parallel run using the wavelet basis-set
Posted: Mon Jun 30, 2014 10:46 am
Hi I encountered some problem when doing the tutorial lesson paral_gswvl section 2. I executed the command
mpirun -np 3 abinit<tgswvl_01.files>&log
but it failed and this error appear at the end of the log file:
*** glibc detected *** abinit: munmap_chunk(): invalid pointer: 0x0000000004afc0f0 ***
My gcc compiler is version 4.9.0 and openmpi is 1.8.1.
The generated log file cannot be attached for some reason, so I paste it as below. Thank you.
mpirun -np 3 abinit<tgswvl_01.files>&log
but it failed and this error appear at the end of the log file:
*** glibc detected *** abinit: munmap_chunk(): invalid pointer: 0x0000000004afc0f0 ***
My gcc compiler is version 4.9.0 and openmpi is 1.8.1.
The generated log file cannot be attached for some reason, so I paste it as below. Thank you.
Code: Select all
ABINIT
Give name for formatted input file:
tgswvl_01.in
Give name for formatted output file:
tgswvl_01.out
Give root name for generic input files:
tgswvl_01.i
Give root name for generic output files:
tgswvl_01.o
Give root name for generic temporary files:
tgswvl_01.tmp
.Version 7.6.2 of ABINIT
.(MPI version, prepared for a x86_64_linux_gnu4.4 computer)
.Copyright (C) 1998-2013 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
ABINIT is a project of the Universite Catholique de Louvain,
Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see http://www.abinit.org .
.Starting date : Tue 1 Jul 2014.
- ( at 00h26 )
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=== Build Information ===
Version : 7.6.2
Build target : x86_64_linux_gnu4.4
Build date : 20140414
=== Compiler Suite ===
C compiler : gnu4.4
CFLAGS : -g -O2 -mtune=native -march=native
C++ compiler : gnu4.4
CXXFLAGS : -g -O2 -mtune=native -march=native
Fortran compiler : gnu4.4
FCFLAGS : -g -ffree-line-length-none -fopenmp
FC_LDFLAGS :
=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : intel_xeon
=== Multicore ===
Parallel build : yes
Parallel I/O : yes
Time tracing : no
openMP support : yes
GPU support : no
=== Connectors / Fallbacks ===
Connectors on : yes
Fallbacks on : yes
DFT flavor : libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback
FFT flavor : fftw3
LINALG flavor : atlas
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : netcdf+etsf_io-fallback
=== Experimental features ===
Bindings : no
Exports : no
GW double-precision : yes
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -mtune=native -march=native
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:
CC_GNU CXX_GNU FC_GNU
HAVE_DFT_ATOMPAW HAVE_DFT_BIGDFT HAVE_DFT_LIBXC
HAVE_DFT_WANNIER90 HAVE_FC_ALLOCATABLE_DT... HAVE_FC_COMMAND_ARGUMENT
HAVE_FC_CPUTIME HAVE_FC_EXIT HAVE_FC_FLUSH
HAVE_FC_GAMMA HAVE_FC_GETENV HAVE_FC_INT_QUAD
HAVE_FC_IOMSG HAVE_FC_ISO_C_BINDING HAVE_FC_LONG_LINES
HAVE_FC_NULL HAVE_FC_STREAM_IO HAVE_FC_SYSTEM
HAVE_FFT HAVE_FFT_FFTW3 HAVE_FFT_MPI
HAVE_FFT_SERIAL HAVE_FORTRAN2003 HAVE_GW_DPC
HAVE_LIBPAW_ABINIT HAVE_LINALG HAVE_LINALG_SERIAL
HAVE_MPI HAVE_MPI2 HAVE_MPI_IO
HAVE_MPI_TYPE_CREATE_S... HAVE_NUMPY HAVE_OMP_COLLAPSE
HAVE_OPENMP HAVE_OS_LINUX HAVE_TIMER
HAVE_TIMER_ABINIT HAVE_TIMER_MPI HAVE_TIMER_SERIAL
HAVE_TRIO_ETSF_IO HAVE_TRIO_NETCDF USE_MACROAVE
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- input file -> tgswvl_01.in
- output file -> tgswvl_01.out
- root for input files -> tgswvl_01.i
- root for output files -> tgswvl_01.o
-instrng : 37 lines of input have been read from file tgswvl_01.in
iofn2 : Please give name of formatted atomic psp file
iofn2 : for atom type 1 , psp file is B-q3
read the values zionpsp= 3.0 , pspcod= 10 , lmax= 1
inpspheads : deduce mpsang = 2, n1xccc = 0.
invars1m : enter jdtset=0
invars1 : treat image number 1
symlatt : the Bravais lattice is cP (primitive cubic)
xangst is defined in input file
ingeo : takes atomic coordinates from input array xangst
--- !WARNING
message: |
Because icoulomb is 1, the average center of coordinates of the system has been translated to (0.5,0.5,0.5)
src_file: ingeo.F90
src_line: 1068
...
symlatt : the Bravais lattice is cP (primitive cubic)
symlatt : the Bravais lattice is cP (primitive cubic)
--- !COMMENT
message: |
The Bravais lattice determined only from the primitive
vectors, bravais(1)= 7, is more symmetric
than the real one, iholohedry= 1, obtained by taking into
account the atomic positions. Start deforming the primitive vector set.
src_file: symbrav.F90
src_line: 201
...
symlatt : the Bravais lattice is hR (rhombohedral)
--- !COMMENT
message: |
The Bravais lattice determined from modified primitive
vectors, bravais(1)= 5, has a lower symmetry than before,
but is still more symmetric than the real one, iholohedry= 1
obtained by taking into account the atomic positions.
src_file: symbrav.F90
src_line: 210
...
symlatt : the Bravais lattice is mC (one-face-centered monoclinic)
--- !COMMENT
message: |
The Bravais lattice determined from modified primitive
vectors, bravais(1)= 2, has a lower symmetry than before,
but is still more symmetric than the real one, iholohedry= 1
obtained by taking into account the atomic positions.
src_file: symbrav.F90
src_line: 210
...
symlatt : the Bravais lattice is aP (primitive triclinic)
symspgr : spgroup= 1 P1 (=C1^1)
getkgrid : length of smallest supercell vector (bohr)= 4.000000E+01
Simple Lattice Grid
getkgrid : length of smallest supercell vector (bohr)= 8.000000E+01
Simple Lattice Grid
getkgrid : length of smallest supercell vector (bohr)= 4.000000E+01
Simple Lattice Grid
invars2: take the default value of fband= 0.00000000E+00
getkgrid : length of smallest supercell vector (bohr)= 4.000000E+01
Simple Lattice Grid
getkgrid : length of smallest supercell vector (bohr)= 8.000000E+01
Simple Lattice Grid
getkgrid : length of smallest supercell vector (bohr)= 4.000000E+01
Simple Lattice Grid
dtset%nelect= 42.000000000000000
chkneu : initialized the occupation numbers for occopt= 1
spin-unpolarized case :
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
npfft, npband, npspinor and npkpt: 1 1 1 3
mpi_setup: mkmem undefined in the input file.Use default mkmem = nkpt
mpi_setup: With nkpt_me=1 and mkmem = 1, ground state wf handled in core.
mpi_setup: mkqmem undefined in the input file.Use default mkqmem = nkpt
mpi_setup: With nkpt_me=1 and mkqmem = 1, ground state wf handled in core.
mpi_setup: mk1mem undefined in the input file.Use default mk1mem = nkpt
mpi_setup: With nkpt_me=1 and mk1mem = 1, ground state wf handled in core.
For input ecut= -1.000000E+00 best grid ngfft= 2 2 2
max ecut= 1.233701E-02
==== FFT mesh ====
FFT mesh divisions ........................ 2 2 2
Augmented FFT divisions ................... 3 3 2
FFT algorithm ............................. 312
FFT cache size ............................ 16
Symmetries : space group P1 (# 1); Bravais aP (primitive triclinic)
getdim_nloc : deduce lmnmax = 4, lnmax = 2,
lmnmaxso= 7, lnmaxso= 3.
wvl_memory : analysis of memory needs
================================================================================
Values of the parameters that define the memory need for DATASET 1 (WVL).
wvl_hgrid = 0.450 nwfshist = 6 wvl_crmult = 5.000 wvl_frmult = 8.000
tl_radius = 0.000 tl_nprccg = 30
natom = 14 ntypat = 1 nstates = 21 nsppol = 1
================================================================================
Shifted atomic positions, Atomic Units: grid spacing units:
1 At. ty 9.75129E+00 1.91100E+01 1.46116E+01 21.670 42.467 32.470
2 At. ty 1.02011E+01 2.02089E+01 1.19390E+01 22.669 44.909 26.531
3 At. ty 9.43165E+00 1.69584E+01 1.21284E+01 20.959 37.685 26.952
4 At. ty 1.27168E+01 1.81898E+01 1.27727E+01 28.260 40.422 28.384
5 At. ty 9.91222E+00 1.39169E+01 1.12314E+01 22.027 30.926 24.959
6 At. ty 1.26235E+01 1.27783E+01 1.32344E+01 28.052 28.396 29.410
7 At. ty 1.12712E+01 1.59191E+01 9.40972E+00 25.047 35.376 20.910
8 At. ty 1.53183E+01 1.32861E+01 1.49638E+01 34.041 29.525 33.253
9 At. ty 1.15131E+01 1.87709E+01 9.76123E+00 25.585 41.713 21.692
10 At. ty 1.23890E+01 9.49108E+00 1.30395E+01 27.531 21.091 28.977
11 At. ty 1.14741E+01 1.71281E+01 1.57903E+01 25.498 38.062 35.090
12 At. ty 1.39303E+01 1.58270E+01 1.45728E+01 30.956 35.171 32.384
13 At. ty 1.02859E+01 1.10701E+01 1.17720E+01 22.857 24.600 26.160
14 At. ty 1.46770E+01 1.04896E+01 1.44316E+01 32.616 23.310 32.070
Shift of= 1.82110E+00 5.22459E+00 2.83274E+00 H grids= 0.4500 0.4500 0.4500
Box Sizes= 2.47500E+01 2.97000E+01 2.52000E+01 55 66 56
Extremes for the high resolution grid points: 15<40 15<51 15<41
wavelet localization is ON
------------------------------------------------- Wavefunctions Descriptors Creation
Coarse resolution grid: Number of segments= 2890 points= 102323
Fine resolution grid: Number of segments= 717 points= 9448
------------------------------------------------------------------ Memory Estimation
Number of atoms= 14 Number of orbitals= 21 Sim. Box Dimensions= 55 66 56
Estimation performed for 3 processors.
Memory occupation for principal arrays:
Poisson Solver Kernel (K): 9 MB 147 KB
Poisson Solver Density (D): 8 MB 880 KB
Single Wavefunction for one orbital: 1 MB 293 KB
All Wavefunctions for each processor: 26 MB 1014 KB
Wavefunctions + DIIS per proc (W): 134 MB 974 KB
Nonlocal Pseudopotential Arrays (P): 0 MB 0 KB
Arrays of full uncompressed grid (U): 25 MB 77 KB
Estimation of Memory requirements for principal code sections:
Kernel calculation | Density Construction | Poisson Solver | Hamiltonian application
~19*K | W+~3*U+~ 5*D+K+P | ~12*D+K+W+P | W+~3*U+~ 5*D+K+P
173MB | 255MB | 250MB | 259MB
The overall memory requirement needed for this calculation is thus: 259 MB
By reducing the DIIS history and/or increasing the number of processors the amount of
memory can be reduced but for this system it will never be less than 103 MB
TODO, remove me
================================================================================
--------------------------------------------------------------------------------
------------- Echo of variables that govern the present computation ------------
--------------------------------------------------------------------------------
-
- outvars: echo of selected default values
- accesswff0 = 0 , fftalg0 =312 , wfoptalg0 = 0
-
- outvars: echo of global parameters not present in the input file
- max_nthreads = 8
-
-outvars: echo values of preprocessed input variables --------
These variables are accessible in NetCDF format (tgswvl_01.o_OUT.nc)
acell 2.0000000000E+01 2.0000000000E+01 2.0000000000E+01 Bohr
amu 1.08110000E+01
icoulomb 1
iscf 2
ixc 11
kpt 0.00000000E+00 2.50000000E-01 0.00000000E+00
kptrlatt 1 0 0 0 2 0 0 0 1
kptrlen 4.00000000E+01
natom 14
nband 21
ngfft 2 2 2
nkpt 1
nsym 1
ntypat 1
nwfshist 6
occ 2.000000 2.000000 2.000000 2.000000 2.000000 2.000000
2.000000 2.000000 2.000000 2.000000 2.000000 2.000000
2.000000 2.000000 2.000000 2.000000 2.000000 2.000000
2.000000 2.000000 2.000000
optstress 0
prtden 0
prteig 0
prtwf 0
shiftk 0.00000000E+00 5.00000000E-01 0.00000000E+00
spgroup 1
tolwfr 1.00000000E-04
typat 1 1 1 1 1 1 1 1 1 1 1 1 1 1
usewvl 1
wvl_crmult 5.00000000E+00
wvl_frmult 8.00000000E+00
wvl_hgrid 4.50000000E-01
xangst 4.1964754037E+00 7.3478409358E+00 6.2330890229E+00
4.4344859212E+00 7.9293663548E+00 4.8188200267E+00
4.0273316519E+00 6.2092633085E+00 4.9190650537E+00
5.7657480525E+00 6.8609103051E+00 5.2600091052E+00
4.2816336192E+00 4.5997735955E+00 4.4443996219E+00
5.7163744520E+00 3.9972479358E+00 5.5042971993E+00
5.0007619463E+00 5.6592842557E+00 3.4803868736E+00
7.1424339990E+00 4.2659412726E+00 6.4194983245E+00
5.1287814495E+00 7.1683950895E+00 3.6663988976E+00
5.5923165650E+00 2.2577267329E+00 5.4011609246E+00
5.1081451763E+00 6.2990677022E+00 6.8568343061E+00
6.4079032923E+00 5.6105534339E+00 6.2125519657E+00
4.4793534021E+00 3.0933124217E+00 4.7304541691E+00
6.8030642714E+00 2.7861258585E+00 6.1378437118E+00
xcart 7.9301892364E+00 1.3885407037E+01 1.1778831215E+01
8.3799639311E+00 1.4984330818E+01 9.1062501341E+00
7.6105538685E+00 1.1733807140E+01 9.2956857814E+00
1.0895684771E+01 1.2965241499E+01 9.9399766652E+00
8.0911149417E+00 8.6923123689E+00 8.3986981104E+00
1.0802382187E+01 7.5537038839E+00 1.0401614261E+01
9.4500705343E+00 1.0694497351E+01 6.5769780276E+00
1.3497244180E+01 8.0614607041E+00 1.2131093744E+01
9.6919923350E+00 1.3546303531E+01 6.9284898104E+00
1.0567946756E+01 4.2664852081E+00 1.0206714947E+01
9.6529954302E+00 1.1903512850E+01 1.2957538977E+01
1.2109182309E+01 1.0602409444E+01 1.1740021802E+01
8.4647511825E+00 5.8455133206E+00 8.9392628637E+00
1.2855928337E+01 5.2650148443E+00 1.1598843662E+01
xred 3.9650946182E-01 6.9427035183E-01 5.8894156076E-01
4.1899819656E-01 7.4921654089E-01 4.5531250671E-01
3.8052769342E-01 5.8669035701E-01 4.6478428907E-01
5.4478423853E-01 6.4826207495E-01 4.9699883326E-01
4.0455574708E-01 4.3461561844E-01 4.1993490552E-01
5.4011910936E-01 3.7768519420E-01 5.2008071304E-01
4.7250352672E-01 5.3472486757E-01 3.2884890138E-01
6.7486220901E-01 4.0307303521E-01 6.0655468719E-01
4.8459961675E-01 6.7731517657E-01 3.4642449052E-01
5.2839733781E-01 2.1332426041E-01 5.1033574735E-01
4.8264977151E-01 5.9517564249E-01 6.4787694886E-01
6.0545911543E-01 5.3012047220E-01 5.8700109008E-01
4.2323755912E-01 2.9227566603E-01 4.4696314319E-01
6.4279641687E-01 2.6325074222E-01 5.7994218309E-01
znucl 5.00000
================================================================================
chkinp: machine precision is 2.2204460492503131E-16
chkinp: Checking input parameters for consistency.
--- !COMMENT
message: |
Comparison between wvl_hgrid and ecut
real-space mesh | eq. Ec around atoms | eq. Ec further from atoms
src_file: chkinp.F90
src_line: 2970
...
0.450 bohr | 97.5 Ht | 24.4 Ht
--- !WARNING
message: |
Restart files from wavelets in non ETSF format does not follow
the ABINIT standards.
Put accesswff to 3 to use ETSF retart files.
src_file: chkinp.F90
src_line: 2992
...
DATA TYPE INFORMATION:
REAL: Data type name: REAL(DP)
Kind value: 8
Precision: 15
Smallest nonnegligible quantity relative to 1: 0.22204460E-15
Smallest positive number: 0.22250739-307
Largest representable number: 0.17976931+309
INTEGER: Data type name: INTEGER(default)
Kind value: 4
Bit size: 32
Largest representable number: 2147483647
LOGICAL: Data type name: LOGICAL
Kind value: 4
CHARACTER: Data type name: CHARACTER Kind value: 1
==== OpenMP parallelism is ON ====
- Max_threads: 8
- Num_threads: 1
- Num_procs: 8
- Dynamic: F
- Nested: F
==== Using MPI-2 specifications ====
MPI-IO support is ON
xmpi_tag_ub ................ 536870911
xmpi_bsize_ch .............. 1
xmpi_bsize_int ............. 4
xmpi_bsize_sp .............. 4
xmpi_bsize_dp .............. 8
xmpi_bsize_spc ............. 8
xmpi_bsize_dpc ............. 16
xmpio_bsize_frm ............ 4
xmpi_address_kind .......... 8
xmpi_offset_kind ........... 8
MPI_WTICK .................. 9.99999999999999955E-007
================================================================================
== DATASET 1 ==================================================================
- nproc = 3
getdim_nloc : deduce lmnmax = 4, lnmax = 2,
lmnmaxso= 7, lnmaxso= 3.
Exchange-correlation functional for the present dataset will be:
GGA: Perdew-Burke-Ernzerhof functional - ixc=11
Citation for XC functional:
J.P.Perdew, K.Burke, M.Ernzerhof, PRL 77, 3865 (1996)
Unit cell volume ucvol= 8.0000000E+03 bohr^3
Angles (23,13,12)= 9.00000000E+01 9.00000000E+01 9.00000000E+01 degrees
- pspini: atom type 1 psp file is B-q3
- pspatm: opening atomic psp file B-q3
- Goedecker pseudopotential for B
- 5.00000 3.00000 70301 znucl, zion, pspdat
10 11 1 2 2001 0.00000 pspcod,pspxc,lmax,lloc,mmax,r2well
rloc= 0.4189914
cc(1:2)= -5.8594617 0.9037564
for angular momentum l = 0 r(l) = 0.3713205
h11, h12, h13 = 6.2972802 0.0000000 0.0000000
h22, h23 = 0.0000000 0.0000000
h33 = 0.0000000
for angular momentum l = 1 r(l) = 0.3645631
h11, h12, h13 = 0.0000000 0.0000000 0.0000000
h22, h23 = 0.0000000 0.0000000
h33 = 0.0000000
k11, k12, k13 = 0.0008550 0.0000000 0.0000000
k22, k23 = 0.0000000 0.0000000
k33 = 0.0000000
radii_cf(1)= 1.9131800; radii_cf(2)= 0.3603900; rad_cov= 0.6962259
- Local part computed in reciprocal space.
pspatm : COMMENT -
the projectors are not normalized,
so that the KB energies are not consistent with
definition in PRB44, 8503 (1991).
However, this does not influence the results obtained hereafter.
pspatm: epsatm= -0.33797878
--- l ekb(1:nproj) -->
0 1.142890
1 0.000000
pspatm: atomic psp has been read and splines computed
-1.98731523E+02 ecore*ucvol(ha*bohr**3)
wvl_setBoxGeometry : Changing the box for wavelets computation.
Shifted atomic positions, Atomic Units: grid spacing units:
1 B 9.75129E+00 1.91100E+01 1.46116E+01 21.670 42.467 32.470
2 B 1.02011E+01 2.02089E+01 1.19390E+01 22.669 44.909 26.531
3 B 9.43165E+00 1.69584E+01 1.21284E+01 20.959 37.685 26.952
4 B 1.27168E+01 1.81898E+01 1.27727E+01 28.260 40.422 28.384
5 B 9.91222E+00 1.39169E+01 1.12314E+01 22.027 30.926 24.959
6 B 1.26235E+01 1.27783E+01 1.32344E+01 28.052 28.396 29.410
7 B 1.12712E+01 1.59191E+01 9.40972E+00 25.047 35.376 20.910
8 B 1.53183E+01 1.32861E+01 1.49638E+01 34.041 29.525 33.253
9 B 1.15131E+01 1.87709E+01 9.76123E+00 25.585 41.713 21.692
10 B 1.23890E+01 9.49108E+00 1.30395E+01 27.531 21.091 28.977
11 B 1.14741E+01 1.71281E+01 1.57903E+01 25.498 38.062 35.090
12 B 1.39303E+01 1.58270E+01 1.45728E+01 30.956 35.171 32.384
13 B 1.02859E+01 1.10701E+01 1.17720E+01 22.857 24.600 26.160
14 B 1.46770E+01 1.04896E+01 1.44316E+01 32.616 23.310 32.070
Shift of= 1.82110E+00 5.22459E+00 2.83274E+00 H grids= 0.4500 0.4500 0.4500
Box Sizes= 2.47500E+01 2.97000E+01 2.52000E+01 55 66 56
Extremes for the high resolution grid points: 15<40 15<51 15<41
wavelet localization is ON
| acell is now: 24.750000 29.700000 25.200000
| nfl1, nfu1: 15 40
| nfl2, nfu2: 15 51
| nfl3, nfu3: 15 41
| box size for datas: 141 163 143
| box size for wavelets: 55 66 56
wvl_denspot_set: Create wavelet type denspot.
Psolver_kernel() : building kernel...
| data dimensions: 141 163 143
------------------------------------------------------------ Poisson Kernel Creation
Calculating Poisson solver kernel, free BC...done.
Memory occ. per proc. (Bytes): Density=9289728 Kernel=9587400
Full Grid Arrays=26292552
Load Balancing for Poisson Solver related operations:
LB_density : processors 0 - 2 work at 100%
LB_kernel : processors 0 - 1 work at 100%
processor 2 works at 96%
Complete LB per proc.= 1/3 LB_density + 2/3 LB_kernel
wvl_setngfft : Changing the FFT grid definition.
| ngfft(1:3) is now: 141 163 143
| ngfft(4:6) is now: 141 163 143
wvl_descr_atoms_set_sym: Create symmetries for the wvl%atoms object.
wvl_wfs_set: Create access keys for wavefunctions.
------------------------------------------------- Wavefunctions Descriptors Creation
Coarse resolution grid: Number of segments= 2890 points= 102323
Fine resolution grid: Number of segments= 710 points= 9260
| all orbitals have coarse segments, elements: 2890 102323
| all orbitals have fine segments, elements: 710 64820
------------------------------------------------------------ PSP Projectors Creation
Type Name Number of atoms Number of projectors
1 B 14 1
------ On-the-fly projectors application
Total number of projectors = 14
Total number of components = 31432
Percent of zero components = 0
wvl_projectors_set : allocate projectors data,
size of the compressed array: 31432
wvl_wfsinp_scratch: wavefunction initialisation.
mklocl_wavelets: Create local potential from ions.
----------------------------------------------------------- Ionic Potential Creation
total ionic charge, leaked charge -41.999999999997 0.000E+00
Poisson Solver:
BC : Isolated
Dimensions : [ 141, 163, 143 ]
MPI tasks : 3
Total No. of Atomic Input Orbitals : 56
*** glibc detected *** abinit: munmap_chunk(): invalid pointer: 0x0000000004afc0f0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3189876166]
abinit[0x4f4f0a]
abinit[0x4d87ec]
abinit[0x47bbb5]
abinit[0x41fb1a]
abinit[0x4139fb]
abinit[0x409ef7]
abinit[0x19eb96a]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x318981ed1d]
abinit[0x409389]
======= Memory map: ========
00400000-01bba000 r-xp 00000000 fd:00 958244 /usr/local/bin/abinit
01dba000-01de3000 rw-p 017ba000 fd:00 958244 /usr/local/bin/abinit
01de3000-035a7000 rw-p 00000000 00:00 0
03ec6000-062c5000 rw-p 00000000 00:00 0 [heap]
3189400000-3189420000 r-xp 00000000 fd:00 1182598 /lib64/ld-2.12.so
318961f000-3189620000 r--p 0001f000 fd:00 1182598 /lib64/ld-2.12.so
3189620000-3189621000 rw-p 00020000 fd:00 1182598 /lib64/ld-2.12.so
3189621000-3189622000 rw-p 00000000 00:00 0
3189800000-318998b000 r-xp 00000000 fd:00 1182600 /lib64/libc-2.12.so
318998b000-3189b8a000 ---p 0018b000 fd:00 1182600 /lib64/libc-2.12.so
3189b8a000-3189b8e000 r--p 0018a000 fd:00 1182600 /lib64/libc-2.12.so
3189b8e000-3189b8f000 rw-p 0018e000 fd:00 1182600 /lib64/libc-2.12.so
3189b8f000-3189b94000 rw-p 00000000 00:00 0
3189c00000-3189c83000 r-xp 00000000 fd:00 1194926 /lib64/libm-2.12.so
3189c83000-3189e82000 ---p 00083000 fd:00 1194926 /lib64/libm-2.12.so
3189e82000-3189e83000 r--p 00082000 fd:00 1194926 /lib64/libm-2.12.so
3189e83000-3189e84000 rw-p 00083000 fd:00 1194926 /lib64/libm-2.12.so
318a000000-318a002000 r-xp 00000000 fd:00 1194933 /lib64/libdl-2.12.so
318a002000-318a202000 ---p 00002000 fd:00 1194933 /lib64/libdl-2.12.so
318a202000-318a203000 r--p 00002000 fd:00 1194933 /lib64/libdl-2.12.so
318a203000-318a204000 rw-p 00003000 fd:00 1194933 /lib64/libdl-2.12.so
318a400000-318a417000 r-xp 00000000 fd:00 1194920 /lib64/libpthread-2.12.so
318a417000-318a617000 ---p 00017000 fd:00 1194920 /lib64/libpthread-2.12.so
318a617000-318a618000 r--p 00017000 fd:00 1194920 /lib64/libpthread-2.12.so
318a618000-318a619000 rw-p 00018000 fd:00 1194920 /lib64/libpthread-2.12.so
318a619000-318a61d000 rw-p 00000000 00:00 0
318a800000-318a815000 r-xp 00000000 fd:00 1194932 /lib64/libz.so.1.2.3
318a815000-318aa14000 ---p 00015000 fd:00 1194932 /lib64/libz.so.1.2.3
318aa14000-318aa15000 r--p 00014000 fd:00 1194932 /lib64/libz.so.1.2.3
318aa15000-318aa16000 rw-p 00015000 fd:00 1194932 /lib64/libz.so.1.2.3
318ac00000-318ac07000 r-xp 00000000 fd:00 1194921 /lib64/librt-2.12.so
318ac07000-318ae06000 ---p 00007000 fd:00 1194921 /lib64/librt-2.12.so
318ae06000-318ae07000 r--p 00006000 fd:00 1194921 /lib64/librt-2.12.so
318ae07000-318ae08000 rw-p 00007000 fd:00 1194921 /lib64/librt-2.12.so
318b000000-318b0c7000 r-xp 00000000 fd:00 943144 /usr/lib64/libnetcdf.so.7.0.1
318b0c7000-318b2c6000 ---p 000c7000 fd:00 943144 /usr/lib64/libnetcdf.so.7.0.1
318b2c6000-318b316000 rw-p 000c6000 fd:00 943144 /usr/lib64/libnetcdf.so.7.0.1
318b316000-318b321000 rw-p 00000000 00:00 0
318b400000-318b40d000 r-xp 00000000 fd:00 958343 /usr/lib64/libgomp.so.1.0.0
318b40d000-318b60c000 ---p 0000d000 fd:00 958343 /usr/lib64/libgomp.so.1.0.0
318b60c000-318b60d000 rw-p 0000c000 fd:00 958343 /usr/lib64/libgomp.so.1.0.0
318b800000-318b816000 r-xp 00000000 fd:00 1194940 /lib64/libresolv-2.12.so
318b816000-318ba16000 ---p 00016000 fd:00 1194940 /lib64/libresolv-2.12.so
318ba16000-318ba17000 r--p 00016000 fd:00 1194940 /lib64/libresolv-2.12.so
318ba17000-318ba18000 rw-p 00017000 fd:00 1194940 /lib64/libresolv-2.12.so
318ba18000-318ba1a000 rw-p 00000000 00:00 0
3193c00000-3193c16000 r-xp 00000000 fd:00 1196730 /lib64/libgcc_s-4.4.7-20120601.so.1
3193c16000-3193e15000 ---p 00016000 fd:00 1196730 /lib64/libgcc_s-4.4.7-20120601.so.1
3193e15000-3193e16000 rw-p 00015000 fd:00 1196730 /lib64/libgcc_s-4.4.7-20120601.so.1
3194400000-3194471000 r-xp 00000000 fd:00 1196737 /lib64/libfreebl3.so
3194471000-3194670000 ---p 00071000 fd:00 1196737 /lib64/libfreebl3.so
3194670000-3194672000 r--p 00070000 fd:00 1196737 /lib64/libfreebl3.so
3194672000-3194673000 rw-p 00072000 fd:00 1196737 /lib64/libfreebl3.so
3194673000-3194677000 rw-p 00000000 00:00 0
3194800000-3194807000 r-xp 00000000 fd:00 1196738 /lib64/libcrypt-2.12.so
3194807000-3194a07000 ---p 00007000 fd:00 1196738 /lib64/libcrypt-2.12.so
3194a07000-3194a08000 r--p 00007000 fd:00 1196738 /lib64/libcrypt-2.12.so
3194a08000-3194a09000 rw-p 00008000 fd:00 1196738 /lib64/libcrypt-2.12.so
3194a09000-3194a37000 rw-p 00000000 00:00 0
3195000000-3195032000 r-xp 00000000 fd:00 1196761 /lib64/libidn.so.11.6.1
3195032000-3195231000 ---p 00032000 fd:00 1196761 /lib64/libidn.so.11.6.1
3195231000-3195232000 rw-p 00031000 fd:00 1196761 /lib64/libidn.so.11.6.1
3195400000-3195403000 r-xp 00000000 fd:00 1196734 /lib64/libcom_err.so.2.1
3195403000-3195602000 ---p 00003000 fd:00 1196734 /lib64/libcom_err.so.2.1
3195602000-3195603000 r--p 00002000 fd:00 1196734 /lib64/libcom_err.so.2.1
3195603000-3195604000 rw-p 00003000 fd:00 1196734 /lib64/libcom_err.so.2.1
3195c00000-3195c19000 r-xp 00000000 fd:00 958286 /usr/lib64/libsasl2.so.2.0.23
3195c19000-3195e18000 ---p 00019000 fd:00 958286 /usr/lib64/libsasl2.so.2.0.23
3195e18000-3195e19000 r--p 00018000 fd:00 958286 /usr/lib64/libsasl2.so.2.0.23
3195e19000-3195e1a000 rw-p 00019000 fd:00 958286 /usr/lib64/libsasl2.so.2.0.23
3196000000-319600a000 r-xp 00000000 fd:00 1196732 /lib64/libkrb5support.so.0.1
319600a000-3196209000 ---p 0000a000 fd:00 1196732 /lib64/libkrb5support.so.0.1
3196209000-319620a000 r--p 00009000 fd:00 1196732 /lib64/libkrb5support.so.0.1
319620a000-319620b000 rw-p 0000a000 fd:00 1196732 /lib64/libkrb5support.so.0.1
3196400000-31965b5000 r-xp 00000000 fd:00 932236 /usr/lib64/libcrypto.so.1.0.1e
31965b5000-31967b5000 ---p 001b5000 fd:00 932236 /usr/lib64/libcrypto.so.1.0.1e
31967b5000-31967d0000 r--p 001b5000 fd:00 932236 /usr/lib64/libcrypto.so.1.0.1e
31967d0000-31967dc000 rw-p 001d0000 fd:00 932236 /usr/lib64/libcrypto.so.1.0.1e
31967dc000-31967e0000 rw-p 00000000 00:00 0
3196800000-3196802000 r-xp 00000000 fd:00 1196731 /lib64/libkeyutils.so.1.3
3196802000-3196a01000 ---p 00002000 fd:00 1196731 /lib64/libkeyutils.so.1.3
3196a01000-3196a02000 r--p 00001000 fd:00 1196731 /lib64/libkeyutils.so.1.3
3196a02000-3196a03000 rw-p 00002000 fd:00 1196731 /lib64/libkeyutils.so.1.3
3196c00000-3196c29000 r-xp 00000000 fd:00 1196733 /lib64/libk5crypto.so.3.1
3196c29000-3196e29000 ---p 00029000 fd:00 1196733 /lib64/libk5crypto.so.3.1
3196e29000-3196e2a000 r--p 00029000 fd:00 1196733 /lib64/libk5crypto.so.3.1
3196e2a000-3196e2b000 rw-p 0002a000 fd:00 1196733 /lib64/libk5crypto.so.3.1
3196e2b000-3196e2c000 rw-p 00000000 00:00 0
3197000000-31970db000 r-xp 00000000 fd:00 1196735 /lib64/libkrb5.so.3.3
31970db000-31972da000 ---p 000db000 fd:00 1196735 /lib64/libkrb5.so.3.3
31972da000-31972e4000 r--p 000da000 fd:00 1196735 /lib64/libkrb5.so.3.3
31972e4000-31972e6000 rw-p 000e4000 fd:00 1196735 /lib64/libkrb5.so.3.3
3197800000-3197841000 r-xp 00000000 fd:00 1196736 /lib64/libgssapi_krb5.so.2.2
3197841000-3197a41000 ---p 00041000 fd:00 1196736 /lib64/libgssapi_krb5.so.2.2
3197a41000-3197a42000 r--p 00041000 fd:00 1196736 /lib64/libgssapi_krb5.so.2.2
3197a42000-3197a44000 rw-p 00042000 fd:00 1196736 /lib64/libgssapi_krb5.so.2.2
3198000000-3198039000 r-xp 00000000 fd:00 1196739 /lib64/libnspr4.so
3198039000-3198238000 ---p 00039000 fd:00 1196739 /lib64/libnspr4.so
3198238000-3198239000 r--p 00038000 fd:00 1196739 /lib64/libnspr4.so
3198239000-319823b000 rw-p 00039000 fd:00 1196739 /lib64/libnspr4.so
319823b000-319823d000 rw-p 00000000 00:00 0
3198400000-3198404000 r-xp 00000000 fd:00 1196740 /lib64/libplc4.so
3198404000-3198603000 ---p 00004000 fd:00 1196740 /lib64/libplc4.so
3198603000-3198604000 r--p 00003000 fd:00 1196740 /lib64/libplc4.so
3198604000-3198605000 rw-p 00004000 fd:00 1196740 /lib64/libplc4.so
3198800000-3198803000 r-xp 00000000 fd:00 1196741 /lib64/libplds4.so
3198803000-3198a02000 ---p 00003000 fd:00 1196741 /lib64/libplds4.so
3198a02000-3198a03000 r--p 00002000 fd:00 1196741 /lib64/libplds4.so
3198a03000-3198a04000 rw-p 00003000 fd:00 1196741 /lib64/libplds4.so
3198c00000-3198c61000 r-xp 00000000 fd:00 958281 /usr/lib64/libssl.so.1.0.1e
3198c61000-3198e61000 ---p 00061000 fd:00 958281 /usr/lib64/libssl.so.1.0.1e
3198e61000-3198e65000 r--p 00061000 fd:00 958281 /usr/lib64/libssl.so.1.0.1e
3198e65000-3198e6c000 rw-p 00065000 fd:00 958281 /usr/lib64/libssl.so.1.0.1e
3199400000-3199425000 r-xp 00000000 fd:00 958282 /usr/lib64/libnssutil3.so
3199425000-3199625000 ---p 00025000 fd:00 958282 /usr/lib64/libnssutil3.so
3199625000-319962b000 r--p 00025000 fd:00 958282 /usr/lib64/libnssutil3.so
319962b000-319962c000 rw-p 0002b000 fd:00 958282 /usr/lib64/libnssutil3.so
3199800000-3199935000 r-xp 00000000 fd:00 958283 /usr/lib64/libnss3.so
3199935000-3199b35000 ---p 00135000 fd:00 958283 /usr/lib64/libnss3.so
3199b35000-3199b3a000 r--p 00135000 fd:00 958283 /usr/lib64/libnss3.so
3199b3a000-3199b3c000 rw-p 0013a000 fd:00 958283 /usr/lib64/libnss3.so
3199b3c000-3199b3e000 rw-p 00000000 00:00 0
3199c00000-3199c39000 r-xp 00000000 fd:00 958284 /usr/lib64/libssl3.so
3199c39000-3199e39000 ---p 00039000 fd:00 958284 /usr/lib64/libssl3.so
3199e39000-3199e3c000 r--p 00039000 fd:00 958284 /usr/lib64/libssl3.so
3199e3c000-3199e3d000 rw-p 0003c000 fd:00 958284 /usr/lib64/libssl3.so
3199e3d000-3199e3e000 rw-p 00000000 00:00 0
319a000000-319a028000 r-xp 00000000 fd:00 958285 /usr/lib64/libsmime3.so
319a028000-319a227000 ---p 00028000 fd:00 958285 /usr/lib64/libsmime3.so
319a227000-319a22b000 r--p 00027000 fd:00 958285 /usr/lib64/libsmime3.so
319a22b000-319a22c000 rw-p 0002b000 fd:00 958285 /usr/lib64/libsmime3.so
319c400000-319c40e000 r-xp 00000000 fd:00 1196742 /lib64/liblber-2.4.so.2.5.6
319c40e000-319c60d000 ---p 0000e000 fd:00 1196742 /lib64/liblber-2.4.so.2.5.6
319c60d000-319c60e000 r--p 0000d000 fd:00 1196742 /lib64/liblber-2.4.so.2.5.6
319c60e000-319c60f000 rw-p 0000e000 fd:00 1196742 /lib64/liblber-2.4.so.2.5.6
319e000000-319e049000 r-xp 00000000 fd:00 1196762 /lib64/libldap-2.4.so.2.5.6
319e049000-319e249000 ---p 00049000 fd:00 1196762 /lib64/libldap-2.4.so.2.5.6
319e249000-319e24b000 r--p 00049000 fd:00 1196762 /lib64/libldap-2.4.so.2.5.6
319e24b000-319e24d000 rw-p 0004b000 fd:00 1196762 /lib64/libldap-2.4.so.2.5.6
319ec00000-319ec27000 r-xp 00000000 fd:00 958302 /usr/lib64/libssh2.so.1.0.1
319ec27000-319ee26000 ---p 00027000 fd:00 958302 /usr/lib64/libssh2.so.1.0.1
319ee26000-319ee27000 rw-p 00026000 fd:00 958302 /usr/lib64/libssh2.so.1.0.1
319ee27000-319ee28000 rw-p 00000000 00:00 0
319f000000-319f052000 r-xp 00000000 fd:00 958303 /usr/lib64/libcurl.so.4.1.1
319f052000-319f251000 ---p 00052000 fd:00 958303 /usr/lib64/libcurl.so.4.1.1
319f251000-319f254000 rw-p 00051000 fd:00 958303 /usr/lib64/libcurl.so.4.1.1
7f02ec084000-7f02ec0c5000 rw-s 00000000 00:10 110961915 /dev/shm/mpich_shar_tmpMnXJa6 (deleted)
7f02ec0c5000-7f02ec106000 rw-s 00000000 00:10 110961912 /dev/shm/mpich_shar_tmp3lwwjH (deleted)
7f02ee4bc000-7f02fbaf8000 rw-p 00000000 00:00 0
7f02fbaf8000-7f02fbaf9000 ---p 00000000 00:00 0
7f02fbaf9000-7f02fc4f9000 rw-p 00000000 00:00 0
7f02fc4f9000-7f02fc4fa000 ---p 00000000 00:00 0
7f02fc4fa000-7f02fcefa000 rw-p 00000000 00:00 0
7f02fcefa000-7f02fcefb000 ---p 00000000 00:00 0
7f02fcefb000-7f02fd8fb000 rw-p 00000000 00:00 0
7f02fd8fb000-7f02fd8fc000 ---p 00000000 00:00 0
7f02fd8fc000-7f02fe2fc000 rw-p 00000000 00:00 0
7f02fe2fc000-7f02fe2fd000 ---p 00000000 00:00 0
7f02fe2fd000-7f02fecfd000 rw-p 00000000 00:00 0
7f02fecfd000-7f02fecfe000 ---p 00000000 00:00 0
7f02fecfe000-7f02ff6fe000 rw-p 00000000 00:00 0
7f02ff6fe000-7f02ff6ff000 ---p 00000000 00:00 0
7f02ff6ff000-7f0302633000 rw-p 00000000 00:00 0
7f0302633000-7f030263f000 r-xp 00000000 fd:00 1182599 /lib64/libnss_files-2.12.so
7f030263f000-7f030283f000 ---p 0000c000 fd:00 1182599 /lib64/libnss_files-2.12.so
7f030283f000-7f0302840000 r--p 0000c000 fd:00 1182599 /lib64/libnss_files-2.12.so
7f0302840000-7f0302841000 rw-p 0000d000 fd:00 1182599 /lib64/libnss_files-2.12.so
7f0302841000-7f03034a2000 rw-s 00000000 00:10 110958431 /dev/shm/mpich_shar_tmpC18Hpw (deleted)
7f03034a2000-7f03034a8000 rw-p 00000000 00:00 0
7f03034a8000-7f03034c5000 r-xp 00000000 fd:00 1194956 /lib64/libselinux.so.1
7f03034c5000-7f03036c4000 ---p 0001d000 fd:00 1194956 /lib64/libselinux.so.1
7f03036c4000-7f03036c5000 r--p 0001c000 fd:00 1194956 /lib64/libselinux.so.1
7f03036c5000-7f03036c6000 rw-p 0001d000 fd:00 1194956 /lib64/libselinux.so.1
7f03036c6000-7f03036d2000 rw-p 00000000 00:00 0
7f03036d2000-7f03037c2000 r-xp 00000000 fd:00 923947 /usr/lib64/libgfortran.so.3.0.0
7f03037c2000-7f03039c1000 ---p 000f0000 fd:00 923947 /usr/lib64/libgfortran.so.3.0.0
7f03039c1000-7f03039c3000 rw-p 000ef000 fd:00 923947 /usr/lib64/libgfortran.so.3.0.0
7f03039c3000-7f03039c4000 rw-p 00000000 00:00 0
7f03039c4000-7f03039c8000 r-xp 00000000 fd:00 957404 /usr/local/lib/libmpl.so.1.0.0
7f03039c8000-7f0303bc7000 ---p 00004000 fd:00 957404 /usr/local/lib/libmpl.so.1.0.0
7f0303bc7000-7f0303bc8000 rw-p 00003000 fd:00 957404 /usr/local/lib/libmpl.so.1.0.0
7f0303bc8000-7f0303bc9000 rw-p 00000000 00:00 0
7f0303bc9000-7f0303bca000 r-xp 00000000 fd:00 957408 /usr/local/lib/libopa.so.1.0.0
7f0303bca000-7f0303dc9000 ---p 00001000 fd:00 957408 /usr/local/lib/libopa.so.1.0.0
7f0303dc9000-7f0303dca000 rw-p 00000000 fd:00 957408 /usr/local/lib/libopa.so.1.0.0
7f0303dca000-7f030400b000 r-xp 00000000 fd:00 957426 /usr/local/lib/libmpich.so.12.0.0
7f030400b000-7f030420a000 ---p 00241000 fd:00 957426 /usr/local/lib/libmpich.so.12.0.0
7f030420a000-7f030421c000 rw-p 00240000 fd:00 957426 /usr/local/lib/libmpich.so.12.0.0
7f030421c000-7f0304256000 rw-p 00000000 00:00 0
7f0304256000-7f0304258000 r-xp 00000000 fd:00 957438 /usr/local/lib/libmpichf90.so.12.0.0
7f0304258000-7f0304457000 ---p 00002000 fd:00 957438 /usr/local/lib/libmpichf90.so.12.0.0
7f0304457000-7f0304458000 rw-p 00001000 fd:00 957438 /usr/local/lib/libmpichf90.so.12.0.0
7f0304458000-7f0304459000 rw-p 00000000 00:00 0
7f0304459000-7f03048ab000 r-xp 00000000 fd:00 930957 /usr/lib64/atlas/libatlas.so.3.0
7f03048ab000-7f0304aab000 ---p 00452000 fd:00 930957 /usr/lib64/atlas/libatlas.so.3.0
7f0304aab000-7f0304ab5000 rw-p 00452000 fd:00 930957 /usr/lib64/atlas/libatlas.so.3.0
7f0304ab5000-7f0304ad5000 r-xp 00000000 fd:00 930959 /usr/lib64/atlas/libcblas.so.3.0
7f0304ad5000-7f0304cd4000 ---p 00020000 fd:00 930959 /usr/lib64/atlas/libcblas.so.3.0
7f0304cd4000-7f0304cd5000 rw-p 0001f000 fd:00 930959 /usr/lib64/atlas/libcblas.so.3.0
7f0304cd5000-7f0304cd6000 rw-p 00000000 00:00 0
7f0304cd6000-7f0304cf5000 r-xp 00000000 fd:00 930963 /usr/lib64/atlas/libf77blas.so.3.0
7f0304cf5000-7f0304ef4000 ---p 0001f000 fd:00 930963 /usr/lib64/atlas/libf77blas.so.3.0
7f0304ef4000-7f0304ef5000 rw-p 0001e000 fd:00 930963 /usr/lib64/atlas/libf77blas.so.3.0
7f0304ef5000-7f0305406000 r-xp 00000000 fd:00 930965 /usr/lib64/atlas/liblapack.so.3.0
7f0305406000-7f0305605000 ---p 00511000 fd:00 930965 /usr/lib64/atlas/liblapack.so.3.0
7f0305605000-7f0305608000 rw-p 00510000 fd:00 930965 /usr/lib64/atlas/liblapack.so.3.0
7f0305608000-7f0305716000 rw-p 00000000 00:00 0
7f0305716000-7f0305771000 r-xp 00000000 fd:00 958178 /usr/lib64/libnetcdff.so.5.1.0
7f0305771000-7f0305970000 ---p 0005b000 fd:00 958178 /usr/lib64/libnetcdff.so.5.1.0
7f0305970000-7f0305971000 rw-p 0005a000 fd:00 958178 /usr/lib64/libnetcdff.so.5.1.0
7f0305971000-7f0305972000 rw-p 00000000 00:00 0
7f030598b000-7f030598d000 rw-p 00000000 00:00 0
7fff81e7c000-7fff8243d000 rw-p 00000000 00:00 0 [stack]
7fff82510000-7fff82511000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 5960 RUNNING AT theory1
= EXIT CODE: 134
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions