[gmx-users] make manual fails

[Michael Brunsteiner]

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