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Re: [charm] For problems concerning compiling NAMD


Chronological Thread 
  • From: "hqzhou" <hqzhou AT nju.edu.cn>
  • To: "黄须啟" <huangxuqi14 AT mails.ucas.ac.cn>, "Phil Miller" <mille121 AT illinois.edu>
  • Cc: "Charm Mailing List" <charm AT cs.illinois.edu>
  • Subject: Re: [charm] For problems concerning compiling NAMD
  • Date: Fri, 13 Nov 2015 13:33:58 +0800

Hi,

Actually, the error message is very clear, SEEK_XXX have already been defined in both

mpi.h and stdio.h.

you need to add

-DMPICH_IGNORE_CXX_SEEK

to your command line.

 
Huiqun Zhou
@Earth Sciences, Nanjing University, China
 
 
------------------ Original ------------------
From:  "黄须啟"<huangxuqi14 AT mails.ucas.ac.cn>;
Date:  Fri, Nov 13, 2015 10:13 AM
To:  "Phil Miller"<mille121 AT illinois.edu>;
Cc:  "Charm Mailing List"<charm AT cs.illinois.edu>;
Subject:  Re: [charm] For problems concerning compiling NAMD
 
Dear Professor:
        The following concrete content is what you need:
       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 `/lustre/researcher/huangxuqi/NAMD_2.10b2_Source/charm-6.6.1/mpi-linux-x86_64/tmp/libs/ck-libs/completion'
../../../../bin/charmc -optimize -production   -c completion.ci
../../../../bin/charmc -optimize -production   -I../../../../tmp -o completion.o completion.C
../../../../bin/charmc -optimize -production   -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 `/lustre/researcher/huangxuqi/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  -optimize -production   -I.   -c -o trace-common.o trace-common.C
../bin/charmc  -optimize -production   -I.   -c -o tracec.o tracec.C
../bin/charmc  -optimize -production   -I.   -c -o tracef.o tracef.C
../bin/charmc  -optimize -production   -I.   -c -o init.o init.C
../bin/charmc  -optimize -production   -I.   -c -o register.o register.C
../bin/charmc  -optimize -production   -I.   -c -o qd.o qd.C
../bin/charmc  -optimize -production   -I.   -c -o ck.o ck.C
../bin/charmc  -optimize -production   -I.   -c -o msgalloc.o msgalloc.C
../bin/charmc  -optimize -production   -I.   -c -o ckfutures.o ckfutures.C
../bin/charmc  -optimize -production   -I.   -c -o ckIgetControl.o ckIgetControl.C
../bin/charmc  -optimize -production   -I.   -c -o debug-message.o debug-message.C
../bin/charmc  -optimize -production   -I.   -c -o debug-charm.o debug-charm.C
../bin/charmc  -optimize -production   -I.   -c -o ckcallback.o ckcallback.C
../bin/charmc  -optimize -production   -I.   -c -o cklocation.o cklocation.C
../bin/charmc  -optimize -production   -I.   -c -o ckarray.o ckarray.C
../bin/charmc  -optimize -production   -I.   -c -o ckreduction.o ckreduction.C
../bin/charmc  -optimize -production   -I.   -c -o ckarrayreductionmgr.o ckarrayreductionmgr.C
../bin/charmc  -optimize -production   -I.   -c -o tempo.o tempo.C
../bin/charmc  -optimize -production   -I.   -c -o waitqd.o waitqd.C
../bin/charmc  -optimize -production   -I.   -c -o LBDatabase.o LBDatabase.C
../bin/charmc  -optimize -production   -I.   -c -o MetaBalancer.o MetaBalancer.C
../bin/charmc  -optimize -production   -I.   -c -o lbdb.o lbdb.C
../bin/charmc  -optimize -production   -I.   -c -o lbdbf.o lbdbf.C
../bin/charmc  -optimize -production   -I.   -c -o ckobjQ.o ckobjQ.C
../bin/charmc  -optimize -production   -I.   -c -o LBAgent.o LBAgent.C
../bin/charmc  -optimize -production   -I.   -c -o LBProfit.o LBProfit.C
../bin/charmc  -optimize -production   -I.   -c -o ckcheckpoint.o ckcheckpoint.C
../bin/charmc  -optimize -production   -I.   -c -o ckmemcheckpoint.o ckmemcheckpoint.C
../bin/charmc  -optimize -production   -I.   -c -o ckevacuation.o ckevacuation.C
../bin/charmc  -optimize -production   -I.   -c -o ckmessagelogging.o ckmessagelogging.C
../bin/charmc  -optimize -production   -I.   -c -o ckcausalmlog.o ckcausalmlog.C
../bin/charmc  -optimize -production   -I.   -c -o ckobjid.o ckobjid.C
../bin/charmc  -optimize -production   -I.   -c -o LBDBManager.o LBDBManager.C
../bin/charmc  -optimize -production   -I.   -c -o LBComm.o LBComm.C
../bin/charmc  -optimize -production   -I.   -c -o LBObj.o LBObj.C
../bin/charmc  -optimize -production   -I.   -c -o LBMachineUtil.o LBMachineUtil.C
../bin/charmc  -optimize -production   -I.   -c -o CentralPredictor.o CentralPredictor.C
../bin/charmc  -optimize -production   -I.   -c -o BaseLB.o BaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o CentralLB.o CentralLB.C
../bin/charmc  -optimize -production   -I.   -c -o HybridBaseLB.o HybridBaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o NborBaseLB.o NborBaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o DistBaseLB.o DistBaseLB.C
../bin/charmc  -optimize -production   -I.   -c -o ckgraphTemp.o ckgraphTemp.C
../bin/charmc  -optimize -production   -I.   -c -o ckgraph.o ckgraph.C
../bin/charmc  -optimize -production   -I.   -c -o LButil.o LButil.C
../bin/charmc  -optimize -production   -I.   -c -o RefinerTemp.o RefinerTemp.C
../bin/charmc  -optimize -production   -I.   -c -o Refiner.o Refiner.C
../bin/charmc  -optimize -production   -I.   -c -o RefinerApprox.o RefinerApprox.C
../bin/charmc  -optimize -production   -I.   -c -o RefinerComm.o RefinerComm.C
../bin/charmc  -optimize -production   -I.   -c -o bitvecset.o bitvecset.c
../bin/charmc  -optimize -production   -I.   -c -o ckset.o ckset.C
../bin/charmc  -optimize -production   -I.   -c -o ckheap.o ckheap.C
../bin/charmc  -optimize -production   -I.   -c -o CommLBHeap.o CommLBHeap.C
../bin/charmc  -optimize -production   -I.   -c -o NullLB.o NullLB.C
../bin/charmc  -optimize -production   -I.   -c -o LBSimulation.o LBSimulation.C
../bin/charmc  -optimize -production   -I.   -c -o ComlibModuleInterface.o ComlibModuleInterface.C
../bin/charmc  -optimize -production   -I.   -c -o modifyScheduler.o modifyScheduler.C
../bin/charmc  -optimize -production   -I.   -c -o charmProjections.o charmProjections.C
../bin/charmc  -optimize -production   -I.   -c -o cktiming.o cktiming.C
../bin/charmc  -optimize -production   -I.   -c -o ckbitvector.o ckbitvector.C
../bin/charmc  -optimize -production   -I.   -c -o pathHistory.o pathHistory.C
../bin/charmc  -optimize -production   -I.   -c -o controlPoints.o controlPoints.C
../bin/charmc  -optimize -production   -I.   -c -o arrayRedistributor.o arrayRedistributor.C
../bin/charmc  -optimize -production   -I.   -c -o cp_effects.o cp_effects.C
../bin/charmc  -optimize -production   -I.   -c -o trace-controlPoints.o trace-controlPoints.C
../bin/charmc  -optimize -production   -I.   -c -o mpi-interoperate.o mpi-interoperate.C
In file included from /opt/intel/impi/4.1.1.036/intel64/include/mpi.h:1279,
                 from mpi-interoperate.h:9,
                 from mpi-interoperate.C:3:
/opt/intel/impi/4.1.1.036/intel64/include/mpicxx.h:95:2: error: #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
/opt/intel/impi/4.1.1.036/intel64/include/mpicxx.h:99:2: error: #error "SEEK_CUR is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"
/opt/intel/impi/4.1.1.036/intel64/include/mpicxx.h:104:2: 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 /lustre/researcher/huangxuqi/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. -O2 -U_FORTIFY_SOURCE -fno-stack-protector -c mpi-interoperate.C -o mpi-interoperate.o returned error code 1
charmc exiting...
gmake: *** [mpi-interoperate.o] Error 1

   I'm not good at compiling charm ,if you can teel me the detailed procedure, i will be very appreciate of you .
   I'm looking forward to your reply!
   sincerely
   huangxuqi

在2015-11-13 00:21:31,黄须啟<huangxuqi14 AT mails.ucas.ac.cn>写道:
> Hi Huangxuqi,
>
> We'll need to see a few lines of output preceding that message, to see
> the actual compilation error.
>
> Also, it looks like you're compiling an older version of NAMD. 2.10
> was released quite some time ago, and a beta for 2.11 was either just
> posted, or will be shortly. For reasons of performance and
> correctness, users are generally recommended to use the most recent
> release.
>
> Phil
>
> On Thu, Nov 12, 2015 at 7:01 AM, 黄须啟 <huangxuqi14 AT mails.ucas.ac.cn> wrote:
> >
> >
> > Dear Professor:
> >
> >        There is something wrong with my comiling NAMD progress for using the
> > following command :
> >
> >         tar xvf NAMD_2.10b2_Source.tar.gz
> >
> >         cd NAMD_2.10b2_Source
> >
> >         tar xf charm-6.6.1.tar
> >
> >         cd charm-6.6.1
> >
> >       env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --with-production
> >
> >     it shows one fatal error:
> >
> >     Fatal Error by charmc in directory
> > /lustre/researcher/huangxuqi/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. -O2 -U_FORTIFY_SOURCE -fno-stack-protector -c
> > mpi-interoperate.C -o mpi-interoperate.o returned error code 1
> > charmc exiting...
> > gmake: *** [mpi-interoperate.o] Error 1
> >
> >     I'm looking forward to your reply!
> >
> >     sincerely
> >
> >     huangxuqi
> >
> >
> >
> >
> >
> >
> >







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