Hello Cíntia,
On 02/01/2013 04:19 PM, Cintia C. Vequi-Suplicy wrote:
Hello Ricardo,
I tried to decrease the integration time but I got the same error.
The system is running fine in my local core.
I have two questions:
1) What do you mean by "I balance the domain decomposition for the
larger number of core"?
When you run at your local hardware, the 8 cores handles your system
differently than the 1024, 2048 (or more) cores in bluegene. So you
must balance the number of cores with your system size. If you try to
run a small system in too many cores, an error may appear:
http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
So you must decrease their number, or assign different numbers of cores
only for PME (mdrun options). There's also the scalability/performance
issue....
2) Are you running simulations at Bluegene P at Rice University?
Yes!
Thank you,
Cíntia
On 30/01/2013 20:48, Ricardo Soares wrote:
Hello,
before submitting to Bluegene, I always test the system in my local 8
core
cpu, and if it works, it will also work in Bluegene, as long as I
balance the
domain decomposition for the larger number of cores. If your system
insists in
exploding, even after energy minimization, you could try to decrease the
integration timestep (dt) to something lower than 2 fs, maybe to 1fs
or, in
some cases even 0.5 fs. Did you tried that?
Cheers,
Ricardo.
On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote
Mark,
Thank you for your answer.
I did an energy minimization with the file em.mdp (below) and then I
did a 40 ns simulation with the same md.mdp I send before. These
two steps were done in my local cluster. After that I took the
configuration for the simulation in the bluegene and I got these
error. I notice that the step that the error occurs depends on the
number of nodes I use. I am also including the end of the min.out file.
I also tried others integrators for the energy minimization but I
always get the same error.
Thank you again,
Cíntia
-------------------------------------------------------
em.mdp
integrator = steep
tinit = 0.0
dt = 0.002
nsteps = 5000000
nstcomm = 1
comm-grps = Other SOL
nstxout = 100
nstvout = 100
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 100
xtc_precision = 100
xtc-grps =
energygrps = Other SOL
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = reaction-field
rcoulomb = 1.4
epsilon_rf = 66
vdw_type = cut-off
rvdw = 1.4
DispCorr = No
constraints = none
-------------------------------------------------------
min.out
...
Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 5199 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.79302464181879e+06
Maximum force = 6.65022934447791e+02 on atom 22015
Norm of force = 4.90065871184878e+00
gcq#0: Thanx for Using GROMACS - Have a Nice Day
-------------------------------------------------------
-------------------------------------------------------
md.mdp file
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 5000000
nstcomm = 5
comm-grps = Other SOL
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
xtc-grps =
energygrps = Other SOL
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = reaction-field
rcoulomb = 1.4
epsilon_rf = 66
vdw_type = cut-off
rvdw = 1.4
DispCorr = No
tcoupl = v-rescale
tc-grps = Other SOL
tau_t = 0.4 0.4
ref_t = 296 296
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 0.2 0.2
compressibility = 4.51e-5 4.51e-5
ref_p = 1.0 1.0
constraints = hbonds
constraint_algorithm = lincs
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