[gmx-users] Regarding submitting a job in the cluster

[Dilip H N]

Hello,

We have a new cluster now, and gromacs has been installed in it.
Now if i want to want to call gromacs and run the command, i have to type:

/apps/gromacs-2016.2/bin/gmx_mpi grompp -f nptmd.mdp -c npt.gro -t npt.cpt
-p topol.top -o nptmd.tpr
/apps/gromacs-2016.2/bin/gmx_mpi mdrun -v -s nptmd.tpr -deffnm nptmd

and it running as follows:
--------------------------------------------------------------------------
WARNING: There is at least non-excluded one OpenFabrics device found,
but there are no active ports detected (or Open MPI was unable to use
them).  This is most certainly not what you wanted.  Check your
cables, subnet manager configuration, etc.  The openib BTL will be
ignored for this job.

  Local host: master
--------------------------------------------------------------------------
[1517328530.673617] [master:10000:0]         sys.c:744  MXM  WARN
Conflicting CPU frequencies detected, using: 1664.99
[1517328530.676824] [master:10000:0]      ib_dev.c:695  MXM  ERROR There
are no Mellanox cards detected.
[1517328530.690993] [master:10000:0]      ib_dev.c:695  MXM  ERROR There
are no Mellanox cards detected.
[1517328530.700884] [master:10000:0]         sys.c:744  MXM  WARN
Conflicting CPU frequencies detected, using: 1664.99
                      :-) GROMACS - gmx mdrun, 2016.2 (-:
.
.
Command line:
  gmx_mpi mdrun -v -s nptmd.tpr -deffnm nptmd
NOTE: Error occurred during GPU detection:
      CUDA driver version is insufficient for CUDA runtime version
      Can not use GPU acceleration, will fall back to CPU kernels.
Running on 1 node with total 16 cores, 16 logical cores, 0 compatible GPUs
Hardware detected on host master (the node of MPI rank 0):
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256

 Hardware topology: Basic
Reading file nptmd.tpr, VERSION 2016.2 (single precision)
Changing nstlist from 10 to 40, rlist from 1.2 to 1.217

Using 1 MPI process
Using 16 OpenMP threads

My question is
1] Is it every time should i call the gromacs (ie., /apps/gromacs/bin...)
and then give the commands..??
2] By default it is taking 16 cores ... why is it so..?? (but our cluster
has 32 cores in master node and 160 cores in compute nodes)
3] the time taken to finish this production run is almost 3 hrs, (but if i
run the same job in my desktop, it is taking the same time. where on my
desktop it was showing as
    Running on 1 node with total 4 cores, 8 logical cores
    Hardware detected:
   CPU info:
    Vendor: Intel
    Brand:  Intel(R) Core(TM) i7-4770 CPU @ 3.40GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256
   Hardware topology: Basic
   Reading file nvt.tpr, VERSION 2016.2 (single precision)
  Changing nstlist from 10 to 25, rlist from 1.2 to 1.224
  Using 1 MPI thread
  Using 8 OpenMP threads ).

So the cluster should be taking less time right to finish the job...?? but
this is not happening...

Do i need to write any script..?? in order to describe how many nodes,
cores etc., should be taken..??


Any suggestions are highly appreciated.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student




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