From: Minh, David D. (daveminh_at_anl.gov)
Date: Mon Jan 31 2011 - 12:25:40 CST
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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