Re: Problems compiling NAMD on 8-core Mac

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Jan 31 2011 - 16:44:23 CST

Which compiler are you using? The default apple gcc or another, such as
the gcc series in macports?

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
"Minh, David D." <daveminh_at_anl.gov> writes:
> Date: Mon, 31 Jan 2011 12:25:40 -0600
> From: "Minh, David D." <daveminh_at_anl.gov>
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Problems compiling NAMD on 8-core Mac
> X-Mailer: Apple Mail (2.936)
> 
> 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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