Re: Problems compiling NAMD on 8-core Mac

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Jan 31 2011 - 22:49:39 CST

I believe I've reproduced the error, though without the full error it's
hard to be completely certain.

Tried using our default "tcl for namd on macosx-x86_64" and also building
tcl8.4.19 natively. Same linker error for both.

David, can you confirm this is similar to your error?

Undefined symbols:
  "_CFRunLoopRunInMode", referenced from:
      _Tcl_WaitForEvent in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFRunLoopWakeUp", referenced from:
      _Tcl_AlertNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
      _NotifierThreadProc in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFLocaleCopyCurrent", referenced from:
      _TclpSetVariables in libnamdtcl8.4.a(tclUnixInit.o)
  "_CFURLGetFileSystemRepresentation", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFBundleCopyResourceURL", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFRunLoopCopyCurrentMode", referenced from:
      _Tcl_WaitForEvent in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "___CFConstantStringClassReference", referenced from:
      cfstring=Versions in libnamdtcl8.4.a(tclMacOSXBundle.o)
      cfstring=Scripts in libnamdtcl8.4.a(tclMacOSXBundle.o)
      cfstring=com.tcltk.tclEventsOnlyRunLoopMode in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_kCFRunLoopDefaultMode", referenced from:
      _Tcl_WaitForEvent in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFBundleCopyBundleURL", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFRelease", referenced from:
      _TclpSetVariables in libnamdtcl8.4.a(tclUnixInit.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _AtForkChild in libnamdtcl8.4.a(tclMacOSXNotify.o)
      _Tcl_FinalizeNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
      _Tcl_WaitForEvent in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_kCFRunLoopCommonModes", referenced from:
      _Tcl_InitNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFRunLoopAddSource", referenced from:
      _Tcl_InitNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
      _Tcl_InitNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFRunLoopGetCurrent", referenced from:
      _Tcl_InitNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFRunLoopSourceInvalidate", referenced from:
      _Tcl_FinalizeNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFStringCreateWithCString", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFStringGetCString", referenced from:
      _TclpSetVariables in libnamdtcl8.4.a(tclUnixInit.o)
  "_CFRunLoopSourceSignal", referenced from:
      _Tcl_AlertNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
      _NotifierThreadProc in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFBundleCreate", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFRunLoopSourceCreate", referenced from:
      _Tcl_InitNotifier in libnamdtcl8.4.a(tclMacOSXNotify.o)
  "_CFURLCreateCopyAppendingPathComponent", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFLocaleGetIdentifier", referenced from:
      _TclpSetVariables in libnamdtcl8.4.a(tclUnixInit.o)
  "_CFURLCopyLastPathComponent", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFStringCompare", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
  "_CFBundleGetBundleWithIdentifier", referenced from:
      _Tcl_MacOSXOpenVersionedBundleResources in libnamdtcl8.4.a(tclMacOSXBundle.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /Users/char/src/namd2/namd2-cvs-2011.01.31/MacOSX-x86_64-g++
   Command g++ -m64 -fPIC -dynamic -fno-common -multiply_defined suppress -rdynamic -O3 -L.rootdir/tcl/lib -L.rootdir/fftw/lib -I.rootdir/charmpp/net-darwin-x86_64/include -o namd2 -L.rootdir/charmpp/net-darwin-x86_64/bin/../lib -I.rootdir/charmpp/net-darwin-x86_64/bin/../include .rootdir/charmpp/net-darwin-x86_64/bin/../lib/libldb-rand.o obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.o obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o obj/ComputeAniso.o obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o obj/ComputeGBISser.o obj/ComputeGBIS.o obj/ComputeFullDirect.o obj/Comp
uteHomePatch.o obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o obj/ComputeNonbondedCUDAExcl.o obj/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/OptPme.o obj/OptPmeRealSpace.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.o obj/ConfigList.o obj/Controller.o obj/ccsinterface.o obj/DataStream.o obj/DumpBench.o obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/GlobalMaster.o obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o obj/GlobalMaste!
 rTcl.o o
bj/GlobalMasterSMD.o obj/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvarmodule.o obj/colvarparse.o obj/colvar.o obj/colvarvalue.o obj/colvarbias.o obj/colvarbias_abf.o obj/colvarbias_meta.o obj/colvaratoms.o obj/colvarcomp.o obj/colvarcomp_angles.o obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o obj/colvarcomp_protein.o obj/colvarcomp_rotations.o obj/colvarproxy_namd.o obj/colvargrid.o obj/GridForceGrid.o obj/GromacsTopFile.o obj/heap.o obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o obj/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.o obj/Molecule2.o obj/NamdCentLB.o obj/NamdNborLB.o obj/NamdHybridLB.o obj/NamdDummyLB.o obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeBase.o obj/PmeKSpace.o obj/PmeRealSpace.o ob
j/ProcessorPrivate.o obj/ProxyMgr.o obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o obj/RefineOnly.o obj/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o obj/pdbplugin.o obj/psfplugin.o moduleinit98959.o -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB .rootdir/charmpp/net-darwin-x86_64/bin/../lib/libmemory-default.o .rootdir/charmpp/net-darwin-x86_64/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -lnamdtcl8.4 -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lm returned error code 1
charmc exiting...

Best,
Chris 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Jim Phillips <jim_at_ks.uiuc.edu> writes:
> Date: Mon, 31 Jan 2011 16:39:49 -0600 (CST)
> From: Jim Phillips <jim_at_ks.uiuc.edu>
> To: "Minh, David D." <daveminh_at_anl.gov>
> cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: Problems compiling NAMD on 8-core Mac
> 
> 
> The true error message isn't shown there, but I'm guessing the
> problem is that you're using 32-bit fftw and tcl libraries in a
> 64-bit build.  I've never actually built a 64-bit Mac binary, and
> I'm guessing the person who checked in that .arch file didn't use
> Tcl.  Try without fftw and tcl to see if that works first.
> 
> -Jim
> 
> On Mon, 31 Jan 2011, Minh, David D. wrote:
> 
> >Hello,
> >
> >I'm interested in making some minor modifications to the targeted
> >MD module of NAMD.  However, I've been having trouble compiling
> >the code on my desktop computer, which is a:
> >
> >Mac Pro3,1
> >Mac OS X Version 10.5.8
> >2 x 2.8 GHz Quad-Core Intel Xeon
> >
> >I downloaded the NAMD 2.7 source files.  Then I built Charmm++ with:
> >
> >./build charm++ net-darwin-x86_64 --no-build-shared -with-production
> >
> >The "megatest" runs with no problems.  I downloaded the TCL and
> >FFTW libraries and renamed them to fftw and tcl, respectively, in
> >the NAMD_2.7_Source directory.  Then I ran the following config
> >command:
> >
> >./config MacOSX-x86_64-g++ --charm-arch net-darwin-x86_64
> >
> >Finally I went to the MacOSX-x86_64-g++ directory and entered
> >make.  The compilation went for a while before these final lines:
> >
> >Adding registration for module NeighborLB
> >Adding registration for module HybridLB
> >Adding registration for module RefineLB
> >Adding registration for module GreedyLB
> >charmc> All libraries are:
> >-L.rootdir/charm-6.2.2/net-darwin-x86_64/bin/../lib
> >-I.rootdir/charm-6.2.2/net-darwin-x86_64/bin/../include
> >.rootdir/charm-6.2.2/net-darwin-x86_64/bin/../lib/libldb-rand.o
> >obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.o
> >obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o
> >obj/AlgSeven.o obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o
> >obj/BackEnd.o obj/BroadcastMgr.o obj/BroadcastClient.o
> >obj/CollectionMaster.o obj/CollectionMgr.o obj/Communicate.o
> >obj/Compute.o obj/ComputeAngles.o obj/ComputeAniso.o
> >obj/ComputeBonds.o obj/ComputeConsForce.o
> >obj/ComputeConsForceMsgs.o obj/ComputeCrossterms.o
> >obj/ComputeCylindricalBC.o obj/ComputeDihedrals.o
> >obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o
> >obj/ComputeEField.o obj/ComputeEwald.o obj/ComputeExt.o
> >obj/ComputeFullDirect.o obj/ComputeHomePatch.o
> >obj/ComputeHomePatches.o obj/ComputeImpropers.o
> >obj/ComputeGlobal.o obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o
> >obj/ComputeMap.o obj/ComputeMgr.o obj/ComputeNonbondedSelf.o
> >obj/ComputeNonbondedPair.o obj/ComputeNonbondedUtil.o
> >obj/ComputeNonbondedStd.o obj/ComputeNonbondedFEP.o
> >obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o
> >obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o
> >obj/ComputeNonbondedCUDAExcl.o obj/ComputePatch.o
> >obj/ComputePatchPair.o obj/ComputePme.o obj/OptPme.o
> >obj/OptPmeRealSpace.o obj/ComputeRestraints.o
> >obj/ComputeSphericalBC.o obj/ComputeStir.o obj/ComputeTclBC.o
> >obj/ComputeThole.o obj/ConfigList.o obj/Controller.o
> >obj/ccsinterface.o obj/DataStream.o obj/DumpBench.o
> >obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o
> >obj/FreeEnergyLambda.o obj/FreeEnergyLambdMgr.o
> >obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o
> >obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/GlobalMaster.o
> >obj/GlobalMasterServer.o obj/GlobalMasterTest.o
> >obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o
> >obj/GlobalMasterTMD.o obj/GlobalMasterFreeEnergy.o
> >obj/GlobalMasterEasy.o obj/GlobalMasterMisc.o obj/colvarmodule.o
> >obj/colvarparse.o obj/colvar.o obj/colvarvalue.o obj/colvarbias.o
> >obj/colvarbias_abf.o obj/colvarbias_meta.o obj/colvaratoms.o
> >obj/colvarcomp.o obj/colvarcomp_angles.o
> >obj/colvarcomp_coordnums.o obj/colvarcomp_distances.o
> >obj/colvarcomp_protein.o obj/colvarcomp_rotations.o
> >obj/colvarproxy_namd.o obj/colvargrid.o obj/GridForceGrid.o
> >obj/GromacsTopFile.o obj/heap.o obj/HomePatch.o obj/IMDOutput.o
> >obj/InfoStream.o obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o
> >obj/MGridforceParams.o obj/MStream.o obj/MigrateAtomsMsg.o
> >obj/Molecule.o obj/Molecule2.o obj/NamdCentLB.o obj/NamdNborLB.o
> >obj/NamdHybridLB.o obj/NamdDummyLB.o obj/NamdState.o
> >obj/NamdOneTools.o obj/Node.o obj/Output.o obj/Parameters.o
> >obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o obj/PatchMap.o
> >obj/PDB.o obj/PDBData.o obj/PmeBase.o obj/PmeKSpace.o
> >obj/PmeRealSpace.o obj/ProcessorPrivate.o obj/ProxyMgr.o
> >obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o
> >obj/ReductionMgr.o obj/RefineOnly.o obj/RefineTorusLB.o
> >obj/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o
> >obj/SimParameters.o obj/SortAtoms.o obj/Sync.o obj/TclCommands.o
> >obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o
> >obj/parm.o obj/imd.o obj/CompressPsf.o obj/PluginIOMgr.o
> >obj/ParallelIOMgr.o obj/AtomsDisInfo.o obj/FileIO.o
> >obj/dcdplugin.o obj/jsplugin.o obj/pdbplugin.o obj/psfplugin.o
> >moduleinit85635.o -lmoduleNeighborLB -lmoduleHybridLB
> >-lmoduleRefineLB -lmoduleGreedyLB .rootdir/charm-6.2.2/net-darwin-x86_64/bin/../lib/libmemory-default.o .rootdir/charm-6.2.2/net-darwin-x86_64/bin/../lib/libthreads-default.o
> >-lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl
> >-lnamdtcl8.4 -lsrfftw -lsfftw -lm -lmoduleNeighborLB
> >-lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB -lm
> >rm -f moduleinit85635.C moduleinit85635.o
> >make: *** [namd2] Error 1
> >
> >Does anybody know what could cause this error and how to get around it?
> >
> >Thanks,
> >David Minh
>

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