FFTW Regarding

Hi steve,

I am trying to simulate PPPM using FFTW which I have installed for first time.

I encountered the following error during simulation:

LAMMPS (25 Mar 2011)
Scanning data file …
2 = max bonds/atom
1 = max angles/atom
Reading data file …
orthogonal box = (0 0 0) to (3.10737 3.10737 3.10737)
1 by 1 by 1 processor grid
3 atoms
2 bonds
1 angles
Finding 1-2 1-3 1-4 neighbors …
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Replicating atoms …
orthogonal box = (0 0 0) to (31.0737 31.0737 31.0737)
1 by 1 by 1 processor grid
3000 atoms
2000 bonds
1000 angles
Finding 1-2 1-3 1-4 neighbors …
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Finding SHAKE clusters …
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
1000 = # of frozen angles
PPPM initialization …
G vector = 0.315973
grid = 20 20 20
stencil order = 5
RMS precision = 5.50411e-05
brick FFT buffer size/proc = 19683 8000 8748
Setting up run …
*** glibc detected *** ./lmp_serial: free(): invalid next size (normal): 0x0a200d60 ***
======= Backtrace: =========
/lib/libc.so.6(+0x6c501)[0xb74c8501]
/lib/libc.so.6(+0x6dd70)[0xb74c9d70]
/lib/libc.so.6(cfree+0x6d)[0xb74cce5d]
./lmp_serial[0x815d027]
./lmp_serial[0x8067445]
./lmp_serial[0x8063a4d]
./lmp_serial[0x807bb4b]
./lmp_serial[0x8220133]
./lmp_serial[0x8205216]
./lmp_serial[0x81542e2]
./lmp_serial[0x8154727]
./lmp_serial[0x815ce78]
/lib/libc.so.6(__libc_start_main+0xe7)[0xb7472ce7]
./lmp_serial[0x80494e1]
======= Memory map: ========
08048000-08295000 r-xp 00000000 08:07 5312340 /home/saurav/Desktop/water/lmp_serial
08295000-08296000 r–p 0024c000 08:07 5312340 /home/saurav/Desktop/water/lmp_serial
08296000-08297000 rw-p 0024d000 08:07 5312340 /home/saurav/Desktop/water/lmp_serial
0a158000-0a6dd000 rw-p 00000000 00:00 0 [heap]
b7000000-b7021000 rw-p 00000000 00:00 0
b7021000-b7100000 —p 00000000 00:00 0
b7106000-b718d000 rw-p 00000000 00:00 0
b718d000-b7214000 rw-p 00000000 00:00 0
b7214000-b72b3000 rw-p 00000000 00:00 0
b72bc000-b7387000 rw-p 00000000 00:00 0
b739a000-b745c000 rw-p 00000000 00:00 0
b745c000-b75b3000 r-xp 00000000 08:07 1572985 /lib/libc-2.12.1.so
b75b3000-b75b5000 r–p 00157000 08:07 1572985 /lib/libc-2.12.1.so
b75b5000-b75b6000 rw-p 00159000 08:07 1572985 /lib/libc-2.12.1.so
b75b6000-b75b9000 rw-p 00000000 00:00 0
b75b9000-b75d3000 r-xp 00000000 08:07 1572887 /lib/libgcc_s.so.1
b75d3000-b75d4000 r–p 00019000 08:07 1572887 /lib/libgcc_s.so.1
b75d4000-b75d5000 rw-p 0001a000 08:07 1572887 /lib/libgcc_s.so.1
b75d5000-b75d6000 rw-p 00000000 00:00 0
b75d6000-b75fa000 r-xp 00000000 08:07 1572994 /lib/libm-2.12.1.so
b75fa000-b75fb000 r–p 00023000 08:07 1572994 /lib/libm-2.12.1.so
b75fb000-b75fc000 rw-p 00024000 08:07 1572994 /lib/libm-2.12.1.so
b75fc000-b76db000 r-xp 00000000 08:07 3999353 /usr/lib/libstdc++.so.6.0.14
b76db000-b76df000 r–p 000de000 08:07 3999353 /usr/lib/libstdc++.so.6.0.14
b76df000-b76e0000 rw-p 000e2000 08:07 3999353 /usr/lib/libstdc++.so.6.0.14
b76e0000-b76e7000 rw-p 00000000 00:00 0
b76f7000-b76fc000 rw-p 00000000 00:00 0
b76fc000-b76fd000 r-xp 00000000 00:00 0 [vdso]
b76fd000-b7719000 r-xp 00000000 08:07 1572971 /lib/ld-2.12.1.so
b7719000-b771a000 r–p 0001b000 08:07 1572971 /lib/ld-2.12.1.so
b771a000-b771b000 rw-p 0001c000 08:07 1572971 /lib/ld-2.12.1.so
bfc91000-bfcb2000 rw-p 00000000 00:00 0 [stack]
Aborted

I would try the latest fully-patched version and see
if the problem goes away. Some recent changes to
memory allocation introduced a few bugs which
have hopefully now been eliminated.

Steve

Hi Steve,

Thanks for your response… I will await your confirmation.

Regards,
Saurav

If you are awaiting confirmation, you may have misread Steve’s reply. When someone says “I would try …” in this context, you can replace it with “If I were you, I would try …”. He is expecting you to try the latest version.

Lisa

Hi Lisa,

Thanks for your email & clarification. Earlier, I tried in the latest version of 25th March 2010.
Taking your email into consideration I’ll try it once again on 29th March 2010 version now.

Regards,
Saurav