having difficulties building hoomd

[julian...@gmail.com]

hi,

I'm trying to build hoomd with gpu enabled, but I am having difficulties doing so. The error seems to be with CUDA

~/hoomd-blue/build-gpu$ cmake -ENABLE_MPI_CUDA=ON ../ -DCMAKE_INSTALL_PREFIX=${SOFTWARE_ROOT}/lib/python
-- Configuring HOOMD v2.1.0-1-g1494322
-- Updating git submodules
-- Found Sqlite3: /usr/lib/x86_64-linux-gnu/libsqlite3.so
-- Could NOT find MKL (missing:  MKL_LIBRARIES MKL_INCLUDE_DIR)
-- Multi-threaded library not found, looking for single-threaded
-- Could NOT find ACML (missing:  ACML_INCLUDES ACML_LIBRARIES)
-- No CPU FFT library found, falling back on SLOW internal radix-2 FFT
-- Configuring done
-- Generating done
-- Build files have been written to: /home/labuser/hoomd-blue/build-gpu
labuser@calculon:~/hoomd-blue/build-gpu$ make -j20
[  1%] Copy hoomd/CMake/hoomd/HOOMDCommonLibsSetup.cmake
[  2%] Built target copy_deprecated
[  3%] Built target copy_dem
[  2%] Copy hoomd/CMake/libgetar/Findlibgetar.cmake
[  2%] Copy hoomd/CMake/git/GetGitRevisionDescription.cmake
[  2%] Copy hoomd/CMake/hoomd/HOOMDCFlagsSetup.cmake
[  3%] Built target copy_cgcmm
[  3%] Copy hoomd/CMake/git/FindGit.cmake
[  4%] Copy hoomd/CMake/hoomd/HOOMDNumpySetup.cmake
[  4%] Copy hoomd/CMake/hoomd/HOOMDMPISetup.cmake
[  4%] Copy hoomd/CMake/thrust/FindThrust.cmake
[  7%] Built target copy_hoomd
[  7%] Copy hoomd/CMake/hoomd/HOOMDPythonSetup.cmake
[  7%] Copy hoomd/CMake/hoomd/HOOMDCUDASetup.cmake
[  7%] Built target copy_metal
[  7%] Copy hoomd/CMake/hoomd/HOOMDMacros.cmake
[  7%] Copy hoomd/CMake/hoomd/HOOMDOSSpecificSetup.cmake
[  7%] Copy hoomd/CMake_build_options.cmake
[  8%] Built target copy_example_plugin
[  8%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CellListGPU.cu.o
[ 11%] Built target copy_md
[ 13%] Built target copy_hpmc
[ 13%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/extern/cuda_compile_generated_mgpucontext.cu.o
[ 14%] Copy hoomd/CMake_src_setup.cmake
[ 14%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleData.cu.o
[ 14%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CommunicatorGPU.cu.o
[ 14%] Copy hoomd/CMake_install_options.cmake
[ 14%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_SFCPackUpdaterGPU.cu.o
[ 15%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_LoadBalancerGPU.cu.o
[ 16%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_BondedGroupData.cu.o
[ 16%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ComputeThermoGPU.cu.o
[ 16%] Copy hoomd/CMake_version_options.cmake
[ 16%] Copy hoomd/CMake_preprocessor_flags.cmake
[ 16%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleGroup.cu.o
[ 16%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_Integrator.cu.o
[ 16%] Built target copy_cmake
/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_00004112_00000000-16_ParticleGroup.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_ParticleGroup.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_ParticleGroup.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:3550: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleGroup.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleGroup.cu.o] Error 1
make[2]: *** Waiting for unfinished jobs....
/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_0000413e_00000000-16_CellListGPU.compute_50.cpp1.ii".
/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_00004117_00000000-16_Integrator.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_CellListGPU.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_CellListGPU.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:758: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CellListGPU.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CellListGPU.cu.o] Error 1
CMake Error at cuda_compile_generated_Integrator.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_Integrator.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:2125: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_Integrator.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_Integrator.cu.o] Error 1
2 errors detected in the compilation of "/tmp/tmpxft_00004126_00000000-16_mgpucontext.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_mgpucontext.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir/extern/./cuda_compile_generated_mgpucontext.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:4221: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/extern/cuda_compile_generated_mgpucontext.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/extern/cuda_compile_generated_mgpucontext.cu.o] Error 1
2 errors detected in the compilation of "/tmp/tmpxft_00004120_00000000-16_SFCPackUpdaterGPU.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_SFCPackUpdaterGPU.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_SFCPackUpdaterGPU.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:3896: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_SFCPackUpdaterGPU.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_SFCPackUpdaterGPU.cu.o] Error 1
/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_00004149_00000000-16_LoadBalancerGPU.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_LoadBalancerGPU.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_LoadBalancerGPU.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:2571: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_LoadBalancerGPU.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_LoadBalancerGPU.cu.o] Error 1
2 errors detected in the compilation of "/tmp/tmpxft_00004131_00000000-16_ComputeThermoGPU.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_ComputeThermoGPU.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_ComputeThermoGPU.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:1795: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ComputeThermoGPU.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ComputeThermoGPU.cu.o] Error 1
2 errors detected in the compilation of "/tmp/tmpxft_00004157_00000000-16_BondedGroupData.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_BondedGroupData.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_BondedGroupData.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:407: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_BondedGroupData.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_BondedGroupData.cu.o] Error 1
/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_00004164_00000000-16_ParticleData.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_ParticleData.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_ParticleData.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:3208: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleData.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleData.cu.o] Error 1
2 errors detected in the compilation of "/tmp/tmpxft_00004173_00000000-16_CommunicatorGPU.compute_50.cpp1.ii".
CMake Error at cuda_compile_generated_CommunicatorGPU.cu.o.cmake:266 (message):
  Error generating file
  /home/labuser/hoomd-blue/build-gpu/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_CommunicatorGPU.cu.o


hoomd/CMakeFiles/_hoomd.dir/build.make:1464: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CommunicatorGPU.cu.o' failed
make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CommunicatorGPU.cu.o] Error 1
CMakeFiles/Makefile2:409: recipe for target 'hoomd/CMakeFiles/_hoomd.dir/all' failed
make[1]: *** [hoomd/CMakeFiles/_hoomd.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2

[Nando V]

I am getting very similar error. Compiling with Ubuntu the 2.1.7 version of HOOMD in single precision.

After make -j20:

make -j20

Scanning dependencies of target copy_metal

Scanning dependencies of target copy_hoomd

Scanning dependencies of target copy_md

Scanning dependencies of target copy_cmake

[  1%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_BondedGroupData.cu.o

Scanning dependencies of target copy_dem

[  1%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_Integrator.cu.o

[  1%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ComputeThermoGPU.cu.o

[  1%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleData.cu.o

[  1%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_SFCPackUpdaterGPU.cu.o

Scanning dependencies of target copy_example_plugin

Scanning dependencies of target copy_deprecated

Scanning dependencies of target copy_hpmc

[  1%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/extern/cuda_compile_generated_mgpucontext.cu.o

[  2%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_LoadBalancerGPU.cu.o

[  2%] Copy hoomd/benchmark.py

[  2%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CellListGPU.cu.o

[  2%] Copy hoomd/analyze.py

Scanning dependencies of target copy_cgcmm

[  2%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleGroup.cu.o

[  2%] Copy hoomd/CMake/hoomd/HOOMDCFlagsSetup.cmake

[  2%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CommunicatorGPU.cu.o

[  3%] Copy hoomd/example_plugin/__init__.py

[  3%] Copy hoomd/metal/__init__.py

[  3%] Copy hoomd/dem/__init__.py

[  3%] Copy hoomd/md/__init__.py

[  4%] Copy hoomd/cgcmm/__init__.py

[  5%] Copy hoomd/hpmc/analyze.py

[  5%] Copy hoomd/dem/pair.py

[  5%] Copy hoomd/cite.py

[  5%] Copy hoomd/deprecated/__init__.py

[  5%] Copy hoomd/example_plugin/update.py

[  5%] Copy hoomd/CMake/hoomd/HOOMDCommonLibsSetup.cmake

[  5%] Copy hoomd/deprecated/analyze.py

[  5%] Copy hoomd/dem/params.py

[  5%] Copy hoomd/metal/pair.py

[  5%] Copy hoomd/deprecated/dump.py

[  6%] Copy hoomd/comm.py

[  6%] Copy hoomd/md/angle.py

[  7%] Copy hoomd/CMake/hoomd/HOOMDCUDASetup.cmake

[  7%] Copy hoomd/cgcmm/angle.py

[  7%] Built target copy_example_plugin

[  7%] Copy hoomd/CMake/hoomd/test.cc

[  7%] Built target copy_metal

[  7%] Copy hoomd/md/charge.py

[  7%] Copy hoomd/compute.py

[  7%] Copy hoomd/CMake/hoomd/HOOMDMacros.cmake

[  8%] Copy hoomd/dem/utils.py

[  8%] Copy hoomd/md/constrain.py

[  8%] Copy hoomd/cgcmm/pair.py

[  8%] Copy hoomd/deprecated/init.py

[  8%] Copy hoomd/hpmc/compute.py

[  8%] Built target copy_deprecated

[  9%] Copy hoomd/CMake/hoomd/HOOMDNumpySetup.cmake

[ 10%] Copy hoomd/md/bond.py

[ 10%] Copy hoomd/CMake/hoomd/HOOMDPythonSetup.cmake

[ 10%] Copy hoomd/CMake/hoomd/HOOMDMPISetup.cmake

[ 10%] Copy hoomd/md/dihedral.py

[ 10%] Copy hoomd/dump.py

[ 10%] Copy hoomd/hpmc/data.py

[ 10%] Copy hoomd/data.py

[ 10%] Copy hoomd/context.py

[ 10%] Built target copy_cgcmm

[ 10%] Copy hoomd/__init__.py

[ 10%] Built target copy_dem

[ 10%] Copy hoomd/md/external.py

[ 11%] Copy hoomd/group.py

[ 11%] Copy hoomd/CMake/hoomd/HOOMDOSSpecificSetup.cmake

[ 12%] Copy hoomd/hpmc/update.py

[ 13%] Copy hoomd/md/force.py

[ 13%] Copy hoomd/hpmc/__init__.py

[ 13%] Copy hoomd/md/improper.py

[ 13%] Copy hoomd/hpmc/integrate.py

[ 13%] Copy hoomd/init.py

[ 13%] Copy hoomd/CMake/git/FindGit.cmake

[ 14%] Copy hoomd/option.py

[ 14%] Copy hoomd/meta.py

[ 14%] Copy hoomd/integrate.py

[ 14%] Copy hoomd/hpmc/util.py

[ 14%] Copy hoomd/CMake/git/GetGitRevisionDescription.cmake

[ 14%] Copy hoomd/hpmc/field.py

[ 15%] Copy hoomd/CMake/libgetar/Findlibgetar.cmake

[ 15%] Copy hoomd/md/integrate.py

[ 15%] Copy hoomd/CMake/thrust/FindThrust.cmake

[ 15%] Copy hoomd/md/nlist.py

[ 15%] Copy hoomd/update.py

[ 15%] Copy hoomd/md/pair.py

[ 15%] Copy hoomd/variant.py

[ 15%] Copy hoomd/lattice.py

[ 15%] Copy hoomd/util.py

[ 15%] Copy hoomd/md/wall.py

[ 15%] Copy hoomd/md/special_pair.py

[ 15%] Copy hoomd/CMake_version_options.cmake

[ 16%] Copy hoomd/CMake_src_setup.cmake

[ 16%] Built target copy_hpmc

[ 17%] Copy hoomd/md/update.py

[ 17%] Copy hoomd/CMake_preprocessor_flags.cmake

[ 17%] Copy hoomd/CMake_install_options.cmake

[ 17%] Copy hoomd/CMake_build_options.cmake

[ 17%] Built target copy_hoomd

[ 17%] Built target copy_md

[ 17%] Built target copy_cmake

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_000025c7_00000000-13_CellListGPU.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_CellListGPU.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_CellListGPU.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:70: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CellListGPU.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CellListGPU.cu.o] Error 1

make[2]: *** Waiting for unfinished jobs....

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_000025d9_00000000-13_ComputeThermoGPU.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_ComputeThermoGPU.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_ComputeThermoGPU.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:84: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ComputeThermoGPU.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ComputeThermoGPU.cu.o] Error 1

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_000025d5_00000000-13_ParticleGroup.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_ParticleGroup.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_ParticleGroup.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:112: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleGroup.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleGroup.cu.o] Error 1

2 errors detected in the compilation of "/tmp/tmpxft_000025f1_00000000-13_mgpucontext.compute_50.cpp1.ii".

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

CMake Error at cuda_compile_generated_mgpucontext.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir/extern/./cuda_compile_generated_mgpucontext.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:126: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/extern/cuda_compile_generated_mgpucontext.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/extern/cuda_compile_generated_mgpucontext.cu.o] Error 1

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_000025fc_00000000-13_Integrator.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_Integrator.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_Integrator.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:91: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_Integrator.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_Integrator.cu.o] Error 1

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(36): error: identifier "__builtin_ia32_monitorx" is undefined

/usr/lib/gcc/x86_64-linux-gnu/5/include/mwaitxintrin.h(42): error: identifier "__builtin_ia32_mwaitx" is undefined

2 errors detected in the compilation of "/tmp/tmpxft_0000260c_00000000-13_BondedGroupData.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_BondedGroupData.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_BondedGroupData.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:63: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_BondedGroupData.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_BondedGroupData.cu.o] Error 1

2 errors detected in the compilation of "/tmp/tmpxft_000025e7_00000000-13_SFCPackUpdaterGPU.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_SFCPackUpdaterGPU.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_SFCPackUpdaterGPU.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:119: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_SFCPackUpdaterGPU.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_SFCPackUpdaterGPU.cu.o] Error 1

2 errors detected in the compilation of "/tmp/tmpxft_00002618_00000000-13_LoadBalancerGPU.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_LoadBalancerGPU.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_LoadBalancerGPU.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:98: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_LoadBalancerGPU.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_LoadBalancerGPU.cu.o] Error 1

2 errors detected in the compilation of "/tmp/tmpxft_00002605_00000000-13_ParticleData.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_ParticleData.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_ParticleData.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:105: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleData.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_ParticleData.cu.o] Error 1

2 errors detected in the compilation of "/tmp/tmpxft_00002629_00000000-13_CommunicatorGPU.compute_50.cpp1.ii".

CMake Error at cuda_compile_generated_CommunicatorGPU.cu.o.Release.cmake:267 (message):

  Error generating file

  /home/nando/compileHOOMD/hoomd-blue/build/hoomd/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_CommunicatorGPU.cu.o

hoomd/CMakeFiles/_hoomd.dir/build.make:77: recipe for target 'hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CommunicatorGPU.cu.o' failed

make[2]: *** [hoomd/CMakeFiles/cuda_compile.dir/cuda_compile_generated_CommunicatorGPU.cu.o] Error 1

CMakeFiles/Makefile2:446: recipe for target 'hoomd/CMakeFiles/_hoomd.dir/all' failed

[Nando V]

In my case, the configure was:

cmake ../ -DCMAKE_INSTALL_PREFIX=${SOFTWARE_ROOT}/lib/python -SINGLE_PRECISION=ON

-- The C compiler identification is GNU 5.4.0

-- The CXX compiler identification is GNU 5.4.0

-- Check for working C compiler: /usr/bin/cc

-- Check for working C compiler: /usr/bin/cc -- works

-- Detecting C compiler ABI info

-- Checking if C linker supports --verbose

-- Checking if C linker supports --verbose - yes

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

-- Check for working CXX compiler: /usr/bin/c++

-- Check for working CXX compiler: /usr/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Checking if CXX linker supports --verbose

-- Checking if CXX linker supports --verbose - yes

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Configuring HOOMD v2.1.7

-- Looking for pthread.h

-- Looking for pthread.h - found

-- Looking for pthread_create

-- Looking for pthread_create - not found

-- Looking for pthread_create in pthreads

-- Looking for pthread_create in pthreads - not found

-- Looking for pthread_create in pthread

-- Looking for pthread_create in pthread - found

-- Found Threads: TRUE

-- Found MPI_C: /home/nando/miniconda2/lib/libmpich.so;/home/nando/miniconda2/lib/libopa.so;/home/nando/miniconda2/lib/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so

-- Found MPI_CXX: /home/nando/miniconda2/lib/libmpichcxx.so;/home/nando/miniconda2/lib/libmpich.so;/home/nando/miniconda2/lib/libopa.so;/home/nando/miniconda2/lib/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/x86_64-linux-gnu/libpthread.so

-- MPI<->CUDA interoperability does not appear to be available.

-- Found PythonInterp: /home/nando/miniconda2/bin/python (found version "2.7.13")

-- Found PythonLibs: /home/nando/miniconda2/lib/libpython2.7.so

-- Found CUDA: /usr/local/cuda-7.5 (found suitable version "7.5", minimum required is "7.0")

-- Found Thrust: /usr/local/cuda-7.5/include (found suitable version "1.8.2", minimum required is "1.5.0")

-- Found cusolver: /usr/local/cuda-7.5/lib64/libcusolver.so

-- Overriding CMake's default CFLAGS (this should appear only once)

-- GCC_ARCH env var not set, setting -march to native

-- Found numpy: /home/nando/miniconda2/lib/python2.7/site-packages/numpy/core/include

-- Updating git submodules

-- Found PkgConfig: /home/nando/miniconda2/bin/pkg-config (found version "0.28")

-- Checking for module 'sqlite3'

--   Found sqlite3, version 3.13.0

-- Found Sqlite3: /home/nando/miniconda2/lib/libsqlite3.so

-- Found MKL: /home/nando/miniconda2/lib/libmkl_rt.so;mkl_intel_ilp64;mkl_intel_thread;mkl_core;pthread;m

-- Multi-threaded library not found, looking for single-threaded

-- Could NOT find ACML (missing:  ACML_INCLUDES ACML_LIBRARIES)

-- Configuring done

-- Generating done

-- Build files have been written to: /home/nando/compileHOOMD/hoomd-blue/build

[Joshua Anderson]

CUDA 7.5 does not support gcc 5.4. Either upgrade to CUDA 8.0 or use gcc 4.x: https://stackoverflow.com/questions/34996295/trying-to-get-cuda-7-5-to-work-with-gcc-5-x

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
http://www-personal.umich.edu/~joaander/

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[Nando V]

Thank you Joshua, that partially fixed my problem.

Now the make step complains about the mkl library:

[ 52%] Building CXX object hoomd/md/CMakeFiles/_md.dir/ActiveForceCompute.cc.o

In file included from /home/nando/compileHOOMD/hoomd-blue/hoomd/extern/dfftlib/src/dfft_local_fft_config.h:12:0,

                 from /home/nando/compileHOOMD/hoomd-blue/hoomd/extern/dfftlib/src/dfft_common.h:9,

                 from /home/nando/compileHOOMD/hoomd-blue/hoomd/extern/dfftlib/src/dfft_host.h:11,

                 from /home/nando/compileHOOMD/hoomd-blue/hoomd/md/PPPMForceCompute.h:13,

                 from /home/nando/compileHOOMD/hoomd-blue/hoomd/md/module-md.cc:41:

/home/nando/compileHOOMD/hoomd-blue/hoomd/extern/dfftlib/src/mkl_single_interface.h:8:17: fatal error: mkl.h: No such file or directory

compilation terminated.

hoomd/md/CMakeFiles/_md.dir/build.make:314: recipe for target 'hoomd/md/CMakeFiles/_md.dir/module-md.cc.o' failed

make[2]: *** [hoomd/md/CMakeFiles/_md.dir/module-md.cc.o] Error 1

But this I already installed through conda:

$ conda install mkl

Fetching package metadata ...........

Solving package specifications: .

# All requested packages already installed.

# packages in environment at /home/nando/miniconda2:

#

mkl                       2017.0.1                      0

Even though I can see that the config step seems to detect it in the previous step:

$ cmake ../ -DCMAKE_INSTALL_PREFIX=${SOFTWARE_ROOT}/lib/python

-- Found CUDA: /usr/local/cuda-8.0 (found suitable version "8.0", minimum required is "7.0")

-- Found Thrust: /usr/local/cuda-8.0/include (found suitable version "1.8.3", minimum required is "1.5.0")

-- Found cusolver: /usr/local/cuda-8.0/lib64/libcusolver.so

-- Overriding CMake's default CFLAGS (this should appear only once)

-- GCC_ARCH env var not set, setting -march to native

-- Found numpy: /home/nando/miniconda2/lib/python2.7/site-packages/numpy/core/include

-- Updating git submodules

-- Found PkgConfig: /home/nando/miniconda2/bin/pkg-config (found version "0.28")

-- Checking for module 'sqlite3'

--   Found sqlite3, version 3.13.0

-- Found Sqlite3: /home/nando/miniconda2/lib/libsqlite3.so

-- Found MKL: /home/nando/miniconda2/lib/libmkl_rt.so;mkl_intel_ilp64;mkl_intel_thread;mkl_core;pthread;m

-- Multi-threaded library not found, looking for single-threaded

-- Could NOT find ACML (missing:  ACML_INCLUDES ACML_LIBRARIES)

-- Configuring done

-- Generating done

-- Build files have been written to: /home/nando/compileHOOMD/hoomd-blue/build

I hope you can enlighten me once again.

Thank you!

[Julian Cuevas-Zepeda]

I currently have the same issue. I'm wondering if you ever figured out how to fix it?

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[Nando V]

Hi Julian,

I still can't solve it, so I'm stuck to HOOMD 1.3.3 (I would love to use the newest version, but the binary comes only in double precision, so I need to compile it to get single).

The issue seems to be with the miniconda. Compiler cannot find the mkl.h library.

Usually, it should be in miniconda directory/include, but its not there

Only mkl I can find are in the minicondadirectory/lib, but those are the libmkl_avx2.so type

Then, when calling ccmake I can't put the correct paths for:

 MKL_INCLUDE_DIR                 ------

 MKL_LIBRARIES                    /home/nando/miniconda2/lib/libmkl_rt.so

I found some information in other forums, but still cant solve it:

https://github.com/BVLC/caffe/issues/3884

http://debugjournal.tumblr.com/post/98401758462/intel-mkl-dynamic-link-library-error

https://github.com/dmlc/mxnet/issues/928

Any idea?

[Joshua Anderson]

This has been discussed on the mailing list before: see the solution in https://groups.google.com/forum/#!searchin/hoomd-users/MKL|sort:relevance/hoomd-users/wexjoqNElTY/ESLjJLNOEQAJ for full details.

Configure with: -DMKL_LIBRARIES="" to disable the MKL library.

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
http://www-personal.umich.edu/~joaander/

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