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@t <nata...@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 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/Contents/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/FEdWd6gC/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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.