Problem in compiling LEM in SDumont computers

#1

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/intel-psxe-2017.sh

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.

then

  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/libtbb_debug.so -DTBB_tbb_LIBRARY_RELEASE=/scratch/app/tbb/2018.2/lib/gcc-6/libtbb.so 

the message obtained was:




What is my mistake?

#2

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)
include_directories(${SQLITE_INCLUDE_DIR})
link_libraries(${SQLITE_LIBRARIES})

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

#3

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

#4

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/libtbb_debug.so -DTBB_tbb_LIBRARY_RELEASE=/scratch/app/tbb/2018.2/lib/gcc-6/libtbb.so -DSQLITE_INCLUDE_DIR=/scratch/app/sqlite/3.24/include -DSQLITE_LIBRARIES=/scratch/app/sqlite/3.24/lib/libsqlite3.so -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.

#5

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.

#6

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

#7

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

#8

We load the follows modules:

* source /scratch/app/modulos/intel-psxe-2017.sh
* 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/libtbb_debug.so -DTBB_tbb_LIBRARY_RELEASE=/scratch/app/tbb/2018.2/lib/gcc-6/libtbb.so -DSQLITE_INCLUDE_DIR=/scratch/app/sqlite/3.24/include -DSQLITE_LIBRARIES=/scratch/app/sqlite/3.24/lib/libsqlite3.so -DCMAKE_CXX_FLAGS=" $CPPFLAGS" -DCMAKE_C_FLAGS=" $CPPFLAGS" -DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc
Errors when compiling LEM code in Savio
#9

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

closed #10