<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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.<div><br></div><div>Matt</div><div><br><div><br></div><div><br><div><div>On May 24, 2011, at 8:22 PM, <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Courier New'; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; ">1. Re: Re: Gromacs Installation Error on Powerbook G4 Running OS<br> 10.5.8</span></blockquote></div><br><div><br></div><div>Matthew Bick wrote:<br><blockquote type="cite"><br></blockquote><blockquote type="cite">On May 23, 2011, at 4:24 PM, <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br></blockquote><blockquote type="cite"><<a href="mailto:gmx-users-request@gromacs.org">mailto:gmx-users-request@gromacs.org</a>> wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Re: Gromacs Installation Error on Powerbook G$ Running OS<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> 10.5.8<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi Justin. Thanks for you response. See my responses below, embedded<br></blockquote><blockquote type="cite">in the original message:<br></blockquote><blockquote type="cite">Matthew Bick wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Dear Gromacs community. I am attempting to install the latest version<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8). I<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">have successfully installed FFTW following the instructions provided<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">on the Gromacs installation page.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">"./configure --with-fft=fftw3" appears to work properly, but when I<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">perform "Make" I get the following errors:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">ld: symbol(s) not found<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">collect2: ld returned 1 exit status<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">make[4]: *** [libgmx.la] Error 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">make[3]: *** [all-recursive] Error 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">make[2]: *** [all-recursive] Error 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">make[1]: *** [all] Error 2<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">make: *** [all-recursive] Error 1<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">|The information about the actual missing symbols should be just above this<br></blockquote><blockquote type="cite">|output, so that would be useful information. Also pertinent would be the<br></blockquote><blockquote type="cite">|compiler versions you're using. From what you've posted below it looks<br></blockquote><blockquote type="cite">like<br></blockquote><blockquote type="cite">|GCC, but which version?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am using the latest Developer's tools for Leopard 10.5.8. So that<br></blockquote><blockquote type="cite">comes with gcc 4.0 and 4.2. I<br></blockquote><blockquote type="cite"> can't say for certain which version was used during<br></blockquote><blockquote type="cite">configuration. I do know that when 'configuration'<br></blockquote><blockquote type="cite"> looks for gcc it finds it.<br></blockquote><blockquote type="cite"><br></blockquote><br>If you're not specifying a custom PATH, then your default gcc is being detected.<br> gcc -v will tell you which is being used.<br><br><blockquote type="cite"> Here are the missing symbols, plus the error codes once again:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Undefined symbols:<br></blockquote><blockquote type="cite">"___sync_lock_test_and_set", referenced from:<br></blockquote><blockquote type="cite">_tMPI_Lock_trylock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Lock_lock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Type_commit in type.o<br></blockquote><blockquote type="cite">_tMPI_Type_contiguous in type.o<br></blockquote><blockquote type="cite">"___sync_bool_compare_and_swap", referenced from:<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_detach in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_push in list.o<br></blockquote><blockquote type="cite">_tMPI_Stack_pop in list.o<br></blockquote><blockquote type="cite">_tMPI_Once_wait in once.o<br></blockquote><blockquote type="cite">_tMPI_Once in once.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Prep_send_envelope in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Wait_process_incoming in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Wait_process_incoming in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Wait_process_incoming in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Wait_process_incoming in p2p_protocol.o<br></blockquote><blockquote type="cite">"___sync_fetch_and_add", referenced from:<br></blockquote><blockquote type="cite">_tMPI_Once_wait in once.o<br></blockquote><blockquote type="cite">"___sync_lock_release", referenced from:<br></blockquote><blockquote type="cite">_tMPI_Lock_unlock in lock.o<br></blockquote><blockquote type="cite">_tMPI_Type_commit in type.o<br></blockquote><blockquote type="cite">_tMPI_Type_contiguous in type.o<br></blockquote><blockquote type="cite">"___sync_add_and_fetch", referenced from:<br></blockquote><blockquote type="cite">_tMPI_Alltoallv in alltoall.o<br></blockquote><blockquote type="cite">_tMPI_Alltoall in alltoall.o<br></blockquote><blockquote type="cite">_tMPI_Barrier_wait in barrier.o<br></blockquote><blockquote type="cite">_tMPI_Mult_recv in collective.o<br></blockquote><blockquote type="cite">_tMPI_Mult_recv in collective.o<br></blockquote><blockquote type="cite">_tMPI_Post_multi in collective.o<br></blockquote><blockquote type="cite">_tMPI_Post_multi in collective.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Xfer in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Xfer in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Wait_process_incoming in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Reduce_fast in reduce.o<br></blockquote><blockquote type="cite">_tMPI_Reduce_fast in reduce.o<br></blockquote><blockquote type="cite">_tMPI_Scatterv in scatter.o<br></blockquote><blockquote type="cite">_tMPI_Scatter in scatter.o<br></blockquote><blockquote type="cite">"___sync_synchronize", referenced from:<br></blockquote><blockquote type="cite">_tMPI_Alltoallv in alltoall.o<br></blockquote><blockquote type="cite">_tMPI_Alltoallv in alltoall.o<br></blockquote><blockquote type="cite">_tMPI_Alltoall in alltoall.o<br></blockquote><blockquote type="cite">_tMPI_Alltoall in alltoall.o<br></blockquote><blockquote type="cite">_tMPI_Barrier_wait in barrier.o<br></blockquote><blockquote type="cite">_tMPI_Barrier_wait in barrier.o<br></blockquote><blockquote type="cite">_tMPI_Mult_recv in collective.o<br></blockquote><blockquote type="cite">_tMPI_Mult_recv in collective.o<br></blockquote><blockquote type="cite">_tMPI_Post_multi in collective.o<br></blockquote><blockquote type="cite">_tMPI_Post_multi in collective.o<br></blockquote><blockquote type="cite">_tMPI_Post_multi in collective.o<br></blockquote><blockquote type="cite">_tMPI_Event_wait in event.o<br></blockquote><blockquote type="cite">_tMPI_Lock_islocked in lock.o<br></blockquote><blockquote type="cite">_tMPI_Once_wait in once.o<br></blockquote><blockquote type="cite">_tMPI_Once_wait in once.o<br></blockquote><blockquote type="cite">_tMPI_Once_wait in once.o<br></blockquote><blockquote type="cite">_tMPI_Post_send in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Xfer in p2p_protocol.o<br></blockquote><blockquote type="cite">_tMPI_Reduce_fast in reduce.o<br></blockquote><blockquote type="cite">_tMPI_Reduce_fast in reduce.o<br></blockquote><blockquote type="cite">_tMPI_Scatterv in scatter.o<br></blockquote><blockquote type="cite">_tMPI_Scatterv in scatter.o<br></blockquote><blockquote type="cite">_tMPI_Scatter in scatter.o<br></blockquote><blockquote type="cite">_tMPI_Scatter in scatter.o<br></blockquote><blockquote type="cite"> ld: symbol(s) not found<br></blockquote><blockquote type="cite"> collect2: ld returned 1 exit status<br></blockquote><blockquote type="cite"> make[4]: *** [libgmx.la] Error 1<br></blockquote><blockquote type="cite"> make[3]: *** [all-recursive] Error 1<br></blockquote><blockquote type="cite"> make[2]: *** [all-recursive] Error 1<br></blockquote><blockquote type="cite"> make[1]: *** [all] Error 2<br></blockquote><blockquote type="cite"> make: *** [all-recursive] Error 1<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><br>Threading is breaking down. I believe the ability to build Gromacs with<br>threading support is compiler dependent, and you may need a newer gcc, although<br>I could be wrong. I seem to recall having to upgrade to gcc 4.4.4 before the<br>newer features would work.<br><br>To test, configure with --disable-threads. In this case, you'd have to<br>--enable-mpi for mdrun if you have multiple cores, and therefore invoke<br>mdrun_mpi via mpirun rather than through the internal threading library.<br><br>-Justin<br><br><blockquote type="cite">|I don't think those warnings are particularly harmful, but I know that<br></blockquote><blockquote type="cite">trying to<br></blockquote><blockquote type="cite">|install a new version of Gromacs on PowerPC can be a challenge. If your<br></blockquote><blockquote type="cite">|compiler is relatively old, you may have to disable some of the newer<br></blockquote><blockquote type="cite">features,<br></blockquote><blockquote type="cite">|like threading, although that should have been caught during configuration.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">|Is the ./configure command given above the exact command you used? If not,<br></blockquote><blockquote type="cite">|posting that would be useful.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Yes, that ./configure command is the exact command I used.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Thank you again for any suggestions. I know everyone is busy.<br></blockquote><blockquote type="cite">-Matt<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-Justin<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">I did configure my shell (bash) environment, as per the Gromacs<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">installation instructions. "Make" runs for about 10 minutes before I<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">get these errors. I have searched the mailing list, and have seen<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">people report problems similar to mine, but couldn't determine how<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">those problems were resolved. Also from the mailing list, I<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">understand that the errors I've listed above aren't that informative.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If it helps, I repeatedly get the following warnings during "Make":<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">function ???tMPI_Atomic_add_return???:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">warning: implicit declaration of function ???__sync_add_and_fetch???<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">function ???tMPI_Atomic_fetch_add???:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">warning: implicit declaration of function ???__sync_fetch_and_add???<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">function ???tMPI_Atomic_cas???:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">warning: implicit declaration of function<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">???__sync_bool_compare_and_swap???<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If anyone has any suggestions, they would be greatly appreciated.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Matthew Bick<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Rockefeller University<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">========================================<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Justin A. Lemkul<br></blockquote><blockquote type="cite">Ph.D. Candidate<br></blockquote><blockquote type="cite">ICTAS Doctoral Scholar<br></blockquote><blockquote type="cite">MILES-IGERT Trainee<br></blockquote><blockquote type="cite">Department of Biochemistry<br></blockquote><blockquote type="cite">Virginia Tech<br></blockquote><blockquote type="cite">Blacksburg, VA<br></blockquote><blockquote type="cite">jalemkul[at]vt.edu | (540) 231-9080<br></blockquote><blockquote type="cite"><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br></blockquote><blockquote type="cite"><br></blockquote><br>--<br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br></div></div></div></body></html>