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

Thu Aug 3 03:10:59 CEST 2017

Hi,

Usually this means, like it says, that the linker isn't able to do the
required job. I don't know whether the stock RHEL 7.2 linker can, but I
imagine that's the issue. Usually using a devtoolset e.g.
https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/ is the way
to get a machine with useful tools on it rather than one with "stable" =
"old" tools, particularly when you want to use the latest hardware...

Mark

On Thu, Aug 3, 2017 at 1:28 AM Guyen Gn <guyen000 at gmail.com> wrote:

> Any update on this one??
>
> On Fri, Jul 14, 2017 at 1:30 PM, Guyen Gn <guyen000 at gmail.com> wrote:
>
> > 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_sim
> >> d_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.
> >
>
>
>
> --
> Guyen G.
> --
> 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.
>