Dear friends ,
I am facing unusual problem with mpi version of AMBER 11 pmemd_cuda
compiled with mvapitch
My job stops writing output (trajectories, restart, .out) after some time
but while using top and pbs commands it shows pmemd in running status.
It is not even producing any error file also. After it if I kill it and
submit it again it start running.
Have anyone faced it ? If yes please let me know the problem as I am not
able to figure out it .
*
The machine is *
CUDA Device Name: Tesla M2090
*
Here is my input file
*
Initial minimization w/ position restraints on DNA, 9.0 cut
&cntrl
nmropt = 0,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
ntwprt = 0, ntwr = 500,
ntf = 2, ntb = 1, dielc = 1.0,
cut = 9.0, nsnb = 10,
ipol = 0,
ibelly = 0, ntr = 0,
imin = 0,
maxcyc = 5000,
ncyc = 2000,
ntmin = 1, dx0 = 0.1, dxm = 0.5, drms = 0.0001,
nstlim = 500000
nscm = 1000,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 10.0,
ig = 71277, heat = 0.0,
ntt = 1, dtemp = 0.0,
tautp = 1.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 0.5,
ntc = 2, tol = 0.0005,
&end
&ewald
a = 62.9065214, b = 46.8818659, c = 192.6251811,
&end
Thanks in advance
--
*With Regards,
HIMANSHU JOSHI
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
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Received on Wed Jun 27 2012 - 00:00:03 PDT
