Re: Problems compiling NAMD on 8-core Mac

From: Jim Phillips (
Date: Mon Jan 31 2011 - 16:39:49 CST

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.


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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