[mpich-discuss] undefined symbol: MPIR_Thread

Matthias Demuzere Matthias.demuzere at ees.kuleuven.be
Wed Feb 2 11:11:50 CST 2011 

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
-------------------------------------------------------------

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