[gmx-users] mdrun initialises, fails to run, no error message

Natalie Tatum nataliejtatum at gmail.com
Tue Jan 3 16:43:35 CET 2017

Dear all,

I'm hoping you can shed light on (a) what my mdrun problem is and (b) where
to start fixing it.

I'm simulating different mutants of a protein dimer on DNA, for 10 ns
a-piece. I have successfully run this protocol on the wild-type protein, on
two single residue mutants, and on a double mutant. I came to run the same
on a fourth, single site mutant. I have followed the same protocols and
utilised the same MDP settings throughout. All were subject to 5000 steps
of steepest-descent energy minimisation, then 200 ps of equilibration in
the NVT ensemble, then the same in the NPT. For this particular mutant
there were no issues apparent going into production MD. Therefore, I don't
think it's an issue of my MDP setup or system...

So I have two compatible (OpenCL 1.2) AMD Radeon HD Firepro D300 GPUs, and
I have one mutant (run/process) assigned to each.

For this mutant I call mdrun with:

gmx mdrun -deffnm md -gpu_id 1 &

Whereas the other is on -gpu_id 0, and walk away. This worked successfully
in the week prior for two other systems. It's New Year, then I come back to
what should be completed simulations this morning to get my hands dirty in

Run on gpu 0 has completed successfully, all is grand.

Mutant on gpu 1 has not. Attempts to resume/restart fail (on either GPU, or
both, or calling neither explicitly). All output looks like this:

GROMACS:      gmx mdrun, VERSION 5.1.3

Executable:   /usr/local/gromacs/bin/gmx

Data prefix:  /usr/local/gromacs

Command line:

  gmx mdrun -deffnm md

GROMACS version:    VERSION 5.1.3

Precision:          single

Memory model:       64 bit

MPI library:        thread_mpi

OpenMP support:     disabled

GPU support:        enabled

OpenCL support:     enabled

invsqrt routine:    gmx_software_invsqrt(x)

SIMD instructions:  AVX_256

FFT library:        fftw-3.3.4-sse2

RDTSCP usage:       enabled

C++11 compilation:  disabled

TNG support:        enabled

Tracing support:    disabled

Built on:           Mon  1 Aug 2016 17:20:18 BST

Built by:           natalie at t <natalie at nicr00353.ncl.ac.uk>
hemachineIuse.here.there [CMAKE]

Build OS/arch:      Darwin 15.5.0 x86_64

Build CPU vendor:   GenuineIntel

Build CPU brand:    Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz

Build CPU family:   6   Model: 62   Stepping: 4

Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx
msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
sse3 sse4.1 sse4.2 ssse3 tdt x2apic

C compiler:         /Applications/Xcode.app/Contents/Developer/Toolchains/
XcodeDefault.xctoolchain/usr/bin/cc Clang

C compiler flags:    -mavx    -Wall -Wno-unused -Wunused-value
-Wunused-parameter -Wno-unknown-pragmas  -O3 -DNDEBUG

C++ compiler:       /Applications/Xcode.app/Contents/Developer/Toolchains/
XcodeDefault.xctoolchain/usr/bin/c++ Clang

C++ compiler flags:  -mavx    -Wextra -Wno-missing-field-initializers
-Wpointer-arith -Wall -Wno-unused-function -Wno-unknown-pragmas  -O3

Boost version:      1.60.0 (external)

OpenCL include dir: /System/Library/Frameworks/OpenCL.framework

OpenCL library:     /System/Library/Frameworks/OPENCL.framework

OpenCL version:     1.2

And there it ends. No files except the log shown above - and though this
initial output looks identical in content to the beginnings of logs for
successful simulations, mdrun does not then seem to engage with the
GPU/CPUs available.

There are no error messages, no apparent indication as to where this has
gone wrong... And now I can't run mdrun at all, for any system.

I've checked my disk space (fine, >100 GB available), I'm able to call and
execute other gmx commands, but mdrun does the above.

The closest error I can find with my google-fu is three years ago where
this user (
) got no error but a killed process, but I don't even get as far as
detection of CPUs/GPUs or domain decomposition.

Any suggestions much appreciated,


*Dr. Natalie J. Tatum*
Post-doctoral Research Associate
Northern Institute for Cancer Research
Newcastle University

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