segmentation fault

[mdasta]

Hello,

I am using the bader code for a zeolite type of material containing 408 atoms and a non-orthogonal (bcc primitive) unit cell. I am using VASP with PAW and am trying to test the convergence of the bader charges with respect to NGXF,Y,Z. In running bader for a 480x480x480 mesh, I run into a segmentaiton fault. The output of the code is given below. Please let me know what you suggest.

Thanks for your help!


GRID BASED BADER ANALYSIS (v0.26a 08/07/09)

OPEN ... CHGCAR
VASP-STYLE INPUT FILE
FFT-grid: 480 x 480 x 480
CLOSE ... CHGCAR

RUN TIME: 88.92 SECONDS

OPEN ... CHGCAR_sum
VASP-STYLE INPUT FILE
FFT-grid: 480 x 480 x 480
CLOSE ... CHGCAR_sum

RUN TIME: 90.29 SECONDS

CALCULATING BADER CHARGE DISTRIBUTION
0 10 25 50 75 100
PERCENT DONE: **********************

REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 98256719

REASSIGNED POINTS:17706496
ITERATION: 2
CHECKED POINTS: 84049741
REASSIGNED POINTS: 102831
ITERATION: 3
CHECKED POINTS: 1225362
REASSIGNED POINTS: 25288
ITERATION: 4
CHECKED POINTS: 309719
REASSIGNED POINTS: 9167
ITERATION: 5
CHECKED POINTS: 115334
REASSIGNED POINTS: 4207
ITERATION: 6
CHECKED POINTS: 53560
REASSIGNED POINTS: 2078
ITERATION: 7
CHECKED POINTS: 28570
REASSIGNED POINTS: 1037
ITERATION: 8
CHECKED POINTS: 15642
REASSIGNED POINTS: 587
ITERATION: 9
CHECKED POINTS: 9768
REASSIGNED POINTS: 353
ITERATION:10
CHECKED POINTS: 5762
REASSIGNED POINTS: 217
ITERATION:11
CHECKED POINTS: 3478
REASSIGNED POINTS: 142
ITERATION:12
CHECKED POINTS: 2364
REASSIGNED POINTS: 117
ITERATION:13
CHECKED POINTS: 1867
REASSIGNED POINTS: 101
ITERATION:14
CHECKED POINTS: 1555
REASSIGNED POINTS: 80
ITERATION:15
CHECKED POINTS: 1142
REASSIGNED POINTS: 82
ITERATION:16
CHECKED POINTS: 1029
REASSIGNED POINTS: 86
ITERATION:17
CHECKED POINTS: 888
REASSIGNED POINTS: 101
ITERATION:18
CHECKED POINTS: 965
REASSIGNED POINTS: 119
ITERATION:19
CHECKED POINTS: 1118
REASSIGNED POINTS: 108
ITERATION:20
CHECKED POINTS: 1044
REASSIGNED POINTS: 99
ITERATION:21
CHECKED POINTS: 878
REASSIGNED POINTS: 77
ITERATION:22
CHECKED POINTS: 778
REASSIGNED POINTS: 32
ITERATION:23
CHECKED POINTS: 462
REASSIGNED POINTS: 12
ITERATION:24
CHECKED POINTS: 198
REASSIGNED POINTS: 7
ITERATION:25
CHECKED POINTS: 126
REASSIGNED POINTS: 2
ITERATION:26
CHECKED POINTS: 47
REASSIGNED POINTS: 0
RUN TIME: 5142.31 SECONDS

CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************

RUN TIME: 138.60 SECONDS
Segmentation fault

[graeme]

My guess is that the program has run out of memory. Can you post the command that you ran? If you asked it to print any of the Bader or Atomic volumes, try turning that off. You could also just monitor the memory use as it runs and see if it hits the machine limit. The calculation is basically done at the point of the seg fault, so it may just be one last temporary array that is allocated for printing.

[mdasta]

The command I used was:

./bader CHGCAR -ref CHGCAR_sum

Your guess seems to be correct. I moved the job to a machine with more memory (8 Gigs instead of 4) and that solved the problem.