Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-28 Thread Szilárd Páll
Dear Makoto Yoneya, Thank you for the feedback, it is of great help! I will try to reproduce the issue because mdrun should not segfault with any gcc version 4.3 and above. Could you please provide two more things: - a log file of the failed run using the latest code from git; - run mdrun with

[gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-27 Thread Makoto Yoneya
Dear GROMACS users: On Gromacs 4.6 segmentation fault with mdrun, I'd also met the same segmentation fault problem with gromacs-4.6. on my linux box with GTX-580. For my case, change the compilor solved this problem. Raf Ponsaerts wrote he used gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-23 Thread Raf Ponsaerts
Hi Szilárd and Roland, Thanks for the clear explanation! I will compile release-4.6 (instead of the nbnxn_hybrid_acc branch) and do some further testing in a few weeks since I'm currently using the machine for production-runs with gmx-4.5.5. Thanks for your time and effort! regards, raf On

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-21 Thread Szilárd Páll
Roland, He explicitly stated that he is using 20da718 which is also from the nbnxn_hybrid_acc branch. Raf, as Roland said, get the release-4-6 ad try again! There's an important thing to mention: your hardware configuration is probably quite imbalanced and the default settings are certainly

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-16 Thread Roland Schulz
Hi Raf, which version of Gromacs did you use? If you used branch nbnxn_hybrid_acc please use branch release-4-6 instead and see whether that fixes your issue. If not please open a bug and upload your log file and your tpr. Roland On Thu, Nov 15, 2012 at 5:13 PM, Raf Ponsaerts

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-15 Thread Raf Ponsaerts
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)] 0x761de301

[gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-12 Thread sebastian
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

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-12 Thread sebastian
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

Re: [gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-12 Thread Szilárd Páll
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