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

[Justin A. Lemkul]

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

========================================