Errors when compiling LEM code in Savio

#1

Here are modules I loaded.

Then I cloned lem and lem-benchmarks from github. When I tried to compile the code, several error occured and the message is as below.

[zhenxiang_su@ln003 lem]$ cd build
[zhenxiang_su@ln003 build]$ cmake -DCMAKE_BUILD_TYPE=Release /global/home/users/zhenxiang_su/LEM/lem
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/c++
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found Eigen3: /global/software/sl-7.x86_64/modules/tools/eigen/3.3.3/include/eigen3 (Required is at least version "2.91.0")
-- Found VOROPLUSPLUS: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/voropp-0.4.6-ppabzmsivi53vcj6wescw                            chkkzmrhx35/include/voro++
-- Found TBB: /global/software/sl-7.x86_64/modules/langs/intel/2016.4.072/tbb/include (found version "4.4")
-- Could NOT find MKL (missing:  MKL_INCLUDE_DIR MKL_LIBRARIES)
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing:  CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
CMake Warning at cmake/FindBoost.cmake:564 (message):
  Imported targets and dependency information not available for Boost version
  (all versions older than 1.33)
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Warning at cmake/FindBoost.cmake:564 (message):
  Imported targets and dependency information not available for Boost version
  (all versions older than 1.33)
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Error at cmake/FindBoost.cmake:1956 (message):
  Unable to find the requested Boost libraries.

  Unable to find the Boost header files.  Please set BOOST_ROOT to the root
  directory containing Boost or BOOST_INCLUDEDIR to the directory containing
  Boost's headers.
Call Stack (most recent call first):
  CMakeLists.txt:76 (find_package)


-- The C compiler identification is GNU 6.3.0
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
CMake Error at cmake/FindHDF5.cmake:363 (separate_arguments):
  separate_arguments given unknown argument NATIVE_COMMAND
Call Stack (most recent call first):
  cmake/FindHDF5.cmake:588 (_HDF5_parse_compile_line)
  CMakeLists.txt:87 (find_package)


-- Could NOT find HDF5 (missing:  HDF5_LIBRARIES HDF5_HL_LIBRARIES) (found version "1.10.1")
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Checking for module 'sqlite3'
--   Found sqlite3, version 3.22.0
-- Found Sqlite: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzd                            m2fdbv/include
-- Configuring incomplete, errors occurred!
See also "/global/home/users/zhenxiang_su/LEM/lem/build/CMakeFiles/CMakeOutput.log".

It seems that several dependencies can’t be found, even though I already load the module (boost library, HDF5…), why does it happen? And how should I solve this error? Thanks.

And by the way, should I also install the optional MLK and CUDA?

#2

Try adding a compiler flag like g++ to cmake and see if that helps so something like this: -DCMAKE_CXX_COMPILER=g++

#3

In build folder, I did, cmake -DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release ..

And it seems the same error occure, error message,

[zhenxiang_su@ln002 lem]$ mkdir build
[zhenxiang_su@ln002 lem]$ cd build/
[zhenxiang_su@ln002 build]$ cmake -DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release ..
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found Eigen3: /global/software/sl-7.x86_64/modules/tools/eigen/3.3.3/include/eigen3 (Required is at least version "2.91.0")
-- Found VOROPLUSPLUS: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/voropp-0.4.6-ppabzmsivi53vcj6wescwchkkzmrhx35/include/voro++
-- Found TBB: /global/software/sl-7.x86_64/modules/langs/intel/2016.4.072/tbb/include (found version "4.4")
-- Could NOT find MKL (missing:  MKL_INCLUDE_DIR MKL_LIBRARIES)
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Found CUDA: /global/software/sl-7.x86_64/modules/langs/cuda/9.0 (found version "9.0")
CMake Warning at cmake/FindBoost.cmake:564 (message):
  Imported targets and dependency information not available for Boost version
  (all versions older than 1.33)
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Warning at cmake/FindBoost.cmake:564 (message):
  Imported targets and dependency information not available for Boost version
  (all versions older than 1.33)
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Error at cmake/FindBoost.cmake:1956 (message):
  Unable to find the requested Boost libraries.

  Unable to find the Boost header files.  Please set BOOST_ROOT to the root
  directory containing Boost or BOOST_INCLUDEDIR to the directory containing
  Boost's headers.
Call Stack (most recent call first):
  CMakeLists.txt:76 (find_package)


-- The C compiler identification is GNU 6.3.0
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
CMake Error at cmake/FindHDF5.cmake:363 (separate_arguments):
  separate_arguments given unknown argument NATIVE_COMMAND
Call Stack (most recent call first):
  cmake/FindHDF5.cmake:588 (_HDF5_parse_compile_line)
  CMakeLists.txt:87 (find_package)


-- Could NOT find HDF5 (missing:  HDF5_LIBRARIES HDF5_HL_LIBRARIES) (found version "1.10.1")
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Checking for module 'sqlite3'
--   Found sqlite3, version 3.22.0
-- Found Sqlite: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/include
-- Configuring incomplete, errors occurred!
See also "/global/home/users/zhenxiang_su/LEM/lem/build/CMakeFiles/CMakeOutput.log".
#4

It is not picking up boost, could you try spack install boost+filesystem to install Boost using Spack?

#5

I used spack to install boost and load it,

Untitled

Now the message becomes,

[zhenxiang_su@ln002 lem]$ mkdir build && cd build
[zhenxiang_su@ln002 build]$ cmake -DCMAKE_CXX_COMPILER=g++ -DCMAKE_BUILD_TYPE=Release ..
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found Eigen3: /global/software/sl-7.x86_64/modules/tools/eigen/3.3.3/include/eigen3 (Required is at least version "2.91.0")
-- Found VOROPLUSPLUS: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/voropp-0.4.6-ppabzmsivi53vcj6wescwchkkzmrhx35/include/voro++
-- Found TBB: /global/software/sl-7.x86_64/modules/langs/intel/2016.4.072/tbb/include (found version "4.4")
-- Could NOT find MKL (missing:  MKL_INCLUDE_DIR MKL_LIBRARIES)
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Found CUDA: /global/software/sl-7.x86_64/modules/langs/cuda/9.0 (found version "9.0")
CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   system
--   filesystem
-- The C compiler identification is GNU 6.3.0
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
CMake Error at cmake/FindHDF5.cmake:363 (separate_arguments):
  separate_arguments given unknown argument NATIVE_COMMAND
Call Stack (most recent call first):
  cmake/FindHDF5.cmake:588 (_HDF5_parse_compile_line)
  CMakeLists.txt:87 (find_package)


-- Could NOT find HDF5 (missing:  HDF5_LIBRARIES HDF5_HL_LIBRARIES) (found version "1.10.1")
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Checking for module 'sqlite3'
--   Found sqlite3, version 3.22.0
-- Found Sqlite: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/include
-- Configuring incomplete, errors occurred!
See also "/global/home/users/zhenxiang_su/LEM/lem/build/CMakeFiles/CMakeOutput.log".

Is the warning, “New Boost version may have incorrect or missing dependencies and imported
targets” ok?

And there still the problem with hdf5, how can I solve it?

#6

I install hdf5 manually as you said here in #44 Running MPM code with Berkeley Savio

The compile message is follow.

[zhenxiang_su@ln003 build]$ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++ -DHDF5_ROOT=$HOME/hdf5/HDF5-1.10.1-Linu            x/HDF_Group/HDF5/1.10.1/ ..
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found Eigen3: /global/software/sl-7.x86_64/modules/tools/eigen/3.3.3/include/eigen3 (Required is at least version "2.91.0"            )
-- Found VOROPLUSPLUS: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/voropp-0.4.6-ppabzmsivi53            vcj6wescwchkkzmrhx35/include/voro++
-- Found TBB: /global/software/sl-7.x86_64/modules/langs/intel/2016.4.072/tbb/include (found version "4.4")
-- Could NOT find MKL (missing:  MKL_INCLUDE_DIR MKL_LIBRARIES)
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Found CUDA: /global/software/sl-7.x86_64/modules/langs/cuda/9.0 (found version "9.0")
CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   system
--   filesystem
-- The C compiler identification is GNU 6.3.0
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found HDF5: /global/home/users/zhenxiang_su/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/lib/libhdf5_cpp.a;/global/home/us            ers/zhenxiang_su/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/lib/libhdf5.a (found version "1.10.1") found components:  CXX H            L
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Checking for module 'sqlite3'
--   Found sqlite3, version 3.22.0
-- Found Sqlite: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvj            liydn3zzdm2fdbv/include
-- Configuring done
-- Generating done
-- Build files have been written to: /global/home/users/zhenxiang_su/LEM/lem/build

It seems work in compiling? But when I do make -j8 , following error occured.

[zhenxiang_su@ln003 build]$ make -j8
Scanning dependencies of target lem
Scanning dependencies of target lemtest
[  6%] Building CXX object CMakeFiles/lemtest.dir/tests/test.cc.o
[ 13%] Building CXX object CMakeFiles/lemtest.dir/tests/node_base_3d_test.cc.o
[ 20%] Linking CXX executable lemtest
[ 26%] Building CXX object CMakeFiles/lem.dir/src/cg_gpu.cc.o
[ 40%] Building CXX object CMakeFiles/lem.dir/src/lem.cc.o
[ 40%] Building CXX object CMakeFiles/lem.dir/src/beam_element.cc.o
[ 46%] Building CXX object CMakeFiles/lem.dir/src/spring_element.cc.o
[ 66%] Building CXX object CMakeFiles/lem.dir/src/eigen_matrix_assembler.cc.o
[ 66%] Building CXX object CMakeFiles/lem.dir/src/shear_element.cc.o
[ 66%] Building CXX object CMakeFiles/lem.dir/src/io.cc.o
[ 73%] Building CXX object CMakeFiles/lem.dir/src/cg_eigen.cc.o
[ 80%] Building CXX object CMakeFiles/lem.dir/src/distribution_generator.cc.o
[ 86%] Building CXX object CMakeFiles/lem.dir/src/vtk_writer.cc.o
[ 93%] Building CXX object CMakeFiles/lem.dir/src/main.cc.o
[100%] Linking CXX executable lem
[100%] Built target lemtest
CMakeFiles/lem.dir/src/lem.cc.o: In function `sqlite::database_binder::sql[abi:cxx11]()':
lem.cc:(.text._ZN6sqlite15database_binder3sqlB5cxx11Ev[_ZN6sqlite15database_binder3sqlB5cxx11Ev]+0xf): undefined reference to `sqlite3_expanded_sql'
collect2: error: ld returned 1 exit status
make[2]: *** [lem] Error 1
make[1]: *** [CMakeFiles/lem.dir/all] Error 2
make: *** [all] Error 2

When’s the problem here? Is still with hdf5 or something else? And how can I possibly solve it?

#7

The problem is SQLite not HDF5, you need to load SQLite.

#8

I already loaded SQLite with spack,

Untitled

And as the configuring message showed above, it can be found when configuring

-- Checking for module 'sqlite3'
--   Found sqlite3, version 3.22.0
-- Found Sqlite: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/include
-- Configuring done

But the error happened at make -j8

#9

It’s a linker error, it is failing to link to a SQL library file.

#10

So how can I possibly solve this error?

#11

Try a spack version instead of the loaded SQLite version

#12

Or try passing the path to the SQLite library file like shown here: Problem in compiling LEM in SDumont computers

#13

I’m using spack version, as Savio didn’t provide SQLite in the system.

As shown in that link, I use this command to compile,

cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++ -DSQLITE_INCLUDE_DIR=/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/include -DSLITE_LIBRARIES=/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/lib/libsqlite3.so -DHDF5_ROOT=$HOME/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/ ..

And got following configuring message,

[zhenxiang_su@ln002 build]$ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++ -DSQLITE_INCLUDE_DIR=/global/home/user                      s/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/include -DSLITE_L                      IBRARIES=/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3z                      zdm2fdbv/lib/libsqlite3.so -DHDF5_ROOT=$HOME/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/ ..
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found Eigen3: /global/software/sl-7.x86_64/modules/tools/eigen/3.3.3/include/eigen3 (Required is at least version "2.91.0                      ")
-- Found VOROPLUSPLUS: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/voropp-0.4.6-ppabzmsivi5                      3vcj6wescwchkkzmrhx35/include/voro++
-- Found TBB: /global/software/sl-7.x86_64/modules/langs/intel/2016.4.072/tbb/include (found version "4.4")
-- Could NOT find MKL (missing:  MKL_INCLUDE_DIR MKL_LIBRARIES)
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Found CUDA: /global/software/sl-7.x86_64/modules/langs/cuda/9.0 (found version "9.0")
CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   system
--   filesystem
-- The C compiler identification is GNU 6.3.0
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found HDF5: /global/home/users/zhenxiang_su/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/lib/libhdf5_cpp.a;/global/home/u                      sers/zhenxiang_su/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/lib/libhdf5.a (found version "1.10.1") found components:  CXX                       HL
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Checking for module 'sqlite3'
--   Found sqlite3, version 3.22.0
-- Found Sqlite: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczv                      jliydn3zzdm2fdbv/include
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    SLITE_LIBRARIES

It seems that the manually-specified paths were not used? as the warning message,

   CMake Warning:
      Manually-specified variables were not used by the project:

        SLITE_LIBRARIES

And when I do make -j8, same error happened.

[zhenxiang_su@ln002 build]$ make -j8
Scanning dependencies of target lemtest
Scanning dependencies of target lem
[  6%] Building CXX object CMakeFiles/lemtest.dir/tests/test.cc.o
[ 13%] Building CXX object CMakeFiles/lemtest.dir/tests/node_base_3d_test.cc.o
[ 20%] Building CXX object CMakeFiles/lem.dir/src/cg_gpu.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/spring_element.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/shear_element.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/eigen_matrix_assembler.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/beam_element.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/lem.cc.o
[ 60%] Building CXX object CMakeFiles/lem.dir/src/io.cc.o
[ 66%] Linking CXX executable lemtest
[ 73%] Building CXX object CMakeFiles/lem.dir/src/cg_eigen.cc.o
[ 80%] Building CXX object CMakeFiles/lem.dir/src/distribution_generator.cc.o
[ 86%] Building CXX object CMakeFiles/lem.dir/src/vtk_writer.cc.o
[ 93%] Building CXX object CMakeFiles/lem.dir/src/main.cc.o
[ 93%] Built target lemtest
[100%] Linking CXX executable lem
CMakeFiles/lem.dir/src/lem.cc.o: In function `sqlite::database_binder::sql[abi:cxx11]()':
lem.cc:(.text._ZN6sqlite15database_binder3sqlB5cxx11Ev[_ZN6sqlite15database_binder3sqlB5cxx11Ev]+0xf): undefined reference to `sqlite3_expanded_sql'
collect2: error: ld returned 1 exit status
make[2]: *** [lem] Error 1
make[1]: *** [CMakeFiles/lem.dir/all] Error 2
make: *** [all] Error 2
#14

You seem to have misspelt -DSQLITE

#15

Okay…I fixed it and got following compile message,

[zhenxiang_su@ln002 build]$ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++ -DSQLITE_INCLUDE_DIR=/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/include -DSQLITE_LIBRARIES=/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/sqlite-3.23.1-vyraaazhr2misczvjliydn3zzdm2fdbv/lib/libsqlite3.so -DHDF5_ROOT=$HOME/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/ ..
-- The CXX compiler identification is GNU 6.3.0
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++
-- Check for working CXX compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Found Eigen3: /global/software/sl-7.x86_64/modules/tools/eigen/3.3.3/include/eigen3 (Required is at least version "2.91.0")
-- Found VOROPLUSPLUS: /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/voropp-0.4.6-ppabzmsivi53vcj6wescwchkkzmrhx35/include/voro++
-- Found TBB: /global/software/sl-7.x86_64/modules/langs/intel/2016.4.072/tbb/include (found version "4.4")
-- Could NOT find MKL (missing:  MKL_INCLUDE_DIR MKL_LIBRARIES)
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Found CUDA: /global/software/sl-7.x86_64/modules/langs/cuda/9.0 (found version "9.0")
CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


CMake Warning at cmake/FindBoost.cmake:798 (message):
  New Boost version may have incorrect or missing dependencies and imported
  targets
Call Stack (most recent call first):
  cmake/FindBoost.cmake:903 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/FindBoost.cmake:1571 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:76 (find_package)


-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   system
--   filesystem
-- The C compiler identification is GNU 6.3.0
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc
-- Check for working C compiler: /global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found HDF5: /global/home/users/zhenxiang_su/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/lib/libhdf5_cpp.a;/global/home/users/zhenxiang_su/hdf5/HDF5-1.10.1-Linux/HDF_Group/HDF5/1.10.1/lib/libhdf5.a (found version "1.10.1") found components:  CXX HL
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Checking for module 'sqlite3'
--   Found sqlite3, version 3.22.0
-- Configuring done
-- Generating done
-- Build files have been written to: /global/home/users/zhenxiang_su/LEM/lem/build

But still same error when I did make -j8

[zhenxiang_su@ln002 build]$ make -j8
Scanning dependencies of target lemtest
Scanning dependencies of target lem
[  6%] Building CXX object CMakeFiles/lemtest.dir/tests/test.cc.o
[ 13%] Building CXX object CMakeFiles/lemtest.dir/tests/node_base_3d_test.cc.o
[ 20%] Building CXX object CMakeFiles/lem.dir/src/cg_gpu.cc.o
[ 33%] Building CXX object CMakeFiles/lem.dir/src/lem.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/beam_element.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/shear_element.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/spring_element.cc.o
[ 53%] Building CXX object CMakeFiles/lem.dir/src/eigen_matrix_assembler.cc.o
[ 60%] Building CXX object CMakeFiles/lem.dir/src/io.cc.o
[ 66%] Linking CXX executable lemtest
[ 66%] Built target lemtest
[ 73%] Building CXX object CMakeFiles/lem.dir/src/cg_eigen.cc.o
[ 80%] Building CXX object CMakeFiles/lem.dir/src/distribution_generator.cc.o
[ 86%] Building CXX object CMakeFiles/lem.dir/src/vtk_writer.cc.o
[ 93%] Building CXX object CMakeFiles/lem.dir/src/main.cc.o
[100%] Linking CXX executable lem
CMakeFiles/lem.dir/src/lem.cc.o: In function `sqlite::database_binder::sql[abi:cxx11]()':
lem.cc:(.text._ZN6sqlite15database_binder3sqlB5cxx11Ev[_ZN6sqlite15database_binder3sqlB5cxx11Ev]+0xf): undefined reference to `sqlite3_expanded_sql'
collect2: error: ld returned 1 exit status
make[2]: *** [lem] Error 1
make[1]: *** [CMakeFiles/lem.dir/all] Error 2
make: *** [all] Error 2
#16

Try make VERBOSE=1 -j8 and grep (search) if it has the -lsqlite3 flag included during compilation.

#17

These are the messages when I did grep -w -e "-lsqlite3" output.txt… I copyed those output message into the output.txt. The output here is incomplete as the word limit.

[zhenxiang_su@ln002 build]$ grep -w -e "-lsqlite3" output.txt
/global/software/sl-7.x86_64/modules/langs/gcc/6.3.0/bin/g++    -fopenmp  -O3 -DNDEBUG    CMakeFiles/lemtest.dir/tests/test.cc.o CMakeFiles/lemtest.dir/tests/node_base_3d_test.cc.o  -o lemtest -Wl,-rpath,/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/freetype-2.7.1-w5in3r4s3x6q4u2ocltovohsbe3gnlbu/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/zlib-1.2.11-vhzh5cfaki5lx5sjuth5iuojq5azdkbd/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lz4-1.8.1.2-q7awix3zctt2axesr4l5t4n53ybbh4s4/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/expat-2.2.5-om6ee3rj6bvlny3mqrvytlpbdxkjn6jm/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libjpeg-9c-h3otql3efinsybz6paustdg23dpavvdr/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libpng-1.6.34-4kfv2v35phzldswsqw4wtculghkswqhz/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libtiff-4.0.9-eerxq3wqte32mukinx6kbmrgzeknctgz/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/hdf5-1.10.3-3dd2amevcc5fhwuft2oaokroax7ibwcl/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/openmpi-3.1.2-r642gk4u6vzukgvdpvtesn3wodn36vgc/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/netcdf-4.6.1-6gb26w2pj3tk5eb6fko6t7h2iq7buvlr/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libharu-2.3.0-4dk55m2cos3wq7dkkuag4rh3ynv5m2r2/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libxml2-2.9.8-ffzbok4dcvwikwe4jekeyb5geabbwddg/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/netcdf-cxx-4.2-czq4esxcb5ndxg67x5aysn7e73vldazx/lib:/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/jsoncpp-1.7.3-bkceia5s32rj3s3ssumusxqxl56gsmyy/lib -rdynamic -Wl,-Bstatic -lvoro++ -Wl,-Bdynamic -ltbb -Wl,-Bstatic -lcudart_static -Wl,-Bdynamic -ldl -lrt -lcublas -Wl,-Bstatic -lcublas_device -Wl,-Bdynamic -lcusparse -lboost_filesystem-mt -lboost_system-mt /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/freetype-2.7.1-w5in3r4s3x6q4u2ocltovohsbe3gnlbu/lib/libfreetype.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/zlib-1.2.11-vhzh5cfaki5lx5sjuth5iuojq5azdkbd/lib/libz.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/lz4-1.8.1.2-q7awix3zctt2axesr4l5t4n53ybbh4s4/lib/liblz4.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/expat-2.2.5-om6ee3rj6bvlny3mqrvytlpbdxkjn6jm/lib/libexpat.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkDomainsChemistryOpenGL2-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersFlowPaths-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersGeneric-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersHyperTree-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersParallelImaging-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersPoints-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersProgrammable-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersSMP-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersSelection-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersTexture-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersTopology-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkFiltersVerdict-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkverdict-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkGeovisCore-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libjpeg-9c-h3otql3efinsybz6paustdg23dpavvdr/lib/libjpeg.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libpng-1.6.34-4kfv2v35phzldswsqw4wtculghkswqhz/lib/libpng.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libtiff-4.0.9-eerxq3wqte32mukinx6kbmrgzeknctgz/lib/libtiff.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkproj4-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkIOAMR-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/hdf5-1.10.3-3dd2amevcc5fhwuft2oaokroax7ibwcl/lib/libhdf5.so -ldl -lm /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/openmpi-3.1.2-r642gk4u6vzukgvdpvtesn3wodn36vgc/lib/libmpi.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/openmpi-3.1.2-r642gk4u6vzukgvdpvtesn3wodn36vgc/lib/libmpi_cxx.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/hdf5-1.10.3-3dd2amevcc5fhwuft2oaokroax7ibwcl/lib/libhdf5_hl.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkIOEnSight-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/vtk-8.0.1-3qqjjcmtmu4u4zt3q4bkzrxgzp3mi3rw/lib/libvtkIOExodus-8.0.so.1 /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/netcdf-4.6.1-6gb26w2pj3tk5eb6fko6t7h2iq7buvlr/lib/libnetcdf.so /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libharu-2.3.0-4dk55m2cos3wq7dkkuag4rh3ynv5m2r2/lib/libhpdf.so 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I also copy those message into a word file and search there, and there did have “-lsqlite3” flag.

#18

I don’t know, could you ask if Savio team can help you install SQLite3 with headers?

#19

I contacted Savio support, there may be some progress on the problem but haven’t solve it.

Do you have any idea about how to solve this version problem mentioned in above pictures? And would you consider to convert the previous Docker image to Singularity, which we may use it easily?
https://research-it.berkeley.edu/services/high-performance-computing/using-singularity-savio
http://singularity.lbl.gov/docs-docker

#20

I’m aware of Singularity, we have a Singularity file for LEM. However, it might be better if we can try and figure out why we have this issue on Savio. Like in the email, can you try to fix which version of SQLite3 is found in CMake?