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
/Users/gmatteo/git_repos/pymatgen/pymatgen/util/testing.py:42: UserWarning: It is recommended that you set the PMG_TEST_FILES_DIR environment variable explicity. Now using a fallback location based on relative path from this module.
  warnings.warn(
AbiPy Manager:
[Qadapter 0]
ShellAdapter:gmac
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 ..................    1.0000000000000002E-006

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 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_GW_DPC                 HAVE_HDF5        HAVE_LIBPAW_ABINIT
 
      HAVE_LIBTETRA_ABINIT                HAVE_LIBXC         HAVE_LINALG_AXPBY
 
        HAVE_LINALG_GEMM3M     HAVE_LINALG_ZDOTC_B*G     HAVE_LINALG_ZDOTU_B*G
 
                  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_TIMER_ABINIT
 
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

 === Build Information === 
  Version       : 9.5.3
  Build target  : x86_64_darwin20.3.0_gnu8.2
  Build date    : 20210702

 === Compiler Suite === 
  C compiler       : gnu8.2
  C++ compiler     : gnu8.2
  Fortran compiler : gnu8.2
  CFLAGS           : -g -O2 -mtune=native -march=native
  CXXFLAGS         : -g -O2 -mtune=native -march=native
  FCFLAGS          : -g -O2 -fbacktrace -ffree-line-length-none   -I/Users/gmatteo/local/build_gcc_820/include -I/Users/gmatteo/local/build_gcc_820/include
  FC_LDFLAGS       : 

 === Optimizations === 
  Debug level        : basic
  Optimization level : standard
  Architecture       : unknown_unknown

 === Multicore === 
  Parallel build : /Users/gmatteo/local/build_gcc_820/
  Parallel I/O   : yes
  openMP support : no
  GPU support    : 

 === Connectors / Fallbacks === 
  LINALG flavor  : openblas
  FFT flavor     : fftw3
  HDF5           : yes
  NetCDF         : yes
  NetCDF Fortran : yes
  LibXC          : yes
  Wannier90      : no

 === Experimental features === 
  Exports             : 
  GW double-precision : yes

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 Default optimizations:
   --- None ---


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


 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 ..................    1.0000000000000002E-006

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 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_GW_DPC                 HAVE_HDF5        HAVE_LIBPAW_ABINIT
 
      HAVE_LIBTETRA_ABINIT                HAVE_LIBXC         HAVE_LINALG_AXPBY
 
        HAVE_LINALG_GEMM3M     HAVE_LINALG_ZDOTC_B*G     HAVE_LINALG_ZDOTU_B*G
 
                  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_TIMER_ABINIT
 
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

 === Build Information === 
  Version       : 9.5.3
  Build target  : x86_64_darwin20.3.0_gnu8.2
  Build date    : 20210702

 === Compiler Suite === 
  C compiler       : gnu8.2
  C++ compiler     : gnu8.2
  Fortran compiler : gnu8.2
  CFLAGS           : -g -O2 -mtune=native -march=native
  CXXFLAGS         : -g -O2 -mtune=native -march=native
  FCFLAGS          : -g -O2 -fbacktrace -ffree-line-length-none   -I/Users/gmatteo/local/build_gcc_820/include -I/Users/gmatteo/local/build_gcc_820/include
  FC_LDFLAGS       : 

 === Optimizations === 
  Debug level        : basic
  Optimization level : standard
  Architecture       : unknown_unknown

 === Multicore === 
  Parallel build : /Users/gmatteo/local/build_gcc_820/
  Parallel I/O   : yes
  openMP support : no
  GPU support    : 

 === Connectors / Fallbacks === 
  LINALG flavor  : openblas
  FFT flavor     : fftw3
  HDF5           : yes
  NetCDF         : yes
  NetCDF Fortran : yes
  LibXC          : yes
  Wannier90      : no

 === Experimental features === 
  Exports             : 
  GW double-precision : yes

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 Default optimizations:
   --- None ---


 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Abinitbuild:
Abinit Build Information:
    Abinit version: 9.5.3
    MPI: True, MPI-IO: True, OpenMP: False
    Netcdf: True

Abipy Scheduler:
PyFlowScheduler, Pid: 14100
Scheduler options: {'weeks': 0, 'days': 0, 'hours': 0, 'minutes': 0, 'seconds': 8}

Installed packages:
Package         Version
--------------  ---------
system          Darwin
python_version  3.8.0
numpy           1.21.0
scipy           1.6.2
netCDF4         1.5.6
apscheduler     3.7.0
pydispatch      2.0.5
yaml            5.4.1
boken           2.3.2
panel           0.11.3
plotly          5.1.0
ase             3.21.1
phonopy         2.9.3
monty           2021.3.3
pymatgen        2022.0.8
abipy           0.9.1


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