[gmx-users] GPU running problem with GMX-4.6 beta2

[Szilárd Páll]

Hi,

That unfortunately tell exactly about the reason why mdrun is stuck. Can
you reproduce the issue on another machines or with different launch
configurations? At which step does it get stuck (-stepout 1 can help)?

Please try the following:
- try running on a single GPU;
- try running on CPUs only (-nb cpu and to match closer the GPU setup with
-ntomp 12);
- try running in GPU emulation mode with the GMX_EMULATE_GPU=1 env. var
set (and to match closer the GPU setup with -ntomp 12)
- provide a backtrace (using gdb).

Cheers,

--
Szilárd



On Mon, Dec 17, 2012 at 5:37 PM, Albert <mailmd2011 at gmail.com> wrote:

> hello:
>
>  I am running GMX-4.6 beta2 GPU work in a 24 CPU core workstation with two
> GTX590, it stacked there without any output i.e the .xtc file size is
> always 0 after hours of running. Here is the md.log file I found:
>
>
> Using CUDA 8x8x8 non-bonded kernels
>
> Potential shift: LJ r^-12: 0.112 r^-6 0.335, Ewald 1.000e-05
> Initialized non-bonded Ewald correction tables, spacing: 7.82e-04 size:
> 1536
>
> Removing pbc first time
> Pinning to Hyper-Threading cores with 12 physical cores in a compute node
> There are 1 flexible constraints
>
> WARNING: step size for flexible constraining = 0
>          All flexible constraints will be rigid.
>          Will try to keep all flexible constraints at their original
> length,
>          but the lengths may exhibit some drift.
>
> Initializing Parallel LINear Constraint Solver
> Linking all bonded interactions to atoms
> There are 161872 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: X 1
> The initial domain decomposition cell size is: X 1.83 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
>                  non-bonded interactions           1.200 nm
> (the following are initial values, they could change due to box
> deformation)
>             two-body bonded interactions  (-rdd)   1.200 nm
>           multi-body bonded interactions  (-rdd)   1.200 nm
>   atoms separated by up to 5 constraints  (-rcon)  1.826 nm
>
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1
> The minimum size for domain decomposition cells is 1.200 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.66
> The maximum allowed distance for charge groups involved in interactions is:
>                  non-bonded interactions           1.200 nm
>             two-body bonded interactions  (-rdd)   1.200 nm
>           multi-body bonded interactions  (-rdd)   1.200 nm
>   atoms separated by up to 5 constraints  (-rcon)  1.200 nm
>
> Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  Protein_LIG_POPC
>   1:  Water_and_ions
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> G. Bussi, D. Donadio and M. Parrinello
> Canonical sampling through velocity rescaling
> J. Chem. Phys. 126 (2007) pp. 014101
> -------- -------- --- Thank You --- -------- --------
>
>
>
> THX
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<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 gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>