<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On May 23, 2011, at 4:24 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; ">Re: Gromacs Installation Error on Powerbook G$ Running OS<br> 10.5.8</span></blockquote></div><div><br></div><div><br></div>Hi Justin. Thanks for you response. See my responses below, embedded in the original message:<br><div>Matthew Bick wrote:</div><div><br></div><div><br><blockquote type="cite">Dear Gromacs community. I am attempting to install the latest version<br></blockquote><blockquote type="cite">of Gromcs (4.5.4) on my Mac Powerbook G4 (1.67 MHz, OS 10.5.8). I<br></blockquote><blockquote type="cite">have successfully installed FFTW following the instructions provided<br></blockquote><blockquote type="cite">on the Gromacs installation page.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">"./configure --with-fft=fftw3" appears to work properly, but when I<br></blockquote><blockquote type="cite">perform "Make" I get the following errors:<br></blockquote><blockquote type="cite"><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><br>|The information about the actual missing symbols should be just above this<br>|output, so that would be useful information. Also pertinent would be the<br>|compiler versions you're using. From what you've posted below it looks like<br>|GCC, but which version?</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I am using the latest Developer's tools for Leopard 10.5.8. So that comes with gcc 4.0 and 4.2. I </div><div> can't say for certain which version was used during configuration. I do know that when 'configuration' </div><div> looks for gcc it finds it.</div><div><br></div><div> Here are the missing symbols, plus the error codes once again:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Undefined symbols: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "___sync_lock_test_and_set", referenced from: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_trylock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_lock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Type_commit in type.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Type_contiguous in type.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "___sync_bool_compare_and_swap", referenced from: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_detach in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_push in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Stack_pop in list.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Once_wait in once.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Once in once.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Prep_send_envelope in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Wait_process_incoming in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Wait_process_incoming in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Wait_process_incoming in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Wait_process_incoming in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "___sync_fetch_and_add", referenced from: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Once_wait in once.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "___sync_lock_release", referenced from: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_unlock in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Type_commit in type.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Type_contiguous in type.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "___sync_add_and_fetch", referenced from: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Alltoallv in alltoall.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Alltoall in alltoall.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Barrier_wait in barrier.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Mult_recv in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Mult_recv in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_multi in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_multi in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Xfer in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Xfer in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Wait_process_incoming in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Reduce_fast in reduce.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Reduce_fast in reduce.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Scatterv in scatter.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Scatter in scatter.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> "___sync_synchronize", referenced from: </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Alltoallv in alltoall.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Alltoallv in alltoall.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Alltoall in alltoall.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Alltoall in alltoall.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Barrier_wait in barrier.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Barrier_wait in barrier.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Mult_recv in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Mult_recv in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_multi in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_multi in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_multi in collective.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Event_wait in event.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Lock_islocked in lock.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Once_wait in once.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Once_wait in once.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Once_wait in once.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Post_send in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Xfer in p2p_protocol.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Reduce_fast in reduce.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Reduce_fast in reduce.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Scatterv in scatter.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Scatterv in scatter.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Scatter in scatter.o </div><div><span class="Apple-tab-span" style="white-space:pre"> </span> _tMPI_Scatter in scatter.o </div><div> ld: symbol(s) not found </div><div> collect2: ld returned 1 exit status </div><div> make[4]: *** [libgmx.la] Error 1 </div><div> make[3]: *** [all-recursive] Error 1 </div><div> make[2]: *** [all-recursive] Error 1 </div><div> make[1]: *** [all] Error 2 </div><div> make: *** [all-recursive] Error 1 </div><div><br><br>|I don't think those warnings are particularly harmful, but I know that trying to<br>|install a new version of Gromacs on PowerPC can be a challenge. If your<br>|compiler is relatively old, you may have to disable some of the newer features,<br>|like threading, although that should have been caught during configuration.<br><br>|Is the ./configure command given above the exact command you used? If not,<br>|posting that would be useful.</div><div><br></div><div><br></div><div> Yes, that ./configure command is the exact command I used.</div><div><br></div><div> Thank you again for any suggestions. I know everyone is busy.<span class="Apple-tab-span" style="white-space:pre"> </span></div><div><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"> </span></div><div><span class="Apple-tab-span" style="white-space:pre"></span><span class="Apple-tab-span" style="white-space:pre"> </span>-Matt</div><div><span class="Apple-tab-span" style="white-space:pre"> </span></div><div><br><br>-Justin</div><div><br></div><div><br></div><div><br><blockquote type="cite">I did configure my shell (bash) environment, as per the Gromacs<br></blockquote><blockquote type="cite">installation instructions. "Make" runs for about 10 minutes before I<br></blockquote><blockquote type="cite">get these errors. I have searched the mailing list, and have seen<br></blockquote><blockquote type="cite">people report problems similar to mine, but couldn't determine how<br></blockquote><blockquote type="cite">those problems were resolved. Also from the mailing list, I<br></blockquote><blockquote type="cite">understand that the errors I've listed above aren't that informative.<br></blockquote><blockquote type="cite">If it helps, I repeatedly get the following warnings during "Make":<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In<br></blockquote><blockquote type="cite">function ???tMPI_Atomic_add_return???:<br></blockquote><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:46:<br></blockquote><blockquote type="cite">warning: implicit declaration of function ???__sync_add_and_fetch???<br></blockquote><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In<br></blockquote><blockquote type="cite">function ???tMPI_Atomic_fetch_add???:<br></blockquote><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:51:<br></blockquote><blockquote type="cite">warning: implicit declaration of function ???__sync_fetch_and_add???<br></blockquote><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h: In<br></blockquote><blockquote type="cite">function ???tMPI_Atomic_cas???:<br></blockquote><blockquote type="cite">../../../../include/types/../thread_mpi/atomic/gcc_intrinsics.h:57:<br></blockquote><blockquote type="cite">warning: implicit declaration of function<br></blockquote><blockquote type="cite">???__sync_bool_compare_and_swap???<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If anyone has any suggestions, they would be greatly appreciated.<br></blockquote><blockquote type="cite">Thanks.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Matthew Bick<br></blockquote><blockquote type="cite">Rockefeller University<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></body></html>