Charm++ parallel programming system

[Nikhil Jain <nikhil.jain AT acm.org>]

Hello Huangxuqi

Your build command looks correct and is known to work in the past. Can you share the output of the OPTS file generated by the build?

$cat mpi-linux-x86_64/tmp/OPTS

--Nikhil

黄须啟

February 24, 2016 at 01:38 via Postbox

Dear Professor:

  There is something wrong with compiling NAMD progress for using following command:

 

tar xvf NAMD_2.10b2_Source.tar.gz   cd NAMD_2.10b2_Source   tar xvf charm-6.6.1.tar   cd charm-6.6.1   env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production -DMPICH_IGNORE_CXX_SEEK
    but it shows some error:  gmake[1]: Leaving directory `/home/xyli/software/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp'
touch basics
Performing '/usr/bin/gmake charm++ OPTS= QUIET=' in mpi-linux-x86_64/tmp
Makefile:1083: Variable OPTS is defined to an empty string. Are you sure this is what you want?
../bin/charmc   -I.   -c -o DummyLB.o DummyLB.C
../bin/charmc   -o ../lib/libmoduleDummyLB.a DummyLB.o
ar: creating ../lib/libmoduleDummyLB.a
../bin/charmc   -I.   -c -o GreedyLB.o GreedyLB.C
../bin/charmc   -o ../lib/libmoduleGreedyLB.a GreedyLB.o
ar: creating ../lib/libmoduleGreedyLB.a
../bin/charmc   -I.   -c -o CommLB.o CommLB.C
../bin/charmc   -o ../lib/libmoduleCommLB.a CommLB.o
ar: creating ../lib/libmoduleCommLB.a
../bin/charmc   -I.   -c -o RandCentLB.o RandCentLB.C
../bin/charmc   -o ../lib/libmoduleRandCentLB.a RandCentLB.o
ar: creating ../lib/libmoduleRandCentLB.a
../bin/charmc   -I.   -c -o RefineLB.o RefineLB.C
../bin/charmc   -o ../lib/libmoduleRefineLB.a RefineLB.o
ar: creating ../lib/libmoduleRefineLB.a
../bin/charmc   -I.   -c -o RefineCommLB.o RefineCommLB.C
../bin/charmc   -o ../lib/libmoduleRefineCommLB.a RefineCommLB.o
ar: creating ../lib/libmoduleRefineCommLB.a
cp -f libmoduleRefineCommLB.dep ../lib/
../bin/charmc   -I.   -c -o RotateLB.o RotateLB.C
../bin/charmc   -o ../lib/libmoduleRotateLB.a RotateLB.o
ar: creating ../lib/libmoduleRotateLB.a
../bin/charmc   -I.   -c -o DistributedLB.o DistributedLB.C
../bin/charmc   -o ../lib/libmoduleDistributedLB.a DistributedLB.o
ar: creating ../lib/libmoduleDistributedLB.a
../bin/charmc   -I.   -c -o HybridLB.o HybridLB.C
../bin/charmc   -o ../lib/libmoduleHybridLB.a HybridLB.o
ar: creating ../lib/libmoduleHybridLB.a
../bin/charmc   -I.   -c -o ComboCentLB.o ComboCentLB.C
../bin/charmc   -o ../lib/libmoduleComboCentLB.a ComboCentLB.o
ar: creating ../lib/libmoduleComboCentLB.a
../bin/charmc   -I.   -c -o RefineSwapLB.o RefineSwapLB.C
../bin/charmc   -o ../lib/libmoduleRefineSwapLB.a RefineSwapLB.o
ar: creating ../lib/libmoduleRefineSwapLB.a
../bin/charmc   -I.   -c -o NeighborLB.o NeighborLB.C
../bin/charmc   -o ../lib/libmoduleNeighborLB.a NeighborLB.o
ar: creating ../lib/libmoduleNeighborLB.a
../bin/charmc   -I.   -c -o OrbLB.o OrbLB.C
../bin/charmc   -o ../lib/libmoduleOrbLB.a OrbLB.o
ar: creating ../lib/libmoduleOrbLB.a
../bin/charmc   -I.   -c -o BlockLB.o BlockLB.C
../bin/charmc   -o ../lib/libmoduleBlockLB.a BlockLB.o
ar: creating ../lib/libmoduleBlockLB.a
../bin/charmc   -I.   -c -o GreedyCommLB.o GreedyCommLB.C
../bin/charmc   -I.   -c -o manager.o manager.C
../bin/charmc   -o ../lib/libmoduleGreedyCommLB.a GreedyCommLB.o manager.o
ar: creating ../lib/libmoduleGreedyCommLB.a
../bin/charmc   -I.   -c -o CommonLBs.o CommonLBs.C
../bin/charmc   -o ../lib/libmoduleCommonLBs.a CommonLBs.o DummyLB.o GreedyLB.o CommLB.o RandCentLB.o RefineLB.o RefineCommLB.o RotateLB.o DistributedLB.o HybridLB.o ComboCentLB.o RefineSwapLB.o NeighborLB.o OrbLB.o BlockLB.o GreedyCommLB.o manager.o
ar: creating ../lib/libmoduleCommonLBs.a
/usr/bin/gmake -C libs/ck-libs/completion
gmake[1]: Entering directory `/home/xyli/software/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp/libs/ck-libs/completion'
../../../../bin/charmc  -c completion.ci
../../../../bin/charmc  -I../../../../tmp -o completion.o completion.C
../../../../bin/charmc  -o ../../../../lib/libmodulecompletion.a completion.o
ar: creating ../../../../lib/libmodulecompletion.a
/bin/cp completion.decl.h ../../../../include
/bin/cp completion.def.h ../../../../include
/bin/cp completion.h ../../../../include
gmake[1]: Leaving directory `/home/xyli/software/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp/libs/ck-libs/completion'
../bin/charmc -seq  -DCMK_NOT_USE_CONVERSE=1 -o sockRoutines-seq.o sockRoutines.c
../bin/charmc   -I.   -c -o trace-common.o trace-common.C
../bin/charmc   -I.   -c -o tracec.o tracec.C
../bin/charmc   -I.   -c -o tracef.o tracef.C
../bin/charmc   -I.   -c -o init.o init.C
../bin/charmc   -I.   -c -o register.o register.C
../bin/charmc   -I.   -c -o qd.o qd.C
../bin/charmc   -I.   -c -o ck.o ck.C
../bin/charmc   -I.   -c -o msgalloc.o msgalloc.C
../bin/charmc   -I.   -c -o ckfutures.o ckfutures.C
../bin/charmc   -I.   -c -o ckIgetControl.o ckIgetControl.C
../bin/charmc   -I.   -c -o debug-message.o debug-message.C
../bin/charmc   -I.   -c -o debug-charm.o debug-charm.C
../bin/charmc   -I.   -c -o ckcallback.o ckcallback.C
../bin/charmc   -I.   -c -o cklocation.o cklocation.C
../bin/charmc   -I.   -c -o ckarray.o ckarray.C
../bin/charmc   -I.   -c -o ckreduction.o ckreduction.C
../bin/charmc   -I.   -c -o ckarrayreductionmgr.o ckarrayreductionmgr.C
../bin/charmc   -I.   -c -o tempo.o tempo.C
../bin/charmc   -I.   -c -o waitqd.o waitqd.C
../bin/charmc   -I.   -c -o LBDatabase.o LBDatabase.C
../bin/charmc   -I.   -c -o MetaBalancer.o MetaBalancer.C
../bin/charmc   -I.   -c -o lbdb.o lbdb.C
../bin/charmc   -I.   -c -o lbdbf.o lbdbf.C
../bin/charmc   -I.   -c -o ckobjQ.o ckobjQ.C
../bin/charmc   -I.   -c -o LBAgent.o LBAgent.C
../bin/charmc   -I.   -c -o LBProfit.o LBProfit.C
../bin/charmc   -I.   -c -o ckcheckpoint.o ckcheckpoint.C
../bin/charmc   -I.   -c -o ckmemcheckpoint.o ckmemcheckpoint.C
../bin/charmc   -I.   -c -o ckevacuation.o ckevacuation.C
../bin/charmc   -I.   -c -o ckmessagelogging.o ckmessagelogging.C
../bin/charmc   -I.   -c -o ckcausalmlog.o ckcausalmlog.C
../bin/charmc   -I.   -c -o ckobjid.o ckobjid.C
../bin/charmc   -I.   -c -o LBDBManager.o LBDBManager.C
../bin/charmc   -I.   -c -o LBComm.o LBComm.C
../bin/charmc   -I.   -c -o LBObj.o LBObj.C
../bin/charmc   -I.   -c -o LBMachineUtil.o LBMachineUtil.C
../bin/charmc   -I.   -c -o CentralPredictor.o CentralPredictor.C
../bin/charmc   -I.   -c -o BaseLB.o BaseLB.C
../bin/charmc   -I.   -c -o CentralLB.o CentralLB.C
../bin/charmc   -I.   -c -o HybridBaseLB.o HybridBaseLB.C
../bin/charmc   -I.   -c -o NborBaseLB.o NborBaseLB.C
../bin/charmc   -I.   -c -o DistBaseLB.o DistBaseLB.C
../bin/charmc   -I.   -c -o ckgraphTemp.o ckgraphTemp.C
../bin/charmc   -I.   -c -o ckgraph.o ckgraph.C
../bin/charmc   -I.   -c -o LButil.o LButil.C
../bin/charmc   -I.   -c -o RefinerTemp.o RefinerTemp.C
../bin/charmc   -I.   -c -o Refiner.o Refiner.C
../bin/charmc   -I.   -c -o RefinerApprox.o RefinerApprox.C
../bin/charmc   -I.   -c -o RefinerComm.o RefinerComm.C
../bin/charmc   -I.   -c -o bitvecset.o bitvecset.c
../bin/charmc   -I.   -c -o ckset.o ckset.C
../bin/charmc   -I.   -c -o ckheap.o ckheap.C
../bin/charmc   -I.   -c -o CommLBHeap.o CommLBHeap.C
../bin/charmc   -I.   -c -o NullLB.o NullLB.C
../bin/charmc   -I.   -c -o LBSimulation.o LBSimulation.C
../bin/charmc   -I.   -c -o ComlibModuleInterface.o ComlibModuleInterface.C
../bin/charmc   -I.   -c -o modifyScheduler.o modifyScheduler.C
../bin/charmc   -I.   -c -o charmProjections.o charmProjections.C
../bin/charmc   -I.   -c -o cktiming.o cktiming.C
../bin/charmc   -I.   -c -o ckbitvector.o ckbitvector.C
../bin/charmc   -I.   -c -o pathHistory.o pathHistory.C
../bin/charmc   -I.   -c -o controlPoints.o controlPoints.C
../bin/charmc   -I.   -c -o arrayRedistributor.o arrayRedistributor.C
../bin/charmc   -I.   -c -o cp_effects.o cp_effects.C
../bin/charmc   -I.   -c -o trace-controlPoints.o trace-controlPoints.C
../bin/charmc   -I.   -c -o mpi-interoperate.o mpi-interoperate.C
In file included from /share/apps/intel2012/impi/4.0.3.008/intel64/include/mpi.h:1221,
                 from mpi-interoperate.h:9,
                 from mpi-interoperate.C:3:
/share/apps/intel2012/impi/4.0.3.008/intel64/include/mpicxx.h:93:2: error: #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
/share/apps/intel2012/impi/4.0.3.008/intel64/include/mpicxx.h:97:2: error: #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
/share/apps/intel2012/impi/4.0.3.008/intel64/include/mpicxx.h:102:2: error: #error "SEEK_END is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
Fatal Error by charmc in directory /home/xyli/software/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp
   Command mpicxx -m64 -fPIC -DCMK_GFORTRAN -I../bin/../include -D__CHARMC__=1 -I. -fno-stack-protector -c mpi-interoperate.C -o mpi-interoperate.o returned error code 1
charmc exiting...
gmake: *** [mpi-interoperate.o] Error 1
-------------------------------------------------
     what sould i do to fix this problem in detail,I am not good at compiling somthing.      I 'm looking forward to your reply!      sincerely      huangxuqi

--
Nikhil Jain, nikhil.jain AT acm.org, http://charm.cs.uiuc.edu/people/nikhil Doctoral Candidate @ CS, UIUC