[Pw_forum] "xspectra.x" crashed with segmentation fault
Abdulrafiu Raji
abdulrafiuraji at gmail.com
Fri Jul 22 12:53:00 CEST 2011
Thank you. I compiled the xspectra.x and pw.x executables with the same
compiler on the same machine. The program ran for few seconds and the
initial error message :"cannot open
/home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/charge-density.dat file" did
not appear anymore. However, the program stopped abruptly. I write below,
respectively, the output and the accompanying error messages.
Please note that the Xspectra examples in the code ran perfectly well on the
machine.
Thanks for your attention
Abdulrafiu Tunde Raji
ICTP, Trieste.
Italy.
============
Program XSPECTRA v.4.2.1 starts on 22Jul2011 at 11:48:23
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please acknowledge
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details
at
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
Parallel version (MPI), running on 8 processors
R & G space division: proc/pool = 8
bef
Planes per process (thick) : nr3 = 80 npp = 10 ncplane = 5625
Planes per process (smooth): nr3s= 60 npps= 8 ncplanes= 2916
Proc/ planes cols G planes cols G columns G
Pool (dense grid) (smooth grid) (wavefct grid)
1 10 447 23677 8 238 9232 73 1579
2 10 446 23674 8 238 9228 73 1579
3 10 446 23674 8 238 9222 73 1579
4 10 446 23674 8 238 9216 73 1579
5 10 446 23674 7 238 9210 73 1579
6 10 446 23674 7 238 9200 73 1579
7 10 446 23674 7 238 9202 73 1579
8 10 448 23676 7 237 9199 72 1574
tot 80 3571 189397 60 1903 73709 583 12627
af
k-points : nkstot= 27
-------------- Crystal Structure ------------
celldm(1:6)
18.57259936 0.00000000 1.10010000
0.00000000 0.00000000 0.00000000
direct lattice vectors
1.00000000 -0.50000000 0.00000000
0.00000000 0.86602540 0.00000000
0.00000000 0.00000000 1.10010000
reciprocal lattice vectors
1.00000000 0.00000000 0.00000000
0.57735027 1.15470054 -0.00000000
-0.00000000 0.00000000 0.90900827
nks= 27 nkstot= 27
----k-point list [units 2*pi/celldm(1)], weight---------
1 0.00000000 0.00000000 0.00000000 0.07407407
2 0.00000000 0.00000000 0.30300276 0.07407407
3 0.00000000 0.00000000 0.60600551 0.07407407
4 0.00000000 0.38490018 0.00000000 0.07407407
5 0.00000000 0.38490018 0.30300276 0.07407407
6 0.00000000 0.38490018 0.60600551 0.07407407
7 0.00000000 0.76980036 0.00000000 0.07407407
8 0.00000000 0.76980036 0.30300276 0.07407407
9 0.00000000 0.76980036 0.60600551 0.07407407
10 0.33333333 0.19245009 0.00000000 0.07407407
11 0.33333333 0.19245009 0.30300276 0.07407407
12 0.33333333 0.19245009 0.60600551 0.07407407
13 0.33333333 0.57735027 0.00000000 0.07407407
14 0.33333333 0.57735027 0.30300276 0.07407407
15 0.33333333 0.57735027 0.60600551 0.07407407
16 0.33333333 0.96225045 0.00000000 0.07407407
17 0.33333333 0.96225045 0.30300276 0.07407407
18 0.33333333 0.96225045 0.60600551 0.07407407
19 0.66666667 0.38490018 0.00000000 0.07407407
20 0.66666667 0.38490018 0.30300276 0.07407407
21 0.66666667 0.38490018 0.60600551 0.07407407
22 0.66666667 0.76980036 0.00000000 0.07407407
23 0.66666667 0.76980036 0.30300276 0.07407407
24 0.66666667 0.76980036 0.60600551 0.07407407
25 0.66666667 1.15470054 0.00000000 0.07407407
26 0.66666667 1.15470054 0.30300276 0.07407407
27 0.66666667 1.15470054 0.60600551 0.07407407
-------------------------------------------------
--- Polarisation and k vector [cartesian coordinates]----
xepsilon(:)= 0.50000000 0.86602540 0.00000000
xkvec(:)= 1.00000000 0.00000000 0.00000000
xmesh= 899
====================================
[node26:10484] *** Process received signal ***
[node26:10485] *** Process received signal ***
[node26:10485] Signal: Segmentation fault (11)
[node26:10485] Signal code: Address not mapped (1)
[node26:10485] Failing at address: 0x111d00
[node26:10482] *** Process received signal ***
[node26:10482] Signal: Segmentation fault (11)
[node26:10482] Signal code: Address not mapped (1)
[node26:10482] Failing at address: 0x111d00
[node26:10484] Signal: Segmentation fault (11)
[node26:10484] Signal code: Address not mapped (1)
[node26:10484] Failing at address: 0x111d00
[node26:10481] *** Process received signal ***
[node26:10481] Signal: Segmentation fault (11)
[node26:10481] Signal code: Address not mapped (1)
[node26:10481] Failing at address: 0x111d00
[node26:10485] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10485] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10485] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10485] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10485] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10485] *** End of error message ***
[node26:10482] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10482] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10482] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10482] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10482] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10482] *** End of error message ***
[node26:10484] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10484] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10484] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10484] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10484] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10484] *** End of error message ***
[node26:10487] *** Process received signal ***
[node26:10487] Signal: Segmentation fault (11)
[node26:10487] Signal code: Address not mapped (1)
[node26:10487] Failing at address: 0x111d00
[node26:10487] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10487] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10487] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10487] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10487] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10487] *** End of error message ***
[node26:10481] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10481] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10481] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10481] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10481] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10481] *** End of error message ***
[node26:10480] *** Process received signal ***
[node26:10480] Signal: Segmentation fault (11)
[node26:10480] Signal code: Address not mapped (1)
[node26:10480] Failing at address: 0x111d00
[node26:10483] *** Process received signal ***
[node26:10483] Signal: Segmentation fault (11)
[node26:10483] Signal code: Address not mapped (1)
[node26:10483] Failing at address: 0x111d00
[node26:10486] *** Process received signal ***
[node26:10486] Signal: Segmentation fault (11)
[node26:10486] Signal code: Address not mapped (1)
[node26:10486] Failing at address: 0x111d00
[node26:10480] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10480] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10480] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10480] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10480] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10480] *** End of error message ***
[node26:10483] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10483] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10483] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10483] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10483] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10483] *** End of error message ***
[node26:10486] [ 0] /lib64/libpthread.so.0 [0x3c7080eb10]
[node26:10486] [ 1] /home/araji/espresso-4.2.1/bin/xspectra.x(MAIN__+0x39e3)
[0x444d93]
[node26:10486] [ 2] /home/araji/espresso-4.2.1/bin/xspectra.x(main+0x2a)
[0x68967a]
[node26:10486] [ 3] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c7001d994]
[node26:10486] [ 4] /home/araji/espresso-4.2.1/bin/xspectra.x [0x42a659]
[node26:10486] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 10482 on node node26.hpc exited
on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
3. Re: Pw_forum Digest, Vol 49, Issue 53 (Paolo Giannozzi)
>
> Message: 3
> Date: Wed, 20 Jul 2011 21:15:56 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 49, Issue 53
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <7F4B01A5-0DC1-457A-9A67-A8A2F9D19D8D at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On Jul 20, 2011, at 18:52 , Abdulrafiu Raji wrote:
>
> > cannot open /home/araji/XAS_SiO2_scr.1/qtz_ar1SCF_kp2.save/
> > charge-density.dat file
>
> it is not there, or it is corrupted, or empty, or not in the right
> format.
> Note that it is a binary file that should be written by and read by
> executables compiled with the same compiler on th same machine,
> as a rule
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
>
>
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