Small systems crash with -nb cpu on tcbs28
Another bug found when using Michael Shirt's ethanol system from the virginia tutorial. The system has 2694 atoms and works fine when setting the number of openMP threads automatically, or when using GPUs. However, if we force cpu execution with "-nb cpu", mdrun crashes with an error about atoms that have moved too far.
For this system and machine, Gromacs picked 16 MPI processes each with two OpenMP threads.
#1 Updated by Roland Schulz over 6 years ago
Could you attach a TPR? You say "works fine when setting the number of openMP threads automatically" and "Gromacs picked 16 MPI processes each with two OpenMP threads". If 2 is automatically picked and the automatically picked works, what number of OpenMP threads causes the problem?
#3 Updated by Erik Lindahl over 6 years ago
Sorry, didn't have much time in Bangalore last week.
After creating The attached system crashes after one step when run (on tcbs28) with the output
Program mdrun, VERSION 5.0.1-dev-20140820-bad36c3
Source code file: /nethome/lindahl/Code/gmx/git/50/gromacs/src/gromacs/mdlib/pme.c, line: 754
33 particles communicated to PME rank 11 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
When run with the command:
"mdrun -v -deffnm test -nb cpu -nt 32 -ntomp 2"
When using "mdrun -v -deffnm test -nb cpu -nt 32 -ntomp 1" it works fine.