Hi Szilárd, I assume I get the same segmentation fault error as Sebastian (don't shoot if not so). I have 2 NVIDA GTX580 cards (and 4x12-core amd64 opteron 6174).
in brief : Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffc07f8700 (LWP 32035)] 0x00007ffff61de301 in nbnxn_make_pairlist.omp_fn.2 () from /usr/local/gromacs/bin/../lib/libmd.so.6 Also -nb cpu with Verlet cutoff-scheme results in this error... gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1 CMake 2.8.7 If I attach the mdrun.debug output file to this mail, the mail to the list gets bounced by the mailserver (because mdrun.debug > 50 Kb). Hoping this might help, regards, raf =========== compiled code : commit 20da7188b18722adcd53088ec30e5f256af62f20 Author: Szilard Pall <[email protected]> Date: Tue Oct 2 00:29:33 2012 +0200 =========== (gdb) exec mdrun (gdb) run -debug 1 -v -s test.tpr Reading file test.tpr, VERSION 4.6-dev-20121002-20da718 (single precision) [New Thread 0x7ffff3844700 (LWP 31986)] [Thread 0x7ffff3844700 (LWP 31986) exited] [New Thread 0x7ffff3844700 (LWP 31987)] [Thread 0x7ffff3844700 (LWP 31987) exited] Changing nstlist from 10 to 50, rlist from 2 to 2.156 Starting 2 tMPI threads [New Thread 0x7ffff3844700 (LWP 31992)] Using 2 MPI threads Using 24 OpenMP threads per tMPI thread 2 GPUs detected: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible 2 GPUs auto-selected to be used for this run: #0, #1 Back Off! I just backed up ctab14.xvg to ./#ctab14.xvg.1# Initialized GPU ID #1: GeForce GTX 580 [New Thread 0x7ffff3043700 (LWP 31993)] Back Off! I just backed up dtab14.xvg to ./#dtab14.xvg.1# Back Off! I just backed up rtab14.xvg to ./#rtab14.xvg.1# [New Thread 0x7ffff1b3c700 (LWP 31995)] [New Thread 0x7ffff133b700 (LWP 31996)] [New Thread 0x7ffff0b3a700 (LWP 31997)] [New Thread 0x7fffebfff700 (LWP 31998)] [New Thread 0x7fffeb7fe700 (LWP 31999)] [New Thread 0x7fffeaffd700 (LWP 32000)] [New Thread 0x7fffea7fc700 (LWP 32001)] [New Thread 0x7fffe9ffb700 (LWP 32002)] [New Thread 0x7fffe97fa700 (LWP 32003)] [New Thread 0x7fffe8ff9700 (LWP 32004)] [New Thread 0x7fffe87f8700 (LWP 32005)] [New Thread 0x7fffe7ff7700 (LWP 32006)] [New Thread 0x7fffe77f6700 (LWP 32007)] [New Thread 0x7fffe6ff5700 (LWP 32008)] [New Thread 0x7fffe67f4700 (LWP 32009)] [New Thread 0x7fffe5ff3700 (LWP 32010)] [New Thread 0x7fffe57f2700 (LWP 32011)] [New Thread 0x7fffe4ff1700 (LWP 32012)] [New Thread 0x7fffe47f0700 (LWP 32013)] [New Thread 0x7fffe3fef700 (LWP 32014)] [New Thread 0x7fffe37ee700 (LWP 32015)] [New Thread 0x7fffe2fed700 (LWP 32016)] [New Thread 0x7fffe27ec700 (LWP 32017)] Initialized GPU ID #0: GeForce GTX 580 Using CUDA 8x8x8 non-bonded kernels [New Thread 0x7fffe1feb700 (LWP 32018)] [New Thread 0x7fffe0ae4700 (LWP 32019)] [New Thread 0x7fffcbfff700 (LWP 32020)] [New Thread 0x7fffcb7fe700 (LWP 32021)] [New Thread 0x7fffcaffd700 (LWP 32022)] [New Thread 0x7fffca7fc700 (LWP 32023)] [New Thread 0x7fffc9ffb700 (LWP 32024)] [New Thread 0x7fffc97fa700 (LWP 32025)] [New Thread 0x7fffc8ff9700 (LWP 32026)] [New Thread 0x7fffc3fff700 (LWP 32027)] [New Thread 0x7fffc37fe700 (LWP 32028)] [New Thread 0x7fffc2ffd700 (LWP 32029)] [New Thread 0x7fffc27fc700 (LWP 32031)] [New Thread 0x7fffc1ffb700 (LWP 32032)] [New Thread 0x7fffc17fa700 (LWP 32033)] [New Thread 0x7fffc0ff9700 (LWP 32034)] [New Thread 0x7fffc07f8700 (LWP 32035)] [New Thread 0x7fffbfff7700 (LWP 32036)] [New Thread 0x7fffbf7f6700 (LWP 32037)] [New Thread 0x7fffbeff5700 (LWP 32038)] [New Thread 0x7fffbe7f4700 (LWP 32039)] [New Thread 0x7fffbdff3700 (LWP 32040)] [New Thread 0x7fffbd7f2700 (LWP 32042)] [New Thread 0x7fffbcff1700 (LWP 32043)] Making 1D domain decomposition 2 x 1 x 1 * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * We have just committed the new CPU detection code in this branch, and will commit new SSE/AVX kernels in a few days. However, this means that currently only the NxN kernels are accelerated! In the mean time, you might want to avoid production runs in 4.6. Back Off! I just backed up traj.trr to ./#traj.trr.1# Back Off! I just backed up traj.xtc to ./#traj.xtc.1# Back Off! I just backed up ener.edr to ./#ener.edr.1# starting mdrun 'Protein in water' 100000 steps, 200.0 ps. Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffc07f8700 (LWP 32035)] 0x00007ffff61de301 in nbnxn_make_pairlist.omp_fn.2 () from /usr/local/gromacs/bin/../lib/libmd.so.6 (gdb) ============================================ Verlet, nb by cpu only: (gdb) run -debug 1 -nb cpu -v -s test.tpr Reading file test.tpr, VERSION 4.6-dev-20121002-20da718 (single precision) [New Thread 0x7ffff3844700 (LWP 32050)] [Thread 0x7ffff3844700 (LWP 32050) exited] [New Thread 0x7ffff3844700 (LWP 32051)] [Thread 0x7ffff3844700 (LWP 32051) exited] Starting 48 tMPI threads [New Thread 0x7ffff3844700 (LWP 32058)] [New Thread 0x7ffff3043700 (LWP 32059)] [New Thread 0x7ffff2842700 (LWP 32060)] [New Thread 0x7ffff2041700 (LWP 32061)] [New Thread 0x7ffff1840700 (LWP 32062)] [New Thread 0x7ffff103f700 (LWP 32063)] [New Thread 0x7ffff083e700 (LWP 32064)] [New Thread 0x7fffe3fff700 (LWP 32065)] [New Thread 0x7fffe37fe700 (LWP 32066)] [New Thread 0x7fffe2ffd700 (LWP 32067)] [New Thread 0x7fffe27fc700 (LWP 32068)] [New Thread 0x7fffe1ffb700 (LWP 32069)] [New Thread 0x7fffe17fa700 (LWP 32070)] [New Thread 0x7fffe0ff9700 (LWP 32071)] [New Thread 0x7fffdbfff700 (LWP 32072)] [New Thread 0x7fffdb7fe700 (LWP 32073)] [New Thread 0x7fffdaffd700 (LWP 32074)] [New Thread 0x7fffda7fc700 (LWP 32075)] [New Thread 0x7fffd9ffb700 (LWP 32076)] [New Thread 0x7fffd97fa700 (LWP 32077)] [New Thread 0x7fffd8ff9700 (LWP 32078)] [New Thread 0x7fffd3fff700 (LWP 32079)] [New Thread 0x7fffd37fe700 (LWP 32080)] [New Thread 0x7fffd2ffd700 (LWP 32081)] [New Thread 0x7fffd27fc700 (LWP 32082)] [New Thread 0x7fffd1ffb700 (LWP 32083)] [New Thread 0x7fffd17fa700 (LWP 32084)] [New Thread 0x7fffd0ff9700 (LWP 32085)] [New Thread 0x7fffd07f8700 (LWP 32086)] [New Thread 0x7fffcfff7700 (LWP 32087)] [New Thread 0x7fffcf7f6700 (LWP 32088)] [New Thread 0x7fffceff5700 (LWP 32089)] [New Thread 0x7fffce7f4700 (LWP 32090)] [New Thread 0x7fffcdff3700 (LWP 32091)] [New Thread 0x7fffcd7f2700 (LWP 32092)] [New Thread 0x7fffccff1700 (LWP 32093)] [New Thread 0x7fffcc7f0700 (LWP 32094)] [New Thread 0x7fffcbfef700 (LWP 32095)] [New Thread 0x7fffcb7ee700 (LWP 32096)] [New Thread 0x7fffcafed700 (LWP 32097)] [New Thread 0x7fffca7ec700 (LWP 32098)] [New Thread 0x7fffc9feb700 (LWP 32099)] [New Thread 0x7fffc97ea700 (LWP 32100)] [New Thread 0x7fffc8fe9700 (LWP 32101)] [New Thread 0x7fffc87e8700 (LWP 32102)] [New Thread 0x7fffc7fe7700 (LWP 32103)] [New Thread 0x7fffc77e6700 (LWP 32104)] Will use 45 particle-particle and 3 PME only nodes This is a guess, check the performance at the end of the log file Using 48 MPI threads Using 1 OpenMP thread per tMPI thread 2 GPUs detected: #0: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible #1: NVIDIA GeForce GTX 580, compute cap.: 2.0, ECC: no, stat: compatible Back Off! I just backed up ctab14.xvg to ./#ctab14.xvg.2# Back Off! I just backed up dtab14.xvg to ./#dtab14.xvg.2# Back Off! I just backed up rtab14.xvg to ./#rtab14.xvg.2# Using SSE2 4x4 non-bonded kernels Making 3D domain decomposition 3 x 5 x 3 * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * We have just committed the new CPU detection code in this branch, and will commit new SSE/AVX kernels in a few days. However, this means that currently only the NxN kernels are accelerated! In the mean time, you might want to avoid production runs in 4.6. Back Off! I just backed up traj.trr to ./#traj.trr.2# Back Off! I just backed up traj.xtc to ./#traj.xtc.2# Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'Protein in water' 100000 steps, 200.0 ps. Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffcd7f2700 (LWP 32092)] 0x00007ffff61db499 in nbnxn_make_pairlist.omp_fn.2 () from /usr/local/gromacs/bin/../lib/libmd.so.6 (gdb) ============================================= On Mon, 2012-11-12 at 19:37 +0100, Szilárd Páll wrote: > Hi Sebastian, > > That is very likely a bug so I'd appreciate if you could provide a bit more > information, like: > > - OS, compiler > > - results of runs with the following configurations: > - "mdrun -nb cpu" (to run CPU-only with Verlet scheme) > - "GMX_EMULATE_GPU=1 mdrun -nb gpu" (to run GPU emulation using plain C > kernels); > - "mdrun" without any arguments (which will use 2x(n/2 cores + 1 GPU)) > - "mdrun -ntmpi 1" without any other arguments (which will use n cores + > the first GPU) > > - please attach the log files of all failed and a successful run as well as > the mdrun.debug file from a failed runs that you can obtain with "mdrun > -debug 1" > > Note that a backtrace would be very useful and if you can get one I'd > be grateful, but for now the above should be minimum effort and I'll > provide simple introductions to get a backtrace later (if needed). > > Thanks, > > -- > Szilárd > > > On Mon, Nov 12, 2012 at 6:22 PM, sebastian < > [email protected]> wrote: > > > On 11/12/2012 04:12 PM, sebastian wrote: > > > Dear GROMACS user, > > > > > > I am running in major problems trying to use gromacs 4.6 on my desktop > > > with two GTX 670 GPU's and one i7 cpu. On the system I installed the > > > CUDA 4.2, running fine for many different test programs. > > > Compiling the git version of gromacs 4.6 with hybrid acceleration I get > > > one error message of a missing libxml2 but it compiles with no further > > > complaints. The tools I tested (like g_rdf or grompp usw.) work fine as > > > long as I generate the tpr files with the right gromacs version. > > > Now, if I try to use mdrun (GMX_GPU_ID=1 mdrun -nt 1 -v -deffnm ....) > > > the preparation seems to work fine until it starts the actual run. It > > > stops with a segmentation fault: > > > > > > Reading file pdz_cis_ex_200ns_test.tpr, VERSION > > > 4.6-dev-20121002-20da718-dirty (single precision) > > > > > > Using 1 MPI thread > > > > > > Using 1 OpenMP thread > > > > > > > > > 2 GPUs detected: > > > > > > #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: > > compatible > > > > > > #1: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: > > compatible > > > > > > > > > 1 GPU user-selected to be used for this run: #1 > > > > > > > > > Using CUDA 8x8x8 non-bonded kernels > > > > > > > > > * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * > > > > > > We have just committed the new CPU detection code in this branch, > > > > > > and will commit new SSE/AVX kernels in a few days. However, this > > > > > > means that currently only the NxN kernels are accelerated! > > > > > > > Since it does run on a pure CPU run (without the verlet cut-off scheme) > > does it maybe help to change the NxN kernels manually in the .mdp file > > (how can I do so)? Or is there something wrong using the CUDA 4.2 > > version or what so ever. The libxml2 should not be a problem since the > > pure CPU run works. > > > > > In the mean time, you might want to avoid production runs in 4.6. > > > > > > > > > Back Off! I just backed up pdz_cis_ex_200ns_test.trr to > > > ./#pdz_cis_ex_200ns_test.trr.4# > > > > > > > > > Back Off! I just backed up pdz_cis_ex_200ns_test.xtc to > > > ./#pdz_cis_ex_200ns_test.xtc.4# > > > > > > > > > Back Off! I just backed up pdz_cis_ex_200ns_test.edr to > > > ./#pdz_cis_ex_200ns_test.edr.4# > > > > > > starting mdrun 'Protein in water' > > > > > > 3500000 steps, 7000.0 ps. > > > > > > Segmentation fault > > > > > > > > > Since I have no idea whats going wrong any help is welcomed. > > > Attached you find the log file. > > > > > > > Help is really appreciated since I want to use my new desktop including > > the GPU's > > > > > Thanks a lot > > > > > > Sebastian > > > > > > > > > > > > > > > > > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
