thanks Szilard for the reply! below is the output of the cmake and make command, i doesn't find sphinx, but then i doesn't seem to look for it either ...anyway, on this second attempt I get a different error, no idea why, only diff: the first time i first made gromacsand only then the manual, this time i made the manual direcctly after the cmake command. see below,looks as if my sphinx version (1.8.4-1) misses something ... but then i guess this is a minor issue, what i tryto make here is an exact copy of the online version, isn't it?mic
prompt> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=gcc-7 -DCMAKE_CXX_COMPILER=g++-7 -DGMX_GPU=on -DCMAKE_INSTALL_PREFIX=/home/michael/local/gromacs-2019-3-bin -DGMX_BUILD_MANUAL=on-- The C compiler identification is GNU 7.4.0 -- The CXX compiler identification is GNU 7.4.0 -- Check for working C compiler: /usr/bin/gcc-7 -- Check for working C compiler: /usr/bin/gcc-7 -- 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/g++-7 -- Check for working CXX compiler: /usr/bin/g++-7 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- 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 -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Number of NVIDIA GPUs detected: 1 -- Found CUDA: /usr/local/cuda (found suitable version "10.0", minimum required is "7.0") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: -- Found Hwloc: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable version "1.11.6", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Adding work-around for issue compiling CUDA code with glibc 2.23 string.h -- Check for working NVCC/C++ compiler combination with nvcc '/usr/local/cuda/bin/nvcc' -- Check for working NVCC/C++ compiler combination - works -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz -- Detected build CPU family - 6 -- Detected build CPU model - 45 -- Detected build CPU stepping - 7 -- Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Enabling RDTSCP support - detected on the build host -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- Detecting best SIMD instructions for this CPU -- Detected best SIMD instructions for this CPU - AVX_256 -- Performing Test C_mavx_FLAG_ACCEPTED -- Performing Test C_mavx_FLAG_ACCEPTED - Success -- Performing Test C_mavx_COMPILE_WORKS -- Performing Test C_mavx_COMPILE_WORKS - Success -- Performing Test CXX_mavx_FLAG_ACCEPTED -- Performing Test CXX_mavx_FLAG_ACCEPTED - Success -- Performing Test CXX_mavx_COMPILE_WORKS -- Performing Test CXX_mavx_COMPILE_WORKS - Success -- Enabling 256-bit AVX SIMD instructions using CXX flags: -mavx -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test C_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test C_mavx512f_mfma_FLAG_ACCEPTED - Success -- Performing Test C_mavx512f_mfma_COMPILE_WORKS -- Performing Test C_mavx512f_mfma_COMPILE_WORKS - Success -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_qopt_zmm_usage_high_FLAG_ACCEPTED - Failed -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED -- Performing Test CXX_xCORE_AVX512_FLAG_ACCEPTED - Failed -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED -- Performing Test CXX_mavx512f_mfma_FLAG_ACCEPTED - Success -- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS -- Performing Test CXX_mavx512f_mfma_COMPILE_WORKS - Success -- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -mavx512f -mfma -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED -- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Failed -- Performing Test _callconv___regcall -- Performing Test _callconv___regcall - Failed -- Performing Test _callconv_ -- Performing Test _callconv_ - Success -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;--enable-avx;--enable-avx2;--enable-avx512 -- Using external FFT library - FFTW3 build managed by GROMACS -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.16", minimum required is "2.7") -- Found LATEX: /usr/bin/latex -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /home/michael/local/gromacs-2019.3/build prompt> make manual[...][ 96%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o [ 96%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o [ 97%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o [ 97%] Linking CXX shared library ../../lib/libgromacs.so [ 97%] Built target libgromacs Scanning dependencies of target view_objlib [ 97%] Building CXX object src/programs/CMakeFiles/view_objlib.dir/view/view.cpp.o [ 97%] Built target view_objlib Scanning dependencies of target gmx [ 98%] Building CXX object src/programs/CMakeFiles/gmx.dir/gmx.cpp.o [ 98%] Building CXX object src/programs/CMakeFiles/gmx.dir/legacymodules.cpp.o [ 98%] Linking CXX executable ../../bin/gmx [ 98%] Built target gmx Scanning dependencies of target sphinx-programs [ 98%] Generating reStructuredText help [ 98%] Built target sphinx-programs Scanning dependencies of target pdf [100%] Preparing PDF manual LaTeX input files Configuration error: There is a programmable error in your configuration file: Traceback (most recent call last): File "/usr/lib/python3/dist-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/usr/lib/python3/dist-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/michael/local/gromacs-2019.3/build/docs/sphinx-input/conf.py", line 53, in <module> execfile('conf-vars.py') NameError: name 'execfile' is not defined -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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