[gmx-users] [gmx-developers] GTX 680 non detected on OS X

Mark Abraham mark.j.abraham at gmail.com
Thu May 26 21:12:34 CEST 2016


Hi,

Is clang 3.8 supported by CUDA on Mac?

Mark

On Thu, 26 May 2016 21:05 Uliano Guerrini <uliano.guerrini at unimi.it> wrote:

> here is part of the log:
>
> GROMACS version:    VERSION 5.1.2
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:        enabled
> OpenCL support:     disabled
> invsqrt routine:    gmx_software_invsqrt(x)
> SIMD instructions:  SSE4.1
> FFT library:        fftw-3.3.4-sse2-avx
> RDTSCP usage:       enabled
> C++11 compilation:  disabled
> TNG support:        enabled
> Tracing support:    disabled
> Built on:           Gio 26 Mag 2016 20:29:04 CEST
> Built by:           uliano at MacPro.lan [CMAKE]
> Build OS/arch:      Darwin 15.5.0 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:    Intel(R) Xeon(R) CPU           W3680  @ 3.33GHz
> Build CPU family:   6   Model: 44   Stepping: 2
> Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
> sse4.2 ssse3
> C compiler:         /opt/local/bin/clang Clang 3.8.0
> C compiler flags:    -msse4.1    -Wall -Wno-unused -Wunused-value
> -Wunused-parameter  -O3 -DNDEBUG
> C++ compiler:       /opt/local/bin/clang++ Clang 3.8.0
> C++ compiler flags:  -msse4.1    -Wextra -Wno-missing-field-initializers
> -Wpointer-arith -Wall -Wno-unused-function  -O3 -DNDEBUG
> Boost version:      1.55.0 (internal)
> CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
> compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
> Mon_Apr_11_13:23:40_CDT_2016;Cuda compilation tools, release 7.5, V7.5.26
> CUDA compiler
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_52,code=compute_52;-use_fast_math;;
> ;-msse4.1;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;
> CUDA driver:        0.0
> CUDA runtime:       0.0
>
>
> NOTE: Error occurred during GPU detection:
>       CUDA driver version is insufficient for CUDA runtime version
>       Can not use GPU acceleration, will fall back to CPU kernels.
>
> regarding osx equivalent of ldd I found otool -L
>
> uliano at MacPro:/opt/gromacs/bin$ otool -L gmx
> gmx:
>         @rpath/libgromacs.1.dylib (compatibility version 1.0.0, current
> version 1.2.0)
>         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1226.10.1)
>         /opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current
> version 1.2.8)
>         /opt/local/lib/libfftw3f.3.dylib (compatibility version 8.0.0,
> current version 8.4.0)
>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> (compatibility version 1.0.0, current version 4.0.0)
>         /opt/local/lib/libomp/libomp.dylib (compatibility version 5.0.0,
> current version 5.0.0)
>         /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current
> version 120.1.0)
>
> and
>
> uliano at MacPro:/opt/gromacs/lib$ otool -L libgromacs.1.dylib
> libgromacs.1.dylib:
>         @rpath/libgromacs.1.dylib (compatibility version 1.0.0, current
> version 1.2.0)
>         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 1226.10.1)
>         /opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current
> version 1.2.8)
>         /opt/local/lib/libfftw3f.3.dylib (compatibility version 8.0.0,
> current version 8.4.0)
>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> (compatibility version 1.0.0, current version 4.0.0)
>         /opt/local/lib/libomp/libomp.dylib (compatibility version 5.0.0,
> current version 5.0.0)
>         /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current
> version 120.1.0)
>
> no sign of cuda here, however cmake did find it
>
> ...
> -- Found CUDA: /usr/local/cuda (found suitable version "7.5", minimum
> required is "4.0”)
>>
> and the build process didn’t gave any error
>
> here is a report of export DYLD_PRINT_LIBRARIES=TRUE that prints libraries
> as they are loaded
>
> uliano at MacPro:~/demo$ /opt/gromacs/bin/gmx mdrun -v -deffnm md_0_1
> dyld: loaded: /opt/gromacs/bin/gmx
> dyld: loaded: /opt/gromacs/bin/../lib/libgromacs.1.dylib
> dyld: loaded: /usr/lib/libSystem.B.dylib
> dyld: loaded: /opt/local/lib/libz.1.dylib
> dyld: loaded: /opt/local/lib/libfftw3f.3.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> dyld: loaded: /opt/local/lib/libomp/libomp.dylib
> dyld: loaded: /usr/lib/libc++.1.dylib
> dyld: loaded: /usr/lib/system/libcache.dylib
> dyld: loaded: /usr/lib/system/libcommonCrypto.dylib
> dyld: loaded: /usr/lib/system/libcompiler_rt.dylib
> dyld: loaded: /usr/lib/system/libcopyfile.dylib
> dyld: loaded: /usr/lib/system/libcorecrypto.dylib
> dyld: loaded: /usr/lib/system/libdispatch.dylib
> dyld: loaded: /usr/lib/system/libdyld.dylib
> dyld: loaded: /usr/lib/system/libkeymgr.dylib
> dyld: loaded: /usr/lib/system/liblaunch.dylib
> dyld: loaded: /usr/lib/system/libmacho.dylib
> dyld: loaded: /usr/lib/system/libquarantine.dylib
> dyld: loaded: /usr/lib/system/libremovefile.dylib
> dyld: loaded: /usr/lib/system/libsystem_asl.dylib
> dyld: loaded: /usr/lib/system/libsystem_blocks.dylib
> dyld: loaded: /usr/lib/system/libsystem_c.dylib
> dyld: loaded: /usr/lib/system/libsystem_configuration.dylib
> dyld: loaded: /usr/lib/system/libsystem_coreservices.dylib
> dyld: loaded: /usr/lib/system/libsystem_coretls.dylib
> dyld: loaded: /usr/lib/system/libsystem_dnssd.dylib
> dyld: loaded: /usr/lib/system/libsystem_info.dylib
> dyld: loaded: /usr/lib/system/libsystem_kernel.dylib
> dyld: loaded: /usr/lib/system/libsystem_m.dylib
> dyld: loaded: /usr/lib/system/libsystem_malloc.dylib
> dyld: loaded: /usr/lib/system/libsystem_network.dylib
> dyld: loaded: /usr/lib/system/libsystem_networkextension.dylib
> dyld: loaded: /usr/lib/system/libsystem_notify.dylib
> dyld: loaded: /usr/lib/system/libsystem_platform.dylib
> dyld: loaded: /usr/lib/system/libsystem_pthread.dylib
> dyld: loaded: /usr/lib/system/libsystem_sandbox.dylib
> dyld: loaded: /usr/lib/system/libsystem_secinit.dylib
> dyld: loaded: /usr/lib/system/libsystem_trace.dylib
> dyld: loaded: /usr/lib/system/libunc.dylib
> dyld: loaded: /usr/lib/system/libunwind.dylib
> dyld: loaded: /usr/lib/system/libxpc.dylib
> dyld: loaded: /usr/lib/libobjc.A.dylib
> dyld: loaded: /usr/lib/libauto.dylib
> dyld: loaded: /usr/lib/libc++abi.dylib
> dyld: loaded: /usr/lib/libDiagnosticMessagesClient.dylib
> dyld: loaded: /opt/local/lib/openmpi-mp/libmpi.12.dylib
> dyld: loaded: /opt/local/lib/openmpi-mp/libopen-rte.12.dylib
> dyld: loaded: /opt/local/lib/openmpi-mp/libopen-pal.13.dylib
> dyld: loaded: /opt/local/lib/libhwloc.5.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
> dyld: loaded:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
>                    :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>
> no sign of cuda either
>
> uliano
>
>
> > Il giorno 26 mag 2016, alle ore 03:01, Szilárd Páll <
> pall.szilard at gmail.com> ha scritto:
> >
> > On Wed, May 25, 2016 at 8:20 PM, Uliano Guerrini <
> uliano.guerrini at unimi.it>
> > wrote:
> >
> >>
> >>> Il giorno 25 mag 2016, alle ore 16:30, Szilárd Páll <
> >> pall.szilard at gmail.com> ha scritto:
> >>>
> >>> On Wed, May 25, 2016 at 12:58 PM, Uliano Guerrini <
> >> uliano.guerrini at unimi.it <mailto:uliano.guerrini at unimi.it>> wrote:
> >>> On OSX 11.5 I instelled cuda 7.5, compiled samples and when I run:
> >>>
> >>> ./deviceQuery Starting...
> >>>
> >>> CUDA Device Query (Runtime API) version (CUDART static linking)
> >>>
> >>> Detected 1 CUDA Capable device(s)
> >>>
> >>> Device 0: "GeForce GTX 680"
> >>>  CUDA Driver Version / Runtime Version          7.5 / 7.5
> >>>  CUDA Capability Major/Minor version number:    3.0
> >>>  Total amount of global memory:                 4096 MBytes (4294508544
> >> bytes)
> >>>  ...
> >>>
> >>> and so on, so I presume my CUDA installation is correct driver is ok
> and
> >> card is supported. Then I compiled from source using openMP enabled
> clang
> >> from macport (the one from apple is useless and gcc isn’t supported
> anymore
> >> by NVIDIA on OSX) configuring with:
> >>>
> >>> cmake ../gromacs-5.1.2 -DCMAKE_C_COMPILER=clang
> >> -DCMAKE_CXX_COMPILER=clang++ -DGMX_GPU=on -DCMAKE_PREFIX_PATH=/opt/local
> >> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> >>>
> >>> All goes apparently well, apart from:
> >>>
> >>> -- Could not detect NVIDIA GPUs
> >>>
> >>> and:
> >>>
> >>> -- Could NOT find NVML (missing:  NVML_LIBRARY NVML_INCLUDE_DIR)
> >>>
> >>> which I presume I can ignore as on OSX platform NVIDIA doesn’t offer
> >> NVML and GPU detection is based on that library (I also read on the net
> of
> >> people safely ignoring these warnings).
> >>>
> >>> Nevertheless when I run gmx mdrun I get the following message:
> >>>
> >>> NOTE: Error occurred during GPU detection:
> >>>      CUDA driver version is insufficient for CUDA runtime version
> >>>      Can not use GPU acceleration, will fall back to CPU kernels.
> >>>
> >>> My limited abilities (just some printf here and there) led me to find
> >> that the call to cudaGetDeviceCount on line 602 of the file
> gpu_utils.cu <
> >> http://gpu_utils.cu/> within gromacs/gmxlib/gpu_utils of the untarred
> >> 5.1.2 gromacs version fails.
> >>>
> >>> Any suggestions?
> >>>
> >>> Your questions are not related to development, please post such
> >> questions to the users' list (CCd, please continue there).
> >>
> >> Sorry for that, I gave an (admittedly fast) glance to user’s list and I
> >> found there lots of chemistry question so I subscribed to the wrong
> list.
> >> I’ll continue on the right one.
> >>
> >
> > Thanks!
> >
> >
> >>
> >>>
> >>> Secondly, this is intriguing, could it be that you are using a newer
> >> runtime form a different path with GROMACS than with the deviceQuery SDK
> >> sample?
> >>
> >> I (believe to) have only one (CUDA?) runtime as I installed it today.
> >>
> >
> > In that case, I'm not sure what could be the issue. Perhaps a dynamic
> > library path is missing? You can check with the equivalent of ldd on OS
> X.
> > The GROMACS log header should contain runtime and driver versions, what
> > does your log file show?
> >
> >
> >>
> >>>
> >>> BTW, I do think this should work, but to the best of my knowledge Apple
> >> has no official hardware that ships with or can be upgraded to GTX 680,
> >> right?
> >>
> >> Wrong: this is a macpro compatible (EFI firmware) GTX680 (now
> >> discontinued, there have been quite a lot out there, still easily found
> on
> >> ebay or similar) on a macpro 5,1 official Apple hardware.
> >>
> >> Apple itself didn’sell any GTX board (but sold some Quadro). They were
> >> however quite common among Adobe Suite (and  other software) users.
> >>
> >
> > Thanks for the correction, I was not aware of that!
> >
> > --
> > Szilárd
> >
> >
> >
> >>
> >> uliano
> >>
> >>>
> >>> Cheers,
> >>> --
> >>> Szilárd
> >>
> >>
> >> --
> >> Gromacs Users mailing list
> >>
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> >> posting!
> >>
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