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

Abhishek Acharya abhi117acharya at gmail.com
Mon Jul 3 07:28:50 CEST 2017

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

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.

Abhishek Acharya
Research Associate,
Department of Molecular Nutrition
CSIR-Central Food Technological Research Institute,

More information about the gromacs.org_gmx-users mailing list