[DFTB-Plus-User] MPI Version crashes

Silvio a Beccara s.abeccara at gmail.com
Tue Sep 3 13:08:13 CEST 2013


Dear DFTB+ developers,

I have tried to compile the MPI parallel version of DFTB+.

After correcting a few issues, such as array allocationswhich did not go 
through, at least with the GCCcompilers suite, I managed to obtain 
anexecutable,
but it crashes nearly immediatelyupon execution. I tried to locate the 
source of the problem, and it seems that some structures are used 
without being properly initialised.

This is the output of GDB:


--------------------------------------------------------------------------------
Starting initialization...

Program received signal SIGSEGV, Segmentation fault.
0x000000000062e658 in blacsgrid_module::initgrids (self=..., ngrid=1, 
nrow=1,
      ncol=2,
colmajor=<error reading variable: Cannot access memory at address 0x0>,
masterrow=<error reading variable: Cannot access memory at address 0x0>,
mastercol=<error reading variable: Cannot access memory at address 0x0>,
context=<error reading variable: Cannot access memory at address 0x0>,
mastergrid=<error reading variable: Cannot access memory at address 0x0>)
      at blacsgrid.f90:158

--------------------------------------------------------------------------------


I am attaching the input and the log files.

Kind regards

Silvio a Beccara
LISC - Fondazione Bruno Kessler
18 via Sommarive
38123 Povo TN
ITALY

-------------- next part --------------
================================================================================
==
==   DFTB+ (Density Functional Tight Binding and much more)
==
==                          Unofficial release (r4423)
==
==                            (ParserVersion = 4)
==
================================================================================

********************************************************************************
** Parsing and initializing
********************************************************************************

Interpreting input file 'dftb_in.hsd'
--------------------------------------------------------------------------------
Reading SK-files:
  C-C.skf
  C-N.skf
  C-O.skf
  C-S.skf
  C-H.skf
  N-C.skf
  N-N.skf
  N-O.skf
  N-S.skf
  N-H.skf
  O-C.skf
  O-N.skf
  O-O.skf
  O-S.skf
  O-H.skf
  S-C.skf
  S-N.skf
  S-O.skf
  S-S.skf
  S-H.skf
  H-C.skf
  H-N.skf
  H-O.skf
  H-S.skf
  H-H.skf
Done.
[lares:05389] *** Process received signal ***
[lares:05389] Signal: Segmentation fault (11)
[lares:05389] Signal code: Address not mapped (1)
[lares:05389] Failing at address: 0x8
[lares:05389] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f068b7e24a0]


Processed input in HSD format written to 'dftb_pin.hsd'

Starting initialization...
--------------------------------------------------------------------------------
[lares:05389] [ 1] /home/silvio/bin/dftb_mpi(__blacsgrid_module_MOD_initgrids+0x4d) [0x62e658]
[lares:05387] *** Process received signal ***
[lares:05389] [ 2] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initgrids+0x623) [0x490157]
[lares:05389] [ 3] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initprogramvariables+0x54c7) [0x495a6d]
[lares:05389] [ 4] /home/silvio/bin/dftb_mpi(__dftbplus_MOD_dftbp+0xa62) [0x424e69]
[lares:05389] [ 5] /home/silvio/bin/dftb_mpi() [0x4210ac]
[lares:05389] [ 6] /home/silvio/bin/dftb_mpi(main+0x34) [0x4210ec]
[lares:05389] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f068b7cd76d]
[lares:05389] [ 8] /home/silvio/bin/dftb_mpi() [0x420fd9]
[lares:05389] *** End of error message ***
[lares:05387] Signal: Segmentation fault (11)
[lares:05387] Signal code: Address not mapped (1)
[lares:05387] Failing at address: 0x8
[lares:05387] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7fe7871c74a0]
[lares:05387] [ 1] /home/silvio/bin/dftb_mpi(__blacsgrid_module_MOD_initgrids+0x4d) [0x62e658]
[lares:05387] [ 2] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initgrids+0x623) [0x490157]
[lares:05387] [ 3] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initprogramvariables+0x54c7) [0x495a6d]
[lares:05387] [ 4] /home/silvio/bin/dftb_mpi(__dftbplus_MOD_dftbp+0xa62) [0x424e69]
[lares:05387] [ 5] /home/silvio/bin/dftb_mpi() [0x4210ac]
[lares:05387] [ 6] /home/silvio/bin/dftb_mpi(main+0x34) [0x4210ec]
[lares:05387] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fe7871b276d]
[lares:05387] [ 8] /home/silvio/bin/dftb_mpi() [0x420fd9]
[lares:05387] *** End of error message ***
[lares:05388] *** Process received signal ***
[lares:05388] Signal: Segmentation fault (11)
[lares:05388] Signal code: Address not mapped (1)
[lares:05388] Failing at address: 0x8
[lares:05388] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7fe53aa274a0]
[lares:05388] [ 1] /home/silvio/bin/dftb_mpi(__blacsgrid_module_MOD_initgrids+0x4d) [0x62e658]
[lares:05388] [ 2] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initgrids+0x623) [0x490157]
[lares:05388] [ 3] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initprogramvariables+0x54c7) [0x495a6d]
[lares:05388] [ 4] /home/silvio/bin/dftb_mpi(__dftbplus_MOD_dftbp+0xa62) [0x424e69]
[lares:05388] [ 5] /home/silvio/bin/dftb_mpi() [0x4210ac]
[lares:05388] [ 6] /home/silvio/bin/dftb_mpi(main+0x34) [0x4210ec]
[lares:05388] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7fe53aa1276d]
[lares:05388] [ 8] /home/silvio/bin/dftb_mpi() [0x420fd9]
[lares:05388] *** End of error message ***
[lares:05390] *** Process received signal ***
[lares:05390] Signal: Segmentation fault (11)
[lares:05390] Signal code: Address not mapped (1)
[lares:05390] Failing at address: 0x8
[lares:05390] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x364a0) [0x7f582e0694a0]
[lares:05390] [ 1] /home/silvio/bin/dftb_mpi(__blacsgrid_module_MOD_initgrids+0x4d) [0x62e658]
[lares:05390] [ 2] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initgrids+0x623) [0x490157]
[lares:05390] [ 3] /home/silvio/bin/dftb_mpi(__initprogram_MOD_initprogramvariables+0x54c7) [0x495a6d]
[lares:05390] [ 4] /home/silvio/bin/dftb_mpi(__dftbplus_MOD_dftbp+0xa62) [0x424e69]
[lares:05390] [ 5] /home/silvio/bin/dftb_mpi() [0x4210ac]
[lares:05390] [ 6] /home/silvio/bin/dftb_mpi(main+0x34) [0x4210ec]
[lares:05390] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f582e05476d]
[lares:05390] [ 8] /home/silvio/bin/dftb_mpi() [0x420fd9]
[lares:05390] *** End of error message ***
--------------------------------------------------------------------------
mpirun.openmpi noticed that process rank 2 with PID 5389 on node lares exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
-------------- next part --------------
Geometry = GenFormat {
<<< "closed-mopopt.gen"
}
Driver = {}
Hamiltonian = DFTB {
SCC = no
Dispersion = lennardjones {
Parameters = UFFParameters {}
}
SlaterKosterFiles {
C-C = "C-C.skf"
C-N = "C-N.skf"
C-S = "C-S.skf"
C-O = "C-O.skf"
O-C = "O-C.skf"
O-O = "O-O.skf"
O-S = "O-S.skf"
O-H = "O-H.skf"
H-O = "H-O.skf"
S-O = "S-O.skf"
S-C = "S-C.skf"
C-H = "C-H.skf"
H-C = "H-C.skf"
H-S = "H-S.skf"
N-N = "N-N.skf"
N-C = "N-C.skf"
N-O = "N-O.skf"
N-S = "N-S.skf"
N-H = "N-H.skf"
H-N = "H-N.skf"
S-N = "S-N.skf"
O-N = "O-N.skf"
S-H = "S-H.skf"
S-S = "S-S.skf"
H-H = "H-H.skf"
}
MaxAngularMomentum {
H = "s"
C = "p"
N = "p"
O = "p"
S = "d"
}
Filling = Fermi {
Temperature [Kelvin] = 0.0
}
}
Options {
WriteEigenvectors = no 
CalculateForces = yes
}
ParserOptions {
ParserVersion = 4
}


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