Re: Struggling with the compilation of NAMD 2.6 on a PBS Cluster with LAM/MPI

From: Frank Thommen (frank.thommen_at_embl-heidelberg.de)
Date: Fri Aug 29 2008 - 11:59:54 CDT

Hi Axel,

> [...]
>
> FT> make: *** [obj/ComputeTclBC.o] Error 1
> FT> [xsoft_at_clnode154 Linux-amd64-MPI]$
> FT>
> FT>
> FT> Any ideas about this one?
>
> was discussed here recently. you have tcl version 8.4 or 8.5, right?

Correct. 8.4 is installed on our cluster nodes.

> NAMD 2.6 assumes version 8.3. you can add -DUSE_COMPAT_CONST or
> -DUSE_NON_CONST (but not both) to the TCLFLAGS line in arch/Linux-amd64.tcl
> to work around it.

Hmm. With '-DUSE_COMPAT_CONST' I get the following error with make
(this is the second run of `make`):

[xsoft_at_clnode154 Linux-amd64-MPI]$ make
g++
-I/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include
-DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include -I/usr/include
-I/home/xsoft/tcl/include -DNAMD_TCL -DUSE_COMPAT_CONST
-I/usr/struct/pack/fftw-2.1.5/include -I/home/xsoft/fftw/include
-DNAMD_FFTW -DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-amd64-MPI\"
  -O3 -m64 -fexpensive-optimizations -ffast-math -o obj/ComputeTclBC.o
-c src/ComputeTclBC.C
src/ComputeTclBC.C: In constructor `ComputeTclBC::ComputeTclBC(ComputeID)':
src/ComputeTclBC.C:63: error: invalid conversion from `const char*' to
`char*'
src/ComputeTclBC.C:66: error: invalid conversion from `const char*' to
`char*'
src/ComputeTclBC.C: In member function `virtual void
ComputeTclBC::doWork()':
src/ComputeTclBC.C:122: error: invalid conversion from `const char*' to
`char*'
make: *** [obj/ComputeTclBC.o] Error 1
[xsoft_at_clnode154 Linux-amd64-MPI]$

Whereas with '-DUSE_NON_CONST' it still seems to be looking for libtcl8.3:

# make
[... removed lots of output ...]
charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module commlib
charmc: Executing mpiCC -m64 -fPIC -D__CHARMC__=1 -c moduleinit22680.C
-o moduleinit22680.o
charmc: Executing mpiCC -m64 -fPIC -rdynamic -L/usr/lib
-L/home/xsoft/tcl/lib -L/usr/struct/pack/fftw-2.1.5/lib
-L/home/xsoft/fftw/lib
-I/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -m64 -fexpensive-optimizations
-ffast-math -o namd2
-L/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib
-I/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../include
/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/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/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
moduleinit22680.o -lmoduleNeighborLB -lmodulecommlib
/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libmemory-default.o
/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/charm-5.9/mpi-linux-amd64/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -lmpi -ldl -ltcl8.3
-ldl -lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib -lmpi -lm
/usr/bin/ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
/usr/bin/ld: skipping incompatible /usr/lib/libdl.a when searching for -ldl
/usr/bin/ld: cannot find -ltcl8.3
collect2: ld returned 1 exit status
mpiCC: No such file or directory
Fatal Error by charmc in directory
/usr/struct/pack/namd2_mpi-2.0.6/SRC/NAMD_2.6_Source/Linux-amd64-MPI

    Command [...very long command removed...] returned error code 1
charmc exiting...
rm -f moduleinit22680.C moduleinit22680.o
make: *** [namd2] Error 1
[xsoft_at_clnode154 Linux-amd64-MPI]$

Can you give me the link to the thread where this problem has been
discussed before? I haven't found it and it may contain other ideas how
to work around this problem.

Cheers

     frank

-- 
Frank Thommen - Structures IT Management and Support - EMBL Heidelberg
frank.thommen_at_embl-heidelberg.de - +49 6221 387 8353

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