Re: Charm++ nodelist commands

From: Gadi Oron (gadi_at_proteologics.com)
Date: Tue Dec 30 2003 - 08:10:29 CST

Hi again,

On Wed, 2003-12-24 at 01:22, Gengbin Zheng wrote:
> We are not completely without hope... :-)

Thank you for your efforts...

> I have compiled Charm++/NAMD on both of my Laptop(Linux RH9 2GHz P4) and a

Nice laptop :-)))

> desktop (running Windows XP and Cygwin, 2.4G P4) at home and now I am
> running NAMD happily on both them using 100M switch broadband router for
> Apoa1 benchmark. I got about 4.52 seconds per step, while running on my
> laptop Linux alone, I got 7.49s per step, so not bad - that is about
> speedup of 1.66 on 2 cpus.
>
> To do this, one needs to use /Zp4 for VC++ to pack structures in a 4 bytes
> boundry (default is 8 bytes, while gcc uses 4 bytes), and needs the charmd
> from the latest version with my previous fixes. I also have the Cygwin
> version of NAMD2 compiled using Cygwin/g++ working too.

Well, I was trying to compile NAMD under Cygwin, but encountered some
problems compiling NAMD:

- Apparently the Cygwin-i686.plugins file is missing.
- (using config without plugins) gcc complains it cannot find
strstream.h, wich seems to be missing in GCC 3.3.
- (When downgrading to GCC 3.2) Linking crashes. The log of the crash
command in an attached document.

Charm++ compiles Ok.

Would it be too much to ask for a copy of the binaries for Win32?

> Here is a sample nodelist file when I start charmrun on Cygwin box.
> (192.168.2.100)
>
> group main
> host 192.168.2.102 ++pathfix /home/work/ /home/gzheng/
> host 192.168.2.100 ++pathfix /home/work/ C:\cygwin\home\work\

So, here you launch NAMD from a computer where your files are in
"/home/work/..." on 2 nodes in the first the files are in
"/home/gzheng/..." and the second (Win) "c:\cygwin\home\work\". Am I
right?

Another question: is it possible to set process priority (nice level)
for NAMD node programs?

Best regards

-- 
================= Gadi ORON, PhD -o- Proteologics ======================
========== gadi/at/proteologics.com ========== +972 8 9475666 ==========
If you lose your temper at a newspaper columnist, he'll get rich, 
or famous or both.

rm -f obj/buildinfo.C; echo 'const char *namd_build_date = ' \"`date`\"\; > obj/buildinfo.C; echo 'const char *namd_build_user = ' \"administrator\"\; >> obj/buildinfo.C; echo 'const char *namd_build_machine = ' \"`hostname`\"\; >> obj/buildinfo.C; cat obj/buildinfo.C; g++ -I/usr/include/w32api -I/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/include -DCMK_OPTIMIZE=1 -Isrc -Iinc -I/cygdrive/c/NAMD_2.5_Source/tcl/win32/include -DNAMD_TCL -DUSE_NON_CONST -I/cygdrive/c/NAMD_2.5_Source/fftw-cygwin/include -DNAMD_FFTW -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Cygwin-i686\" -O3 -Wall -march=pentiumpro -ffast-math -o obj/buildinfo.o -c obj/buildinfo.C
const char *namd_build_date = "Tue Dec 30 16:01:59 JST 2003";
const char *namd_build_user = "administrator";
const char *namd_build_machine = "argos";
cc1plus: warning: changing search order for system directory "/usr/include/w32api"
cc1plus: warning: as it has already been specified as a non-system directory
cc1plus: warning: changing search order for system directory "/usr/i686-pc-cygwin/lib/../../include/w32api"
cc1plus: warning: as it is the same as non-system directory "/usr/include/w32api"
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/charmc -verbose -ld++-option \
"-I/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -Wall -march=pentiumpro -ffast-math" \
-module NeighborLB -module commlib -language charm++ \
obj/buildinfo.o \
obj/common.o obj/dcdlib.o obj/erf.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/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.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/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.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/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 \
 \
 \
-L/cygdrive/c/NAMD_2.5_Source/tcl/win32/lib -ltcl8.3 \
-L/cygdrive/c/NAMD_2.5_Source/fftw-cygwin/lib -lsrfftw -lsfftw \
 \
-lm -o namd2
Verbose mode set
passing unrecognized option -march=pentiumpro to all compilers and linkers
passing unrecognized option -ffast-math to all compilers and linkers
Adding file obj/buildinfo.o...
Adding file obj/common.o...
Adding file obj/dcdlib.o...
Adding file obj/erf.o...
Adding file obj/main.o...
Adding file obj/mainfunc.o...
Adding file obj/memusage.o...
Adding file obj/strlib.o...
Adding file obj/AlgSeven.o...
Adding file obj/AlgRecBisection.o...
Adding file obj/AlgNbor.o...
Adding file obj/AtomMap.o...
Adding file obj/BackEnd.o...
Adding file obj/BroadcastMgr.o...
Adding file obj/BroadcastClient.o...
Adding file obj/CollectionMaster.o...
Adding file obj/CollectionMgr.o...
Adding file obj/Communicate.o...
Adding file obj/Compute.o...
Adding file obj/ComputeAngles.o...
Adding file obj/ComputeBonds.o...
Adding file obj/ComputeConsForce.o...
Adding file obj/ComputeConsForceMsgs.o...
Adding file obj/ComputeCylindricalBC.o...
Adding file obj/ComputeDihedrals.o...
Adding file obj/ComputeDPME.o...
Adding file obj/ComputeDPMEMsgs.o...
Adding file obj/ComputeDPMTA.o...
Adding file obj/ComputeEField.o...
Adding file obj/ComputeExt.o...
Adding file obj/ComputeFullDirect.o...
Adding file obj/ComputeHomePatch.o...
Adding file obj/ComputeHomePatches.o...
Adding file obj/ComputeImpropers.o...
Adding file obj/ComputeGlobal.o...
Adding file obj/ComputeGlobalMsgs.o...
Adding file obj/ComputeMap.o...
Adding file obj/ComputeMgr.o...
Adding file obj/ComputeNonbondedSelf.o...
Adding file obj/ComputeNonbondedPair.o...
Adding file obj/ComputeNonbondedUtil.o...
Adding file obj/ComputeNonbondedStd.o...
Adding file obj/ComputeNonbondedFEP.o...
Adding file obj/ComputeNonbondedLES.o...
Adding file obj/ComputePatch.o...
Adding file obj/ComputePatchPair.o...
Adding file obj/ComputePme.o...
Adding file obj/ComputeRestraints.o...
Adding file obj/ComputeSphericalBC.o...
Adding file obj/ComputeStir.o...
Adding file obj/ConfigList.o...
Adding file obj/Controller.o...
Adding file obj/ccsinterface.o...
Adding file obj/DataStream.o...
Adding file obj/DumpBench.o...
Adding file obj/FreeEnergyAssert.o...
Adding file obj/FreeEnergyGroup.o...
Adding file obj/FreeEnergyLambda.o...
Adding file obj/FreeEnergyLambdMgr.o...
Adding file obj/FreeEnergyParse.o...
Adding file obj/FreeEnergyRestrain.o...
Adding file obj/FreeEnergyRMgr.o...
Adding file obj/FreeEnergyVector.o...
Adding file obj/GlobalMaster.o...
Adding file obj/GlobalMasterServer.o...
Adding file obj/GlobalMasterTest.o...
Adding file obj/GlobalMasterIMD.o...
Adding file obj/GlobalMasterTcl.o...
Adding file obj/GlobalMasterSMD.o...
Adding file obj/GlobalMasterFreeEnergy.o...
Adding file obj/GlobalMasterEasy.o...
Adding file obj/GlobalMasterMisc.o...
Adding file obj/GromacsTopFile.o...
Adding file obj/heap.o...
Adding file obj/HomePatch.o...
Adding file obj/IMDOutput.o...
Adding file obj/InfoStream.o...
Adding file obj/LdbCoordinator.o...
Adding file obj/LJTable.o...
Adding file obj/Measure.o...
Adding file obj/MStream.o...
Adding file obj/MigrateAtomsMsg.o...
Adding file obj/Molecule.o...
Adding file obj/NamdCentLB.o...
Adding file obj/NamdNborLB.o...
Adding file obj/NamdState.o...
Adding file obj/NamdOneTools.o...
Adding file obj/Node.o...
Adding file obj/Output.o...
Adding file obj/Parameters.o...
Adding file obj/ParseOptions.o...
Adding file obj/Patch.o...
Adding file obj/PatchMgr.o...
Adding file obj/PatchMap.o...
Adding file obj/PDB.o...
Adding file obj/PDBData.o...
Adding file obj/PmeBase.o...
Adding file obj/PmeKSpace.o...
Adding file obj/PmeRealSpace.o...
Adding file obj/ProcessorPrivate.o...
Adding file obj/ProxyMgr.o...
Adding file obj/ProxyPatch.o...
Adding file obj/Rebalancer.o...
Adding file obj/RecBisection.o...
Adding file obj/ReductionMgr.o...
Adding file obj/RefineOnly.o...
Adding file obj/ScriptTcl.o...
Adding file obj/Sequencer.o...
Adding file obj/Set.o...
Adding file obj/Settle.o...
Adding file obj/SimParameters.o...
Adding file obj/Sync.o...
Adding file obj/TclCommands.o...
Adding file obj/WorkDistrib.o...
Adding file obj/pub3dfft.o...
Adding file obj/vmdsock.o...
Adding file obj/parm.o...
Adding file obj/imd.o...
charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing g++ -Wno-deprecated -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -Wall -march=pentiumpro -ffast-math -c moduleinit.C -o moduleinit.o
charmc: Executing g++ -Wno-deprecated -O3 -Wall -march=pentiumpro -ffast-math -L/cygdrive/c/NAMD_2.5_Source/tcl/win32/lib -L/cygdrive/c/NAMD_2.5_Source/fftw-cygwin/lib -I/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/include -o namd2 -L/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib -I/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../include /cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libldb-rand.o obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.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/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.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/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.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/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 moduleinit.o -lmoduleNeighborLB -lmodulecommlib /cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmemory-default.o /cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lz -ltcl8.3 -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTV10NeighborLB+0x0):NeighborLB.C: multiple definition of `vtable for NeighborLB'
obj/NamdNborLB.o(.data$_ZTV10NeighborLB+0x0):NamdNborLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTI10NeighborLB+0x0):NeighborLB.C: multiple definition of `typeinfo for NeighborLB'
obj/NamdNborLB.o(.data$_ZTI10NeighborLB+0x0):NamdNborLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTS10NeighborLB+0x0):NeighborLB.C: multiple definition of `typeinfo name for NeighborLB'
obj/NamdNborLB.o(.text$_ZTS10NeighborLB+0x0):NamdNborLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTI10NborBaseLB+0x0):NeighborLB.C: multiple definition of `typeinfo for NborBaseLB'
obj/NamdNborLB.o(.data$_ZTI10NborBaseLB+0x0):NamdNborLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTS10NborBaseLB+0x0):NeighborLB.C: multiple definition of `typeinfo name for NborBaseLB'
obj/NamdNborLB.o(.text$_ZTS10NborBaseLB+0x0):NamdNborLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTI6BaseLB+0x0):NeighborLB.C: multiple definition of `typeinfo for BaseLB'
obj/NamdCentLB.o(.data$_ZTI6BaseLB+0x0):NamdCentLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTS6BaseLB+0x0):NeighborLB.C: multiple definition of `typeinfo name for BaseLB'
obj/NamdCentLB.o(.text$_ZTS6BaseLB+0x0):NamdCentLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTI8IrrGroup+0x0):NeighborLB.C: multiple definition of `typeinfo for IrrGroup'
obj/BroadcastMgr.o(.data$_ZTI8IrrGroup+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTS8IrrGroup+0x0):NeighborLB.C: multiple definition of `typeinfo name for IrrGroup'
obj/BroadcastMgr.o(.text$_ZTS8IrrGroup+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTI5Chare+0x0):NeighborLB.C: multiple definition of `typeinfo for Chare'
obj/main.o(.data$_ZTI5Chare+0x0):main.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmoduleNeighborLB.a(NeighborLB.o)(.rdata$_ZTS5Chare+0x0):NeighborLB.C: multiple definition of `typeinfo name for Chare'
obj/main.o(.text$_ZTS5Chare+0x0):main.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ck.o)(.rdata$_ZTI5Group+0x0):ck.C: multiple definition of `typeinfo for Group'
obj/BroadcastMgr.o(.data$_ZTI5Group+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ck.o)(.rdata$_ZTS5Group+0x0):ck.C: multiple definition of `typeinfo name for Group'
obj/BroadcastMgr.o(.text$_ZTS5Group+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ck.o)(.rdata$_ZTI14CkReductionMgr+0x0):ck.C: multiple definition of `typeinfo for CkReductionMgr'
obj/BroadcastMgr.o(.data$_ZTI14CkReductionMgr+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ck.o)(.rdata$_ZTS14CkReductionMgr+0x0):ck.C: multiple definition of `typeinfo name for CkReductionMgr'
obj/BroadcastMgr.o(.text$_ZTS14CkReductionMgr+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ck.o)(.rdata$_ZTI19CkGroupInitCallback+0x0):ck.C: multiple definition of `typeinfo for CkGroupInitCallback'
obj/BroadcastMgr.o(.data$_ZTI19CkGroupInitCallback+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ck.o)(.rdata$_ZTV19CkGroupInitCallback+0x0):ck.C: multiple definition of `vtable for CkGroupInitCallback'
obj/BroadcastMgr.o(.data$_ZTV19CkGroupInitCallback+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ck.o)(.rdata$_ZTS19CkGroupInitCallback+0x0):ck.C: multiple definition of `typeinfo name for CkGroupInitCallback'
obj/BroadcastMgr.o(.text$_ZTS19CkGroupInitCallback+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(ckreduction.o)(.rdata$_ZTV14CkReductionMgr+0x0):ckreduction.C: multiple definition of `vtable for CkReductionMgr'
obj/BroadcastMgr.o(.data$_ZTV14CkReductionMgr+0x0):BroadcastMgr.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(CentralLB.o)(.rdata$_ZTV9CentralLB+0x0):CentralLB.C: multiple definition of `vtable for CentralLB'
obj/NamdCentLB.o(.data$_ZTV9CentralLB+0x0):NamdCentLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(CentralLB.o)(.rdata$_ZTI9CentralLB+0x0):CentralLB.C: multiple definition of `typeinfo for CentralLB'
obj/NamdCentLB.o(.data$_ZTI9CentralLB+0x0):NamdCentLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(CentralLB.o)(.rdata$_ZTS9CentralLB+0x0):CentralLB.C: multiple definition of `typeinfo name for CentralLB'
obj/NamdCentLB.o(.text$_ZTS9CentralLB+0x0):NamdCentLB.C: first defined here
/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libck.a(BaseLB.o)(.rdata$_ZTV6BaseLB+0x0):BaseLB.C: multiple definition of `vtable for BaseLB'
obj/NamdCentLB.o(.data$_ZTV6BaseLB+0x0):NamdCentLB.C: first defined here
/usr/lib/gcc-lib/i686-pc-cygwin/3.2/../../../../i686-pc-cygwin/bin/ld: cannot find -ltcl8.3
collect2: ld returned 1 exit status
Fatal Error by charmc in directory /cygdrive/c/NAMD_2.5_Source/Cygwin-i686
Command g++ -Wno-deprecated -O3 -Wall -march=pentiumpro -ffast-math -L/cygdrive/c/NAMD_2.5_Source/tcl/win32/lib -L/cygdrive/c/NAMD_2.5_Source/fftw-cygwin/lib -I/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/include -o namd2 -L/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib -I/cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../include /cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libldb-rand.o obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.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/ComputeCylindricalBC.o obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o obj/ComputeDPMTA.o obj/ComputeEField.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/ComputePatch.o obj/ComputePatchPair.o obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o obj/ComputeStir.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/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 moduleinit.o -lmoduleNeighborLB -lmodulecommlib /cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libmemory-default.o /cygdrive/c/NAMD_2.5_Source/charm/net-cygwin/bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lz -ltcl8.3 -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib returned error code 1
charmc exiting...

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