Problems installing NAMD

From: Bruno Rodrigues (bbrodrigues_at_gmail.com)
Date: Sat Jul 31 2010 - 01:12:12 CDT

Hi,

I have a MacOSX with core 2 duo processor. So I think this is a 64 bit
architecture. Based on this fact, I installed Charm 6.2.1 with this command
./build LIBS net-darwin-x86_64 -j2 -O2

Everything worked fine, and I was able to run all the tests.

Then I went to install NAMD_2.7b3. I used this command, after struggling for
a while with the syntax:
./config MacOSX-x86_64-g++ --charm-arch net-darwin-x86_64

First I tried install everything on the 32 bits architecture, and the
installation crashed at the begin after the ./config command.
On the 64 bits it worked fine, with no errors.
Then I cd to MacOSX-x86_64-g++ and typed make.
All the commands were typed with sudo.

I got this message, at the end:

ld: symbol(s) not found
collect2: ld returned 1 exit status
Fatal Error by charmc in directory
/Users/bbrodrigues/Documents/doc_ufmg/programs/source_codes/NAMD_2.7b3_Source/MacOSX-x86_64-g++
   Command g++ -m64 -fPIC -dynamic -fno-common -multiply_defined suppress
-rdynamic -O3 -L.rootdir/tcl/lib -L.rootdir/fftw/lib
-I.rootdir/charm-6.2.1/net-darwin-x86_64/include -o namd2
-L.rootdir/charm-6.2.1/net-darwin-x86_64/bin/../lib
-I.rootdir/charm-6.2.1/net-darwin-x86_64/bin/../include
.rootdir/charm-6.2.1/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 moduleinit5848.o
-lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB
.rootdir/charm-6.2.1/net-darwin-x86_64/bin/../lib/libmemory-default.o
.rootdir/charm-6.2.1/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 returned error code 1
charmc exiting...
rm -f moduleinit5848.C moduleinit5848.o
make: *** [namd2] Error 1

I checked the page
http://debianclusters.org/index.php/NAMD:_Troubleshooting_Errors
and re-built charm++ using this explanation:
"You can fix this by giving the charm++ ./build command a --basedir=. Set
the base directory to be the directory that encompasses where mpi.h is
located. "

But the error continued....

Can anyone help me?

-- 
-- 
Msc. Bruno B. Rodrigues
Prof. de Ensino Básico, Técnico e Tecnologico
Escola Preparatória de Cadetes do Ar - EPCAR

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