[gmx-users] GROMACS 5.0.5 GPU version on K620
Krzysztof Kuczera
kkuczera at ku.edu
Wed Jul 22 00:17:03 CEST 2015
Hi Szilárd ,
The test case worked after I added the flags you recommended, though the
speed was not as high as I had hoped - equivalent to about 6 CPU cores -
I guess my GPU is not so hot.
Below is the output from "mdrun -version". Please let me know if you
see things that might be optimized there.
Thanks for your excellent help!
Krzysztof
-------------------------------
Gromacs version: VERSION 5.0.5
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled GPU support: enabled invsqrt
routine: gmx_software_invsqrt(x)
SIMD instructions: AVX2_256
FFT library: fftw-3.3.4-fma-sse2-avx RDTSCP usage: enabled C++11
compilation: disabled TNG support: enabled
Tracing support: disabled
Built on: Tue Jul 21 16:25:29 CDT 2015
Built by: kuczera at lolipop-chem-ku-edu [CMAKE]Build
OS/arch: Linux 3.10.0-229.4.2.el7.x86_64 x86_64
Build CPU vendor: GenuineIntel
Build CPU brand: Intel(R) Xeon(R) CPU E5-2687W v3 @ 3.10GHzBuild CPU
family: 6 Model: 63 Stepping: 2Build CPU features: aes apic avx
avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm m
mx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apicC compiler: /usr/bin/cc GNU
4.8.3C compiler flags: -march=core-avx2 -Wno-maybe-uninitialized
-Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3
-DNDEBUG -fomit-frame-pointer -funroll-all-
loops -fexcess-precision=fast -Wno-array-bounds
C++ compiler: /usr/bin/c++ GNU 4.8.3
C++ compiler flags: -march=core-avx2 -Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall
-Wno-unused-function -O3 -DNDEBUG -fomit-frame-pointer
-funroll-all-loops -fexcess-precision=fast -Wno-array-bounds
Boost version: 1.53.0 (external)
CUDA compiler: /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda
compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on
Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, V7.0.27
CUDA compiler
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-gencode;arch=compute_50,code=compute_50;-use_fast_math;-Xcompiler;-fPIC
;
;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-fomit-frame-pointer;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
CUDA driver: 7.0
CUDA runtime: 7.0
On 7/17/15 5:39 PM, Szilárd Páll wrote:
> Krzysztof,
>
> Whyle GROMACS 5.0.x build system does not explicitly generate options
> targeting 5.x devices, the binary built should still be compatible with
> your GPU. You can try adding the device-specific optimization flags with the
> -DCUDA_NVCC_FLAGS_RELEASE="-gencode;arch=compute_50,code=sm_50"
> cmake flag, but I'm not sure this fix the issue.
>
> What does gmx -version show?
>
> Cheers,
>
> --
> Szilárd
>
> On Fri, Jul 17, 2015 at 11:49 PM, Krzysztof Kuczera <kkuczera at ku.edu> wrote:
>
>> Hi Group,
>>
>> I am getting a run-time error on my Linux workstation with K620 GPU
>> for the GPU version of GROMACS 5.0.5
>> using gcc 4.8.3 and CUDA Toolkit 7.0 I had no problem compiling the code
>> but got this error when starting a test case:
>>
>> Program mdrun, VERSION 5.0.5
>> Source code file:
>> /home/kuczera/prog/gromacs-5.0.5/src/gromacs/mdlib/nbnxn_cuda/
>> nbnxn_cuda.cu, line: 619
>>
>> Fatal error:
>> cudaStreamSynchronize failed in cu_blockwait_nb: an illegal memory access
>> was encountered
>>
>> Searching the Web, I found that this type of error was already resolved in
>> GROMACS 4.6 some time ago.
>> Could somebody suggest a solution?
>>
>> We have been able to compile and run GROMACS 5.0.4 on an older GPU with
>> compute capability 3.5,
>> my newer K620 has compute capability 5.0 - could this be the problem ?
>>
>> Thanks
>> Krzysztof
>>
>> --
>> Krzysztof Kuczera
>> Departments of Chemistry and Molecular Biosciences
>> The University of Kansas
>> 1251 Wescoe Hall Drive, 5090 Malott Hall
>> Lawrence, KS 66045
>> Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
>> http://oolung.chem.ku.edu/~kuczera/home.html
>>
>> --
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--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
1251 Wescoe Hall Drive, 5090 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
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