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

[Justin Lemkul]

On 1/30/18 11:52 AM, Dilip H N wrote:
> 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.
>

Questions about how to properly use your hardware should be directed to 
your system administrator, not this mailing list. GROMACS is doing what 
it's supposed to; it's up to you to understand what your hardware is and 
how to use it.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================