.
>  gcc -v will tell you which is being used.
>
>    Here are the missing symbols, plus the error codes once again:
>
> Undefined symbols:
>
> "___sync_lock_test_and_set", referenced from:
>
> _tMPI_Lock_trylock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Lock_lock in lock.o
>
> _tMPI_Type_commit in type.o
>
> _tMPI_Type_contiguous in type.o
>
> "___sync_bool_compare_and_swap", referenced from:
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_detach in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_push in list.o
>
> _tMPI_Stack_pop in list.o
>
> _tMPI_Once_wait in once.o
>
> _tMPI_Once in once.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Prep_send_envelope in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Wait_process_incoming in p2p_protocol.o
>
> _tMPI_Wait_process_incoming in p2p_protocol.o
>
> _tMPI_Wait_process_incoming in p2p_protocol.o
>
> _tMPI_Wait_process_incoming in p2p_protocol.o
>
> "___sync_fetch_and_add", referenced from:
>
> _tMPI_Once_wait in once.o
>
> "___sync_lock_release", referenced from:
>
> _tMPI_Lock_unlock in lock.o
>
> _tMPI_Type_commit in type.o
>
> _tMPI_Type_contiguous in type.o
>
> "___sync_add_and_fetch", referenced from:
>
> _tMPI_Alltoallv in alltoall.o
>
> _tMPI_Alltoall in alltoall.o
>
> _tMPI_Barrier_wait in barrier.o
>
> _tMPI_Mult_recv in collective.o
>
> _tMPI_Mult_recv in collective.o
>
> _tMPI_Post_multi in collective.o
>
> _tMPI_Post_multi in collective.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Xfer in p2p_protocol.o
>
> _tMPI_Xfer in p2p_protocol.o
>
> _tMPI_Wait_process_incoming in p2p_protocol.o
>
> _tMPI_Reduce_fast in reduce.o
>
> _tMPI_Reduce_fast in reduce.o
>
> _tMPI_Scatterv in scatter.o
>
> _tMPI_Scatter in scatter.o
>
> "___sync_synchronize", referenced from:
>
> _tMPI_Alltoallv in alltoall.o
>
> _tMPI_Alltoallv in alltoall.o
>
> _tMPI_Alltoall in alltoall.o
>
> _tMPI_Alltoall in alltoall.o
>
> _tMPI_Barrier_wait in barrier.o
>
> _tMPI_Barrier_wait in barrier.o
>
> _tMPI_Mult_recv in collective.o
>
> _tMPI_Mult_recv in collective.o
>
> _tMPI_Post_multi in collective.o
>
> _tMPI_Post_multi in collective.o
>
> _tMPI_Post_multi in collective.o
>
> _tMPI_Event_wait in event.o
>
> _tMPI_Lock_islocked in lock.o
>
> _tMPI_Once_wait in once.o
>
> _tMPI_Once_wait in once.o
>
> _tMPI_Once_wait in once.o
>
> _tMPI_Post_send in p2p_protocol.o
>
> _tMPI_Xfer in p2p_protocol.o
>
> _tMPI_Reduce_fast in reduce.o
>
> _tMPI_Reduce_fast in reduce.o
>
> _tMPI_Scatterv in scatter.o
>
> _tMPI_Scatterv in scatter.o
>
> _tMPI_Scatter in scatter.o
>
> _tMPI_Scatter in scatter.o
>
>     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
>
>
>
> Threading is breaking down.  I believe the ability to build Gromacs with
> threading support is compiler dependent, and you may need a newer gcc,
> although
> I could be wrong.  I seem to recall having to upgrade to gcc 4.4.4 before
> the
> newer features would work.
>
> To test, configure with --disable-threads.  In this case, you'd have to
> --enable-mpi for mdrun if you have multiple cores, and therefore invoke
> mdrun_mpi via mpirun rather than through the internal threading library.
>
> -Justin
>
> |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.
>
>
>      Yes, that ./configure command is the exact command I used.
>
>      Thank you again for any suggestions.  I know everyone is busy.
>
> -Matt
>
>
> -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
>
>
> --
> ========================================
>
> 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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