From: Suxing Hu (suxing_at_t4.lanl.gov)
Date: Thu Dec 09 2004 - 21:08:54 CST
Hi Gengbin,
Thank you very much for your suggestions! I eventually get the NAMD built on the
Myrinet.
Appreciate again.
Suxing
>From: Gengbin Zheng <gzheng_at_ks.uiuc.edu>
>User-Agent: Mozilla Thunderbird 0.9 (Windows/20041103)
>X-Accept-Language: en-us, en
>MIME-Version: 1.0
>To: Suxing Hu <suxing_at_t4.lanl.gov>
>Subject: Re: namd-l: Building NAMD with Portland's C++ Comipler
>Content-Transfer-Encoding: 7bit
>X-PMX-Version: 4.7.0.111621
>
>
>It actually looks good - namd2 binary should have been compiled.
>It failed when compiling some utility programs. ANd you don't need pgcc
>for them, so just define CC in NAMD arch file to gcc and recompile NAMD
>utility programs. (since there is no way to cleanup the existing
>binaries, so you may have to make clean and compile NAMD from scratch)
>
>GEngbin
>
>Suxing Hu wrote:
>
>>Thanks Gengbin,
>>
>>Your receipe of changing "pgCC" to direct "charmc" works for the compiling
>>process. However, it seems the link has some fatal problem:
>>
>>
>>[suxing_at_lepton Linux-i686-MPI]$ make
>>rm -f obj/buildinfo.C; echo 'const char *namd_build_date = ' \"`date`\"\; >
>>obj/buildinfo.C; echo 'const char *namd_build_user = ' \"suxing\"\; >>
>>obj/buildinfo.C; echo 'const char *namd_build_machine = ' \"`hostname`\"\; >>
>>obj/buildinfo.C; cat obj/buildinfo.C;
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/cha
rm
>>c -DSOCKLEN_T=socklen_t
>>-I/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/inclu
de
>>-DCMK_OPTIMIZE=1 -Isrc -Iinc -I/home/lepton/suxing/NAMD2/tcl8.3/include
>>-DNAMD_TCL -DUSE_NON_CONST -I/home/lepton/suxing/NAMD2/fftw-2/include
>>-I/home/lepton/suxing/NAMD2/fftw-2/include -DNAMD_FFTW -DNAMD_VERSION=\"2.5\"
>>-DNAMD_PLATFORM=\"Linux-i686-MPI\" -O2 -o obj/buildinfo.o -c obj/buildinfo.C
>>const char *namd_build_date = "Thu Dec 9 14:20:48 MST 2004";
>>const char *namd_build_user = "suxing";
>>const char *namd_build_machine = "lepton";
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/cha
rm
>>c -verbose -ld++-option \
>>"-I/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/incl
ud
>>e -DCMK_OPTIMIZE=1 -Iinc -Isrc -O2 " \
>>-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/ComputeBField.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/home/lepton/suxing/NAMD2/tcl8.3/lib -ltcl8.3 -ldl \
>>-L/home/lepton/suxing/NAMD2/fftw-2/lib -L/home/lepton/suxing/NAMD2/fftw-2/lib
>>-lsrfftw -lsfftw \
>> \
>>-lm -o namd2
>>Verbose mode set
>>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/ComputeBField.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 pgCC -I /usr/local/vmi/mpich/include -D__CHARMC__=1
>>-DCMK_OPTIMIZE=1 -Iinc -Isrc -O2 -c moduleinit.C -o moduleinit.o
>>charmc: Executing pgCC -L /usr/local/vmi/mpich/lib/pgi -rdynamic -O2
>>-L/home/lepton/suxing/NAMD2/tcl8.3/lib -L/home/lepton/suxing/NAMD2/fftw-2/lib
>>-L/home/lepton/suxing/NAMD2/fftw-2/lib
>>-I/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/inclu
de
>>-o namd2
>>-L/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/.
./
>>lib
>>-I/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/.
./
>>include
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/../
li
>>b/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/ComputeBField.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
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/../
li
>>b/libmemory-default.o
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/../
li
>>b/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt
>>-lpthread -L/usr/local/mpich/lib -lmpich -L/usr/local/src/gm/binary/lib -lgm
>>-Wl,-ldl -lz -ltcl8.3 -ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB
>>-lmodulecommlib
>>pgCC-Warning-Unknown switch: -rdynamic
>>/home/lepton/suxing/NAMD2/tcl8.3/lib/libtcl8.3.a(tclUnixPipe.o): In function
>>`TclpCreateTempFile':
>>tclUnixPipe.o(.text+0xef): the use of `tmpnam' is dangerous, better use
>>`mkstemp'
>>charmc: Executing rm -f charmrun
>>charmc: Executing cp -p
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/cha
rm
>>run charmrun
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/cha
rm
>>c -Isb/src -I/home/lepton/suxing/NAMD2/tcl8.3/include -DNAMD_TCL
>>-DUSE_NON_CONST -DNAMD_VERSION=\"2.5\" -DNAMD_PLATFORM=\"Linux-i686-MPI\" -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/home/lepton/suxing/NAMD2/tcl8.3/lib -ltcl8.3 -ldl -lm
>>pgCC-Warning-Unknown switch: -rdynamic
>>/home/lepton/suxing/NAMD2/tcl8.3/lib/libtcl8.3.a(tclUnixPipe.o): In function
>>`TclpCreateTempFile':
>>tclUnixPipe.o(.text+0xef): the use of `tmpnam' is dangerous, better use
>>`mkstemp'
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/../
li
>>b/libck.a(init.o): In function `_initCharm(int, char **)':
>>init.o(.text+0x1b6f): undefined reference to `CkRegisterMainModule'
>>Fatal Error by charmc in directory
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/Linux-i686-MPI
>> Command pgCC -L /usr/local/vmi/mpich/lib/pgi -rdynamic
>>-L/home/lepton/suxing/NAMD2/tcl8.3/lib -o psfgen
>>-L/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/.
./
>>lib
>>-I/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/.
./
>>include
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/../
li
>>b/libldb-rand.o 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 moduleinit.o -ltcl8.3 -ldl -lm
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/../
li
>>b/libmemory-default.o
>>/home/lepton/suxing/NAMD2/NAMD_2.5_Source/charm-5.8/mpi-linux-gm2-pgcc/bin/../
li
>>b/libthreads-default.o -lck -lconv-cplus-y -lconv-core -lconv-util -lm -lckqt
>>-lpthread -L/usr/local/mpich/lib -lmpich -L/usr/local/src/gm/binary/lib -lgm
>>-Wl,-ldl -lz returned error code 2
>>charmc exiting...
>>make: *** [psfgen] Error 1
>>[suxing_at_lepton Linux-i686-MPI]$
>>
>>
>>
>>
>>Suxing
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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