[Trilinos-Users] [EXTERNAL] [TRILINOS-11.14.1 INSTALLATION ERROR SOLVED]--UNDEFINED REFERENCE TO "CHOLMOD/ SUITESPARSE"--SOLVED
Joseph Ampadu Ofosu
joseph at al.t.u-tokyo.ac.jp
Fri Apr 17 14:06:55 MDT 2015
Siva,
Is it not possible to link static libraries to shared ones, if you build
the static with the '-fPIC' flag configuration option?
Thanks.
On 18/04/2015 01:33, Siva Rajamanickam wrote:
> The reason is Amesos doesn't use CHOLMOD and Amesos2 does and the
> right cholmod libraries are not in
> your link line.
>
> If you don't need CHOLMOD please turn that off. I am starting to
> wonder what is your real usecase ?
> Why do you have so many different direct solvers enabled ?
>
> If you really need CHOLMOD, then you need to link against it properly.
> See Ross's instruction below to see the link line.
>
> Also, why do you link with static libs and configuring Trilinos with
> shared libraries on ?
>
> -Siva
>
> On 04/17/2015 10:20 AM, Ofosu Ampadu Joseph wrote:
>> Dear All,
>>
>> Thanks for the advice.
>>
>> Bartlett,
>> I did not link the executables anymore.
>>
>> First, I turned off the Amesos2 package via :
>> -DTrilinos_ENABLE_Amesos2=OFF
>> Yet this packaged was still part of the configuration output and thus
>> the error was unresolved.
>>
>> I eventually turned the Amesos2 package off via :
>> -DTrilinos_ENABLE_ALL_PACKAGES=OFF, whiles enabling the individual
>> packages I wanted to install.
>>
>> Both the configuration and installation was successful.
>>
>> However, I still do not understand why Amesos configures without
>> errors and yet Amesos2 does with errors.
>>
>> On 17/04/15 21:06, Bartlett, Roscoe A. wrote:
>>>
>>> Link that executable with VERBOSE=1 with:
>>>
>>> $ cd packages/amesos2/src/SuiteSparse/KLU2/Source
>>>
>>> $ make VERBOSE=1 Amesos2_klu2_simple
>>>
>>> That will show you the exact link line and if the libraries are
>>> showing up correctly.
>>>
>>> If the correct libraries are showing in the right order on the link
>>> line, then there must be a problem with the compatibility of the
>>> libraries.
>>>
>>> -Ross
>>>
>>> *From:*trilinos-users-bounces at software.sandia.gov
>>> [mailto:trilinos-users-bounces at software.sandia.gov] *On Behalf Of
>>> *Ofosu Ampadu Joseph
>>> *Sent:* Thursday, April 16, 2015 11:56 PM
>>> *To:* Bruno Turcksin
>>> *Cc:* trilinos-users at software.sandia.gov
>>> *Subject:* Re: [Trilinos-Users] [EXTERNAL] [TRILINOS-11.14.1
>>> INSTALLATION ERROR PERSISTS]--UNDEFINED REFERENCE TO "CHOLMOD/
>>> SUITESPARSE"--CONFIG STATEMENTS
>>>
>>> Hello Bruno,
>>>
>>> I did add the following as you advised:
>>>
>>> -DTPL_UMFPACK_LIBRARIES="/usr/local/lib/libumfpack.5.7.1.a" \
>>> -DTPL_CHOLMOD_LIBRARIES="/usr/local/lib/libcholmod.3.0.5.a" \
>>> -DTPL_SUITESPARSE_LIBRARIES="/usr/local/lib/libsuitesparseconfig.4.4.4.a"
>>> \
>>>
>>> AND AFTER
>>>
>>> 17% of built progress, I had the following errors:
>>>
>>> Scanning dependencies of target Amesos2_klu2_simple
>>> [ 17%] Building CXX object
>>> packages/amesos2/src/SuiteSparse/KLU2/Source/CMakeFiles/Amesos2_klu2_simple.dir/klu2_simple.cpp.o
>>> Linking CXX executable Amesos2_klu2_simple.exe
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `amd_postorder'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `cholmod_start'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `cholmod_finish'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `cholmod_free_factor'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `SuiteSparse_free'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `cholmod_print_common'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `SuiteSparse_time'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `cholmod_free_sparse'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `amd_defaults'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `cholmod_transpose'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `SuiteSparse_config'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `SuiteSparse_malloc'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `amd_2'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `amd_valid'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `cholmod_analyze'
>>> ../../../../../amesos/src/libamesos.so.11.14.1: undefined reference
>>> to `amd_aat'
>>> collect2: error: ld returned 1 exit status
>>> make[2]: ***
>>> [packages/amesos2/src/SuiteSparse/KLU2/Source/Amesos2_klu2_simple.exe]
>>> Error 1
>>> make[1]: ***
>>> [packages/amesos2/src/SuiteSparse/KLU2/Source/CMakeFiles/Amesos2_klu2_simple.dir/all]
>>> Error 2
>>> make: *** [all] Error 2
>>>
>>>
>>> Any specific reasons?
>>>
>>> Thanks once again.
>>>
>>> On 17/04/15 09:00, Bruno Turcksin wrote:
>>>
>>> Joseph,
>>>
>>> you probably want to add something like:
>>>
>>> -DTPL_CHOLMOD_LIBRARIES=path/to/library \
>>> -DTPL_SUITESPARSE_LIBRARIES=path/to/library \
>>>
>>> The linker cannot find where these libraries are. Your
>>> configuration only says where the header files are not the
>>> compiled libraries.
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>> 2015-04-16 17:58 GMT-05:00 Ofosu Ampadu Joseph
>>> <joseph at al.t.u-tokyo.ac.jp <mailto:joseph at al.t.u-tokyo.ac.jp>>:
>>>
>>> Dear All,
>>>
>>> In order to provide a broader picture to the installation
>>> errors, I have provided the configuration statements I used for
>>> configuring below:
>>>
>>> sudo cmake -DTrilinos_ENABLE_Sacado=ON \
>>> -DTrilinos_ENABLE_Stratimikos=ON \
>>> -DCMAKE_BUILD_TYPE=RELEASE \
>>> -DCMAKE_CXX_FLAGS="-g -O3" \
>>> -DCMAKE_C_FLAGS="-g -O3" \
>>> -DCMAKE_FORTRAN_FLAGS="-g -O5" \
>>> -DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
>>> -DTrilinos_ENABLE_ALL_PACKAGES=ON \
>>> -DCMAKE_VERBOSE_MAKEFILE=FALSE \
>>> -DTrilinos_VERBOSE_CONFIGURE=FALSE \
>>> -DTPL_ENABLE_MPI=ON \
>>> -DBUILD_SHARED_LIBS=ON \
>>> -DTPL_ENABLE_UMFPACK=ON \
>>> -DTPL_ENABLE_CHOLMOD=ON \
>>> -DTPL_ENABLE_SUITESPARSE=ON \
>>> -DTPL_ENABLE_SuperLU=ON \
>>> -DTPL_UMFPACK_INCLUDE_DIR="/usr/local/include" \
>>> -DTPL_CHOLMOD_INCLUDE_DIR="/usr/local/include" \
>>> -DTPL_SUITESPARSE_INCLUDE_DIR="/usr/local/include" \
>>> -DSuperLU_INCLUDE_DIRS="/home/ofosu/SuperLU_4.3/SRC" \
>>> -DTPL_SuperLU_LIBRARIES="/home/ofosu/SuperLU_4.3/lib/libsuperlu_4.3.a"
>>> \
>>> -DTPL_ENABLE_MUMPS=ON \
>>> -DTPL_ENABLE_SCALAPACK=ON \
>>> -DTPL_MUMPS_INCLUDE_DIRS="/usr/lib/openmpi/include/openmpi" \
>>> -DTPL_SCALAPACK_LIBRARIES="/home/ofosu/scalapack-2.0.2/libscalapack.a"
>>> \
>>> -DTPL_SWIG_INCLUDE_DIRS="/usr/local/include/share/swig/3.0.5" \
>>> -DCMAKE_INSTALL_PATH="/usr/local/include" \
>>> /home/ofosu/trilinos-11.14.1-Source
>>>
>>>
>>> On 16/04/15 02:08, Siva Rajamanickam wrote:
>>>
>>> Looks like you are configuring Trilinos with CHOLMOD, but the
>>> linker is not able to find the cholmod library.
>>>
>>> -Siva
>>>
>>> On 04/15/2015 10:12 AM, Ofosu Ampadu Joseph wrote:
>>>
>>> Dear All,
>>>
>>> I am new to Trilinos and would like to interface some of the
>>> libraries with Deal II.
>>> I am building on Ubuntu 14.04 LTS OS.
>>> I have been able to successfully configure Trilinos, however
>>> during installation via the command: 'sudo make install' , and
>>> after 27% of built target success, I get the following errors:
>>>
>>> [ 27%] Built target Amesos_Amesos_TESTBASIC_COPY3
>>> Linking CXX executable amesos_test.exe
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `cholmod_start'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `cholmod_finish'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `cholmod_free_factor'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `SuiteSparse_free'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `cholmod_print_common'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `SuiteSparse_time'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `cholmod_free_sparse'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `cholmod_transpose'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `SuiteSparse_config'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `SuiteSparse_malloc'
>>> ../../src/libamesos.so.11.14.1: undefined reference to
>>> `cholmod_analyze'
>>> collect2: error: ld returned 1 exit status
>>> make[2]: *** [packages/amesos/test/Test_Basic/amesos_test.exe]
>>> Error 1
>>> make[1]: ***
>>> [packages/amesos/test/Test_Basic/CMakeFiles/amesos_test.dir/all]
>>> Error 2
>>> make: *** [all] Error 2
>>>
>>> I humbly ask if anyone could assist me with an advice of how to
>>> proceed. Thanks.
>>>
>>>
>>> _______________________________________________
>>> Trilinos-Users mailing list
>>> Trilinos-Users at software.sandia.gov
>>> <mailto:Trilinos-Users at software.sandia.gov>
>>> https://software.sandia.gov/mailman/listinfo/trilinos-users
>>>
>>>
>>> --
>>> ====================================
>>> Ofosu Joseph Ampadu
>>> The University of Tokyo
>>> Graduate Sch. of Frontier Sciences
>>> Department of Advanced Energy
>>> Komurasaki Laboratory
>>> +81-4-7136-4030 <tel:%2B81-4-7136-4030>
>>> ====================================
>>>
>>> _______________________________________________
>>> Trilinos-Users mailing list
>>> Trilinos-Users at software.sandia.gov
>>> <mailto:Trilinos-Users at software.sandia.gov>
>>> https://software.sandia.gov/mailman/listinfo/trilinos-users
>>>
>>>
>>>
>>> --
>>> ====================================
>>> Ofosu Joseph Ampadu
>>> The University of Tokyo
>>> Graduate Sch. of Frontier Sciences
>>> Department of Advanced Energy
>>> Komurasaki Laboratory
>>> +81-4-7136-4030
>>> ====================================
>>
>> --
>> ====================================
>> Ofosu Joseph Ampadu
>> The University of Tokyo
>> Graduate Sch. of Frontier Sciences
>> Department of Advanced Energy
>> Komurasaki Laboratory
>> +81-4-7136-4030
>> ====================================
>>
>>
>> _______________________________________________
>> Trilinos-Users mailing list
>> Trilinos-Users at software.sandia.gov
>> https://software.sandia.gov/mailman/listinfo/trilinos-users
>
--
==================================
Ofosu Joseph Ampadu
The University of Tokyo
Graduate Sch. of Frontier Sciences
Department of Advanced Energy
Komurasaki Laboratory
0081-4-7136-4030
==================================
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