problem about NAMD compile

From: liupeng012 (liupeng012_at_mail.nankai.edu.cn)
Date: Tue Mar 10 2009 - 03:15:27 CDT



HI!
  everyone!
 
  I compile the NAMD .
  
  (1)compiling charm-6.0 is succesful.
  (2)compiling NAMD ,
   when it is finished , i see the message as follow!

charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing mpicxx -m64 -fPIC -D__CHARMC__=1 -c moduleinit3060.C -o moduleinit3060.o
charmc: Executing mpicxx -m64 -fPIC -rdynamic -L/hptc_cluster/NAMD/namd2/tcl/linux-amd64/lib -L/hptc_cluster/NAMD/namd2/fftw/linux-amd64/lib -I.rootdir/charm-6.0//include -DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations -ffast-math -o namd2 -L.rootdir/charm-6.0//bin/../lib -I.rootdir/charm-6.0//bin/../include .rootdir/charm-6.0//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/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/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/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/AtomsDisInfo.o obj/FileIO.o obj/dcdplugin.o moduleinit3060.o -lmoduleNeighborLB -lmodulecommlib .rootdir/charm-6.0//bin/../lib/libmemory-default.o .rootdir/charm-6.0//bin/../lib/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib -lm
/hptc_cluster/NAMD/namd2/tcl/linux-amd64/lib/libtcl8.3.a(tclUnixPipe.o): In function `TclpCreateTempFile':
tclUnixPipe.c:(.text+0xe0): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
charmc: Executing rm -f charmrun
charmc: Executing cp -p .rootdir/charm-6.0//bin/charmrun charmrun
rm -f moduleinit3060.C moduleinit3060.o
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/tcl_main.o -c sb/src/tcl_main.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/tcl_psfgen.o -c sb/src/tcl_psfgen.c
sb/src/tcl_psfgen.c: In function ?newhandle_msga
sb/src/tcl_psfgen.c:40: warning: passing argument 2 of Tcl_Mergea€? from incompatible pointer type
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/charmm_file.o -c sb/src/charmm_file.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/charmm_parse_topo_defs.o -c sb/src/charmm_parse_topo_defs.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/extract_alias.o -c sb/src/extract_alias.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/hash.o -c sb/src/hash.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/hasharray.o -c sb/src/hasharray.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/memarena.o -c sb/src/memarena.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/pdb_file.o -c sb/src/pdb_file.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/pdb_file_extract.o -c sb/src/pdb_file_extract.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/psf_file.o -c sb/src/psf_file.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/psf_file_extract.o -c sb/src/psf_file_extract.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/topo_defs.o -c sb/src/topo_defs.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/topo_mol.o -c sb/src/topo_mol.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/topo_mol_output.o -c sb/src/topo_mol_output.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o obj/stringhash.o -c sb/src/stringhash.c
gcc -Isb/src -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o psfgen obj/tcl_main.o obj/tcl_psfgen.o obj/charmm_file.o obj/charmm_parse_topo_defs.o obj/extract_alias.o obj/hash.o obj/hasharray.o obj/memarena.o obj/pdb_file.o obj/pdb_file_extract.o obj/psf_file.o obj/psf_file_extract.o obj/topo_defs.o obj/topo_mol.o obj/topo_mol_output.o obj/stringhash.o -L/hptc_cluster/NAMD/namd2/tcl/linux-amd64/lib -ltcl8.3 -ldl -lm
/hptc_cluster/NAMD/namd2/tcl/linux-amd64/lib/libtcl8.3.a(tclUnixPipe.o): In function `TclpCreateTempFile':
tclUnixPipe.c:(.text+0xe0): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
gcc -Isrc -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o flipdcd src/flipdcd.c || \
        echo "#!/bin/sh\necho unavailable on this platform" > flipdcd; \
        chmod +x flipdcd
src/flipdcd.c: In function maina:
src/flipdcd.c:39: warning: incompatible implicit declaration of built-in function a€?exita€?
gcc -Isrc -I/hptc_cluster/NAMD/namd2/tcl/linux-amd64/include -DNAMD_TCL -O3 -m64 -fexpensive-optimizations -ffast-math -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRACOPY -o flipbinpdb src/flipbinpdb.c || \
        echo "#!/bin/sh\necho unavailable on this platform" > flipbinpdb; \
        chmod +x flipbinpdb
src/flipbinpdb.c: In function main
src/flipbinpdb.c:28: warning: incompatible implicit declaration of built-in function exit
src/flipbinpdb.c:33: warning: incompatible implicit declaration of built-in function exit
src/flipbinpdb.c:38: warning: incompatible implicit declaration of built-in function exit
src/flipbinpdb.c:45: warning: incompatible implicit declaration of built-in function exit
src/flipbinpdb.c:51: warning: incompatible implicit declaration of built-in function exit
src/flipbinpdb.c:62: warning: incompatible implicit declaration of built-in function exit


 just a lot of warning !
 no error and no the message "sucessful compiled"!

 the binary file namd2 is excutable . and it work!

Is it right??

  any help is appreciated !
                                                                                       thanks!
                                                                                                         peng liu!
   
2009-03-10



liupeng012

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:27 CST