NAMD 2.7b1 with APBS/iAPBS

From: Bjoern Olausson (bjoern.olausson_at_biochemtech.uni-halle.de)
Date: Wed Jul 22 2009 - 02:56:07 CDT

Hi everybody,

I tried to compile NAMD with iAPBS interface to carry out a MD-Simulation with
implicit solvent (water).

So far I didn't manage to compile NAMD linked to APBS.

I tried it with ICC and GCC so far, but no go.

Attached is a complete logfile of the script (install.{txt,sh} which I used to
compile all the stuff (it basically replicates all the manual steps)

I don't know if I can send attachment so here are the files:
http://daten-transport.de/?id=kZgr7FJySXbH

install.log 291,4 Kilobytes
http://daten-transport.de/download.php?id=kZgr7FJySXbH&dateinummer=3862
install.txt 2,5 Kilobytes
http://daten-transport.de/download.php?id=kZgr7FJySXbH&dateinummer=3863

Thanks for any help.

Kind regards
Bjoern

The failing part:
charmc: Executing g++ -fPIC -m64 -m64 -rdynamic -L.rootdir/tcl/lib -
L.rootdir/fftw/lib -L/lib -I.rootdir/charm-6.1/net-linux-x86_64/include -
DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -ffast-math -o
namd2 -L.rootdir/charm-6.1/net-linux-x86_64/bin/../lib -
I.rootdir/charm-6.1/net-linux-x86_64/bin/../include .rootdir/charm-6.1/net-
linux-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/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/ComputeNonbondedCUDA.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/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/GlobalMasterAPBS.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/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/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/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/AtomsDisInfo.o obj/FileIO.o obj/dcdplugin.o obj/jsplugin.o obj/pdbplugin.o
obj/psfplugin.o moduleinit5004.o -lmoduleNeighborLB -lmodulecommlib
.rootdir/charm-6.1/net-linux-x86_64/bin/../lib/libmemory-default.o
.rootdir/charm-6.1/net-linux-x86_64/bin/../lib/libthreads-default.o -lck -
lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -ltcl8.3 -ldl -lsrfftw -
lsfftw -liapbs -lapbsmainroutines -lapbs -lmaloc -lblas -llapack -lvf2c -
lifcore -lm -lmoduleNeighborLB -lmodulecommlib -lm
/usr/bin/ld: cannot find -liapbs
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /home/blub/apbs/NAMD_2.7b1_Source/Linux-
x86_64-g++


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