[gmx-users] AVX related compiler error during build with P100 RHEL7

Fri Jul 14 22:31:11 CEST 2017

Any ideas on this one? Thanks!

On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn <guyen000 at gmail.com> wrote:

> Still did not work. change xMIC to xCore and log is below (if it was other
> way around, then originally it must have not worked).
> Script file is all oneline.
>
> -- Performing Test C_xCORE_AVX512_FLAG_WORKS
> -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed
> -- Performing Test C_mavx512f_mfma_FLAG_WORKS
> -- Performing Test C_mavx512f_mfma_FLAG_WORKS - Failed
> -- Performing Test C_mavx512f_FLAG_WORKS
> -- Performing Test C_mavx512f_FLAG_WORKS - Failed
> -- Performing Test C_arch_AVX_FLAG_WORKS
> -- Performing Test C_arch_AVX_FLAG_WORKS - Failed
> -- Performing Test C_hgnu_FLAG_WORKS
> -- Performing Test C_hgnu_FLAG_WORKS - Failed
> -- Performing Test C_FLAG_WORKS
> -- Performing Test C_FLAG_WORKS - Success
> -- Performing Test C_COMPILE_WORKS
> -- Performing Test C_COMPILE_WORKS - Failed
> -- Compiler flag was valid, but executable did not build - perhaps update
> the binutils package
> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS
> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS - Failed
> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS
> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS - Failed
> -- Performing Test CXX_mavx512f_FLAG_WORKS
> -- Performing Test CXX_mavx512f_FLAG_WORKS - Failed
> -- Performing Test CXX_arch_AVX_FLAG_WORKS
> -- Performing Test CXX_arch_AVX_FLAG_WORKS - Failed
> -- Performing Test CXX_hgnu_FLAG_WORKS
> -- Performing Test CXX_hgnu_FLAG_WORKS - Failed
> -- Performing Test CXX_FLAG_WORKS
> -- Performing Test CXX_FLAG_WORKS - Success
> -- Performing Test CXX_COMPILE_WORKS
> -- Performing Test CXX_COMPILE_WORKS - Failed
> -- Compiler flag was valid, but executable did not build - perhaps update
> the binutils package
> CMake Error at cmake/gmxManageSimd.cmake:92 (message):
>   Found a compiler flag for AVX 512F support, but some other problem
> exists.
>   Update your assembler and/or linker, e.g.  in the binutils package of
> your
>   distribution.
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:314 (gmx_give_fatal_error_when_
> simd_support_not_found)
>   CMakeLists.txt:666 (gmx_manage_simd)
>
>
> -- Configuring incomplete, errors occurred!
>
>
> On Mon, Jul 3, 2017 at 2:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn <guyen000 at gmail.com> wrote:
>>
>> > Sorry for long wait on response, basically i followed the instruction at
>> > nvidia website:
>> >
>> > http://www.nvidia.com/object/gromacs-installation.html
>> >
>> > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After
>> that
>> > it tells to run following:
>> >
>> > CC=gcc CXX=g++ cmake <GROMACS_SRC_DIR> -DGMX_OPENMP=ON -DGMX_GPU=ON -
>> > DGPU_DEPLOYMENT_KIT_ROOT_DIR=<GDK_PATH> -DGMX_BUILD_OWN_FFTW=ON -
>> > DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release -
>> > DCMAKE_INSTALL_PREFIX=<GROMACS_INSTALL_DIR>
>> >
>> > I tweaked as follows to fit my environment I setup (basically just
>> > installation source and run directory:
>> > CC=gcc CXX=g++ cmake /root/gromacs/gromacs-2016 -DGMX_OPENMP=ON
>> > -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda
>> > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON
>> > -DCMAKE_BUILD_TYPE=Release
>> > -DCMAKE_INSTALL_PREFIX=/root/gromacs/gromacs-2016-run inside build.sh
>> shell
>> > script.
>> >
>> > This is the full log, I highlighted toward the end section of code
>> where it
>> > started to fail. It appears something related to AVX. Thanks.,
>> >
>> > [root at localhost gromacs-2016]# ./build.sh
>> > CMake Error: The source directory "/root/gromacs/gromacs-2016/-" does
>> not
>> > exist.
>> > Specify --help for usage, or press the help button on the CMake GUI.
>> > ./build.sh: line 2: -DGMX_BUILD_OWN_FFTW=ON: command not found
>> > ./build.sh: line 3: -DCMAKE_BUILD_TYPE=Release: command not found
>> >
>>
>> All the above is because your script needed editing to handle newlines
>> from
>> your copy-paste.
>>
>>
>> > [root at localhost gromacs-2016]# nano -w build.sh
>> > [root at localhost gromacs-2016]# pwd
>> > /root/gromacs/gromacs-2016
>> > [root at localhost gromacs-2016]# mkdir ~/gromacs/gromacs-run
>> > [root at localhost gromacs-2016]# ./build.sh
>> > -- The C compiler identification is GNU 4.8.5
>> > -- The CXX compiler identification is GNU 4.8.5
>> > -- Check for working C compiler: /usr/bin/gcc
>> > -- Check for working C compiler: /usr/bin/gcc -- works
>> > -- Detecting C compiler ABI info
>> > -- Detecting C compiler ABI info - done
>> > -- Check for working CXX compiler: /usr/bin/g++
>> > -- Check for working CXX compiler: /usr/bin/g++ -- works
>> > -- Detecting CXX compiler ABI info
>> > -- Detecting CXX compiler ABI info - done
>> > -- 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: 2
>> > -- Found CUDA: /usr/local/cuda (found suitable version "8.0", minimum
>> > required is "5.0")
>> > -- Could NOT find NVML (missing:  NVML_INCLUDE_DIR)
>> > -- Checking for GCC x86 inline asm
>> > -- Checking for GCC x86 inline asm - supported
>> > -- Detecting best SIMD instructions for this CPU
>> > -- Detected best SIMD instructions for this CPU - AVX_512
>> > -- Try OpenMP C flag = [-fopenmp]
>> > -- Performing Test OpenMP_FLAG_DETECTED
>> > -- Performing Test OpenMP_FLAG_DETECTED - Success
>> > -- Try OpenMP CXX flag = [-fopenmp]
>> > -- Performing Test OpenMP_FLAG_DETECTED
>> > -- Performing Test OpenMP_FLAG_DETECTED - Success
>> > -- Found OpenMP: -fopenmp
>> > -- 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
>> > -- 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
>> > Searching for static libraries requested, so the GROMACS libraries will
>> > also be static (BUILD_SHARED_LIBS=OFF)
>> > -- Could NOT find Hwloc (missing:  HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS)
>> > (Required is at least version "1.5")
>> > -- Looking for include file pthread.h
>> > -- Looking for include file 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
>> > -- Looking for include file pthread.h
>> > -- Looking for include file pthread.h - found
>> > -- Atomic operations found
>> > -- Performing Test PTHREAD_SETAFFINITY
>> > -- Performing Test PTHREAD_SETAFFINITY - Success
>> > -- 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
>> > -- Enabling single compilation unit for the CUDA non-bonded module.
>> > Multiple compilation units are not compatible with CC 2.x devices, to
>> > enable the feature specify only CC >=3.0 target architectures in
>> > GMX_CUDA_TARGET_SM/GMX_CUDA_TARGET_COMPUTE.
>> > -- Setting build user/date/host/cpu information
>> > -- Setting build user & time - OK
>> > -- 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
>> > -- Performing Test C_xMIC_AVX512_FLAG_WORKS
>>
>>
>> Aha. This is a known issue that we have fixed, but not yet made available
>> in a released version. When we wrote this code, we had no Skylake machines
>> to test on. See
>> https://gerrit.gromacs.org/c/6570/2/cmake/gmxManageSimd.cmake for the
>> form
>> of the fix. You can simply edit that single line in
>> cmake/gmxManageSimd.cmake in your source directory and all will be fine -
>> maybe a fresh build directory will help.
>>
>> Mark
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Guyen G.
>

-- 
Guyen G.