gw_iter rescf=True error

[mbarbry]

Dear @masmansouri and @kovalp

Here is the error that I get when setting rescf=True in gw_iter. However, it occurred at the moment only with this specific system. It did not give issues for small molecules.

AttributeError: 'gw_iter' object has no attribute '_add_suffix'
Exception ignored in: <function VHFOpt.__del__ at 0x7f7a23aaba60>
Traceback (most recent call last):
File "/home/marc/programs/pyscf/pyscf/scf/_vhf.py", line 92, in __del__
libcvhf.CVHFdel_optimizer(ctypes.byref(self._this))
AttributeError: 'VHFOpt' object has no attribute '_this'

gw_iter_error.zip

[kovalp]

Looks new to me. I will try to have a look. El sáb., 30 nov. 2019 9:55, mbarbry <notifications@github.com> escribió:

…

Dear @masmansouri <https://github.com/masmansouri> and @kovalp <https://github.com/kovalp> Here is the error that I get when setting rescf=True in gw_iter. However, it occurred at the moment only with this specific system. It did not give issues for small molecules. AttributeError: 'gw_iter' object has no attribute '_add_suffix' Exception ignored in: <function VHFOpt.__del__ at 0x7f7a23aaba60> Traceback (most recent call last): File "/home/marc/programs/pyscf/pyscf/scf/_vhf.py", line 92, in __del__ libcvhf.CVHFdel_optimizer(ctypes.byref(self._this)) AttributeError: 'VHFOpt' object has no attribute '_this' gw_iter_error.zip <https://github.com/cfm-mpc/pyscf/files/3906925/gw_iter_error.zip> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15?email_source=notifications&email_token=ACAKSHHAHJXSXALAJLT24A3QWITANA5CNFSM4JTFVW62YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H47S2XQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACAKSHFH6AOZPPESU2AEMETQWITANANCNFSM4JTFVW6Q> .

[mbarbry]

It is probably caused by some changes after the rebase with upstream. I get this error on nao2 branch.

[kovalp]

Can you help me with compilation? I follow the instructions in nao/README.md copied the cmake.user.inc cd build cmake .. cmake finds FFTW3 /usr/lib/x86_64-linux-gnu I compile, go to nao/test export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu trying to run the first test. ''' ============================================================================= ERRORS =============================================================================

…

________________________________________________________ ERROR collecting pyscf/nao/test/test_0001_nao.py

________________________________________________________ /home/kovalp/envs/py37-pyside2/lib/python3.7/site-packages/py/_path/local.py:701: in pyimport __import__(modname) ../__init__.py:25: in <module> from .m_ao_matelem import ao_matelem_c ../m_ao_matelem.py:23: in <module> from pyscf.nao.m_gaunt import gaunt_c ../m_gaunt.py:17: in <module> from pyscf.nao.m_thrj import thrj ../m_thrj.py:41: in <module> from pyscf.nao.m_libnao import libnao ../m_libnao.py:16: in <module> libnao = misc.load_library("libnao") ../../lib/misc.py:64: in load_library return numpy.ctypeslib.load_library(libname, _loaderpath) /home/kovalp/envs/py37-pyside2/lib/python3.7/site-packages/numpy/ctypeslib.py:152: in load_library return ctypes.cdll[libpath] /usr/local/lib/python3.7/ctypes/__init__.py:431: in __getitem__ return getattr(self, name) /usr/local/lib/python3.7/ctypes/__init__.py:426: in __getattr__ dll = self._dlltype(name) /usr/local/lib/python3.7/ctypes/__init__.py:356: in __init__ self._handle = _dlopen(self._name, mode) E OSError: /home/kovalp/programs/pyscf/pyscf/lib/libnao.so: undefined symbol: sfftw_destroy_plan_ '''

On Sat, Nov 30, 2019 at 10:12 AM mbarbry ***@***.***> wrote: It is probably caused by some changes after the rebase with upstream. I get this error on nao2 branch. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15?email_source=notifications&email_token=ACAKSHFIRT7ATMLDITUF5WDQWIVBHA5CNFSM4JTFVW62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFP6HUY#issuecomment-559932371>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACAKSHF7CACZPAPB5W7F6ETQWIVBHANCNFSM4JTFVW6Q> .

[kovalp]

@mbarbry

[mbarbry]

To compile I usually use (ubuntu 18.04),

export CC=gcc && export FC=gfortran && export CXX=g++
cd pyscf && git fetch && git checkout nao2 && cd pyscf/lib
cp cmake_user_inc_examples/cmake.user.inc-singularity.anaconda.gnu.mkl cmake.arch.inc
mkdir build && cd build && cmake .. && make VERBOSE=1

Then I export

export PYTHONPATH=/opt/pyscf:$PYTHONPATH
export LD_LIBRARY_PATH=/opt/pyscf/pyscf/lib/deps/lib:${LD_LIBRARY_PATH}

[masmansouri]

Hi,
by following the above procedure which is a standard way to compile pyscf, I just successfully installed it. I used to compile with another arch file like cmake.user.inc-nao-gnu that no longer works due to the inaccessible link for cloning the libxc in tddft.org webpage. After installation using mkl root as you mentioned, when I tried to import pyscf.nao modules, for example in Ipython, it gives an error as follows:

Python 3.7.3 (default, Mar 27 2019, 22:11:17)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.6.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from pyscf.nao import gw

OSError Traceback (most recent call last)
in
----> 1 from pyscf.nao import gw

~/software/pyscf/pyscf/nao/init.py in
23 from .m_ls_part_centers import ls_part_centers
24 from .m_coulomb_am import coulomb_am
---> 25 from .m_ao_matelem import ao_matelem_c
26 from .prod_basis import prod_basis
27 from .m_comp_coulomb_den import comp_coulomb_den

~/software/pyscf/pyscf/nao/m_ao_matelem.py in
21 from pyscf.nao.m_ao_log_hartree import ao_log_hartree
22 from timeit import default_timer as timer
---> 23 from pyscf.nao.m_gaunt import gaunt_c
24
25 #

~/software/pyscf/pyscf/nao/m_gaunt.py in
15 import numpy as np
16 import scipy as sp
---> 17 from pyscf.nao.m_thrj import thrj
18 #from sympy.physics.quantum.cg import Wigner3j as w3j
19 #from sympy.physics.wigner import gaunt as gau

~/software/pyscf/pyscf/nao/m_thrj.py in
39
40 if uselibnao :
---> 41 from pyscf.nao.m_libnao import libnao
42
43 libnao.init_thrj.argtypes = (

~/software/pyscf/pyscf/nao/m_libnao.py in
14
15 from pyscf.lib import misc
---> 16 libnao = misc.load_library("libnao")

~/software/pyscf/pyscf/lib/misc.py in load_library(libname)
62 else:
63 _loaderpath = os.path.dirname(file)
---> 64 return numpy.ctypeslib.load_library(libname, _loaderpath)
65
66 #Fixme, the standard resouce module gives wrong number when objects are released

~/anaconda3/lib/python3.7/site-packages/numpy/ctypeslib.py in load_library(libname, loader_path)
155 raise
156 ## if no successful return in the libname_ext loop:
--> 157 raise OSError("no file with expected extension")
158
159 ctypes_load_library = deprecate(load_library, 'ctypes_load_library',

OSError: no file with expected extension

Apparently, it cannot import most of nao modules. Do you know what the problem is?

[mbarbry]

Looks like it does not find the library somehow.
I will give a try in a virtualbox. Could you send me the cmake.arch that you use.

[masmansouri]

I downgraded the gcc to the older version, i.e. g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0. I also tried different mkl roots in the arch file, but all failed to import modules.

cmake.arch.inc.txt

[mbarbry]

Dear @masmansouri and @kovalp

I managed to install and run pyscf-nao on a clean system (linux mint 19.2) following the instructions below

Instruction to install pyscf-nao

apt-get update
apt-get upgrade
apt-get -y install git wget curl htop gcc gfortran vim build-essential liblapack-dev libfftw3-dev make cmake zlib1g-dev
wget https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh
bash Anaconda3-2019.10-Linux-x86_64.sh
bash
mkdir -p anaconda3/lib/mkl/lib
ln -s ~/anaconda3/lib/libmkl_* ~/anaconda3/lib/mkl/lib/

export CC=gcc && export FC=gfortran && export CXX=g++
git clone https://github.com/cfm-mpc/pyscf.git
cd pyscf
git fetch
git checkout nao2
cd pyscf/lib
cp cmake_user_inc_examples/cmake.user.inc-singularity.anaconda.gnu.mkl cmake.arch.inc

Edit the cmake.arch.inc that it properly find mkl
Use a full path for MKLROOT, and don't use ~ for your home folder path, it could not compile in my case

export LD_LIBRARY_PATH=~/anaconda3/lib/mkl/lib:{LD_LIBRARY_PATH}
mkdir build && cd build
cmake .. && make

Once pyscf is build, add the following variable to your bash

export PYTHONPATH=~/pyscf:${PYTHONPATH}
export LD_LIBRARY_PATH=~/pyscf/pyscf/lib/deps/lib:${LD_LIBRARY_PATH}

then you can go to nao test folder, and you should be able to run the tests

[kovalp]

Thank you. I was not able to do anything so far. I have made a bad experience with anaconda. Therefore, I will try it differently. The best would be to have a pip package. El dom., 1 dic. 2019 12:12, mbarbry <notifications@github.com> escribió:

…

Dear @masmansouri <https://github.com/masmansouri> and @kovalp <https://github.com/kovalp> I managed to install and run pyscf-nao on a clean system (linux mint 19.2) following the instructions below Instruction to install pyscf-nao apt-get update apt-get upgrade apt-get -y install git wget curl htop gcc gfortran vim build-essential liblapack-dev libfftw3-dev make cmake zlib1g-dev wget https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh bash Anaconda3-2019.10-Linux-x86_64.sh bash mkdir -p anaconda3/lib/mkl/lib ln -s ~/anaconda3/lib/libmkl_* ~/anaconda3/lib/mkl/lib/ export CC=gcc && export FC=gfortran && export CXX=g++ git clone https://github.com/cfm-mpc/pyscf.git cd pyscf git fetch git checkout nao2 cd pyscf/lib cp cmake_user_inc_examples/cmake.user.inc-singularity.anaconda.gnu.mkl cmake.arch.inc Edit the cmake.arch.inc that it properly find mkl Use a full path for MKLROOT, and don't use ~ for your home folder path, it could not compile in my case export LD_LIBRARY_PATH=~/anaconda3/lib/mkl/lib:{LD_LIBRARY_PATH} mkdir build && cd build cmake .. && make Once pyscf is build, add the following variable to your bash export PYTHONPATH=~/pyscf:${PYTHONPATH} export LD_LIBRARY_PATH=~/pyscf/pyscf/lib/deps/lib:${LD_LIBRARY_PATH} then you can go to nao test folder, and you should be able to run the tests — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15?email_source=notifications&email_token=ACAKSHCJDISGFWZJMZ5ZWNLQWOL2JA5CNFSM4JTFVW62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFRFTAY#issuecomment-560093571>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACAKSHC4RO7IEXEBAMJL3LTQWOL2JANCNFSM4JTFVW6Q> .

[masmansouri]

Thanks @mbarbry One clarification, which version of gcc you used to compile?

[masmansouri]

@mbarbry by following your recipe and gcc 7.4.0 installed and successfully passed tests.

[masmansouri]

I received a lot of
"NumbaPerformanceWarning: np.dot() is faster on contiguous arrays, called on (array(float64, 2d, C), array(float64, 2d, A))"
in most of the tests in gw class, e.g. test 0055-0058 calling rf0_den. Tests passed much much slower than the former algorithm! Also, a few tests mostly in tddft failed.

[mbarbry]

Hi @kovalp, I agree a pip package would be nice, but difficult to achieve with the number of dependencies.

I think docker is easier for such cases with many dependencies. You should try the singularity packages I wrote.
https://gitlab.com/mbarbry/AbInitioToolkit

The recipe buildPySCF-NAO-Siesta.mkl.gpu is the latest up to date.

@masmansouri I will try to see if I get also the warnings for the tests. I did not see any in the tests I run thought.

[masmansouri]

=============================================================
Starting TEST at 01/12/2019 --- 14:25:41, please wait...IT TAKES A FEW MINS

=============> Report: 142 succeeded and 14 failed.<=================
FAILED TEST are:
test_0044_h2_scf_gto_vs_nao_nao.py
test_0046_tddft_gto_h2.py
test_0049_high_telec.py
test_0053_gw_si_ref.py
test_0068_gw_f_atom.py
test_0077_chlocal_water.py
test_0079_recomp_hamilt_water.py
test_0081_bse_nonin_gto_be.py
test_0082_bse_gw_gto_be.py
test_0083_gw_bse_h2_ae.py
test_0085_mn_scf.py
test_0095_h2_ae_fp_rescf.py
test_0100_fireball.py
test_0160_bse_h2b_uhf_gw.py
=======================FINISHED! AT 15:10:24 ===================

Tests which are failed, mostly have problems with this new algorithm si_correlation in m_rf0 and a few have problems in original pyscf kernel like test 44 for which scf no longer has former attributes.
"AttributeError: 'scf' object has no attribute 'incore_anyway".