[Trilinos-Users] [EXTERNAL] [TRILINOS-11.14.1 INSTALLATION ERROR SOLVED]--UNDEFINED REFERENCE TO "CHOLMOD/ SUITESPARSE"--SOLVED
Siva Rajamanickam
srajama at sandia.gov
Fri Apr 17 10:33:58 MDT 2015
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://software.sandia.gov/pipermail/trilinos-users/attachments/20150417/858fee17/attachment.html>
More information about the Trilinos-Users
mailing list