Compile from source (Ubuntu) problems

[ap-ahero]

Hello everyone,

I'm struggling a bit with the compilation from source in my VM. It is a "brand" new ubuntu 20.04, therefore I assume it should be fine.

During the compilation of dafoam, I have some errors that has been saved in the error_log.txt. Is it normal?

But then when I "pip install .", it says that everything has been successfully installed.

The main problem arise during the DAFoam regression tests. That means when I run this command:

cd $HOME/dafoam/repos/dafoam/tests && ./Allrun

First the folder name in my case is cd $HOME/dafoam/repos/dafoam-3.0.0/tests and second it remains stucked here during the first test:

+--------------------------------------------------------------------------+
| Evaluating Objective Function Sensitivities 001 |
+--------------------------------------------------------------------------+
capi_return is NULL
Call-back cb_slgrad_in_slsqp__user__routines failed.
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:844: UserWarning: addGeoDVLocal will be deprecated, use addLocalDV instead
warnings.warn("addGeoDVLocal will be deprecated, use addLocalDV instead")
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:743: UserWarning: addGeoDVGlobal will be deprecated, use addGlobalDV instead
warnings.warn("addGeoDVGlobal will be deprecated, use addGlobalDV instead")
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pySLSQP/pySLSQP.py:207: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
lw = np.array([lwM], np.int)
runTests_Integration.py:123: ComplexWarning: Casting complex values to real discards the imaginary part
inletU = [float(U0 * np.cos(aoa)), float(U0 * np.sin(aoa)), 0]
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:844: UserWarning: addGeoDVLocal will be deprecated, use addLocalDV instead
warnings.warn("addGeoDVLocal will be deprecated, use addLocalDV instead")
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:743: UserWarning: addGeoDVGlobal will be deprecated, use addGlobalDV instead
warnings.warn("addGeoDVGlobal will be deprecated, use addGlobalDV instead")
runTests_Integration.py:123: ComplexWarning: Casting complex values to real discards the imaginary part
inletU = [float(U0 * np.cos(aoa)), float(U0 * np.sin(aoa)), 0]
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:844: UserWarning: addGeoDVLocal will be deprecated, use addLocalDV instead
warnings.warn("addGeoDVLocal will be deprecated, use addLocalDV instead")
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:743: UserWarning: addGeoDVGlobal will be deprecated, use addGlobalDV instead
warnings.warn("addGeoDVGlobal will be deprecated, use addGlobalDV instead")
runTests_Integration.py:123: ComplexWarning: Casting complex values to real discards the imaginary part
inletU = [float(U0 * np.cos(aoa)), float(U0 * np.sin(aoa)), 0]
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:844: UserWarning: addGeoDVLocal will be deprecated, use addLocalDV instead
warnings.warn("addGeoDVLocal will be deprecated, use addLocalDV instead")
/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py:743: UserWarning: addGeoDVGlobal will be deprecated, use addGlobalDV instead
warnings.warn("addGeoDVGlobal will be deprecated, use addGlobalDV instead")
runTests_Integration.py:123: ComplexWarning: Casting complex values to real discards the imaginary part
inletU = [float(U0 * np.cos(aoa)), float(U0 * np.sin(aoa)), 0]
Traceback (most recent call last):
File "runTests_Integration.py", line 224, in
sol = opt(optProb, sens=optFuncs.calcObjFuncSensMP, storeHistory=histFile)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pySLSQP/pySLSQP.py", line 218, in call
slsqp.slsqp(m, meq, la, n, xs, blx, bux, ff, gg, df, dg, acc, maxit,
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pySLSQP/pySLSQP.py", line 180, in slgrad
gobj, gcon, fail = self._masterFunc(x, ["gobj", "gcon"])
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 321, in _masterFunc
result = self._masterFunc2(*args)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 460, in masterFunc2
args = self.sens(xuser, self.cache["funcs"])
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/optFuncs.py", line 252, in calcObjFuncSensMP
DASolver.writeDeformedFFDs()
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/pyDAFoam.py", line 1168, in writeDeformedFFDs
self.DVGeo.writeTecplot("deformedFFD%03d.dat" % self.nSolveAdjoints)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 2597, in writeTecplot
vol_counter += self._writeVols(f, vol_counter, solutionTime)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 4157, in _writeVols
writeTecplot3D(handle, "FFD_vol%d" % i, self.FFD.vols[i].coef, solutionTime)
TypeError: writeTecplot3D() takes 3 positional arguments but 4 were given
Traceback (most recent call last):
File "runTests_Integration.py", line 224, in
sol = opt(optProb, sens=optFuncs.calcObjFuncSensMP, storeHistory=histFile)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pySLSQP/pySLSQP.py", line 265, in call
self._waitLoop()
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 693, in _waitLoop
self._masterFunc2(*info)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 460, in masterFunc2
args = self.sens(xuser, self.cache["funcs"])
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/optFuncs.py", line 252, in calcObjFuncSensMP
DASolver.writeDeformedFFDs()
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/pyDAFoam.py", line 1168, in writeDeformedFFDs
self.DVGeo.writeTecplot("deformedFFD%03d.dat" % self.nSolveAdjoints)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 2597, in writeTecplot
vol_counter += self._writeVols(f, vol_counter, solutionTime)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 4157, in _writeVols
writeTecplot3D(handle, "FFD_vol%d" % i, self.FFD.vols[i].coef, solutionTime)
TypeError: writeTecplot3D() takes 3 positional arguments but 4 were given
Traceback (most recent call last):
File "runTests_Integration.py", line 224, in
sol = opt(optProb, sens=optFuncs.calcObjFuncSensMP, storeHistory=histFile)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pySLSQP/pySLSQP.py", line 265, in call
self._waitLoop()
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 693, in _waitLoop
self._masterFunc2(*info)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 460, in masterFunc2
args = self.sens(xuser, self.cache["funcs"])
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/optFuncs.py", line 252, in calcObjFuncSensMP
DASolver.writeDeformedFFDs()
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/pyDAFoam.py", line 1168, in writeDeformedFFDs
self.DVGeo.writeTecplot("deformedFFD%03d.dat" % self.nSolveAdjoints)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 2597, in writeTecplot
vol_counter += self._writeVols(f, vol_counter, solutionTime)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 4157, in _writeVols
writeTecplot3D(handle, "FFD_vol%d" % i, self.FFD.vols[i].coef, solutionTime)
TypeError: writeTecplot3D() takes 3 positional arguments but 4 were given
Traceback (most recent call last):
File "runTests_Integration.py", line 224, in
sol = opt(optProb, sens=optFuncs.calcObjFuncSensMP, storeHistory=histFile)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pySLSQP/pySLSQP.py", line 265, in call
self._waitLoop()
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 693, in _waitLoop
self._masterFunc2(*info)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pyoptsparse/pyOpt_optimizer.py", line 460, in masterFunc2
args = self.sens(xuser, self.cache["funcs"])
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/optFuncs.py", line 252, in calcObjFuncSensMP
DASolver.writeDeformedFFDs()
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/dafoam/pyDAFoam.py", line 1168, in writeDeformedFFDs
self.DVGeo.writeTecplot("deformedFFD%03d.dat" % self.nSolveAdjoints)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 2597, in writeTecplot
vol_counter += self._writeVols(f, vol_counter, solutionTime)
File "/home/pedl-20/dafoam/packages/miniconda3/lib/python3.8/site-packages/pygeo/parameterization/DVGeo.py", line 4157, in _writeVols
writeTecplot3D(handle, "FFD_vol%d" % i, self.FFD.vols[i].coef, solutionTime)
TypeError: writeTecplot3D() takes 3 positional arguments but 4 were given
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='deformedFFD_001.dat' mode='w' encoding='UTF-8'>
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='deformedFFD_001.dat' mode='w' encoding='UTF-8'>
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='deformedFFD_001.dat' mode='w' encoding='UTF-8'>

Can anyone help me?
Best
AP

[friedenhe]

Thanks for the feedback. The problem was caused by an issue in the pyGeo version. We have just updated the website with the correct pyGeo version to use. Please re-install pyGeo following here and let us know if it works.

[ap-ahero]

It worked:

---

**************** All DAFoam tests passed! ******************

---

thank you :)