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

Matthew Bick bickm at mail.rockefeller.edu
Thu May 26 01:31:43 CEST 2011 

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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