[gmx-users] Using multiple GPU's

[paul buscemi]

Thanks Kevin. for the rapid response.

I am using 2018. I’ll check the 2018 - make sure - I was look at the proper docs.   I should not note that the  GPUs are not matched.   a gtx 1080ti  and a gtx 1060

below is some pertinent information from the log file.  ( not too sure how to post a link on the user group ) 

Paul

> On Aug 10, 2018, at 12:31 PM, Kevin Boyd <kevin.boyd at uconn.edu> wrote:
> 
> Hi,
> 
> Can you post a link to your log file?
> 
> Also, what version of gromacs are you using? Make sure that the
> documentation you are following corresponds to the right version of
> gromacs. If you are using v 5.1 (as the link suggests), strongly consider
> upgrading to 2018.
> 
> Kevin
> 
> On Fri, Aug 10, 2018 at 12:57 PM, paul buscemi <pbuscemi at q.com> wrote:
> 
>> 
>> Dear Uses,
>> 
>> I’ve been following the examples on https://na01.safelinks.
>> protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.
>> org%2Fdocumentation%2F5.1%2Fuser-guide%2Fmdrun-
>> performance.html&amp;data=02%7C01%7Ckevin.boyd%40uconn.edu%
>> 7Cb67f423cb92a4abac13508d5fee27522%7C17f1a87e2a254eaab9df9d439034
>> b080%7C0%7C1%7C636695170968044387&amp;sdata=TBSbmbdU%
>> 2F5kxRGsaD1IqLXzEbcJUJ6Kqg7ub%2B%2B9m6xc%3D&amp;reserved=0 for setting up
>> multiple GP’s but have not succeeded.
>> Using a single GPU gmx runs well.  Nvidia and gmx see the 2 PGUs. and
>> I‘ve  tried   mdrun with   variations of  -gpu_id  01,    and -ntmpi, but
>> the GPUs are not put to use.
>> 
>> Would someone suggest the proper signals to mdrun for  two GPU’s. ?
>> 
>>  Running on lilnix-min sarah,  I7
>> 
>> thanks
>> Paul
>> --
>> 

GROMACS:      gmx mdrun, version 2018
Executable:   /usr/local/gromacs/bin//gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/rgb/Desktop/PDMS
Command line:
  gmx mdrun -deffnm pdms.sys.nvt -ntmpi 4 -ntomp 2 -gpu_id 01

GROMACS version:    2018
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        CUDA
SIMD instructions:  AVX2_256
FFT library:        fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
Built on:           2018-07-06 18:24:42
Built by:           rgb at RGB [CMAKE]
Build OS/arch:      Linux 4.4.0-21-generic x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz
Build CPU family:   6   Model: 158   Stepping: 9
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:         /usr/bin/gcc GNU 5.4.0
C compiler flags:    -march=core-avx2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
C++ compiler:       /usr/bin/c++ GNU 5.4.0
C++ compiler flags:  -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
CUDA compiler:      /usr/lib/nvidia-cuda-toolkit/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on Tue_Aug_11_14:27:32_CDT_2015;Cuda compilation tools, release 7.5, V7.5.17
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;-D_FORCE_INLINES;; ;-march=core-avx2;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver:        9.0
CUDA runtime:       7.50

===== latest attempt ======= 
Running on 1 node with total 4 cores, 8 logical cores, 2 compatible GPUs
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz
    Family: 6   Model: 158   Stepping: 9
    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  Hardware topology: Basic
    Sockets, cores, and logical processors:
      Socket  0: [   0   4] [   1   5] [   2   6] [   3   7]
  GPU info:
    Number of GPUs detected: 2
    #0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC:  no, stat: compatible
    #1: NVIDIA GeForce GTX 1060 6GB, compute cap.: 6.1, ECC:  no, stat: compatible