[gmx-users] grompp not possible with annealing - Gromacs 2019.1

Tafelmeier, Stefanie Stefanie.Tafelmeier at zae-bayern.de
Fri Sep 13 11:06:30 CEST 2019


Dear Mark,

many thanks for your answer.

Unfortunately I face another problem when installing Gromacs 2019.2 or 2019.3.

The regressiontests fail (no. 42 & 46).
This problem already occur when I installed Gromacs 2019.1. Then the issue was solved by using the newest versions of GCC and CUDA. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/124028.html 

If I want to do this now, I have the problem that the newest CUDA version does not support the newest GCC 
-------
CMake Error at cmake/gmxManageNvccConfig.cmake:192 (message):
  NVCC/C++ compiler combination does not seem to be supported.  CUDA
  frequently does not support the latest versions of the host compiler, so
  you might want to try an earlier C++ compiler version and make sure your
  CUDA compiler and driver are as recent as possible.
-------

Hence, I have to use the GCC 8.2, which then only allows me to use Gromacs 2019.1 and so no annealing is possible. 
This is a bit tricky.

If you have any suggestions on how to use annealing anyway I would appreciate a lot.

Many thanks,
Steffi







-----Ursprüngliche Nachricht-----
Von: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] Im Auftrag von Mark Abraham
Gesendet: Dienstag, 10. September 2019 17:56
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] grompp not possible with annealing - Gromacs 2019.1

Hi,

Thanks for the report - but it's probably fixed already (
http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html#fix-segmentation-fault-when-preparing-simulated-annealing-inputs)
so I suggest you get the latest 2019.x release?

Mark

On Tue, 10 Sep 2019 at 17:15, Tafelmeier, Stefanie <
Stefanie.Tafelmeier at zae-bayern.de> wrote:

> Dear all,
>
> I try to use simulation annealing, but unfortunately the grompp - command
> leads to an error.
> It is not a known Gromacs error, but it doesn't finish the job and it
> says: Speicherzugriffsfehler (Speicherabzug geschrieben) (which means
> something like "Memory Access Error")
>
> The only output file produced is the mdout.mdp, which content seems
> correct.
>
> The screen text is given below as well as the grompp.mdp content and the
> details to the system used.
>
> There have been some issues as well to get Gromacs installed on the
> workstation. Not sure if this could be connected.
> Many thanks already for your help.
>
> Greetings,
> Steffi
>
>
>
> ------------------------------------------------------------------------------------------------
> Screen text:
>
> GROMACS:      gmx grompp, version 2019.1
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:
> /home/pcm-mess/Schreibtisch/StTa/Vergleich_FF/OPLS/fixed_layer/freeze_grp/temp_grps/annealing
> Command line:
>   gmx grompp -f grompp_OPLS_anneal.mdp -v
>
> checking input for internal consistency...
> Setting the LD random seed to -28800458
> processing topology...
> Generated 330891 of the 330891 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 330891 of the 330891 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'Other'
> turning all bonds into constraints...
>
> NOTE 1 [file unknown]:
>   You are using constraints on all bonds, whereas the forcefield has been
>   parametrized only with constraints involving hydrogen atoms. We suggest
>   using constraints = h-bonds instead, this will also improve performance.
>
> processing coordinates...
> double-checking input for internal consistency...
> Setting gen_seed to -1070611718
> Velocities were taken from a Maxwell distribution at 280 K
> Removing all charge groups because cutoff-scheme=Verlet
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Analysing residue names:
> There are:  3600      Other residues
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Speicherzugriffsfehler (Speicherabzug geschrieben)
>
> ------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------------------------
> Content grompp.mdp (as an example):
>
> include                  = -I../top
> define                   =
> cutoff-scheme            = Verlet
> integrator               = md
> dt                       = 0.001
> nsteps                   = 800000
> nstxout                  = 2000
> nstvout                  = 2000
> nstlog                   = 2000
> nstenergy                = 2000
> nstlist                  = 10
> ns-type                  = grid
> pbc                      = xyz
> rlist                    = 1
> coulombtype              = PME
> rcoulomb                 = 1
> rvdw                     = 1
> tcoupl                   = v-rescale
> tc-grps                 = other
> tau-t                    = 0.1
> ref-t                    = 280
> Pcoupl                   = Berendsen
> pcoupltype               = anisotropic
> tau-p                    = 10
> compressibility          = 8.7e-5 8.7e-5 8.7e-5 0 0 0
> ref-p                    = 1.0 1.0 1.0 0 0 0
> constraints              = all-bonds
> gen-vel                  = yes
> gen-temp                 = 280
> gen-seed                 = -1
> annealing               = single
> annealing-npoints       = 2
> annealing-time           = 0 60
> annealing-temp          = 280 280
>
> ------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------------------------
> System details:
>
> GROMACS version:    2019.1
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
> GPU support:        CUDA
> SIMD instructions:  AVX_512
> FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
> RDTSCP usage:       enabled
> TNG support:        enabled
> Hwloc support:      disabled
> Tracing support:    disabled
> C compiler:         /usr/bin/cc GNU 8.2.0
> C compiler flags:    -mavx512f -mfma     -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
> C++ compiler:       /usr/bin/c++ GNU 8.2.0
> C++ compiler flags:  -mavx512f -mfma    -std=c++11   -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> CUDA compiler:      /usr/local/cuda-10.1/bin/nvcc nvcc: NVIDIA (R) Cuda
> compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
> Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105
> 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_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;;
> ;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> CUDA driver:        10.10
> CUDA runtime:       10.10
>
> Running on 1 node with total 44 cores, 88 logical cores, 1 compatible GPU
> Hardware detected:
>   CPU info:
>     Vendor: Intel
>     Brand:  Intel(R) Xeon(R) Gold 6152 CPU @ 2.10GHz
>     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  44] [   1  45] [   2  46] [   3  47] [   4  48] [
>  5  49] [   6  50] [   7  51] [   8  52] [   9  53] [  10  54] [  11  55]
> [  12  56] [  13  57] [  14  58] [  15  59] [  16  60] [  17  61] [  18
> 62] [  19  63] [  20  64] [  21  65]
>       Socket  1: [  22  66] [  23  67] [  24  68] [  25  69] [  26  70] [
> 27  71] [  28  72] [  29  73] [  30  74] [  31  75] [  32  76] [  33  77]
> [  34  78] [  35  79] [  36  80] [  37  81] [  38  82] [  39  83] [  40
> 84] [  41  85] [  42  86] [  43  87]
>   GPU info:
>     Number of GPUs detected: 1
>     #0: NVIDIA Quadro P6000, compute cap.: 6.1, ECC:  no, stat: compatible
>
> ------------------------------------------------------------------------------------------------
>
>
>
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