Re: Problems compiling NAMD on 8-core Mac

From: Jim Phillips (jim_at_ks.uiuc.edu)
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.

-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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