[gmx-users] mdrun initialises, fails to run, no error message
Natalie Tatum
nataliejtatum at gmail.com
Mon Jan 9 16:10:53 CET 2017
Dear Justin,
Thanks for the advice - after a clean up, a reboot, and some careful
application of commands, everything seems to be running nicely again.
Switching the call to below (instead of using -deffnm) is working.
gmx mdrun -s md.tpr -gpu_id 1 &
Many thanks,
Natalie
On 4 January 2017 at 01:02, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 1/3/17 10:43 AM, Natalie Tatum wrote:
>
>> 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
>> analysis.
>>
>> 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
>>
>>
> From the .log, it appears your command was not what you think it was. Is
> it possible that the job failed because mdrun tried to consume all
> available hardware and got hung up?
>
>
>>
>> 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/Conte
>> nts/Developer/Toolchains/
>> XcodeDefault.xctoolchain/usr/bin/cc Clang 7.3.0.7030031
>>
>> C compiler flags: -mavx -Wall -Wno-unused -Wunused-value
>> -Wunused-parameter -Wno-unknown-pragmas -O3 -DNDEBUG
>>
>> C++ compiler: /Applications/Xcode.app/Conte
>> nts/Developer/Toolchains/
>> XcodeDefault.xctoolchain/usr/bin/c++ Clang 7.3.0.7030031
>>
>> C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers
>> -Wpointer-arith -Wall -Wno-unused-function -Wno-unknown-pragmas -O3
>> -DNDEBUG
>>
>> 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.
>>
>>
> Test whether or not your GPU is still accessible and capable of running
> test programs.
>
> -Justin
>
> 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 (
>> http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/FE
>> dWd6gC/mdrun-no-error-but-hangs-no-results
>> ) 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,
>>
>> Natalie
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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--
*Dr. Natalie J. Tatum*
Post-doctoral Research Associate
Northern Institute for Cancer Research
Newcastle University
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