[gmx-users] random initial failure

[Szilárd Páll]

Harry,

That does not seem normal. Have you tried to run on CPU-only and see
if that reproduces the issue (e.g. run mdrun -nsteps 0 -nb cpu -pme
cpu a few times).

--
Szilárd

On Mon, Feb 11, 2019 at 11:25 AM Harry Mark Greenblatt
<harry.greenblatt at weizmann.ac.il> wrote:
>
> BS”D
>
> Dear All,
>
>   Trying to run a system with about 70,000 atoms, including waters, of a trimeric protein.  Went through minimization, PT and NPT equilibration.
>
> Most of the time, it starts and runs fine.  But once in about 5 tries, I get:
>
>
> 125000000 steps, 250000.0 ps.
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2019
> Source file: src/gromacs/mdlib/sim_util.cpp (line 752)
> MPI rank:    4 (out of 6)
>
> Fatal error:
> Step 0: The total potential energy is 3.21792e+36, which is extremely high.
> The LJ and electrostatic contributions to the energy are 28531.2 and -228106,
> respectively. A very high potential energy can be caused by overlapping
> interactions in bonded interactions or very large coordinate values. Usually
> this is caused by a badly- or non-equilibrated initial configuration,
> incorrect interactions or parameters in the topology.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> If the system was truly non-equilibrated, I would have thought it would fail every time.  Yet most runs are fine.
>
>
> Below are the hardware and build details.
>
>
> Please let me know what other details you would like to know.
>
> Thanks
>
> Harry
>
>
> GROMACS version:    2019
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:        CUDA
> SIMD instructions:  AVX_512
> FFT library:        fftw-3.3.7-sse2-avx-avx2-avx2_128-avx512
> RDTSCP usage:       enabled
> TNG support:        enabled
> Hwloc support:      disabled
> Tracing support:    disabled
> C compiler:         /usr/local/gcc/gcc-6.4.0/bin/gcc GNU 6.4.0
> C compiler flags:    -mavx512f -mfma     -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
> C++ compiler:       /usr/local/gcc/gcc-6.4.0/bin/c++ GNU 6.4.0
> C++ compiler flags:  -mavx512f -mfma    -std=c++11   -O2 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
> CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2018 NVIDIA Corporation;Built on Tue_Jun_12_23:07:04_CDT_2018;Cuda compilation tools, release 9.2, V9.2.148
> CUDA compiler flags:-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_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_70,code=compute_70;-use_fast_math;;; ;-mavx512f;-mfma;-std=c++11;-O2;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> CUDA driver:        9.20
> CUDA runtime:       9.20
>
>
> Running on 1 node with total 36 cores, 36 logical cores, 2 compatible GPUs
> Hardware detected:
>   CPU info:
>     Vendor: Intel
>     Brand:  Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz
>     Family: 6   Model: 85   Stepping: 4
>     Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl 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
>     Number of AVX-512 FMA units: 2
>   Hardware topology: Basic
>     Sockets, cores, and logical processors:
>       Socket  0: [   0] [   1] [   2] [   3] [   4] [   5] [   6] [   7] [   8] [   9] [  10] [  11] [  12] [  13] [  14] [  15] [  16] [  17]
>       Socket  1: [  18] [  19] [  20] [  21] [  22] [  23] [  24] [  25] [  26] [  27] [  28] [  29] [  30] [  31] [  32] [  33] [  34] [  35]
>   GPU info:
>     Number of GPUs detected: 2
>     #0: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, stat: compatible
>     #1: NVIDIA Tesla V100-PCIE-16GB, compute cap.: 7.0, ECC: yes, stat: compatible
>
>
> --------------------------------------------------------------------
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<mailto:harry.greenblatt at weizmann.ac.il>
> Weizmann Institute of Science        Phone:  972-8-934-6340
> 234 Herzl St.                        Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
> --
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