# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# * David Maluenda Niubo (dmaluenda@cnb.csic.es) [2]
# *
# * [1] SciLifeLab, Stockholm University
# * [2] Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import json
from datetime import datetime
import pwem
from pyworkflow import Config
import pyworkflow.utils as pwutils
from scipion.install.funcs import CommandDef
from scipion import __version__ as scipionAppVersion
from packaging.version import Version
from .base import *
from .version import *
from .constants import XMIPP_HOME, XMIPP_URL, XMIPP_DLTK_NAME, XMIPP_CUDA_BIN, XMIPP_CUDA_LIB, XMIPP_GIT_URL
_references = ['delaRosaTrevin2013', 'Sorzano2013', 'Strelak2021']
_currentDepVersion = '1.0'
# Requirement version variables
NVIDIA_DRIVERS_MINIMUM_VERSION = 450
type_of_version = version.type_of_version
_logo = version._logo
_binTagVersion = version._binTagVersion
_pluginTagVersion= version._pluginTagVersion
_currentDepVersion = version._currentDepVersion
__version__ = version.__version__
[docs]class Plugin(pwem.Plugin):
_homeVar = XMIPP_HOME
_pathVars = [XMIPP_HOME]
_supportedVersions = []
_url = XMIPP_URL
_condaRootPath = None
# Refressing the plugin
# Inspects the call stack to find 'installPipModule' and sets 'self._plugin' to None.
# Uses CPython's internal API 'PyFrame_LocalsToFast' to sync changes.
# Risky and CPython-specific; use only if redesign is not possible.
try:
import inspect
import ctypes
for frameInfo in inspect.stack():
if frameInfo.function == "installPipModule":
frame = frameInfo[0]
frame.f_locals['self']._plugin = None
ctypes.pythonapi.PyFrame_LocalsToFast(
ctypes.py_object(frame),
ctypes.c_int(1))
except Exception as e:
print(e)
@classmethod
def _defineVariables(cls):
cls._defineEmVar(XMIPP_HOME, pwem.Config.XMIPP_HOME)
cls._defineVar(XMIPP_CUDA_BIN, pwem.Config.CUDA_BIN)
cls._defineVar(XMIPP_CUDA_LIB, pwem.Config.CUDA_LIB)
[docs] @classmethod
def getEnviron(cls, xmippFirst=True):
""" Create the needed environment for Xmipp programs. """
environ = pwutils.Environ(os.environ)
pos = pwutils.Environ.BEGIN if xmippFirst else pwutils.Environ.END
environ.update({
'PATH': cls.getVar(XMIPP_CUDA_BIN),
'LD_LIBRARY_PATH': cls.getVar(XMIPP_CUDA_LIB)
}, position=pwutils.Environ.END)
if os.path.isfile(getXmippPath('xmippEnv.json')):
with open(getXmippPath('xmippEnv.json'), 'r') as f:
compilationEnv = json.load(f)
environ.update(compilationEnv, position=pos)
environ.update({
'PATH': getXmippPath('bin'),
'LD_LIBRARY_PATH': getXmippPath('lib'),
'PYTHONPATH': getXmippPath('pylib')
}, position=pos)
environ['XMIPP_HOME'] = getXmippPath()
# Add path to python lib folder
environ.addLibrary(Config.getPythonLibFolder())
return environ
#TODO: Standardize to just: runProgram
[docs] @classmethod
def runXmippProgram(cls, program, args=""):
""" Internal shortcut function to launch a Xmipp program. """
pwutils.runJob(None, program, args, env=cls.getEnviron())
[docs] @classmethod
def getMatlabEnviron(cls, *toolPaths):
""" Return an Environment prepared for launching Matlab
scripts using the Xmipp binding.
"""
env = pwutils.Environ(os.environ)
env.set('PATH', os.environ.get('MATLAB_BINDIR', ''), pwutils.Environ.BEGIN)
env.set('LD_LIBRARY_PATH', os.environ.get('MATLAB_LIBDIR', ''),
pwutils.Environ.BEGIN)
for toolpath in toolPaths:
env.set('MATLABPATH', toolpath, pwutils.Environ.BEGIN)
env.set('MATLABPATH', os.path.join(os.environ[XMIPP_HOME],
'libraries', 'bindings', 'matlab'),
pwutils.Environ.BEGIN)
return env
[docs] @classmethod
def defineBinaries(cls, env):
""" Define the Xmipp binaries/source available tgz.
In addition, define extra software needed by some Xmipp methods
such as deepLearningToolkit.
Scipion-defined software can be used as dependencies
by using its name as string.
"""
# Determine if we are on a development
bundleDir = cls.__getBundleDirectory()
develMode = bundleDir is not None
COMPILE_TARGETS = [
'dist/bin/xmipp_image_header',
'dist/xmipp.bashrc'
]
# When changing dependencies, increment _currentDepVersion
CONDA_DEPENDENCIES = [
'cmake>=3.17',
'hdf5>=1.18',
'sqlite>=3',
'fftw>=3',
'mpich-mpicxx',
'c-compiler',
'cxx-compiler',
'make',
'openjdk',
'libtiff',
'libjpeg-turbo'
]
if os.environ['CONDA_PREFIX'] is not None: # TODO replace with pyworkflow method when available.
commands = CommandDef('conda install -c conda-forge ' + ' '.join(CONDA_DEPENDENCIES))
env.addPackage(
'xmippDep', version=_currentDepVersion,
tar='void.tgz',
commands=commands.getCommands(),
neededProgs=['conda'],
default=False
)
if develMode:
env.addPackage(
'xmippDev',
tar='void.tgz',
commands=[(f'cd {bundleDir} && ./xmipp', COMPILE_TARGETS)],
neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
updateCuda=True,
default=False
)
xmippSrc = f'xmippSrc-{version._binTagVersion}'
installCommands = [
(f'cd .. && rm -rf {xmippSrc} && '
f'git clone {XMIPP_GIT_URL} {xmippSrc} && '
f'cd {xmippSrc} && '
f'git checkout {version._binTagVersion} && '
f'./xmipp --production True ', COMPILE_TARGETS)
]
env.addPackage(
'xmippSrc', version=version._binTagVersion,
tar='void.tgz',
commands=installCommands,
neededProgs=['git', 'gcc', 'g++', 'cmake', 'make'],
updateCuda=True,
default=not develMode
)
## EXTRA PACKAGES ##
installDeepLearningToolkit(cls, env)
@classmethod
def __getBundleDirectory(cls):
# plugin = scipion-em-xmipp <-- xmipp3 <-- __init__.py
pluginDir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
# bundle = xmipp-bundle <- src <- scipion-em-xmipp
bundleDir = os.path.dirname(os.path.dirname(pluginDir))
isBundle = (os.path.isdir(os.path.join(bundleDir, 'src')) and
os.path.isfile(os.path.join(bundleDir, 'xmipp')))
return bundleDir if isBundle else None
[docs]def getNvidiaDriverVersion(plugin):
""" Several ways to retrieve NVIDIA driver version.
"""
commands = [["nvidia-smi", "--query-gpu=driver_version", "--format=csv,noheader"],
["cat", "/sys/module/nvidia/version"]]
for cmd in commands:
try:
nvidiaDriverVer = subprocess.Popen(cmd,
env=plugin.getEnviron(),
stdout=subprocess.PIPE
).stdout.read().decode('utf-8').split(".")[0]
return nvidiaDriverVer
except (ValueError, TypeError, FileNotFoundError):
continue