Hi all,
I am a newcomer trying to get an abinit install to work on OSX to educate myself in abinit (hw is macbook pro with intel x86_64) according to the install instructions given in the docs. I succeeded to build all libs from source except the linear algebra where I used the system-provided accelerate framework.
My configure was:
../configure --enable-openmp --with-mpi --with-netcdf --with-netcdf-fortran=/usr/local --with-libxc
FCFLAGS_EXTRA="-g -Wall -fallow-argument-mismatch -fallow-argument-mismatch" --enable-zdot-bugfix="yes"
after which everything seems hunky-dory and make -j8 and make install terminate without errors.
The first two simple tutorials work fine but then I get a segmentation fault directly in when running the simple tutorial 3_1:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
Could not print backtrace: executable file is not an executable
#0 0x10f00f86e
#1 0x10f00ea4d
#2 0x7ff806d9bdfc
#3 0x7ff807723d2c
#4 0x10afafc39
#5 0x10a83432b
#6 0x10a20aecb
#7 0x10a2160fe
#8 0x10a1873c5
#9 0x10a19210c
#10 0x10a0a4615
#11 0x10a0ae8bb
#12 0x10a086abc
#13 0x10a02adb3
#14 0x10a0309a7
I guess I made a beginners mistake somewhere, but I don’t know what to include as diagnostics. But maybe you can see whether there is something foul with the package dependencies?
fabian@MBP-FW-2020 Work3 % otool -L /usr/local/bin/abinit
/usr/local/bin/abinit:
/usr/local/opt/libxc/lib/libxc.9.dylib (compatibility version 12.0.0, current version 12.3.0)
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib (compatibility version 1.0.0, current version 1.0.0)
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/local/lib/libnetcdff.7.dylib (compatibility version 9.0.0, current version 9.0.0)
/usr/local/lib/libnetcdf.19.dylib (compatibility version 21.0.0, current version 21.0.0)
/usr/local/lib/libhdf5_hl.200.dylib (compatibility version 202.0.0, current version 202.0.0)
/usr/local/lib/libhdf5.200.dylib (compatibility version 203.0.0, current version 203.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/usr/local/opt/open-mpi/lib/libmpi_usempif08.40.dylib (compatibility version 71.0.0, current version 71.0.0)
/usr/local/opt/open-mpi/lib/libmpi_usempi_ignore_tkr.40.dylib (compatibility version 71.0.0, current version 71.0.0)
/usr/local/opt/open-mpi/lib/libmpi_mpifh.40.dylib (compatibility version 71.0.0, current version 71.0.0)
/usr/local/opt/open-mpi/lib/libmpi.40.dylib (compatibility version 71.0.0, current version 71.4.0)
/usr/local/opt/gcc/lib/gcc/current/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/usr/local/opt/gcc/lib/gcc/current/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
/usr/local/opt/gcc/lib/gcc/current/libgcc_s.1.1.dylib (compatibility version 1.0.0, current version 1.1.0)
/usr/local/opt/gcc/lib/gcc/current/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1311.100.3)
Thanks for reading this far and hoping for a hint how to proceed,
Fabian
Since I cannot upload files yet, I include the log file as quotation:
ABINIT 9.4.2
ABI_PSPDIR found in environment, with value /Users/fabian/Git/abinit/abinit-9.4.2/tests//Psps_for_tests/
-instrng: 75 lines of input have been read from file tbase3_1.abi
--- !COMMENT
src_file: m_dtfil.F90
src_line: 1476
message: |
Output file: tbase3_1.abo already exists.
...
--- !COMMENT
src_file: m_dtfil.F90
src_line: 1500
message: |
Renaming old: tbase3_1.abo to: tbase3_1.abo0004
...
.Version 9.4.2 of ABINIT
.(MPI version, prepared for a x86_64_darwin21.6.0_gnu12.2 computer)
.Copyright (C) 1998-2021 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 https://docs.abinit.org/theory/acknowledgments for suggested
acknowledgments of the ABINIT effort.
For more information, see https://www.abinit.org .
.Starting date : Fri 14 Oct 2022.
- ( at 16h02 )
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=== Build Information ===
Version : 9.4.2
Build target : x86_64_darwin21.6.0_gnu12.2
Build date : 20221014
=== Compiler Suite ===
C compiler : llvm14.0
C++ compiler : llvm14.0
Fortran compiler : gnu12.2
CFLAGS : -g -O2 -mtune=native -mcpu=native
CXXFLAGS : -g -O2 -mtune=native -mcpu=native
FCFLAGS : -g -ffree-line-length-none -fopenmp -I/usr/local/include
FC_LDFLAGS :
=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : unknown_unknown
=== Multicore ===
Parallel build : yes
Parallel I/O :
openMP support : yes
GPU support :
=== Connectors / Fallbacks ===
LINALG flavor : netlib
FFT flavor : goedecker
HDF5 : yes
NetCDF : yes
NetCDF Fortran : yes
LibXC : yes
Wannier90 : no
=== Experimental features ===
Exports :
GW double-precision :
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -mtune=native -march=native
Optimizations for 43_ptgroups:
-O0
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:
CC_LLVM CXX_LLVM FC_GNU
HAVE_FC_ALLOCATABLE_DT... HAVE_FC_ASYNC HAVE_FC_BACKTRACE
HAVE_FC_COMMAND_ARGUMENT HAVE_FC_COMMAND_LINE HAVE_FC_CONTIGUOUS
HAVE_FC_CPUTIME HAVE_FC_EXIT HAVE_FC_FLUSH
HAVE_FC_GAMMA HAVE_FC_GETENV HAVE_FC_IEEE_ARITHMETIC
HAVE_FC_IEEE_EXCEPTIONS HAVE_FC_INT_QUAD HAVE_FC_IOMSG
HAVE_FC_ISO_C_BINDING HAVE_FC_ISO_FORTRAN_2008 HAVE_FC_LONG_LINES
HAVE_FC_MOVE_ALLOC HAVE_FC_ON_THE_FLY_SHAPE HAVE_FC_PRIVATE
HAVE_FC_PROTECTED HAVE_FC_SHIFTLR HAVE_FC_STREAM_IO
HAVE_FC_SYSTEM HAVE_FORTRAN2003 HAVE_HDF5
HAVE_LIBPAW_ABINIT HAVE_LIBTETRA_ABINIT HAVE_LIBXC
HAVE_MPI HAVE_MPI2 HAVE_MPI_IALLGATHER
HAVE_MPI_IALLREDUCE HAVE_MPI_IALLTOALL HAVE_MPI_IALLTOALLV
HAVE_MPI_IBCAST HAVE_MPI_IGATHERV HAVE_MPI_INTEGER16
HAVE_MPI_IO HAVE_MPI_TYPE_CREATE_S... HAVE_NETCDF
HAVE_NETCDF_FORTRAN HAVE_OMP_COLLAPSE HAVE_OPENMP
HAVE_TIMER_ABINIT
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- input file -> tbase3_1.abi
- output file -> tbase3_1.abo
- root for input files -> tbase3_1i
- root for output files -> tbase3_1o
ABI_PSPDIR found in environment, with value /Users/fabian/Git/abinit/abinit-9.4.2/tests//Psps_for_tests/
-instrng: 75 lines of input have been read from file tbase3_1.abi
For atom type 1, psp file is /Users/fabian/Git/abinit/abinit-9.4.2/tests//Psps_for_tests/Pseudodojo_nc_sr_04_pw_standard_psp8/Si.psp8
read the values zionpsp= 4.0 , pspcod= 8 , lmax= 2
inpspheads: deduce mpsang = 3, n1xccc = 2501.
=======================================================
invars1m : enter jdtset= 0
symlatt: the Bravais lattice is cF (face-centered cubic)
xred is defined in input file
ingeo: takes atomic coordinates from input array xred
--- !COMMENT
src_file: m_ingeo.F90
src_line: 900
message: |
The tolerance on symmetries = 1.000E-05 is bigger than 1.0e-8.
In order to avoid spurious effects, the atomic coordinates have been
symmetrized before storing them in the dataset internal variable.
So, do not be surprised by the fact that your input variables (xcart, xred, ...)
do not correspond exactly to the ones echoed by ABINIT, the latter being used to do the calculations.
This is not a problem per se.
Still, in order to avoid this symmetrization (e.g. for specific debugging/development), decrease tolsym to 1.0e-8 or lower,
or (much preferred) use input primitive vectors that are accurate to better than 1.0e-8.
This message will only be printed once, even if there are other datasets where tolsym is bigger than 1.0e-8.
...
symlatt: the Bravais lattice is cF (face-centered cubic)
symlatt: the Bravais lattice is cF (face-centered cubic)
symspgr: spgroup= 227 Fd -3 m (=Oh^7)
symspgr: optical characteristics = isotropic
invars2: take the default value of fband= 1.25000000E-01
For input ecut= 1.200000E+01 best grid ngfft= 24 24 24
max ecut= 1.371408E+01
==== FFT mesh ====
FFT mesh divisions ........................ 24 24 24
Augmented FFT divisions ................... 25 25 24
FFT algorithm ............................. 112
FFT cache size ............................ 16
getmpw: optimal value of mpw= 525
Symmetries : space group Fd -3 m (#227); Bravais cF (face-center cubic)
getdim_nloc : deduce lmnmax = 18, lnmax = 6,
lmnmaxso= 18, lnmaxso= 6.
memory: analysis of memory needs
================================================================================
Values of the parameters that define the memory need of the present run
intxc = 0 ionmov = 0 iscf = 7 lmnmax = 6
lnmax = 6 mgfft = 24 mpssoang = 3 mqgrid = 3001
natom = 2 nloc_mem = 1 nspden = 1 nspinor = 1
nsppol = 1 nsym = 48 n1xccc = 2501 ntypat = 1
occopt = 1 xclevel = 1
- mband = 5 mffmem = 1 mkmem = 2
mpw = 525 nfft = 13824 nkpt = 2
================================================================================
P This job should need less than 4.782 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
_ WF disk file : 0.082 Mbytes ; DEN or POT disk file : 0.107 Mbytes.
================================================================================
Biggest array : f_fftgr(disk), with 1.6895 MBytes.
memana : allocated an array of 1.690 Mbytes, for testing purposes.
memana: allocated 4.782Mbytes, for testing purposes.
The job will continue.
--------------------------------------------------------------------------------
------------- Echo of variables that govern the present computation ------------
--------------------------------------------------------------------------------
-
- outvars: echo of selected default values
- iomode0 = 0 , fftalg0 =112 , 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 (tbase3_1o_OUT.nc)
acell 1.0180000000E+01 1.0180000000E+01 1.0180000000E+01 Bohr
amu 2.80855000E+01
diemac 1.20000000E+01
ecut 1.20000000E+01 Hartree
- fftalg 112
ixc -1012
kpt -2.50000000E-01 5.00000000E-01 0.00000000E+00
-2.50000000E-01 0.00000000E+00 0.00000000E+00
kptrlatt 2 -2 2 -2 2 2 -2 -2 2
kptrlen 2.03600000E+01
P mkmem 2
natom 2
nband 5
ngfft 24 24 24
nkpt 2
nstep 10
nsym 48
ntypat 1
occ 2.000000 2.000000 2.000000 2.000000 0.000000
rprim 0.0000000000E+00 5.0000000000E-01 5.0000000000E-01
5.0000000000E-01 0.0000000000E+00 5.0000000000E-01
5.0000000000E-01 5.0000000000E-01 0.0000000000E+00
shiftk 5.00000000E-01 5.00000000E-01 5.00000000E-01
spgroup 227
symrel 1 0 0 0 1 0 0 0 1 -1 0 0 0 -1 0 0 0 -1
0 -1 1 0 -1 0 1 -1 0 0 1 -1 0 1 0 -1 1 0
-1 0 0 -1 0 1 -1 1 0 1 0 0 1 0 -1 1 -1 0
0 1 -1 1 0 -1 0 0 -1 0 -1 1 -1 0 1 0 0 1
-1 0 0 -1 1 0 -1 0 1 1 0 0 1 -1 0 1 0 -1
0 -1 1 1 -1 0 0 -1 0 0 1 -1 -1 1 0 0 1 0
1 0 0 0 0 1 0 1 0 -1 0 0 0 0 -1 0 -1 0
0 1 -1 0 0 -1 1 0 -1 0 -1 1 0 0 1 -1 0 1
-1 0 1 -1 1 0 -1 0 0 1 0 -1 1 -1 0 1 0 0
0 -1 0 1 -1 0 0 -1 1 0 1 0 -1 1 0 0 1 -1
1 0 -1 0 0 -1 0 1 -1 -1 0 1 0 0 1 0 -1 1
0 1 0 0 0 1 1 0 0 0 -1 0 0 0 -1 -1 0 0
1 0 -1 0 1 -1 0 0 -1 -1 0 1 0 -1 1 0 0 1
0 -1 0 0 -1 1 1 -1 0 0 1 0 0 1 -1 -1 1 0
-1 0 1 -1 0 0 -1 1 0 1 0 -1 1 0 0 1 -1 0
0 1 0 1 0 0 0 0 1 0 -1 0 -1 0 0 0 0 -1
0 0 -1 0 1 -1 1 0 -1 0 0 1 0 -1 1 -1 0 1
1 -1 0 0 -1 1 0 -1 0 -1 1 0 0 1 -1 0 1 0
0 0 1 1 0 0 0 1 0 0 0 -1 -1 0 0 0 -1 0
-1 1 0 -1 0 0 -1 0 1 1 -1 0 1 0 0 1 0 -1
0 0 1 0 1 0 1 0 0 0 0 -1 0 -1 0 -1 0 0
1 -1 0 0 -1 0 0 -1 1 -1 1 0 0 1 0 0 1 -1
0 0 -1 1 0 -1 0 1 -1 0 0 1 -1 0 1 0 -1 1
-1 1 0 -1 0 1 -1 0 0 1 -1 0 1 0 -1 1 0 0
tnons 0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
toldfe 1.00000000E-06 Hartree
typat 1 1
wtk 0.75000 0.25000
xangst 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
1.3467559959E+00 1.3467559959E+00 1.3467559959E+00
xcart 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
2.5450000000E+00 2.5450000000E+00 2.5450000000E+00
xred 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
2.5000000000E-01 2.5000000000E-01 2.5000000000E-01
znucl 14.00000
================================================================================
chkinp: Checking input parameters for consistency.
DATA TYPE INFORMATION:
REAL: Data type name: REAL(DP)
Kind value: 8
Precision: 15
Smallest nonnegligible quantity relative to 1: 0.22204460E-015
Smallest positive number: 0.22250739E-307
Largest representable number: 0.17976931E+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: 8
- Num_procs: 8
- Dynamic: F
- Nested: F
==== Using MPI-2 specifications ====
MPI-IO support is ON
xmpi_tag_ub ................ 2147483647
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 .................. 9.9999999999999995E-007
================================================================================
== DATASET 1 ==================================================================
- mpi_nproc: 1, omp_nthreads: 8 (-1 if OMP is not activated)
--- !COMMENT
src_file: m_xgScalapack.F90
src_line: 236
message: |
xgScalapack in auto mode
...
getdim_nloc : deduce lmnmax = 18, lnmax = 6,
lmnmaxso= 18, lnmaxso= 6.
Slater exchange
P. A. M. Dirac, Math. Proc. Cambridge Philos. Soc. 26, 376 (1930)
F. Bloch, Z. Phys. 57, 545 (1929)
Perdew & Wang