[Smeagol-discuss] running example file

[asa aravindh]

Dear Ivan,
Thanks for your prompt reply.
The KINDS variable sets is for the MPICH threading specific to our system
architecture.

I face problem running most of the examples in parallel and some of the
examples in serial mode, provided with the smeagol distribution.  As I am a
beginner, I haven't tested my own systems . First I am  trying to run the
examples correctly, to learn the  parameter settings and all in detail.
Unforutnately even the examples, which were already tested successfully by
the developers, I am not able to run in my system. I will list out my
experience in running all examples in serial and parallel mode.
----------------------------------------------------------------
SERIAL RUNS
------------------------------------------------------------------
Successful Runs:   Fe, SiH, MgO, H2O, H2O (order N) , Au leads calculation
in the gamma directory, leads in the kpoints directory
----------------------------------------------------------------------------------------------------------------------------------------
Failed Cases: Capacitor and Infinite calculations in the kpoints directory,
Au wire calculation in the gamma directory
The error is: program stops at the same point for all runs, at memory
allocation, and not proceeding at all .

 siesta:                 ===============================
SMEAGOL                 Bias step =    0, V =  0.000 Ry
                            Begin CG move =      0
                        ===============================

InitMesh: MESH =   108 x   108 x   192 =     2239488
InitMesh: Mesh cutoff (required, used) =   200.000   203.052 Ry

* Maximum dynamic memory allocated =   136 MB
---------------------------------------------------------------------------------------------------------------------------------------------
************************************************************************************************************
PARALLEL RUN
************************************************************************************************************
Successful Cases: H2O,H2O(ordr N), SiH,
----------------------------------------------------------------------------------------------------------------------------------------
Failed Cases:  Fe, Auwire.fdf, Au leads ( both  in gamma directory),
Capacitor, Infinite and Leads( in kpoints directory) , MgO

error: In all calculations except for the Fe , program stops at the same
place giving the following error.I am pasting part of one output here.
-------------------------------------------------------------------------------------------

siesta: System type = bulk

siesta: k-grid: Number of k-points =    75
siesta: k-grid: Cutoff             =     7.248 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid:    5   0   0      0.000
siesta: k-grid:    0   5   0      0.000
siesta: k-grid:    0   0   5      0.000
siesta: overlap:  rmaxh   veclen  direction
siesta: overlap:  18.5553  5.4786   1
siesta: overlap:  rmaxh   veclen  direction
siesta: overlap:  18.5553  5.4786   2
siesta: overlap:  rmaxh   veclen  direction
siesta: overlap:  18.5553  5.4786   3

superc: Internal auxiliary supercell:     7 x     7 x     7  =     343
superc: Number of atoms, orbitals, and projectors:    686  1715  4459

* Maximum dynamic memory allocated =     2 MB

siesta:                 ===============================
                            Begin CG move =      0
                        ===============================

outcoor: Atomic coordinates (scaled):
    0.00000000    0.00000000    0.00000000   1  Mg         1
    0.50000000    0.50000000    0.50000000   2  O          2

superc: Internal auxiliary supercell:     7 x     7 x     7  =     343
superc: Number of atoms, orbitals, and projectors:    686  1715  4459
p3_22547:  p4_error: interrupt SIGSEGV: 11
p0_22067:  p4_error: interrupt SIGx: 13
p0_22067: (9.328125) net_send: could not write to fd=4, errno = 32
-------------------------------------------------------------------------------------------------------------------------------------
For Fe, the program proceeds till  23 scf iterations, and then stops with
following error


siesta: E_KS(eV) =             -782.2432

siesta: E_KS - E_eggbox =      -782.2432

siesta: Atomic forces (eV/Ang):
*** glibc detected *** /home/rocks2/smathi/test/smeagol.1.0b/Src/smeagol:
free(): invalid next size (fast): 0x0000000016da2370 ***
*** glibc detected *** /home/rocks2/smathi/test/smeagol.1.0b/Src/smeagol:
free(): invalid next size (fast): 0x0000000008fd82a0 ***
*** glibc detected *** /home/rocks2/smathi/test/smeagol.1.0b/Src/smeagol:
free(): invalid next size (fast): 0x0000000008ecc3d0 ***
p0_13772:  p4_error: interrupt SIGx: 13
-----------------------------------------------------------------------------------------------------------------------------------------

Kindly guide me ,

Thanks and regards
Asa
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