abicheck.py¶
This script checks that the options specified in manager.yml, scheduler.yml,
and the environment on the local machine are properly configured.
Please consult the documentation on the TaskManager for a more detailed description of these YAML files.
$ abicheck.py --no-colors
/usr/share/miniconda/envs/abipy/bin/abicheck.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('abipy==0.9.8')
AbiPy Manager:
[Qadapter 0]
ShellAdapter:github
Hardware:
num_nodes: 1, sockets_per_node: 1, cores_per_socket: 2, mem_per_node 4096,
Qadapter selected: 0
self.info 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
==== Using MPI-2 specifications ====
MPI-IO support is ON
xmpi_tag_ub ................ 268435455
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 .................. 1.0000000000000001E-009
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:
CC_GNU CXX_GNU 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_FFTW3 HAVE_FORTRAN2003
HAVE_HDF5 HAVE_HDF5_MPI HAVE_LIBPAW_ABINIT
HAVE_LIBTETRA_ABINIT HAVE_LIBXC HAVE_MPI
HAVE_MPI2 HAVE_MPI2_INPLACE 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_NETCDF_FORTRAN_MPI HAVE_NETCDF_MPI
HAVE_OS_LINUX HAVE_TIMER_ABINIT
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=== Build Information ===
Version : 10.0.3
Build target : x86_64_linux_gnu13.3
Build date : 20241021
=== Compiler Suite ===
C compiler : gnu
C++ compiler : gnu13.3
Fortran compiler : gnu13.3
CFLAGS : -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protect ...
CXXFLAGS : -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune ...
FCFLAGS : -g -ffree-line-length-none -fallow-argument-mismatch -fallow-argument-mismatch
FC_LDFLAGS :
=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : intel_xeon
=== Multicore ===
Parallel build : yes
Parallel I/O : yes
openMP support :
GPU support :
=== Connectors / Fallbacks ===
LINALG flavor : netlib
FFT flavor : fftw3
HDF5 : yes
NetCDF : yes
NetCDF Fortran : yes
LibXC : yes
Wannier90 : no
=== Experimental features ===
Exports :
GW double-precision :
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -march=nocona -mtune=haswell
Optimizations for 43_ptgroups:
-O0
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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
==== Using MPI-2 specifications ====
MPI-IO support is ON
xmpi_tag_ub ................ 268435455
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 .................. 1.0000000000000001E-009
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:
CC_GNU CXX_GNU 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_FFTW3 HAVE_FORTRAN2003
HAVE_HDF5 HAVE_HDF5_MPI HAVE_LIBPAW_ABINIT
HAVE_LIBTETRA_ABINIT HAVE_LIBXC HAVE_MPI
HAVE_MPI2 HAVE_MPI2_INPLACE 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_NETCDF_FORTRAN_MPI HAVE_NETCDF_MPI
HAVE_OS_LINUX HAVE_TIMER_ABINIT
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=== Build Information ===
Version : 10.0.3
Build target : x86_64_linux_gnu13.3
Build date : 20241021
=== Compiler Suite ===
C compiler : gnu
C++ compiler : gnu13.3
Fortran compiler : gnu13.3
CFLAGS : -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protect ...
CXXFLAGS : -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune ...
FCFLAGS : -g -ffree-line-length-none -fallow-argument-mismatch -fallow-argument-mismatch
FC_LDFLAGS :
=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : intel_xeon
=== Multicore ===
Parallel build : yes
Parallel I/O : yes
openMP support :
GPU support :
=== Connectors / Fallbacks ===
LINALG flavor : netlib
FFT flavor : fftw3
HDF5 : yes
NetCDF : yes
NetCDF Fortran : yes
LibXC : yes
Wannier90 : no
=== Experimental features ===
Exports :
GW double-precision :
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -march=nocona -mtune=haswell
Optimizations for 43_ptgroups:
-O0
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Abinitbuild:
Abinit Build Information:
Abinit version: 10.0.3
MPI: True, MPI-IO: True, OpenMP: True
Netcdf: True
Abipy Scheduler:
PyFlowScheduler, Pid: 3330
Scheduler options:
{'weeks': 0, 'days': 0, 'hours': 0, 'minutes': 0, 'seconds': 5}
Installed packages:
Package Version
-------------- ----------
system Linux
python_version 3.11.8
numpy 1.26.4
scipy 1.14.1
netCDF4 1.7.2
apscheduler 3.10.4
pydispatch 2.0.7
ruamel.yaml 0.18.6
boken 3.6.1
panel 1.5.4
plotly 5.24.1
ase 3.23.0
phonopy 2.31.0
monty 2024.10.21
pymatgen 2024.11.13
abipy 0.9.8
Important Shell Variables:
['/usr/share/miniconda/envs/abipy/bin:/usr/share/miniconda/condabin:/usr/share/miniconda/condabin:/snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/runner/.dotnet/tools',
'',
'']
Abipy requirements are properly configured
The command abicheck.py --with-flow can be used to run a small AbiPy flow in order to
check the interface with the Abinit executables.
Complete command line reference
usage: abicheck.py [-h] [--loglevel LOGLEVEL] [-V] [-v] [--no-colors]
[--with-flow] [-d FLOW_DIR] [-m] [-c] [-f]
Named Arguments¶
- --loglevel
Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG
Default:
'ERROR'- -V, --version
show program’s version number and exit
- -v, --verbose
verbose, can be supplied multiple times to increase verbosity.
Default:
0- --no-colors
Disable ASCII colors.
Default:
False- --with-flow
Build and run small abipy flow for testing.
Default:
False- -d, --flow-dir
Create AbiPy flow in this directory. If None, a default directory is used,
- -m, --show-managers
Print table with manager files provided by AbiPy.
Default:
False- -c, --create-config
Create yaml configuration files in ~/abinit/.abipy with predefined settings.
Default:
False- -f, --force-reinstall
Overwrite yaml configuration files if –create-config and files already exist.
Default:
False