Compile error on bright cluster

[Stefano Salvatori]

Hello 

I´m trying to compile hoomd for a bright cluster but I got some errors during the cmake and then make -j20 (according to the documentation I have all the requirements but I still have error with dependencies). 

This are the modules that I load 

[stefano@bright72 build]$ module list

Currently Loaded Modulefiles:

  1) slurm/15.08.13                        8) intel/compiler/64/16.0.4/2016.4.258  15) acml/intel/fma4/5.3.1

  2) cuda75/toolkit/7.5.18                 9) intel/mkl/mic/2017/0.098             16) python/2.7.13

  3) openmpi/gcc/64/1.10.1                10) intel/mkl/64/11.3.4/2016.4.258       17) cuda80/blas/8.0.44

  4) hdf5/1.6.10                          11) acml/open64/fma4/5.3.1               18) cuda80/fft/8.0.44

  5) fftw2/openmpi/open64/64/float/2.1.5  12) acml/intel-int64/mp/fma4/5.3.1       19) cuda80/nsight/8.0.44

  6) mpiexec/0.84_432                     13) acml/intel-int64/fma4/5.3.1          20) cuda80/profiler/8.0.44

  7) fftw2/openmpi/gcc/64/float/2.1.5     14) acml/intel/mp/fma4/5.3.1             21) cuda80/toolkit/8.0.44

Then the error running cmake

[stefano@bright72 build]$ cmake ../

-- The C compiler identification is GNU 4.4.7

-- The CXX compiler identification is GNU 4.4.7

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

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

-- Detecting C compiler ABI info

-- 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

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Configuring HOOMD v2.1.7-6-gef9cc3a

-- 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: /cm/shared/apps/openmpi/gcc/64/1.10.1/lib64/libmpi.so

-- Found MPI_CXX: /cm/shared/apps/openmpi/gcc/64/1.10.1/lib64/libmpi_cxx.so;/cm/shared/apps/openmpi/gcc/64/1.10.1/lib64/libmpi.so

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

-- Found PythonInterp: /cm/shared/apps/python/2.7.13/bin/python (found version "2.7.13")

-- Found PythonLibs: /cm/shared/apps/python/2.7.13/lib/libpython2.7.so

-- Found CUDA: /cm/shared/apps/cuda80/toolkit/8.0.44 (found suitable version "8.0", minimum required is "7.0")

-- Found Thrust: /cm/shared/apps/cuda80/toolkit/8.0.44/include (found suitable version "1.8.3", minimum required is "1.5.0")

-- Found cusolver: /cm/shared/apps/cuda80/toolkit/8.0.44/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: /cm/shared/apps/python/2.7.13/lib/python2.7/site-packages/numpy/core/include

-- Updating git submodules

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")

-- Checking for module 'sqlite3'

--   Found sqlite3, version 3.6.20

-- Found Sqlite3: /usr/lib64/libsqlite3.so

-- Found MKL: /cm/shared/apps/intel/compilers_and_libraries/2016.4.258/mkl/lib/intel64/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_LIBRARIES)

-- Configuring done

-- Generating done

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

And finally the error for make -j20 

[stefano@bright72 build]$ make -j20

-- Configuring HOOMD v2.1.7-6-gef9cc3a

-- Found cusolver: /cm/shared/apps/cuda80/toolkit/8.0.44/lib64/libcusolver.so

-- Updating git submodules

-- Checking for module 'sqlite3'

--   Found sqlite3, version 3.6.20

-- Found Sqlite3: /usr/lib64/libsqlite3.so

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

-- Could NOT find ACML (missing:  ACML_LIBRARIES)

-- Configuring done

-- Generating done

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

[  0%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/extern/cuda_compile_1_generated_mgpucontext.cu.o

[  0%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_CellListGPU.cu.o

[  3%] Built target copy_hoomd

[  4%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_BondedGroupData.cu.o

[  8%] Built target copy_cmake

[ 11%] Built target copy_md

[ 13%] Built target copy_hpmc

[ 13%] Built target copy_deprecated

[ 14%] Built target copy_dem

[ 15%] Built target copy_cgcmm

[ 14%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_CommunicatorGPU.cu.o

[ 15%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_ComputeThermoGPU.cu.o

[ 15%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_Integrator.cu.o

[ 15%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_ParticleData.cu.o

[ 15%] Built target copy_metal

[ 16%] Built target copy_example_plugin

[ 17%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_LoadBalancerGPU.cu.o

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

[ 17%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_ParticleGroup.cu.o

[ 17%] Building NVCC (Device) object hoomd/CMakeFiles/cuda_compile_1.dir/cuda_compile_1_generated_SFCPackUpdaterGPU.cu.o

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

nvcc warning : The -std=c++11 flag is not supported with the configured host compiler. Flag will be ignored.

/home/stefano/hoomd-blue/hoomd/extern/cub/cub/device/dispatch/dispatch_select_if.cuh: In function ‘void gpu_load_balance_select_off_rank(unsigned int*, unsigned int*, unsigned int*, void*, size_t&, unsigned int, unsigned int)’:

/home/stefano/hoomd-blue/hoomd/extern/cub/cub/device/dispatch/dispatch_select_if.cuh:457: warning: ‘<anonymous>’ may be used uninitialized in this function

/home/stefano/hoomd-blue/hoomd/extern/cub/cub/device/dispatch/dispatch_select_if.cuh:457: note: ‘<anonymous>’ was declared here

Scanning dependencies of target _hoomd

[ 18%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/BondedGroupData.cc.o

[ 18%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/module.cc.o

[ 18%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/BoxResizeUpdater.cc.o

[ 18%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/Analyzer.cc.o

[ 19%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/CallbackAnalyzer.cc.o

[ 19%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/Autotuner.cc.o

[ 19%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/CellList.cc.o

[ 19%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/CellListStencil.cc.o

[ 19%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/ClockSource.cc.o

cc1plus: error: unrecognized command line option "-std=c++11"

cc1plus: error: unrecognized command line option "-std=c++11"

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

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

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/Analyzer.cc.o] Error 1

[ 19%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/Communicator.cc.o

[ 20%] Building CXX object hoomd/CMakeFiles/_hoomd.dir/CommunicatorGPU.cc.o

cc1plus: error: unrecognized command line option "-std=c++11"

cc1plus: error: unrecognized command line option "-std=c++11"

cc1plus: error: unrecognized command line option "-std=c++11"

cc1plus: error: unrecognized command line option "-std=c++11"

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/Communicator.cc.o] Error 1

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/BondedGroupData.cc.o] Error 1

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/Autotuner.cc.o] Error 1

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/ClockSource.cc.o] Error 1

cc1plus: error: unrecognized command line option "-std=c++11"

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/BoxResizeUpdater.cc.o] Error 1

cc1plus: error: unrecognized command line option "-std=c++11"

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/CommunicatorGPU.cc.o] Error 1

cc1plus: error: unrecognized command line option "-std=c++11"

cc1plus: error: unrecognized command line option "-std=c++11"

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/CellListStencil.cc.o] Error 1

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/CallbackAnalyzer.cc.o] Error 1

cc1plus: error: unrecognized command line option "-std=c++11"

make[2]: *** [hoomd/CMakeFiles/_hoomd.dir/CellList.cc.o] Error 1

make[1]: *** [hoomd/CMakeFiles/_hoomd.dir/all] Error 2

make: *** [all] Error 2

[stefano@bright72 build]$

Any ideas about which module i am not loading? 

Thanks in advance 

Best regards

S.

[Joshua Anderson]

You are using GCC 4.4 which does not support C++11. The requirement as listed in the documentation is: "C++ 11 capable compiler (tested with gcc >= 4.8.5, clang 3.5)". Most clusters provide a newer version of gcc as a module, you should check on yours and try loading it.

By the way, did you know that you have both cuda 7.5 and cuda 8.0 loaded? HOOMD found 8.0, but I would suggest that you unload 7.5 to avoid possible any opportunities for confusion.

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

--
You received this message because you are subscribed to the Google Groups "hoomd-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hoomd-users+unsubscribe@googlegroups.com.
To post to this group, send email to hoomd...@googlegroups.com.
Visit this group at https://groups.google.com/group/hoomd-users.
For more options, visit https://groups.google.com/d/optout.

[Stefano Salvatori]

Hi Joshua

I change those libs but still I have some issues with ACML_LIBRARIES

[stefano@bright72 build]$ cmake ../ -DCMAKE_INSTALL_PREFIX=${SOFTWARE_ROOT}/lib/python -DCMAKE_CXX_FLAGS=-march=x86-64 -DCMAKE_C_FLAGS=-march=x86-64 -DENABLE_CUDA=ON -DENABLE_MPI=ON

-- The C compiler identification is GNU 5.2.0

-- The CXX compiler identification is GNU 5.2.0

-- Check for working C compiler: /cm/local/apps/gcc/5.2.0/bin/gcc

-- Check for working C compiler: /cm/local/apps/gcc/5.2.0/bin/gcc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

-- Check for working CXX compiler: /cm/local/apps/gcc/5.2.0/bin/g++

-- Check for working CXX compiler: /cm/local/apps/gcc/5.2.0/bin/g++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Configuring HOOMD v2.1.7-6-gef9cc3a

-- 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: /cm/shared/apps/openmpi/gcc/64/1.10.1/lib64/libmpi.so

-- Found MPI_CXX: /cm/shared/apps/openmpi/gcc/64/1.10.1/lib64/libmpi_cxx.so;/cm/shared/apps/openmpi/gcc/64/1.10.1/lib64/libmpi.so

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

-- Found PythonInterp: /cm/shared/apps/python/3.6.1/bin/python (found version "3.6.1")

-- Found PythonLibs: /cm/shared/apps/python/3.6.1/lib/libpython3.6m.so

-- Found CUDA: /cm/shared/apps/cuda80/toolkit/8.0.44 (found suitable version "8.0", minimum required is "7.0")

-- Found Thrust: /cm/shared/apps/cuda80/toolkit/8.0.44/include (found suitable version "1.8.3", minimum required is "1.5.0")

-- Found cusolver: /cm/shared/apps/cuda80/toolkit/8.0.44/lib64/libcusolver.so

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

-- Found GCC_ARCH env var, setting -march to x86-64

-- Found numpy: /cm/shared/apps/python/3.6.1/lib/python3.6/site-packages/numpy/core/include

-- Updating git submodules

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")

-- Checking for module 'sqlite3'

--   Found sqlite3, version 3.6.20

-- Found Sqlite3: /usr/lib64/libsqlite3.so

-- Found MKL: /cm/shared/apps/intel/compilers_and_libraries/2017.0.098/mkl/lib/intel64/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_LIBRARIES)

-- Configuring done

-- Generating done

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

Then during the compilation i got many deprecated messages like 

/home/stefano/hoomd-blue/hoomd/extern/kernels/../mgpuhost.cuh:796:129: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]

/cm/local/apps/gcc/5.2.0/include/c++/5.2.0/bits/unique_ptr.h:49:25: note: declared here

   template<typename> class auto_ptr;

and at the end many 

../_md.so: undefined reference to `DftiComputeForward'

../_md.so: undefined reference to `DftiSetValue'

../_md.so: undefined reference to `DftiCreateDescriptor_s_1d'

../_md.so: undefined reference to `DftiComputeBackward'

../_md.so: undefined reference to `DftiFreeDescriptor'

../_md.so: undefined reference to `DftiCommitDescriptor'

and finally an error with

[ 81%] Linking CXX shared library _hpmc.so

[ 81%] Built target _hpmc

make: *** [all] Error 2

any ideas

?

To unsubscribe from this group and stop receiving emails from it, send an email to hoomd-users...@googlegroups.com.

[Joshua Anderson]

I cannot help with MKL issues, as MKL is not used by HOOMD but by an embedded library maintained by Jens Glaser. Perhaps he can offer suggestions.

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

To unsubscribe from this group and stop receiving emails from it, send an email to hoomd-users+unsubscribe@googlegroups.com.

[Jens Glaser]

Hi,

it looks like it doesn’t link against MKL.  MKL is not needed for HOOMD, as Josh says, it is just used,

when available, to optimize MPI FFT on the CPU. We should provide a way to disable MKL explicitly.

For now, try unloading the MKL module and do a fresh cmake.

Jens

[Stefano Salvatori]

[ 96%] Built target test_faceted_sphere
[ 96%] Built target test_sphere
[ 96%] Linking CXX executable test_convex_polyhedron
[ 96%] Built target test_convex_polyhedron
[ 96%] Linking CXX executable test_sphinx
[ 96%] Built target test_sphinx
[ 97%] Linking CXX executable test_ellipsoid
[ 97%] Built target test_ellipsoid
[ 97%] Linking CXX executable test_sphere_union
[ 97%] Built target test_sphere_union
[ 98%] Linking CXX executable test_spheropolyhedron
[ 98%] Built target test_spheropolyhedron
[ 98%] Linking CXX shared library _dem.so
[ 98%] Built target _dem
[ 98%] Linking CXX executable test_polyhedron
[ 98%] Built target test_polyhedron
[100%] Linking CXX executable test_neighborlist
[100%] Built target test_neighborlist
[100%] Linking CXX executable test_communication
[100%] Built target test_communication
Scanning dependencies of target test_all
[100%] Built target test_all


It works!

Thanks you guys