Hello everyone:
I am very confused about the command of kspace_style, when I use the
command like this:
pair_style buck/coul/long 10.0
kspace_style ewald 1.0e-4
the in file run thoroughly with no errors, but when I change the command to
kspace_style pppm 1.0e-4
it has errors in the beginning :
Memory usage per processor = 55.8633 Mbytes
Step Temp Press PotEng KinEng TotEng Volume walltemp
0 7291.4465 nan nan 10805.687 nan
153501.75 306.21026
[node1:26971] *** Process received signal ***
[node1:26971] Signal: Segmentation fault (11)
[node1:26971] Signal code: Address not mapped (1)
[node1:26971] Failing at address: 0x2ab989adc4d0
[node1:26971] [ 0] /lib64/libpthread.so.0 [0x2ab9b9308c00]
[node1:26971] [ 1]
./lmp_linux(_ZN9LAMMPS_NS16PairBuckCoulLong7computeEii+0x280)
[0x641db6]
[node1:26971] [ 2] ./lmp_linux(_ZN9LAMMPS_NS6Verlet3runEi+0x4a9) [0x707d0f]
[node1:26971] [ 3] ./lmp_linux(_ZN9LAMMPS_NS3Run7commandEiPPc+0xb77) [0x6e5bab]
[node1:26971] [ 4]
./lmp_linux(_ZN9LAMMPS_NS5Input15execute_commandEv+0x277f) [0x5d30ef]
[node1:26971] [ 5] ./lmp_linux(_ZN9LAMMPS_NS5Input4fileEv+0x299) [0x5d4939]
[node1:26971] [ 6] ./lmp_linux(main+0xa7) [0x5ddddf]
[node1:26971] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2ab9b9f5e184]
[node1:26971] [ 8] ./lmp_linux(_ZNSt8ios_base4InitD1Ev+0x39) [0x4651a9]
[node1:26971] *** End of error message ***
Segmentation fault
I don't know what's wrong with it, could someone help me?
Hello everyone:
I am very confused about the command of kspace_style, when I use the
command like this:
pair_style buck/coul/long 10.0
kspace_style ewald 1.0e-4
the in file run thoroughly with no errors, but when I change the command to
kspace_style pppm 1.0e-4
it has errors in the beginning :
Memory usage per processor = 55.8633 Mbytes
Step Temp Press PotEng KinEng TotEng Volume walltemp
0 7291.4465 nan nan 10805.687 nan
153501.75 306.21026
is your temperature supposed to be this high?
also you potential energy seems to be bust.
are you sure your input is reasonable?
[node1:26971] *** Process received signal ***
[node1:26971] Signal: Segmentation fault (11)
[node1:26971] Signal code: Address not mapped (1)
[node1:26971] Failing at address: 0x2ab989adc4d0
[node1:26971] [ 0] /lib64/libpthread.so.0 [0x2ab9b9308c00]
[node1:26971] [ 1]
./lmp_linux(_ZN9LAMMPS_NS16PairBuckCoulLong7computeEii+0x280)
[0x641db6]
[node1:26971] [ 2] ./lmp_linux(_ZN9LAMMPS_NS6Verlet3runEi+0x4a9) [0x707d0f]
[node1:26971] [ 3] ./lmp_linux(_ZN9LAMMPS_NS3Run7commandEiPPc+0xb77) [0x6e5bab]
[node1:26971] [ 4]
./lmp_linux(_ZN9LAMMPS_NS5Input15execute_commandEv+0x277f) [0x5d30ef]
[node1:26971] [ 5] ./lmp_linux(_ZN9LAMMPS_NS5Input4fileEv+0x299) [0x5d4939]
[node1:26971] [ 6] ./lmp_linux(main+0xa7) [0x5ddddf]
[node1:26971] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2ab9b9f5e184]
[node1:26971] [ 8] ./lmp_linux(_ZNSt8ios_base4InitD1Ev+0x39) [0x4651a9]
[node1:26971] *** End of error message ***
Segmentation fault
I don't know what's wrong with it, could someone help me?
it is impossible to provide specific help without knowing
anything about what you are trying to do and particularly
having the means to reproduce your problem.
cheers,
axel.
sorry, i used a special case in the letter. I want to relax the sio2
system in npt ensemble with the pressure 1bar,while I use the
kspace_style ewald , it goes well and the log file shows this:
Ewald initialization ...
G vector = 0.273155
vectors: actual 1d max = 396 6 1098
Memory usage per processor = 2.74601 Mbytes
Step Temp Press PotEng KinEng TotEng Volume mypress[ mypress[ mypress[
mypress[ mypress[ mypress[
0 299.62917 51877.351 -11149.463 31.332659
-11118.13 10169.163 50021.494 49479.565 56130.994
-139.40275 25.437591 200.36478
1000 299.62917 52166.778 -11148.921 31.332659
-11117.588 10169.163 50617.354 49777.674 56105.306
251.01978 -519.19048 -236.14972
2000 299.62917 52964.171 -11147.458 31.332659
-11116.126 10169.163 51690.799 50571.845 56629.871
620.20029 -1053.6227 -621.33532
3000 299.62917 54256.188 -11145.139 31.332659
-11113.807 10169.163 53232.18 51858.029 57678.354
954.14082 -1575.3949 -954.28551
4000 299.62917 55927.731 -11142.198 31.332659
-11110.866 10169.163 55101.098 53535.775 59146.32
1255.7664 -2082.7187 -1239.3433
5000 299.62917 57823.363 -11138.955 31.332659
-11107.623 10169.163 57124.027 55447.476 60898.584
1497.4503 -2575.1906 -1474.9281
6000 299.62917 59786.725 -11135.747 31.332659
-11104.415 10169.163 59131.771 57455.945 62772.458
1664.7374 -3043.8346 -1665.21
while pppm:
Scanning data file ...
Reading data file ...
orthogonal box = (-0.311 1.042 -0.322) to (25.218 25.608 15.893)
1 by 1 by 1 processor grid
810 atoms
810 velocities
Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
270 atoms in group si
540 atoms in group o
PPPM initialization ...
G vector = 0.224358
grid = 8 8 6
stencil order = 5
RMS precision = 0.00212209
brick FFT buffer size/proc = 1859 384 1521
Setting up run ...
[node1:31183] *** Process received signal ***
[node1:31183] Signal: Segmentation fault (11)
[node1:31183] Signal code: Address not mapped (1)
[node1:31183] Failing at address: (nil)
[node1:31183] [ 0] /lib64/libpthread.so.0 [0x2b3e11a07c00]
[node1:31183] [ 1] ./lmp_buck [0x70d434]
[node1:31183] [ 2] ./lmp_buck(fftw+0xb9) [0x70d5fc]
[node1:31183] [ 3]
./lmp_buck(_Z6fft_3dP12fftw_complexS0_iP11fft_plan_3d+0xd0) [0x51edd0]
[node1:31183] [ 4] ./lmp_buck(_ZN9LAMMPS_NS5FFT3d7computeEPdS1_i+0x18)
[0x51efea]
[node1:31183] [ 5] ./lmp_buck(_ZN9LAMMPS_NS4PPPM7computeEii+0x188) [0x6b3730]
[node1:31183] [ 6] ./lmp_buck(_ZN9LAMMPS_NS6Verlet5setupEv+0x49d) [0x7071d5]
[node1:31183] [ 7] ./lmp_buck(_ZN9LAMMPS_NS3Run7commandEiPPc+0xb33) [0x6e5b67]
[node1:31183] [ 8]
./lmp_buck(_ZN9LAMMPS_NS5Input15execute_commandEv+0x277f) [0x5d30ef]
[node1:31183] [ 9] ./lmp_buck(_ZN9LAMMPS_NS5Input4fileEv+0x299) [0x5d4939]
[node1:31183] [10] ./lmp_buck(main+0xa7) [0x5ddddf]
[node1:31183] [11] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b3e1265d184]
[node1:31183] [12] ./lmp_buck(_ZNSt8ios_base4InitD1Ev+0x39) [0x4651a9]
[node1:31183] *** End of error message ***
Segmentation fault
the system is very simple and there is no specific setup in the input file.
lisa,
that doesn't really help much. it could just be that
your binary is not using the right FFT. please try
the peptide example input in the distribution and
see if pppm works for you at all.
also, what version of LAMMPS are you using and
what platform are you running on.
if the peptide example works correctly.
the only way to track this down would be to
send a small input that reproduces the crash
to the lists, so that somebody can run it in a
debugger (or you would have to do this yourself).
i use pppm all the time and i spent a significant
time testing and reading the code, when i integrated
support for FFTW3 and single precision FFTS into
my tree. it works fine if i feed it the right input, so i
can only assume that you are doing something with
it that is not correct or are using a version with a
known (and fixed) bug.
axel.
I use 8Mar10 version of lammps and run it in Suse LINUX cluster system
with mpirun. where can i found the peptide example? Here is my input
file:
#relax file
units metal
atom_style full
boundary p p p
read_data data.810
timestep 0.000001
pair_style buck/coul/long 10.0
pair_coeff 1 1 3150.462646 0.350699 626.751953
pair_coeff 1 2 27029.419922 0.193851 148.099091
pair_coeff 2 2 659.595398 0.386091 26.836679
neighbor 2.0 bin
neigh_modify every 100 delay 0 check no
kspace_style pppm 1.0e-4
group si type 1
group o type 2
compute mke all ke/atom
compute mytemp all temp
compute mypress all pressure mytemp
compute mycoord all coord/atom 2.0
fix 2 all npt 300.0 300.0 0.0001 aniso 50000.0 50000.0 50000.0 50000.0
50000.0 50000.0 0.0005 drag 0.5
dump 2 all custom 10000 dumpnpt.lammpstrj id type x y z
c_mycoord c_mke
thermo 10000
thermo_style custom step temp press pe ke etotal
vol c_mypress[1] c_mypress[2] c_mypress[3] c_mypress[4]
c_mypress[5] c_mypress[6]
thermo_modify lost warn
run 1000000
write_restart npt.*
data file is attacked.
data.810 (145 KB)
I use 8Mar10 version of lammps and run it in Suse LINUX cluster system
with mpirun. where can i found the peptide example? Here is my input
of course in the example/peptide directory of the lammps distribution.
i tried your input and it works just fine for me. so quite possibly
you have linked a single precision version of fftw2 to lammps executable.
axel.