[mpich-discuss] undefined symbol: MPIR_Thread
Anthony Chan
chan at mcs.anl.gov
Wed Feb 2 09:48:03 CST 2011
All your bldlog files indicate that you set FC to mpif90 and
NOT $(MPICH_PATH)/bin/mpif90 as I suggested earlier. You should
set both LIB_MPI and INC_MPI to empty strings. Do you have other
MPI implementations (older MPICH2 or other MPI implementations)
installed on your system besides MPICH2-1.3.1 ? Do a "which mpif90"
to find out.
A.Chan
----- Original Message -----
> Dear Anthony!
>
> I have now done what you suggested below:
> Set FC and CC to mpif90 and mpicc and removing the inc_ and lib_
> references.
> Again, I could built the executable, but running the latter results in
> ./ccsm.exe: undefined symbol: MPIR_Thread
>
> Therefore, I set everything back to before and added this to the
> LIB_MPI
> LIB_MPI := $(MPICH_PATH)/lib -lmpichf90 -lmpichf90 -lmpich -lopa
> -lmpl -lrt -lpthread
>
> As the last arguments were shown by mpif90 -show. But again, same
> error.
>
> For every module of the model, a log file is saved. I attached the 3
> most important ones:
> - pio: parallel IO
> - lnd: the land module that I would like to test
> - ccsm: the log for building the executable
>
> As far as I can see, there could be something in pio, but I'm not
> sure,
> and it doesn't seem to be enough to stop the compilation process.
>
> Wouldn't there be any other way to deal with this thread problem?
> Kind regards,
>
> Matthias
>
>
>
> On 02/02/2011 01:12 AM, Anthony Chan wrote:
> > I took a quick look at the scripts that you sent but they ain't very
> > helpful
> > as these files source some other files which ain't included in your
> > attachment.
> > In any case, my knowledge on CCSM is limited. Since the build
> > problem is CCSM
> > specific, you may want to contact CCSM developers to see what it
> > should be done.
> >
> > Given your final executable (or one of the executables) has
> > unresolved symbol
> > MPIR_Thread, so it seems it didn't link in MPICH2 libraries
> > correctly.
> > I would first set FC=to $(MPICH_PATH)/bin/mpif90 and
> > CC=$(MPICH_PATH)/bin/mpicc
> > and leave LIB_MPI and INC_MPI empty since mpif90 and mpicc should
> > take care of
> > LIB_MPI and INC_MPI. You may want to save the compile and linking
> > output of
> > whole build process to see what goes wrong.
> >
> > A.Chan
> >
> >
> >
> > ----- Original Message -----
> >> mmm, I am not sure if I can answer this question.
> >> It is a global climate model, with a lot of packages, and in order
> >> to
> >> compile it I follow the installation guide of the model.
> >> So I am not completely sure what I should provide you with?
> >>
> >> There is a seperate Macros files in which I have to adapt libs and
> >> flags
> >> for my system. The contents are as follows:
> >> # Note that CPPDEFS is set in Macros.cppdefs
> >> CPPDEFS += -DLINUX -DSEQ_$(FRAMEWORK) -DFORTRANUNDERSCORE -DNO_R16
> >> -DNO_SHR_VMATH
> >>
> >> ifeq ($(compile_threaded), true)
> >> CPPDEFS += -DTHREADED_OMP
> >> endif
> >>
> >> FC := mpif90
> >> CC := mpicc
> >>
> >> HDF5_PATH := /usr/local/hdf5
> >> HDF5_LIB := $(HDF5_PATH)/lib -lhdf5 -lhdf5_hl
> >> NETCDF_PATH := /usr/local/netcdf-4.1.1
> >> INC_NETCDF := $(NETCDF_PATH)/include
> >> LIB_NETCDF := $(NETCDF_PATH)/lib -lnetcdf -L/usr/local/hdf5/lib
> >> -lhdf5_hl -lhdf5 -L/usr/local/zlib/lib -lz -lm
> >> MOD_NETCDF := $(NETCDF_PATH)/include
> >> MPICH_PATH := /usr/local/mpich2-1.3.1
> >> INC_MPI := $(MPICH_PATH)/include
> >> LIB_MPI := $(MPICH_PATH)/lib
> >> MPI_LIB_NAME := mpich
> >> PNETCDF_PATH :=
> >> INC_PNETCDF :=
> >> LIB_PNETCDF :=
> >> LAPACK_LIBDIR :=
> >> #=====================================================
> >>
> >> CFLAGS := $(CPPDEFS)
> >> FIXEDFLAGS := -132
> >> FREEFLAGS := -FR
> >> ##FFLAGS := $(CPPDEFS) -g -fp-model precise -convert big_endian
> >> -assume byterecl -ftz -traceback
> >> FFLAGS := $(CPPDEFS)-g -O2 -I/usr/local/include
> >> FFLAGS_NOOPT := $(FFLAGS) -O0
> >> FFLAGS_OPT := -O2
> >> LDFLAGS :=
> >> AR := ar
> >> MOD_SUFFIX := mod
> >> CONFIG_SHELL :=
> >>
> >> So maybe something is wrong here???
> >> In attach I also sent you the configure file, and the build file to
> >> compile the model.
> >> That works all fine. Only when running the obtained executable, I
> >> get
> >> the error MPIR_Thread...
> >> to run the .exe, I use the following:
> >> mpirun ./ccsm.exe>&! ccsm.log.$LID
> >>
> >> as is mentioned in the test2.Latitude_E6400.run file in attach.
> >>
> >> I do not know if you can do something with this, if not, please let
> >> me
> >> know....
> >>
> >> Matthias
> >>
> >>
> >> On 02/01/2011 09:17 PM, Anthony Chan wrote:
> >>> ----- Original Message -----
> >>>
> >>>> I can also perform the test as in the installation guide:
> >>>> mpiexec -n 5 ./examples/cpi
> >>>>
> >>>> Process 1 of 5 is on MaffieLE6400
> >>>> Process 3 of 5 is on MaffieLE6400
> >>>> Process 0 of 5 is on MaffieLE6400
> >>>> Process 2 of 5 is on MaffieLE6400
> >>>> Process 4 of 5 is on MaffieLE6400
> >>>> pi is approximately 3.1415926544231230, Error is
> >>>> 0.0000000008333298
> >>>> wall clock time = 0.000435
> >>>>
> >>>> as far as I can see all works fine?
> >>> Yes.
> >>>
> >>>> The reason I configured with the --with-thread-package=none the
> >>>> second
> >>>> time was to deal with the MPIR_Thread error...
> >>>> So I wonder how I can deal with this error?
> >>> Let's just focus on using the mpich2 install that was configured
> >>> without
> >>> --with-thread-package. How did you compile your application ?
> >>>
> >>>> Thanks for your help!
> >>>>
> >>>> Matthias
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> On 02/01/2011 08:24 PM, Anthony Chan wrote:
> >>>>> ----- Original Message -----
> >>>>>> Dear Anthony,
> >>>>>>
> >>>>>> My apologies for posting to the wrong email list. I will
> >>>>>> register
> >>>>>> to
> >>>>>> the
> >>>>>> other one so that in the future I can put my questions there.
> >>>>>> For now i'll post this directly to you, hope that is fine??
> >>>>> Yes. I cc'ed my reply to mpich-discuss as someone else may have
> >>>>> things to add.
> >>>>>
> >>>>>> I am not sure if I understand what you mean with:
> >>>>>>
> >>>>>> Did you use mpif90/mpif77 to link your code or just use above
> >>>>>> link
> >>>>>> command which seems incomplete ?
> >>>>>>
> >>>>>> I used the following line to check how mpich2 was built, as I
> >>>>>> first
> >>>>>> got
> >>>>>> an error with f90 vs f95.
> >>>>>> So with
> >>>>>> /usr/local/mpich2-1.3.1/bin/mpif90 -show
> >>>>>>
> >>>>>> I get finally got:
> >>>>>> gfortran -O2 -I/usr/local/mpich2-1.3.1/include
> >>>>>> -I/usr/local/mpich2-1.3.1/include -L/usr/local/mpich2-1.3.1/lib
> >>>>>> -lmpichf90 -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread
> >>>>>>
> >>>>>> Do you mean that there is something missing here? And should I
> >>>>>> add
> >>>>>> it
> >>>>>> than in my definition of INC_MPI and LIB_MPI?
> >>>>> Let's focus if your mpich2 installation is correct first.
> >>>>>> One other question. I was thinking that it could be useful to
> >>>>>> built
> >>>>>> mpich2 without threading, so I used:
> >>>>>> ./configure -prefix=/usr/local/mpich2-1.3.1
> >>>>>> --with-thread-package=none
> >>>>> Try "./configure --prefix=/usr/local/mpich2-1.3.1", without
> >>>>> --with-thread-package.
> >>>>>
> >>>>> A.Chan
> >>>>>
> >>>>>> But then I get a whole list of errors, e.g.:
> >>>>>> /home/matthias/Downloads/mpich2-1.3.1/lib/libmpich.a(info_getn.o):
> >>>>>> In
> >>>>>> function `MPIU_Thread_CS_exit_lockname_recursive_impl_':
> >>>>>> info_getn.c:(.text+0x124): undefined reference to
> >>>>>> `MPIU_Thread_mutex_unlock'
> >>>>>> /home/matthias/Downloads/mpich2-1.3.1/lib/libmpich.a(info_getnth.o):
> >>>>>> In
> >>>>>> function `MPIU_Thread_CS_enter_lockname_recursive_impl_':
> >>>>>> info_getnth.c:(.text+0x32): undefined reference to
> >>>>>> `MPIU_Thread_mutex_lock'
> >>>>>> /home/matthias/Downloads/mpich2-1.3.1/lib/libmpich.a(info_getnth.o):
> >>>>>> In
> >>>>>> function `MPIU_Thread_CS_exit_lockname_recursive_impl_':
> >>>>>> info_getnth.c:(.text+0xf4): undefined reference to
> >>>>>> `MPIU_Thread_mutex_unlock'
> >>>>>> /home/matthias/Downloads/mpich2-1.3.1/lib/libmpich.a(info_getvallen.o):
> >>>>>> In function `MPIU_Thread_CS_enter_lockname_recursive_impl_':
> >>>>>> info_getvallen.c:(.text+0x32): undefined reference to
> >>>>>> `MPIU_Thread_mutex_lock'
> >>>>>> /home/matthias/Downloads/mpich2-1.3.1/lib/libmpich.a(info_getvallen.o):
> >>>>>> In function `MPIU_Thread_CS_exit_lockname_recursive_impl_':
> >>>>>>
> >>>>>>
> >>>>>> Any ideas here?
> >>>>>> Matthias
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> -------- Original Message --------
> >>>>>> Subject: Re: [mpich2-dev] undefined symbol: MPIR_Thread
> >>>>>> Date: Tue, 1 Feb 2011 19:41:54 +0100
> >>>>>> From: Anthony Chan<chan at mcs.anl.gov>
> >>>>>> Reply-To: Anthony Chan<chan at mcs.anl.gov>,
> >>>>>> "mpich2-dev at mcs.anl.gov"
> >>>>>> <mpich2-dev at mcs.anl.gov>
> >>>>>> To: mpich2-dev at mcs.anl.gov<mpich2-dev at mcs.anl.gov>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> mpich2-dev for mpich2 development not general MPICH usage
> >>>>>> questions,
> >>>>>> please send your question to mpich-discuss at mcs.anl.gov.
> >>>>>>
> >>>>>> ----- Original Message -----
> >>>>>>> All,
> >>>>>>>
> >>>>>>> when running a model with mpirun ./exe
> >>>>>>> I get the following error:
> >>>>>>> ./exe: symbol lookup error: ./exe: undefined symbol:
> >>>>>>> MPIR_Thread
> >>>>>>>
> >>>>>>> I have no idea how to deal with this. I use mpich2-1.3.1,
> >>>>>>> compiled
> >>>>>>> with
> >>>>>>> gfortran, with the following libraries:
> >>>>>>> gfortran -O2 -I/usr/local/mpich2-1.3.1/include
> >>>>>>> -I/usr/local/mpich2-1.3.1/include
> >>>>>>> -L/usr/local/mpich2-1.3.1/lib
> >>>>>>> -lmpichf90 -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread
> >>>>>> Did you use mpif90/mpif77 to link your code or just use above
> >>>>>> link
> >>>>>> command which seems incomplete ?
> >>>>>>
> >>>>>> A.Chan
> >>>>>>
> >>>>>>> Could anybody help me with this?
> >>>>>>>
> >>>>>>> Regards,
> >>>>>>> Matthias
> >>>>>>>
> >>>>>>> --
> >>>>>>>
> >>>>>>>
> >>>>>>> -------------------------------------------------------------
> >>>>>>> FWO Post-doctoral Research Fellow
> >>>>>>> Department of Earth& Environmental Sciences
> >>>>>>> Physical and Regional Geography Research Group
> >>>>>>> Regional climate studies
> >>>>>>>
> >>>>>>> Celestijnenlaan 200E
> >>>>>>> 3001 Heverlee (Leuven)
> >>>>>>> BELGIUM
> >>>>>>>
> >>>>>>> Tel: + 32 16 326424
> >>>>>>> Fax: + 32 16 322980
> >>>>>>>
> >>>>>>> http://geo.kuleuven.be/aow/
> >>>>>>> www.kuleuven.be/geography
> >>>>>>> -------------------------------------------------------------
> >>>> --
> >>>>
> >>>>
> >>>> -------------------------------------------------------------
> >>>> FWO Post-doctoral Research Fellow
> >>>> Department of Earth& Environmental Sciences
> >>>> Physical and Regional Geography Research Group
> >>>> Regional climate studies
> >>>>
> >>>> Celestijnenlaan 200E
> >>>> 3001 Heverlee (Leuven)
> >>>> BELGIUM
> >>>>
> >>>> Tel: + 32 16 326424
> >>>> Fax: + 32 16 322980
> >>>>
> >>>> http://geo.kuleuven.be/aow/
> >>>> www.kuleuven.be/geography
> >>>> -------------------------------------------------------------
> >> --
> >>
> >>
> >> -------------------------------------------------------------
> >> FWO Post-doctoral Research Fellow
> >> Department of Earth& Environmental Sciences
> >> Physical and Regional Geography Research Group
> >> Regional climate studies
> >>
> >> Celestijnenlaan 200E
> >> 3001 Heverlee (Leuven)
> >> BELGIUM
> >>
> >> Tel: + 32 16 326424
> >> Fax: + 32 16 322980
> >>
> >> http://geo.kuleuven.be/aow/
> >> www.kuleuven.be/geography
> >> -------------------------------------------------------------
>
> --
>
>
> -------------------------------------------------------------
> FWO Post-doctoral Research Fellow
> Department of Earth& Environmental Sciences
> Physical and Regional Geography Research Group
> Regional climate studies
>
> Celestijnenlaan 200E
> 3001 Heverlee (Leuven)
> BELGIUM
>
> Tel: + 32 16 326424
> Fax: + 32 16 322980
>
> http://geo.kuleuven.be/aow/
> www.kuleuven.be/geography
> -------------------------------------------------------------
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