[mpich-discuss] undefined symbol: MPIR_Thread

Matthias Demuzere Matthias.demuzere at ees.kuleuven.be
Thu Feb 3 10:09:19 CST 2011 

ok, I removed all other references to mpi in /usr/local/bin and /include 
(strange that this wasn't removed with the synaptic package manager).
I recompiled everything again, but still same error referring to 
MPIR_Thread.

output from the ccsm build log now looks like:

/usr/local/mpich2-1.3.1/bin/mpif90 -c -I.  
-I/usr/local/netcdf-4.1.1/include -I/usr/local/netcdf-4.1.1/include -I. 
-I/usr/workdir/cesm1_0_2/scripts/test1/SourceMods/src.drv 
-I/usr/workdir/cesm1_0_2/models/drv/driver 
-I/usr/workdir/cesm1_0_2/scripts/test1/lib/include   -DMCT_INTERFACE 
-DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH  
-g -fno-range-check -fconvert=big-endian -O2    
/usr/workdir/cesm1_0_2/models/drv/driver/ccsm_driver.F90
/usr/local/mpich2-1.3.1/bin/mpif90 -o 
/usr/workdir/cesm1_0_2/scripts/test1/run/ccsm.exe ccsm_driver.o 
map_atmatm_mct.o map_atmice_mct.o map_atmlnd_mct.o map_atmocn_mct.o 
map_glcglc_mct.o map_iceice_mct.o map_iceocn_mct.o map_lndlnd_mct.o 
map_ocnocn_mct.o map_rofocn_mct.o map_rofrof_mct.o map_snoglc_mct.o 
map_snosno_mct.o mrg_x2a_mct.o mrg_x2g_mct.o mrg_x2i_mct.o mrg_x2l_mct.o 
mrg_x2o_mct.o mrg_x2s_mct.o seq_avdata_mod.o seq_diag_mct.o 
seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o 
seq_rearr_mod.o seq_rest_mod.o 
-L/usr/workdir/cesm1_0_2/scripts/test1/lib -latm -llnd -lice -locn -lglc 
-L/usr/workdir/cesm1_0_2/scripts/test1/lib -lcsm_share -lmct -lmpeu 
-lpio  -L/usr/local/netcdf-4.1.1/lib -lnetcdf -lnetcdff 
-L/usr/local/hdf5/lib -lhdf5_hl -lhdf5  -L/usr/local/zlib/lib -lz -lm 
-lnetcdf   -L/usr/local/lib -lcurl
/usr/bin/ld: Warning: alignment 16 of symbol `mpifcmb4_' in 
/usr/local/mpich2-1.3.1/lib/libmpich.a(setbot.o) is smaller than 32 in 
ccsm_driver.o
/usr/bin/ld: Warning: alignment 16 of symbol `mpifcmb6_' in 
/usr/local/mpich2-1.3.1/lib/libmpich.a(setbot.o) is smaller than 32 in 
ccsm_driver.o
/usr/bin/ld: Warning: alignment 16 of symbol `mpifcmb8_' in 
/usr/local/mpich2-1.3.1/lib/libmpich.a(setbot.o) is smaller than 32 in 
ccsm_driver.o


On 02/03/2011 04:58 PM, Anthony Chan wrote:
> Given you didn't remove ubuntu mpich, you should check
> if /usr/local/include has any mpi.h, mpif.h or mpi.mod files,
> if so remove them as well...  If you do have these files, chances
> are some of your object files are using these headers, so you need
> to recompile everything again...
>
> ----- Original Message -----
>> In your ccsm build log, you have this command and output:
>>
>> /usr/local/mpich2-1.3.1/bin/mpif90 -o
>> /usr/workdir/cesm1_0_2/scripts/test1/run/ccsm.exe ccsm_driver.o
>> map_atmatm_mct.o map_atmice_mct.o map_atmlnd_mct.o map_atmocn_mct.o
>> map_glcglc_mct.o map_iceice_mct.o map_iceocn_mct.o map_lndlnd_mct.o
>> map_ocnocn_mct.o map_rofocn_mct.o map_rofrof_mct.o map_snoglc_mct.o
>> map_snosno_mct.o mrg_x2a_mct.o mrg_x2g_mct.o mrg_x2i_mct.o
>> mrg_x2l_mct.o mrg_x2o_mct.o mrg_x2s_mct.o seq_avdata_mod.o
>> seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o
>> seq_hist_mod.o seq_rearr_mod.o seq_rest_mod.o
>> -L/usr/workdir/cesm1_0_2/scripts/test1/lib -latm -llnd -lice -locn
>> -lglc -L/usr/workdir/cesm1_0_2/scripts/test1/lib -lcsm_share -lmct
>> -lmpeu -lpio -L/usr/local/netcdf-4.1.1/lib -lnetcdf -lnetcdff
>> -L/usr/local/hdf5/lib -lhdf5_hl -lhdf5 -L/usr/local/zlib/lib -lz -lm
>> -lnetcdf -L/usr/local/lib -lcurl
>> /usr/bin/ld: Warning: alignment 16 of symbol `mpifcmb4_' in
>> /usr/local/lib/libmpich.a(setbot.o) is smaller than 32 in
>> ccsm_driver.o
>> /usr/bin/ld: Warning: alignment 16 of symbol `mpifcmb6_' in
>> /usr/local/lib/libmpich.a(setbot.o) is smaller than 32 in
>> ccsm_driver.o
>> /usr/bin/ld: Warning: alignment 16 of symbol `mpifcmb8_' in
>> /usr/local/lib/libmpich.a(setbot.o) is smaller than 32 in
>> ccsm_driver.o
>>
>> Notice that the warning is about /usr/local/lib/libmpich.a which is
>> mpich2 from ubuntu repository (I think
>> mpich2-1.3.1's libmpich.a is in
>> /usr/local/mpich2-1.3.1/lib/libmpich.a), right. Since you need
>> libcurl.a(.so)
>> from /usr/local/lib, you HAVE TO remove /usr/local/lib/libmpich.a,
>> otherwise mpif90 will use libmpich.a from
>> your /usr/local/lib first..
>>
>> A.Chan
>>
>> ----- Original Message -----
>>> yes, ccsm.exe is created again, as a new folder is created each time
>>> I
>>> run the building process (meaning that the old one is removed).
>>> So once the compilation starts, all is stored in folder /test1/....
>>>
>>> In attach the log file for creating the ccsm executable, as mct is
>>> not
>>> the module that creates the ccsm.exe file.
>>>
>>> On 02/03/2011 04:34 PM, Anthony Chan wrote:
>>>> Your MCT build log does not contain the link command that creates
>>>> ccsm.exe,
>>>> so I am not sure if ccsm.exe has actually been recreated with the
>>>> mpich2-1.3.1,
>>>> i.e. you could be still use the old ccsm.exe that was linked with
>>>> ubuntu mpich.
>>>>
>>>> So you need to remove all .o, .a (or .so) and ccsm.exe (or all
>>>> .exe)
>>>> files before
>>>> compiling again to make sure everything is compiled and linked
>>>> correctly with
>>>> mpich2-1.3.1...
>>>>
>>>> A.Chan
>>>>
>>>> ----- Original Message -----
>>>>> 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
>>>>> -------------------------------------------------------------
>>> --
>>>
>>>
>>> -------------------------------------------------------------
>>> 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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