Problem in compiling LEM in SDumont computers

Hello guys, I have to compile the LEM code in SDumont computers.

I follow the steps:

  1. I download the LEM code in the directory:
: /scratch/fhfnlem/julio.cordero/
  1. I load the prerequisites:
module load gcc-6/6.2
module load cmake/3.12
module load boost/1.67_intel
module load eigen/3.3_intel
module load tbb/2018.2_gcc-6
module load hdf5/1.10_openmpi-2.0_intel 
module load voro++/0.4.6_intel
module load vtk/8.1_intel
module load cuda/9.2
source /scratch/app/modulos/

SQlite is not necessary to load because it is Directly available through the Operating System package

  1. use the commands:
cd lem
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..

I had a problem because cmake can not found some libraries.


  1. I used the command:
cmake -DCMAKE_BUILD_TYPE=Release ..  -DEIGEN3_INCLUDE_DIR=/scratch/app/eigen/3.3_intel/include/eigen3 -DVOROPLUSPLUS_INCLUDE_DIR=/scratch/app/voro++/0.4.6_intel/include/voro++ -DVOROPLUSPLUS_LIBRARIES=/scratch/app/voro++/0.4.6_intel/lib/libvoro++.a -DTBB_INCLUDE_DIRS=/scratch/app/tbb/2018.2/include -DTBB_tbb_LIBRARY_DEBUG=/scratch/app/tbb/2018.2/lib/gcc-6/ -DTBB_tbb_LIBRARY_RELEASE=/scratch/app/tbb/2018.2/lib/gcc-6/ 

the message obtained was:

What is my mistake?

Hi @julios158

In your CMakeLists.txt:

Can you add include_directories(${SQLITE_INCLUDE_DIR}) to SQLite? So it looks like this:

# SQLite
find_package(Sqlite REQUIRED)

Run cmake and make -j again. Let me know if that fixes the issue.

Can you run make VERBOSE=1 to show a more detailed compilation output?

Hi guys! I follow your recommendation but I have same erro. The support group of Sdmunont recommend me use the follow command:

cmake -DCMAKE_BUILD_TYPE=Release ..  -DEIGEN3_INCLUDE_DIR=/scratch/app/eigen/3.3_intel/include/eigen3 -DVOROPLUSPLUS_INCLUDE_DIR=/scratch/app/voro++/0.4.6_intel/include/voro++ -DVOROPLUSPLUS_LIBRARIES=/scratch/app/voro++/0.4.6_intel/lib/libvoro++.a -DTBB_INCLUDE_DIRS=/scratch/app/tbb/2018.2/include -DTBB_tbb_LIBRARY_DEBUG=/scratch/app/tbb/2018.2/lib/gcc-6/ -DTBB_tbb_LIBRARY_RELEASE=/scratch/app/tbb/2018.2/lib/gcc-6/ -DSQLITE_INCLUDE_DIR=/scratch/app/sqlite/3.24/include -DSQLITE_LIBRARIES=/scratch/app/sqlite/3.24/lib/ -DCMAKE_CXX_FLAGS=" $CPPFLAGS" -DCMAKE_C_FLAGS=" $CPPFLAGS" -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc

I am going to try and update you if the problem is resolved.

Could you please try with the latest version of lem, which I just pushed. Please do a git pull in the develop branch to fetch the latest version of the code.

SDumont group got compile the LEM. Thanks for your help.

Could you expand on how you got it compiled? as this will help future users?

We load the follows modules:

* source /scratch/app/modulos/
* module load sqlite/3.24 boost/1.67_intel gmp/6.1.1 eigen/3.3_intel hdf5/1.8_intel cmake/3.12 gcc-6/6.2 fftw/3.3.7_intel mathlibs/intel voro++/0.4.6_intel vtk/8.1_intel tbb/2018.2_gcc-6 cuda/9.2

This command is used to compile:

* cmake -DCMAKE_BUILD_TYPE=Release ..  -DEIGEN3_INCLUDE_DIR=/scratch/app/eigen/3.3_intel/include/eigen3 -DVOROPLUSPLUS_INCLUDE_DIR=/scratch/app/voro++/0.4.6_intel/include/voro++ -DVOROPLUSPLUS_LIBRARIES=/scratch/app/voro++/0.4.6_intel/lib/libvoro++.a -DTBB_INCLUDE_DIRS=/scratch/app/tbb/2018.2/include -DTBB_tbb_LIBRARY_DEBUG=/scratch/app/tbb/2018.2/lib/gcc-6/ -DTBB_tbb_LIBRARY_RELEASE=/scratch/app/tbb/2018.2/lib/gcc-6/ -DSQLITE_INCLUDE_DIR=/scratch/app/sqlite/3.24/include -DSQLITE_LIBRARIES=/scratch/app/sqlite/3.24/lib/ -DCMAKE_CXX_FLAGS=" $CPPFLAGS" -DCMAKE_C_FLAGS=" $CPPFLAGS" -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc

Thanks, I see, the missing module was sqlite/3.24.