[mpich-discuss] undefined symbol: MPIR_Thread
Matthias Demuzere
Matthias.demuzere at ees.kuleuven.be
Thu Feb 3 10:49:50 CST 2011
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
-------------------------------------------------------------
More information about the mpich-discuss
mailing list