Re: Problems compiling NAMD on 8-core Mac

From: Minh, David D. (daveminh_at_anl.gov)
Date: Mon Jan 31 2011 - 17:44:01 CST

It is the default apple gcc.

(I will also look into whether fftw and tcl are 32 or 64 bit when I am back at that computer).

On Jan 31, 2011, at 4:44 PM, Chris Harrison wrote:

> 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
>>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:33 CST