NAMD on RedHat Linux

From: godawr_at_rpi.edu
Date: Wed May 23 2007 - 10:04:22 CDT

('binary' encoding is not supported, stored as-is) Hi All
I followed the steps in notes.txt to install NAMD. Following output comes
up during installation. Please guide me so as to where is the problem and
how can i fix it.

charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing g++ -D__CHARMC__=1 -c moduleinit5149.C -o moduleinit5149.o
charmc: Executing g++ -Wl,--allow-multiple-definition -rdynamic
-L/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib
-L/home/godawr/tcl/lib
-L/home/godawr/software/NAMD_2.6_Source/fftw-linux//lib
-I/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static -o
namd2
-L/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib
-I/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../include
/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib/libld
b-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/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/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.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/GlobalMasterTest.o
obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o
obj/GlobalMasterTMD.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o
obj/GlobalMasterMisc.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/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.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/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o
obj/SimParameters.o obj/Sync.o obj/TclCommands.o obj/WorkDistrib.o
obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/dcdplugin.o
moduleinit5149.o -lmoduleNeighborLB -lmodulecommlib
/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib/libme
mory-default.o
/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib/libth
reads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl
-ltcl8.3 -ldl -lm -lmoduleNeighborLB -lmodulecommlib -lm
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclLoadDl.
o)(.text+0x35): In function `TclpLoadFile':
: Using 'dlopen' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclUnixPip
e.o)(.text+0xe2): In function `TclpCreateTempFile':
: the use of `tmpnam' is dangerous, better use `mkstemp'
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclUnixFCm
d.o)(.text+0xc26): In function `GetGroupAttribute':
: Using 'getgrgid' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclUnixFCm
d.o)(.text+0xe38): In function `SetGroupAttribute':
: Using 'getgrnam' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclUnixFCm
d.o)(.text+0xc71): In function `GetGroupAttribute':
: Using 'endgrent' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclUnixFCm
d.o)(.text+0xf4d): In function `SetOwnerAttribute':
: Using 'getpwnam' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
obj/dcdlib.o(.text+0x1066): In function `write_dcdheader(int, char*, int,
int, int, int, int, double, int)':
: Using 'getpwuid' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclUnixFCm
d.o)(.text+0xd31): In function `GetOwnerAttribute':
: Using 'endpwent' in statically linked applications requires at runtime
the shared libraries from the glibc version used for linking
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclUnixCha
n.o)(.text+0xf01): In function `TcpGetOptionProc':
: Using 'gethostbyaddr' in statically linked applications requires at
runtime the shared libraries from the glibc version used for linking
obj/vmdsock.o(.text+0x96): In function `vmdsock_connect(void*, char
const*, int)':
: Using 'gethostbyname' in statically linked applications requires at
runtime the shared libraries from the glibc version used for linking
/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib/libtcl8.3.a(tclIOSock.
o)(.text+0x47): In function `TclSockGetPort':
: Using 'getservbyname' in statically linked applications requires at
runtime the shared libraries from the glibc version used for linking
obj/ComputePme.o(.text+0x1a64): In function
`ComputePmeMgr::initialize(CkQdMsg*)':
: undefined reference to `rfftwnd_create_plan_specific'
obj/ComputePme.o(.text+0x1af2): In function
`ComputePmeMgr::initialize(CkQdMsg*)':
: undefined reference to `fftw_create_plan_specific'
obj/ComputePme.o(.text+0x1b80): In function
`ComputePmeMgr::initialize(CkQdMsg*)':
: undefined reference to `fftw_create_plan_specific'
obj/ComputePme.o(.text+0x1bf7): In function
`ComputePmeMgr::initialize(CkQdMsg*)':
: undefined reference to `rfftwnd_create_plan_specific'
obj/ComputePme.o(.text+0x2d7a): In function `ComputePmeMgr::gridCalc1()':
: undefined reference to `rfftwnd_real_to_complex'
obj/ComputePme.o(.text+0x35fa): In function `ComputePmeMgr::gridCalc2()':
: undefined reference to `fftw'
obj/ComputePme.o(.text+0x369e): In function `ComputePmeMgr::gridCalc2()':
: undefined reference to `fftw'
obj/ComputePme.o(.text+0x3f93): In function `ComputePmeMgr::gridCalc3()':
: undefined reference to `rfftwnd_complex_to_real'
obj/SimParameters.o(.text+0xcaeb): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_import_wisdom_from_file'
obj/SimParameters.o(.text+0xccab): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `rfftwnd_create_plan_specific'
obj/SimParameters.o(.text+0xccb3): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `rfftwnd_destroy_plan'
obj/SimParameters.o(.text+0xcd1f): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_create_plan_specific'
obj/SimParameters.o(.text+0xcd27): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_destroy_plan'
obj/SimParameters.o(.text+0xcd93): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_create_plan_specific'
obj/SimParameters.o(.text+0xcd9b): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_destroy_plan'
obj/SimParameters.o(.text+0xcdff): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_create_plan_specific'
obj/SimParameters.o(.text+0xce07): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_destroy_plan'
obj/SimParameters.o(.text+0xce68): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_create_plan_specific'
obj/SimParameters.o(.text+0xce70): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_destroy_plan'
obj/SimParameters.o(.text+0xcee1): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `rfftwnd_create_plan_specific'
obj/SimParameters.o(.text+0xcee9): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `rfftwnd_destroy_plan'
obj/SimParameters.o(.text+0xcf93): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_export_wisdom_to_file'
obj/SimParameters.o(.text+0xcfa0): In function
`SimParameters::print_config(ParseOptions&, ConfigList*, char*&)':
: undefined reference to `fftw_export_wisdom_to_string'
obj/SimParameters.o(.text+0x1097a): In function
`SimParameters::receive_SimParameters(MIStream*)':
: undefined reference to `fftw_import_wisdom_from_string'
collect2: ld returned 1 exit status
Fatal Error by charmc in directory
/home/godawr/software/NAMD_2.6_Source/Linux-i686-g++
   Command g++ -Wl,--allow-multiple-definition -rdynamic
-L/home/godawr/software/NAMD_2.6_Source/tcl-linux/lib
-L/home/godawr/tcl/lib
-L/home/godawr/software/NAMD_2.6_Source/fftw-linux//lib
-I/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -march=pentiumpro -ffast-math -static -o
namd2
-L/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib
-I/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../include
/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib/libld
b-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/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/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.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/GlobalMasterTest.o
obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o
obj/GlobalMasterTMD.o obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o
obj/GlobalMasterMisc.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/MStream.o obj/MigrateAtomsMsg.o obj/Molecule.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/ScriptTcl.o obj/Sequencer.o obj/Set.o obj/Settle.o
obj/SimParameters.o obj/Sync.o obj/TclCommands.o obj/WorkDistrib.o
obj/pub3dfft.o obj/vmdsock.o obj/parm.o obj/imd.o obj/dcdplugin.o
moduleinit5149.o -lmoduleNeighborLB -lmodulecommlib
/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib/libme
mory-default.o
/home/godawr/software/NAMD_2.6_Source/charm-5.9/net-linux/bin/../lib/libth
reads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl
-ltcl8.3 -ldl -lm -lmoduleNeighborLB -lmodulecommlib -lm returned error code 1
charmc exiting...
rm -f moduleinit5149.C moduleinit5149.o
make: *** [namd2] Error 1

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