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

Matthew Bick bickm at mail.rockefeller.edu
Tue May 24 21:03:43 CEST 2011 

On May 23, 2011, at 4:24 PM, 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.

     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


|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
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