hungpham2017 / pywannier90 Goto Github PK

Dear developer, first of all thanks a lot for the effort to share this useful tool

Unfortunately I have the following issue:

My system:

1. System Ubuntu18.04
2. gfortran7 + gcc7
3. blas and lapack libs installed with apt

wannier90 lib without wannier_lib.F90 from pywannier90 working by testing with resident tool.

after changing wannier_lib.F90 as suggested in pywannier90 installation guide:

1. modified Makefile pywannier90 as per the file attached here 'Makefile.txt'

2. after checking with the command: ' python -c "import libwannier90" ' I received the following error:
   "ImportError: /home/PYWANNIER90/pyWannier90/src/libwannier90.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _gfortran_transfer_complex"

3. to check symbols in the libwannier90 I did 'nm libwannier90.cpython-36m-x86_64-linux-gnu.so' and the result is in the file 'result.txt'

would you be so kind to let me know if you have any thoughts on this? thanks a lot

Regards

Makefile.txt
result.txt

When running test files in lib-test, there seems to be a typecasting error, where the libwannier.cpp is not receiving the data type from test-cu.py file.

While running files in examples, each of the files show some errors.
Running ch4.py file gives the following error:

Traceback (most recent call last):
  File "ch4.py", line 47, in <module>
    w90.kernel()

  File "/home/valayagarawal/Apps/pyscf/pyscf/pbc/tools/pywannier90.py", line 562, in kernel 
    self.A_matrix_loc = self.get_A_mat()

  File "/home/valayagarawal/Apps/pyscf/pyscf/pbc/tools/pywannier90.py", line 683, in get_A_mat
    gr = g_r(coords, abs_site, l, mr, r, zona, x_axis, z_axis, unit = 'B')

  File "/home/valayagarawal/Apps/pyscf/pyscf/pbc/tools/pywannier90.py", line 309, in g_r
    neither_idx = not larger_idx and not smaller_idx

ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Running ch3.py and h2.py gives

Traceback (most recent call last):
  File "ch3.py", line 46, in <module>
    w90 = pywannier90.W90(kmf, cell, nk, num_wann, other_keywords = keywords)
  File "/home/valayagarawal/Apps/pyscf/pyscf/pbc/tools/pywannier90.py", line 477, in __init__
    nao_kpts.append(mo_energy.shape[0])
AttributeError: 'list' object has no attribute 'shape'

Running h2.py generates UNK files, but still has the same error as ch3.py file.

When compling the cpp file, we got an error

/home/qssun/workspace/program/pyWannier90/libwannier90.cpp: In function ‘std::vector<pybind11::array_t<double> > setup(char*, pybind11::array_t<int>, int*, pybind11::array_t<double>, pybind11::array_t<double>, pybind11::array_t<double>, int*, int*, pybind11::array_t<int>, pybind11::array_t<double>, int*, int*)’:
/home/qssun/workspace/program/pyWannier90/libwannier90.cpp:138:3: error: could not convert ‘{nn_, sizeof (int), pybind11::format_descriptor<T, typename std::enable_if<std::is_arithmetic<_Tp>::value, void>::type>::format() [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>](), 3, {nn_dim1, nn_dim2, 4}, {(((long unsigned int)(num_kpts * 4)) * sizeof (int)), (sizeof (int) * 4ul), sizeof (int)}}’ from ‘<brace-enclosed initializer list>’ to ‘pybind11::buffer_info’
   }; 
   ^

Seems the initialization part for buffer_info is not consistent to the newest buffer_info data structure
https://github.com/pybind/pybind11/blob/master/include/pybind11/buffer_info.h#L17

Dear Contributor:

Recently I am trying to install the pywannier90. After I compile the libwannier90, I obtained 2 files, naming as "libwannier90.cpp" and "libwannier90.cpython-37m-x86_64-linux-gnu.so".
But after I move the .so file to /pbc/tools and try [python3 -c "import libwannier90"], I obtain the following error:

Traceback (most recent call last):
File "", line 1, in
ImportError: [my own directory]/python3.8/site-packages/pyscf/pbc/tools/libwannier90.cpython-37m-x86_64-linux-gnu.so: undefined symbol: zgesv_

So is there a compiling error?
I also want to know that, as you mentioned in /pyscf/pbc/tools/pywannier90.py that:
['WARNING: Check the installation of libwannier90 and its path in pyscf/pbc/tools/pywannier90.py']
But actually, I did not find the code that related to the path of libwannier90 in the .py code. Instead, I found in /pyWannier90/src/pywannier90.py that:
[W90LIB = '/burg/home/hqp2000/pyWannier90/src']
I tries changing this line to the related directory, and copy this line to pyscf/pbc/tools/pywannier90.py. Both of my attempts do not work. So is this line necessary in pyscf/pbc/tools/pywannier90.py?

Thank you for reading this and looking forward to your reply.

When trying to run the h2.py example, I get the following error

Traceback (most recent call last):
  File "h2.py", line 47, in <module>
    w90.setup()
  File "/projects/wagner/wawheel2/code/pyscf/pyscf/pbc/tools/pywannier90.py", line 540, in setup
    self.atom_atomic_loc, atoms_cart_loc, self.gamma_only, self.spinors) 
TypeError: setup(): incompatible function arguments. The following argument types are supported:
    1. (arg0: numpy.ndarray[int32], arg1: int, arg2: numpy.ndarray[float64], arg3: numpy.ndarray[float64], arg4: numpy.ndarray[float64], arg5: int, arg6: int, arg7: numpy.ndarray[int32], arg8: numpy.ndarray[float64], arg9: int, arg10: int) -> List[numpy.ndarray[float64]]

Invoked with: 'wannier90', [2, 2, 2], 8, array([3., 0., 0., 0., 3., 0., 0., 0., 3.]), array([2.0943951, 0.       , 0.       , 0.       , 2.0943951, 0.       , 
       0.       , 0.       , 2.0943951]), array([0. , 0. , 0. , 0. , 0. , 0.5, 0. , 0.5, 0. , 0. , 0.5, 0.5, 0.5,  
       0. , 0. , 0.5, 0. , 0.5, 0.5, 0.5, 0. , 0.5, 0.5, 0.5]), 4, 2, [1, 1], array([1.5, 1.5, 1. , 1.5, 1.5, 2. ]), 0, 0

None of the argument types seem wrong, so I'm confused about what the problem is.

I cannot run the examples in the PySCF nor the pyWannier90 repositories, both giving the same error:

You are running Wannier90_setup via pyWannier90
 Error: Problem reading keyword num_wann
Error: examine the output/error file for details

I'll focus on the example in pyscf/pbc/tools/pywannier90.py
The input file for wannier90 is produced successfully and looks fine to me:

! Basic input

num_bands       = 9
num_wann       = 4

Begin Unit_Cell_Cart
 6.3500000   0.0000000   0.0000000
 0.0000000   6.3500000   0.0000000
 0.0000000   0.0000000   6.3500000
End Unit_Cell_Cart

Begin atoms_cart
C  3.1750000  3.1750000  3.1750000
H  2.5462656  2.5462656  2.5462656
H  3.8037344  3.8037344  2.5462656
H  2.5462656  3.8037344  3.8037344
H  3.8037344  2.5462656  3.8037344
End atoms_cart

!Additional keywords

    exclude_bands : 1,6-9
    begin projections
    C:sp3
    end projections
    


mp_grid        = 1 1 1
begin kpoints
0.0000000  0.0000000  0.0000000
End Kpoints

The output prints, after some headers,

Wannier90 is running in LIBRARY MODE via pyWannier90

 Setting up k-point neighbours...

 Exiting.......
 Error: Problem reading keyword num_wann

I am running pywannier90.py on a Linux cluster, and I compiled using GNU compilers, and also followed instructions in #4 (comment)

In the Makefile of pyWannier90,
USE_INTEL =no
LIBDIR = ${HOME}/soft/cp2k/tools/toolchain/install/lapack-3.8.0
LIBS = -L$(LIBDIR)/lib -llapack -lblas -Wl,-rpath,$(W90DIR) -L$(W90DIR) -lwannier
(in which the "libblas.a" and "liblapack.a" are available.)
In "$(W90DIR)", the "libwannier.a" is available, which is compiled using gfortran.

The "libwannier90.cpython-37m-x86_64-linux-gnu.so" was generated normally. The path of "libwannier90.cpython-37m-x86_64-linux-gnu.so" was also added properly into the enviroment variable of "LD_LIBRARY_PATH".

However, the running of "pywannier90.py" still gave an error message:

ImportError: ~/pyWannier90/src/libwannier90.cpython-37m-x86_64-linux-gnu.so: undefined symbol: __w90lib_MOD_wannier_run

Actually, the "__w90lib_MOD_wannier_run" is actaully available in the "libwannier90.cpp".

By running "nm -D" or "ldd -r" libwannier90.cpython-37m-x86_64-linux-gnu.so, I also noted that the status of "__w90lib_MOD_wannier_run" was "-U".

How could I fix it?

Hello, I have reopened issue #5, it seems to still exist even the latest pull request into pyscf.

I just compiled the dev branch of pyscf (with the latest commits), as well as fresh wannier90 and pyWannier90 installations using the GNU compilers and standard LAPACK/BLAS libraries.

When running example 47-pywannier90.py from pyscf, I receive the following error

[sapatha2@golubh3 pbc]$ python 47-pywannier90.py
WARN: Fail to read chkfile. Use MINAO initial guess
converged SCF energy = -7.8727802384689
You are running Wannier90_setup via pyWannier90
Error: Problem reading keyword num_wann
Error: examine the output/error file for details

If I were to instead put in an optional keyword that is read BEFORE num_wann by wannier90 (reference is wannier90/src/parameters.F90 function param_read()), such as timing_level
keywords = \
"""
timing_level = 3

begin projections
Si:sp3
end projections
""",
the following error is received
[sapatha2@golubh3 pbc]$ python 47-pywannier90.py
converged SCF energy = -7.87278023806266
You are running Wannier90_setup via pyWannier90
Error: Problem reading keyword timing_level
Error: examine the output/error file for details

Do you have any idea how to fix this issue? I suspect it has something to do with the formatting of the .win file that is generated by pyWannier90, since it is clearly failing in wannier90/src/parameters.F90 function param_read()

Thanks!

Hi,

Thanks for implementing Wannierization for PySCF. I was wondering if your implementation also works when pseudopotentials are used?

Regards
Vamshi

When I run

$ python -c "import libwannier90"

I get the following error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: /projects/wagner/wawheel2/code/pyWannier90/src/libwannier90.cpython-37m-x86_64-linux-gnu.so: undefined symbol: mpi_reduce_

I'm not sure where the problem is coming from. I've compiled wannier90 using the pyWannier90 version of wannier_lib.F90. The edited lines in the pyWannier90 Makefile are

W90DIR =/projects/wagner/wawheel2/code/wannier90
LIBDIR =/usr/local/intel/parallel_studio_xe_2018/compilers_and_libraries_2018.1.163/linux    /bin/intel64
USE_INTEL = yes 
MPIF90=mpiifort

ifeq ($(USE_INTEL), yes)
  CPP = /usr/local/intel/parallel_studio_xe_2018/compilers_and_libraries_2018.1.163/linux/bin/intel64/icpc
  LIBS = -L$(LIBDIR)/mkl/lib/intel64 -lmkl_core -lmkl_intel_lp64 -lmkl_sequential \
  -Wl,-rpath,$(LIBDIR)/lib/intel64 -L$(LIBDIR)/lib/intel64 -limf -lintlc -liomp5 -lifcore \
  -Wl,-rpath,$(W90DIR) -L$(W90DIR) -lwannier
    all: libwannier90_intel
endif

Do you have any suggestions?