[gmx-users] Re: error compiling gmx 4.5 on Mac 10.6.4

Alan alanwilter at gmail.com
Sat Jul 31 18:15:46 CEST 2010 

To myself.

Removing --enable-shared and compilation went fine.

Alan

On Sat, Jul 31, 2010 at 11:41, Alan <alanwilter at gmail.com> wrote:

> Hi there,
>
> I am trying gmx 4.5 beta on Mac SL 10.6.4 with Fink, doing:
>
> ./configure CPPFLAGS="-I/sw/include" LDFLAGS="-L/sw/lib" --enable-shared
> --with-gsl --with-x
>
> and then 'make' failed with:
>
> (cd .libs/libgmx.lax/libthread_mpi.a && ar x
> /Users/alan/Downloads/gromacs-4.5-beta1/src/gmxlib/thread_mpi/.libs/libthread_mpi.a)
> cc  -dynamiclib  -o .libs/libgmx.6.dylib  .libs/3dview.o .libs/atomprop.o
> .libs/bondfree.o .libs/calcgrid.o .libs/calch.o .libs/chargegroup.o
> .libs/checkpoint.o .libs/confio.o .libs/copyrite.o .libs/disre.o
> .libs/do_fit.o .libs/enxio.o .libs/ewald_util.o .libs/ffscanf.o
> .libs/filenm.o .libs/futil.o .libs/gbutil.o .libs/gmx_fatal.o
> .libs/gmx_sort.o .libs/gmxcpp.o .libs/gmxfio.o .libs/ifunc.o .libs/index.o
> .libs/inputrec.o .libs/cinvsqrtdata.o .libs/invblock.o .libs/macros.o
> .libs/orires.o .libs/sparsematrix.o .libs/main.o .libs/maths.o .libs/matio.o
> .libs/mshift.o .libs/mtop_util.o .libs/mtxio.o .libs/mvdata.o .libs/names.o
> .libs/network.o .libs/nrama.o .libs/nrjac.o .libs/nrnb.o .libs/pargs.o
> .libs/pbc.o .libs/pdbio.o .libs/princ.o .libs/rando.o .libs/random.o
> .libs/gmx_random.o .libs/rbin.o .libs/readinp.o .libs/replace.o
> .libs/rmpbc.o .libs/shift_util.o .libs/sortwater.o .libs/smalloc.o
> .libs/statutil.o .libs/sfactor.o .libs/strdb.o .libs/string2.o
> .libs/symtab.o .libs/topsort.o .libs/tpxio.o .libs/trnio.o .libs/trxio.o
> .libs/txtdump.o .libs/typedefs.o .libs/viewit.o .libs/warninp.o .libs/wgms.o
> .libs/wman.o .libs/writeps.o .libs/xdrd.o .libs/xtcio.o .libs/xvgr.o
> .libs/libxdrf.o .libs/gmx_arpack.o .libs/gmx_matrix.o .libs/dihres.o
> .libs/tcontrol.o .libs/splitter.o .libs/gmx_cyclecounter.o
> .libs/gmx_system_xdr.o .libs/md5.o .libs/vmdio.o .libs/vmddlopen.o
> .libs/sighandler.o .libs/oenv.o .libs/gmxfio_rw.o .libs/gmxfio_asc.o
> .libs/gmxfio_bin.o .libs/gmxfio_xdr.o
>  .libs/libgmx.lax/libnonbonded.a/nb_free_energy.o
> .libs/libgmx.lax/libnonbonded.a/nb_generic.o
> .libs/libgmx.lax/libnonbonded.a/nb_generic_cg.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel010.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel010_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel020.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel030.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel030_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel100.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel100_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel101.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel101_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel102.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel102_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel103.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel103_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel104.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel104_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel110.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel110_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel111.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel111_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel112.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel112_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel113.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel113_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel114.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel114_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel120.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel121.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel122.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel123.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel124.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel130.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel130_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel131.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel131_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel132.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel132_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel133.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel133_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel134.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel134_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel200.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel200_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel201.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel201_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel202.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel202_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel203.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel203_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel204.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel204_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel210.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel210_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel211.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel211_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel212.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel212_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel213.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel213_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel214.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel214_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel220.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel221.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel222.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel223.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel224.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel230.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel230_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel231.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel231_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel232.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel232_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel233.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel233_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel234.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel234_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel300.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel300_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel301.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel301_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel302.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel302_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel303.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel303_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel304.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel304_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel310.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel310_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel311.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel311_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel312.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel312_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel313.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel313_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel314.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel314_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel320.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel321.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel322.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel323.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel324.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel330.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel330_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel331.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel331_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel332.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel332_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel333.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel333_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel334.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel334_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel400.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel400_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel410.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel410_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel420.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel430.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel430_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel_allvsall.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel_allvsall_sse2_single.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel_allvsallgb.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel_allvsallgb_sse2_single.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel_c.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel_x86_64_sse.o
> .libs/libgmx.lax/libnonbonded.a/nb_kernel_x86_64_sse_test_asm.o
> .libs/libgmx.lax/libnonbonded.a/nonbonded.o
>  .libs/libgmx.lax/libselection.a/compiler.o
> .libs/libgmx.lax/libselection.a/evaluate.o
> .libs/libgmx.lax/libselection.a/mempool.o
> .libs/libgmx.lax/libselection.a/params.o
> .libs/libgmx.lax/libselection.a/parser.o
> .libs/libgmx.lax/libselection.a/parsetree.o
> .libs/libgmx.lax/libselection.a/scanner.o
> .libs/libgmx.lax/libselection.a/scanner_internal.o
> .libs/libgmx.lax/libselection.a/selection.o
> .libs/libgmx.lax/libselection.a/selelem.o
> .libs/libgmx.lax/libselection.a/selhelp.o
> .libs/libgmx.lax/libselection.a/selmethod.o
> .libs/libgmx.lax/libselection.a/selvalue.o
> .libs/libgmx.lax/libselection.a/sm_compare.o
> .libs/libgmx.lax/libselection.a/sm_distance.o
> .libs/libgmx.lax/libselection.a/sm_insolidangle.o
> .libs/libgmx.lax/libselection.a/sm_keywords.o
> .libs/libgmx.lax/libselection.a/sm_merge.o
> .libs/libgmx.lax/libselection.a/sm_permute.o
> .libs/libgmx.lax/libselection.a/sm_position.o
> .libs/libgmx.lax/libselection.a/sm_same.o
> .libs/libgmx.lax/libselection.a/sm_simple.o
> .libs/libgmx.lax/libselection.a/symrec.o
>  .libs/libgmx.lax/libstatistics.a/gmx_statistics.o
> .libs/libgmx.lax/libstatistics.a/histogram.o
>  .libs/libgmx.lax/libtrajana.a/centerofmass.o
> .libs/libgmx.lax/libtrajana.a/displacement.o
> .libs/libgmx.lax/libtrajana.a/indexutil.o
> .libs/libgmx.lax/libtrajana.a/nbsearch.o
> .libs/libgmx.lax/libtrajana.a/poscalc.o
> .libs/libgmx.lax/libtrajana.a/position.o
> .libs/libgmx.lax/libtrajana.a/trajana.o
>  .libs/libgmx.lax/libthread_mpi.a/barrier.o
> .libs/libgmx.lax/libthread_mpi.a/collective.o
> .libs/libgmx.lax/libthread_mpi.a/comm.o
> .libs/libgmx.lax/libthread_mpi.a/errhandler.o
> .libs/libgmx.lax/libthread_mpi.a/event.o
> .libs/libgmx.lax/libthread_mpi.a/group.o
> .libs/libgmx.lax/libthread_mpi.a/hwinfo.o
> .libs/libgmx.lax/libthread_mpi.a/list.o
> .libs/libgmx.lax/libthread_mpi.a/lock.o
> .libs/libgmx.lax/libthread_mpi.a/once.o
> .libs/libgmx.lax/libthread_mpi.a/p2p.o
> .libs/libgmx.lax/libthread_mpi.a/profile.o
> .libs/libgmx.lax/libthread_mpi.a/pthreads.o
> .libs/libgmx.lax/libthread_mpi.a/reduce_fast.o
> .libs/libgmx.lax/libthread_mpi.a/tmpi_init.o
> .libs/libgmx.lax/libthread_mpi.a/topology.o
> .libs/libgmx.lax/libthread_mpi.a/type.o   -L/sw/lib -lm  -msse2 -framework
> Accelerate -install_name  /usr/local/gromacs/lib/libgmx.6.dylib
> -compatibility_version 7 -current_version 7.0
> Undefined symbols:
>   "_main", referenced from:
>       _tMPI_Thread_starter in tmpi_init.o
>       _tMPI_Start_threads in tmpi_init.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
>
>
> Any ideas? Thanks,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>



-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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