Re: [ESPResSo-users] [SPAM] Re: activate magnetostatics method DipolarDi

At first, thanks for your quickly reply!

1. The I worte last mail is not clear and I didn't run the run-full.sh with mpirun and just changed the number of cores in the mpirun calls in run-full.sh.

2. I retried the script, and changed the following things:

1) pypresso=./pypresso in run-full.sh

2) since I met the following exception

Exception: Encoutered errors during integrate: ERROR: Please seed the random number generator.
ESPResSo can choose one for you with set_random_state_PRNG().

So, I added the following commands in the gen-system.py and run.py.

g.s.set_random_state_PRNG()

3. Then I executed bash run-full.sh

The same problem occurred again and the whole output is:

# Generate thermalized system
$mpirun -np 32 $pypresso gen-system.py --output_file full_system.pcl --steps 150
+ mpirun -np 32 ./pypresso gen-system.py --output_file full_system.pcl --steps 150
Box too small. Resizing
('box', array([ 142.6954458, 142.6954458, 142.6954458]))
('Moving particles by', array([ 71.3477229, 71.3477229, 71.3477229]))
3.04375
(0, 0.0014575600624084472, 'seconds per time step')
Box too big. Resizing
('box', array([ 120.30563526, 119.13493207, 119.32029661]))
('Moving particles by', array([-10.43444499, -11.66752103, -12.085865 ]))
2.25625
(1, 0.001327979564666748, 'seconds per time step')
Box too big. Resizing
('box', array([ 109.12181639, 108.17245726, 107.41240948]))
('Moving particles by', array([-7.05027172, -5.35029851, -5.54697319]))
2.25625
(2, 0.0015033197402954102, 'seconds per time step')
Box too big. Resizing
('box', array([ 101.08057713, 100.09778332, 99.71040269]))
('Moving particles by', array([-4.14163472, -2.79714755, -4.81336581]))
2.25625
(3, 0.0016785407066345216, 'seconds per time step')
Box too big. Resizing
('box', array([ 93.86391575, 93.57990064, 91.43426866]))
('Moving particles by', array([-4.15346032, -4.40448177, -4.00901207]))
2.25625
(4, 0.0022895312309265136, 'seconds per time step')
2.25625
(5, 0.0017555999755859376, 'seconds per time step')
Box too big. Resizing
('box', array([ 88.59403743, 86.45768828, 84.57835679]))
('Moving particles by', array([-1.75344572, -3.54188878, -3.46579655]))
1.69375
(6, 0.001645679473876953, 'seconds per time step')
1.46875
(7, 0.0018255019187927246, 'seconds per time step')
Box too big. Resizing
('box', array([ 83.04730876, 82.60606041, 84.04076722]))
('Moving particles by', array([-2.32061992, -0.92458869, 0.51134931]))
1.35625
(8, 0.0016590094566345216, 'seconds per time step')
1.35625
(9, 0.0016977190971374512, 'seconds per time step')
Box too big. Resizing
('box', array([ 79.148324 , 80.42770598, 78.99220223]))
('Moving particles by', array([-1.18519868, -0.90613815, -2.81163526]))
1.46875
(10, 0.0015981197357177734, 'seconds per time step')
1.35625
(11, 0.0016547608375549316, 'seconds per time step')
1.35625
(12, 0.0022620010375976564, 'seconds per time step')
1.35625
(13, 0.0018271684646606445, 'seconds per time step')
1.01875
(14, 0.0017157697677612305, 'seconds per time step')
Box too big. Resizing
('box', array([ 78.36157477, 74.10349715, 77.78254409]))
('Moving particles by', array([-0.94444026, -4.49338336, -0.1556677 ]))
1.01875
(15, 0.0015130901336669921, 'seconds per time step')
1.01875
(16, 0.0015798211097717285, 'seconds per time step')
1.35625
(17, 0.0016656303405761718, 'seconds per time step')
('Moving particles by', array([ 1.7529142, -0.638697 , -0.5294174]))
1.35625
(18, 0.0016450285911560059, 'seconds per time step')
('Moving particles by', array([-0.88488321, 0.85033374, 0.03089746]))
1.35625
(19, 0.0017591595649719238, 'seconds per time step')
('Moving particles by', array([-1.19734571, -1.00533589, 0.25366547]))
0.90625
(20, 0.002098069190979004, 'seconds per time step')
1.35625
(21, 0.0017566394805908203, 'seconds per time step')
1.35625
(22, 0.0017087888717651368, 'seconds per time step')
('Moving particles by', array([ 0.65383484, -0.46770508, -0.50826587]))
1.35625
(23, 0.0016969704627990722, 'seconds per time step')
('Moving particles by', array([-0.47322065, 0.27832029, 1.62113617]))
1.35625
(24, 0.0024384498596191407, 'seconds per time step')
1.35625
(25, 0.0016894412040710449, 'seconds per time step')
Box too small. Resizing
('box', array([ 77.90053028, 78.41043806, 78.61666092]))
('Moving particles by', array([-1.45010419, 1.51936425, -0.62638667]))
1.13125
(26, 0.0017900300025939942, 'seconds per time step')
('Moving particles by', array([-1.0504294 , 0.12455737, 1.85348189]))
1.35625
(27, 0.0018353986740112305, 'seconds per time step')
11: misplaced part id 6917. 0x2153bc8 != 0x2153e50
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 11 in communicator MPI_COMMUNICATOR 4
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

The version of Espreso is 4.0.2(Latest release 30-April-2019) and myconfig.hpp is in the attachment. In addition, I also attached the whole scripts I used!

Thanks a lot!

Best regards!

Ricky

From:	address@hidden
Subject:	Re: [ESPResSo-users] [SPAM] Re: activate magnetostatics method DipolarDirectSumCpu
Date:	Sun, 12 May 2019 23:07:00 +0800