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

[Albert]

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