[mpich-discuss] undefined symbol: MPIR_Thread
Anthony Chan
chan at mcs.anl.gov
Thu Feb 3 11:54:42 CST 2011
MPICH2-1.3.1's default process manager is hydra not mpd,
so you don't need to start mpd... Older mpich2 requires
mpd but not 1.3.1 MPIR_Thread is defined in libmpich.a (AFAICT)
I don't know why your ccsm.exe still says it can't find MPIR_Thread.
Is everything in CCSM statically linked ?
----- Original Message -----
> I was wondering whether this has also something to do with the
> problem.
> On a website of a person installing ccsm on his laptop (also using
> mpich2) he states that before running the executable, he has to start
> mpi first
> > mpd &
>
> Now, if I do that, then I get:
> /usr/workdir/cesm1_0_2/scripts$ config: problems opening file
> /etc/mpd.conf for reading: Permission denied
>
> or as root
> listen: Failed to listen on localhost (line 69): Address already in
> use:
>
> Does this mean it is already on, or that there is an error?
>
>
> On 02/02/2011 07:08 PM, Anthony Chan wrote:
> > You indicated mpich2-1.3.1 was installed in /usr/local/mpich2-1.3.1
> > so /usr/local/bin/mpif90 refers to mpif90 from other MPI
> > implementation.
> > So you MUST specify fullpath to mpif90 in all your build scripts
> > and/or
> > makefiles. I also notice your bldlog uses compiler variables besides
> > FC and CC,
> > i.e. MPICC, MPIF90, F90..., and some of these fortran
> >
> > CC = $(MPICH_PATH)/bin/mpicc
> > MPICC = $(MPICH_PATH)/bin/mpicc
> > FC = $(MPICH_PATH)/bin/mpif90
> > F90 = $(MPICH_PATH)/bin/mpif90
> > MPIF90 = $(MPICH_PATH)/bin/mpif90
> >
> > and leave LIB_MPI and INC_MPI blank (that would help you locate
> > which script
> > and/or makefile that set FC to "gfortran" or "mpif90").
> >
> > The other option is to simply prefix your PATH with
> > /usr/local/mpich2-1.3.1 to
> > avoid /usr/local/bin's MPI compiler wrappers being used in CCSM
> > build system,
> > but then you have to check your environment every time running CCSM
> > build system,
> > and your build output won't show correct MPI implementation is being
> > used or not.
> > So I think you should follow the 1st approach that was suggested.
> >
> > A.Chan
> >
> > ----- Original Message -----
> >> The files that I send were indeed with the LIB and INC definitions
> >> included.
> >> But I did the test as well without these indications (and setting
> >> FC
> >> and
> >> CC to MPICH2/etc/etc/...), and the results were the same?
> >> see example built log in attach.
> >>
> >> The "which mpif90" statement gives me:
> >> /usr/local/bin/mpif90
> >>
> >> Matthias
> >>
> >> On 02/02/2011 04:48 PM, Anthony Chan wrote:
> >>> 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
> >>>> -------------------------------------------------------------
> >> --
> >>
> >>
> >> -------------------------------------------------------------
> >> 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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