[gmx-users] Multiple output log. xtc .edr files generated using mpirun

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 3 09:39:22 CEST 2017


You need MPI support to use more than one node at once.


On Mon, 3 Jul 2017 07:29 Abhishek Acharya <abhi117acharya at gmail.com> wrote:

> Hello GROMACS users,
> I am trying to run a simulation on a university cluster; I am using
> gromacs-5.1.2. The problem is while running mdrun, using the following
> command:
> mpirun -np 32 gmx mdrun -s prod.tpr -deffnm prod_out -pin on   ### I
> expected gmx mdrun_mpi here but it was not available.
> I am getting multiple log files, xtc, edr files as the output and all the
> log files say the following:
> Running on 1 node with total 16 cores, 16 logical cores
> Hardware detected:
>   CPU info:
>     Vendor: GenuineIntel
>     Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
>     Family:  6  model: 45  stepping:  7
>     CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
> sse4.2 ssse3 tdt x2apic
>     SIMD instructions most likely to fit this hardware: AVX_256
>     SIMD instructions selected at GROMACS compile time: AVX_256
> This in itself is pretty weird. I am guessing that the package is not
> properly installed by the admin. My question is what is the exact problem
> with the setup and what is the solution; i need to communicate this to the
> admin. Although, I reported the issue previously, but it seems he doesn't
> understand where the problem seems to be.
> Thanks in advance.
> Sincerely,
> Abhishek Acharya
> Research Associate,
> Department of Molecular Nutrition
> CSIR-Central Food Technological Research Institute,
> Mysuru-570020
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