:-) GROMACS - mdrun_mpi, 2020.4 (-:

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  Gerrit Groenhof     Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang  
  Aleksei Iupinov   Christoph Junghans     Joe Jordan     Dimitrios Karkoulis
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  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg     Erik Marklund   
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   Alfons Sijbers     Peter Tieleman      Jon Vincent      Teemu Virolainen 
 Christian Wennberg    Maarten Wolf      Artem Zhmurov   
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

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GROMACS:      mdrun_mpi, version 2020.4
Executable:   /opt/apps/gromacs/2020.4/gcc/8.4.0/cuda/10.1.243/openmpi/4.0.3/bin/mdrun_mpi
Data prefix:  /opt/apps/gromacs/2020.4/gcc/8.4.0/cuda/10.1.243
Working dir:  /data/homezvol1/calmasri/WRKY/WRKY_polyAT/axial/test
Command line:
  mdrun_mpi -ntomp 20 -deffnm pull -pf pullf.xvg -px pullx.xvg

Compiled SIMD: AVX2_128, but for this host/run AVX_512 might be better (see
log).
Reading file pull.tpr, VERSION 2020.4 (single precision)
Changing nstlist from 20 to 100, rlist from 1.418 to 1.53

On host hpc3-gpu-16-02 2 GPUs selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 2 ranks on this node:
  PP:0,PP:1
PP tasks will do (non-perturbed) short-ranged and most bonded interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 2 MPI processes

Non-default thread affinity set, disabling internal thread affinity

Using 20 OpenMP threads per MPI process


NOTE: Your choice of number of MPI ranks and amount of resources results in using 20 OpenMP threads per rank, which is most likely inefficient. The optimum is usually between 2 and 6 threads per rank.

WARNING: This run will generate roughly 8307 Mb of data


NOTE: DLB will not turn on during the first phase of PME tuning
starting mdrun 'Protein in water'
50000000 steps, 100000.0 ps.

step 1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Warning: Triclinic box is too skewed.
Warning: Triclinic box is too skewed.
         Box (3x3):
          Box (3x3):
           Box[    0]={-7.72854e+01,             Box[    0]={-7.72854e+01,  0.00000e+00,  0.00000e+00}
   0.00000e+00,  0.00000e+00}
            Box[    1]={-0.00000e+00, -4.07764e+01, -0.00000e+00          Box[    1]={-0.00000e+00, }
            Box[    2]={-4.07764e+01, -0.00000e+00}
            Box[    2]={-0.00000e+00, -0.00000e+00-0.00000e+00, -0.00000e+00, -3.28580e+01}
         Can not fix pbc.

Warning: Triclinic box is too skewed.
         Box (3x3):
 , -3.28580e+01}
         Can not fix pbc.

           Box[    0]={-7.72854e+01Warning: Triclinic box is too skewed.
         Box (3x3):
            Box[    0]={-7.72854e+01,  0.00000e+00,  0.00000e+00,  0.00000e+00}
            Box[    1]={-0.00000e+00, ,  0.00000e+00}
  -4.07764e+01, -0.00000e+00}
          Box[    1]={-0.00000e+00, -4.07764e+01, -0.00000e+00}
            Box[    2]={-0.00000e+00, -0.00000e+00, -3.28580e+01}
         Can not fix pbc.

            Box[    2]={-0.00000e+00, -0.00000e+00, -3.28580e+01}
         Can not fix pbc.

[hpc3-gpu-16-02:981  :0:1022] Caught signal 11 (Segmentation fault: address not mapped to object at address 0xfffffffe06375640)
[hpc3-gpu-16-02:00981] *** Process received signal ***
[hpc3-gpu-16-02:00981] Signal: Segmentation fault (11)
[hpc3-gpu-16-02:00981] Signal code: Address not mapped (1)
[hpc3-gpu-16-02:00981] Failing at address: 0xfffffffe06375640
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 981 on node hpc3-gpu-16-02 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------