[mpich-discuss] undefined symbol: MPIR_Thread
Matthias Demuzere
Matthias.demuzere at ees.kuleuven.be
Thu Feb 3 08:15:24 CST 2011
Ok!
I realised that in first instance I installed mpich via the ubuntu
repository, and afterwards i built it myself.
That was the reason why I had another MPI installation present.
So I un-installed the first version, and built the other one again, to
be sure.
I have set the references as you said:
FC := /usr/local/mpich2-1.3.1/bin/mpif90
CC := /usr/local/mpich2-1.3.1/bin/mpicc
F90 := /usr/local/mpich2-1.3.1/bin/mpif90
MPICC := /usr/local/mpich2-1.3.1/bin/mpicc
MPIF90 := /usr/local/mpich2-1.3.1/bin/mpif90
and compiled the model again. This went ok, an executable was created
(see attach for example of one of the modules)
Running the executable unfortunately gave me the same error:
./ccsm.exe: symbol lookup error: ./ccsm.exe: undefined symbol: MPIR_Thread
So back to square one?
Any new ideas?
Matthias
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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