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

Uliano Guerrini uliano.guerrini at unimi.it
Thu May 26 21:05:35 CEST 2016 

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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