Re: Compile NAMD - Projections

From: Stefan Richter (stefan.richter_at_h-its.org)
Date: Thu Oct 15 2015 - 04:40:44 CDT

Thank you for this offer, first i would need help to get the standard
compile without projections going.

I always get the error below.

On 10/14/2015 06:45 PM, Kostas Malavazos wrote:
> I want a guide how to compile NAMD with projections on a Linux-64bit
> machine.

Fatal Error by charmc in directory
/zhome/academic/HLRS/xhi/xhiricht/software/NAMD_2.10_Source/CRAY-XC-intel
    Command CC -I/opt/cray/rca/1.0.0-2.0502.57212.2.56.ari/include
-I/opt/cray/alps/5.2.3-2.0502.9295.14.14.ari/include
-I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include
-I/opt/cray/pmi/5.0.9-1.0000.10911.0.0.ari/include
-I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include
-I/opt/cray/wlm_detect/1.0-1.0502.57063.1.1.ari/include
-I/opt/cray/krca/1.0.0-2.0502.57202.2.45.ari/include
-I/opt/cray-hss-devel/7.2.0/include
-I/opt/cray/gni-headers/4.0-1.0502.10317.9.2.ari/include
-I/opt/cray/ugni/6.0-1.0502.10245.9.9.ari/include -O2 -ip -no-vec
-L/zhome/academic/HLRS/xhi/xhiricht/software/NAMD_2.10_Source/tcl-threaded/lib
-L/lib -I.rootdir/charm-6.6.1/gni-crayxc/include -o namd2
-L.rootdir/charm-6.6.1/gni-crayxc/bin/../lib
-I.rootdir/charm-6.6.1/gni-crayxc/bin/../include
.rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libldb-rand.o obj/buildinfo.o
obj/ComputeMoa.o obj/ComputeMsm.o obj/ComputeMsmMsa.o
obj/ComputeMsmSerial.o obj/ComputeFmmSerial.o obj/msm.o
obj/msm_longrng.o obj/msm_longrng_sprec.o obj/msm_setup.o
obj/msm_shortrng.o obj/msm_shortrng_sprec.o obj/wkfutils.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/ComputeAniso.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/ComputeGBISser.o obj/ComputeGBIS.o
obj/ComputeGromacsPair.o obj/ComputeLCPO.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/ComputeNonbondedGo.o obj/ComputeNonbondedTI.o
obj/ComputeNonbondedLES.o obj/ComputeNonbondedPProf.o
obj/ComputeNonbondedTabEnergies.o obj/ComputeNonbondedCUDA.o
obj/ComputeNonbondedCUDAExcl.o obj/ComputeNonbondedMIC.o
obj/ComputeNonbondedMICKernel.o obj/ComputePatch.o
obj/ComputePatchPair.o obj/ComputePme.o obj/OptPme.o
obj/OptPmeRealSpace.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o
obj/ComputeStir.o obj/ComputeTclBC.o obj/ComputeThole.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/fstream_namd.o
obj/GlobalMaster.o obj/GlobalMasterServer.o obj/GlobalMasterTest.o
obj/GlobalMasterIMD.o obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o
obj/GlobalMasterTMD.o obj/Matrix4Symmetry.o obj/GlobalMasterSymmetry.o
obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o
obj/GlobalMasterMisc.o obj/colvar.o obj/colvaratoms.o obj/colvarbias.o
obj/colvarbias_abf.o obj/colvarbias_alb.o obj/colvarbias_meta.o
obj/colvarbias_restraint.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/colvargrid.o
obj/colvarmodule.o obj/colvarparse.o obj/colvarproxy_namd.o
obj/colvarscript.o obj/colvartypes.o obj/colvarvalue.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/Molecule2.o obj/GoMolecule.o obj/NamdCentLB.o
obj/NamdNborLB.o obj/NamdHybridLB.o obj/NamdDummyLB.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/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/SortAtoms.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/PluginIOMgr.o obj/DataExchanger.o
obj/ParallelIOMgr.o obj/dcdplugin.o obj/jsplugin.o obj/namdbinplugin.o
obj/pdbplugin.o obj/psfplugin.o moduleinit26621.o -lmoduleCkMulticast
-lmoduleGreedyLB -lmoduleRefineLB -lmoduleHybridLB -lmoduleNeighborLB
.rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libmemory-default.o
.rootdir/charm-6.6.1/gni-crayxc/bin/../lib/libthreads-default.o -lckmain
-lck -lconv-cplus-y -lconv-core -lconv-util -lconv-partition -lckqt -ldl
-lrt -ltcl8.5 -ldl -lfftw3f -lm
.rootdir/charm-6.6.1/gni-crayxc/bin/../lib/cray_tlbhack.o
-lmoduleNeighborLB -lmoduleHybridLB -lmoduleRefineLB -lmoduleGreedyLB
-lmoduleCkMulticast -lm returned error code 1
charmc exiting...
rm -f moduleinit26621.C moduleinit26621.o
make: *** [namd2] Error 1

-- 
Dr. Stefan Richter
Software and IT Specialist
Molecular and Cellular Modeling Group (MCM)
HITS gGmbH
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Germany
  
phone: +49 - 6221 - 533 279
fax: +49 6221 533298
email: Stefan.Richter_at_h-its.org
http://www.h-its.org
_________________________________________________
Amtsgericht Mannheim / HRB 337446
Managing Director:
Prof. Dr.-Ing. Andreas Reuter

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