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 <jalem...@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@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/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 > > 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. > -- *Dr. Natalie J. Tatum* Post-doctoral Research Associate Northern Institute for Cancer Research Newcastle University -- 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.