Closed giammi56 closed 1 year ago
robertodr
commented
1 year ago Hello, thanks for your interest in VeloxChem. Note that ARM64 is not (yet) officially supported (we have had some success on Apple M1 machines) I suggest you try using the openblas_env.yml file: MKL only is available for linux-64, mkl-64, and osx-64 architectures.
giammi56
commented
1 year ago after puting cppe and and mdanalysis under pip: dependencies, it compiles with the following output:
ubuntu@ubuntu:~/Documents/veloxchem$ conda env create -f openblas_env.yml
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages
openblas-0.3.21 | 8.1 MB | ################################################################################# | 100%
llvm-openmp-15.0.4 | 5.6 MB | ################################################################################# | 100%
libopenblas-0.3.21 | 7.2 MB | ################################################################################# | 100%
_openmp_mutex-4.5 | 6 KB | ################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/home/ubuntu/anaconda3/envs/vlxenv/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/ubuntu/Documents/veloxchem/condaenv.miip21w9.requirements.txt']
Pip subprocess output:
Collecting cppe
Downloading cppe-0.3.1.tar.gz (1.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 22.5 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting mdanalysis
Downloading MDAnalysis-2.3.0.tar.gz (3.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 88.1 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting pybind11>=2.2
Using cached pybind11-2.10.1-py3-none-any.whl (216 kB)
Collecting matplotlib>=1.5.1
Downloading matplotlib-3.6.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 86.5 MB/s eta 0:00:00
Collecting fasteners
Downloading fasteners-0.18-py3-none-any.whl (18 kB)
Collecting GridDataFormats>=0.4.0
Downloading GridDataFormats-1.0.1-py3-none-any.whl (2.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 89.7 MB/s eta 0:00:00
Collecting joblib>=0.12
Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.0/298.0 kB 43.8 MB/s eta 0:00:00
Collecting threadpoolctl
Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Requirement already satisfied: networkx>=2.0 in /home/ubuntu/anaconda3/envs/vlxenv/lib/python3.10/site-packages (from mdanalysis->-r /home/ubuntu/Documents/veloxchem/condaenv.miip21w9.requirements.txt (line 2)) (2.8.8)
Requirement already satisfied: numpy>=1.20.0 in /home/ubuntu/anaconda3/envs/vlxenv/lib/python3.10/site-packages (from mdanalysis->-r /home/ubuntu/Documents/veloxchem/condaenv.miip21w9.requirements.txt (line 2)) (1.23.4)
Requirement already satisfied: packaging in /home/ubuntu/anaconda3/envs/vlxenv/lib/python3.10/site-packages (from mdanalysis->-r /home/ubuntu/Documents/veloxchem/condaenv.miip21w9.requirements.txt (line 2)) (21.3)
Collecting mmtf-python>=1.0.0
Downloading mmtf_python-1.1.3-py2.py3-none-any.whl (25 kB)
Collecting biopython>=1.71
Downloading biopython-1.79.tar.gz (16.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.7/16.7 MB 71.8 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting tqdm>=4.43.0
Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 15.3 MB/s eta 0:00:00
Requirement already satisfied: scipy>=1.5.0 in /home/ubuntu/anaconda3/envs/vlxenv/lib/python3.10/site-packages (from mdanalysis->-r /home/ubuntu/Documents/veloxchem/condaenv.miip21w9.requirements.txt (line 2)) (1.9.3)
Collecting gsd>=1.9.3
Downloading gsd-2.6.1.tar.gz (138 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.0/139.0 kB 25.2 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting mrcfile
Downloading mrcfile-1.4.3-py2.py3-none-any.whl (43 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 kB 8.2 MB/s eta 0:00:00
Collecting pillow>=6.2.0
Downloading Pillow-9.3.0-cp310-cp310-manylinux_2_28_aarch64.whl (3.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 94.9 MB/s eta 0:00:00
Collecting cycler>=0.10
Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Requirement already satisfied: pyparsing>=2.2.1 in /home/ubuntu/anaconda3/envs/vlxenv/lib/python3.10/site-packages (from matplotlib>=1.5.1->mdanalysis->-r /home/ubuntu/Documents/veloxchem/condaenv.miip21w9.requirements.txt (line 2)) (3.0.9)
Collecting python-dateutil>=2.7
Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 13.7 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1
Downloading kiwisolver-1.4.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (1.4 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 85.4 MB/s eta 0:00:00
Collecting fonttools>=4.22.0
Downloading fonttools-4.38.0-py3-none-any.whl (965 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 965.4/965.4 kB 77.0 MB/s eta 0:00:00
Collecting contourpy>=1.0.1
Downloading contourpy-1.0.6-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (278 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 278.9/278.9 kB 37.9 MB/s eta 0:00:00
Collecting msgpack>=1.0.0
Downloading msgpack-1.0.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (309 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 309.5/309.5 kB 13.7 MB/s eta 0:00:00
Requirement already satisfied: six>=1.5 in /home/ubuntu/anaconda3/envs/vlxenv/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib>=1.5.1->mdanalysis->-r /home/ubuntu/Documents/veloxchem/condaenv.miip21w9.requirements.txt (line 2)) (1.16.0)
Building wheels for collected packages: cppe, mdanalysis, biopython, gsd
Building wheel for cppe (setup.py): started
Building wheel for cppe (setup.py): still running...
Building wheel for cppe (setup.py): still running...
Building wheel for cppe (setup.py): finished with status 'done'
Created wheel for cppe: filename=cppe-0.3.1-cp310-cp310-linux_aarch64.whl size=788589 sha256=68853e13f7794bb8e20e5c3ba07564dbd6f8e41fe9b89ac4d18119f32a77b461
Stored in directory: /home/ubuntu/.cache/pip/wheels/13/15/85/d440821f06552e51295384f7ca301052b95e845a6ef6ca1966
Building wheel for mdanalysis (pyproject.toml): started
Building wheel for mdanalysis (pyproject.toml): still running...
Building wheel for mdanalysis (pyproject.toml): finished with status 'done'
Created wheel for mdanalysis: filename=MDAnalysis-2.3.0-cp310-cp310-linux_aarch64.whl size=2366876 sha256=9ead441ebae422d11d732aa0492b329f8dc1cf732b06728c22ed89f70b461f7d
Stored in directory: /home/ubuntu/.cache/pip/wheels/ce/4a/d6/db03fdc9863df639cbe3e0a48fc2b6bf30a2df316c44c3dec2
Building wheel for biopython (setup.py): started
Building wheel for biopython (setup.py): finished with status 'done'
Created wheel for biopython: filename=biopython-1.79-cp310-cp310-linux_aarch64.whl size=2281705 sha256=a4b956cfa8ae0d3ad43c5a99d7e39183ca4b8f35a94722c5ff5e88e758fd4093
Stored in directory: /home/ubuntu/.cache/pip/wheels/09/a0/11/386a7bf373b098a091adbb47abe56ad52762eb0307d5e90074
Building wheel for gsd (pyproject.toml): started
Building wheel for gsd (pyproject.toml): finished with status 'done'
Created wheel for gsd: filename=gsd-2.6.1-cp310-cp310-linux_aarch64.whl size=101221 sha256=d8073e26a942e2529407f8d458e8670d8e505c41068c5d0783efed2a99633e1c
Stored in directory: /home/ubuntu/.cache/pip/wheels/15/56/b4/712f39cd5c6a6882ad497e04177309a86e32a6342069ddcc02
Successfully built cppe mdanalysis biopython gsd
Installing collected packages: msgpack, tqdm, threadpoolctl, python-dateutil, pybind11, pillow, mrcfile, mmtf-python, kiwisolver, joblib, gsd, fonttools, fasteners, cycler, contourpy, biopython, matplotlib, GridDataFormats, cppe, mdanalysis
Successfully installed GridDataFormats-1.0.1 biopython-1.79 contourpy-1.0.6 cppe-0.3.1 cycler-0.11.0 fasteners-0.18 fonttools-4.38.0 gsd-2.6.1 joblib-1.2.0 kiwisolver-1.4.4 matplotlib-3.6.2 mdanalysis-2.3.0 mmtf-python-1.1.3 mrcfile-1.4.3 msgpack-1.0.4 pillow-9.3.0 pybind11-2.10.1 python-dateutil-2.8.2 threadpoolctl-3.1.0 tqdm-4.64.1
done
#
# To activate this environment, use
#
# $ conda activate vlxenv
#
# To deactivate an active environment, use
#
# $ conda deactivate
Retrieving notices: ...working... doneNevertheless, when a job is lunched
$ mpirun python3 -m veloxchem test.ini test.out
I receive an error
home/ubuntu/anaconda3/envs/vlxenv/bin/python3: No module named veloxchem
Checking the list of installed packages, it is indeed true that veloxchem has not been installed:
(vlxenv) ubuntu@ubuntu:~/Documents/veloxchem_jobs$ conda list
# packages in environment at /home/ubuntu/anaconda3/envs/vlxenv:
#
# Name Version Build Channel
_openmp_mutex 4.5 2_kmp_llvm conda-forge
attrs 22.1.0 pyh71513ae_1 conda-forge
binutils 2.39 h64c2a2e_0 conda-forge
binutils_impl_linux-aarch64 2.39 hb04425f_0 conda-forge
binutils_linux-aarch64 2.39 h489c705_11 conda-forge
biopython 1.79 pypi_0 pypi
bzip2 1.0.8 hf897c2e_4 conda-forge
c-ares 1.18.1 hf897c2e_0 conda-forge
c-compiler 1.5.1 h4e544f5_0 conda-forge
ca-certificates 2022.9.24 h4fd8a4c_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cmake 3.24.3 hc6ca916_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
contourpy 1.0.6 pypi_0 pypi
cppe 0.3.1 pypi_0 pypi
cxx-compiler 1.5.1 hdd96247_0 conda-forge
cycler 0.11.0 pypi_0 pypi
distro 1.6.0 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.0.2 pyhd8ed1ab_0 conda-forge
expat 2.5.0 ha18d298_0 conda-forge
fasteners 0.18 pypi_0 pypi
fftw 3.3.10 nompi_ha1d0423_105 conda-forge
fonttools 4.38.0 pypi_0 pypi
gcc 10.4.0 h27fe70b_11 conda-forge
gcc_impl_linux-aarch64 10.4.0 h9569200_19 conda-forge
gcc_linux-aarch64 10.4.0 h72ad2ee_11 conda-forge
geometric 1.0 pyhd8ed1ab_0 conda-forge
gmock 1.11.0 hdd96247_0 conda-forge
griddataformats 1.0.1 pypi_0 pypi
gsd 2.6.1 pypi_0 pypi
gtest 1.11.0 hdd96247_0 conda-forge
gxx 10.4.0 h27fe70b_11 conda-forge
gxx_impl_linux-aarch64 10.4.0 h9569200_19 conda-forge
gxx_linux-aarch64 10.4.0 hb08d869_11 conda-forge
h5py 3.7.0 nompi_py310h81225f4_102 conda-forge
hdf5 1.12.2 nompi_h3900512_100 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
joblib 1.2.0 pypi_0 pypi
kernel-headers_linux-aarch64 4.18.0 h5b4a56d_13 conda-forge
keyutils 1.6.1 h4e544f5_0 conda-forge
kiwisolver 1.4.4 pypi_0 pypi
krb5 1.19.3 h750e270_0 conda-forge
ld_impl_linux-aarch64 2.39 ha75b1e8_0 conda-forge
libblas 3.9.0 16_linuxaarch64_openblas conda-forge
libcblas 3.9.0 16_linuxaarch64_openblas conda-forge
libcurl 7.86.0 h22f3f83_1 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h3557bc0_5 conda-forge
libgcc-devel_linux-aarch64 10.4.0 h3c6860a_19 conda-forge
libgcc-ng 12.2.0 h607ecd0_19 conda-forge
libgfortran-ng 12.2.0 he9431aa_19 conda-forge
libgfortran5 12.2.0 hf695500_19 conda-forge
libgomp 12.2.0 h607ecd0_19 conda-forge
liblapack 3.9.0 16_linuxaarch64_openblas conda-forge
libnghttp2 1.47.0 h674c3cc_1 conda-forge
libnsl 2.0.0 hf897c2e_0 conda-forge
libopenblas 0.3.21 openmp_hcebcb9f_3 conda-forge
libsanitizer 10.4.0 h0e20637_19 conda-forge
libsqlite 3.39.4 hf9034f9_0 conda-forge
libssh2 1.10.0 he5a64b1_3 conda-forge
libstdcxx-devel_linux-aarch64 10.4.0 h3c6860a_19 conda-forge
libstdcxx-ng 12.2.0 hc13a102_19 conda-forge
libuuid 2.32.1 hf897c2e_1000 conda-forge
libuv 1.44.2 h4e544f5_0 conda-forge
libzlib 1.2.13 h4e544f5_4 conda-forge
llvm-openmp 15.0.4 hb2805f8_0 conda-forge
make 4.3 h309ac5b_1 conda-forge
matplotlib 3.6.2 pypi_0 pypi
mctc-lib 0.3.1 h6c8be48_0 conda-forge
mdanalysis 2.3.0 pypi_0 pypi
mmtf-python 1.1.3 pypi_0 pypi
mpi 1.0 mpich conda-forge
mpi4py 3.1.4 py310h6187c17_0 conda-forge
mpich 4.0.3 h26b3c96_100 conda-forge
mrcfile 1.4.3 pypi_0 pypi
msgpack 1.0.4 pypi_0 pypi
ncurses 6.3 headf329_1 conda-forge
networkx 2.8.8 pyhd8ed1ab_0 conda-forge
ninja 1.11.0 hdd96247_0 conda-forge
numpy 1.23.4 py310he617cf3_1 conda-forge
ocl-icd 2.3.1 hf897c2e_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openblas 0.3.21 openmp_h74c59f8_3 conda-forge
openmm 7.7.0 py310h2a864e5_1 conda-forge
openssl 3.0.7 h4e544f5_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pillow 9.3.0 pypi_0 pypi
pip 22.3.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
psutil 5.9.4 py310h761cc84_0 conda-forge
pybind11 2.10.1 pypi_0 pypi
pybind11-global 2.10.1 py310hb15e014_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pytest 7.2.0 pyhd8ed1ab_2 conda-forge
python 3.10.6 h92ab765_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.10 2_cp310 conda-forge
readline 8.1.2 h38e3740_0 conda-forge
rhash 1.4.3 h4e544f5_0 conda-forge
scikit-build 0.16.2 pyhb871ab6_0 conda-forge
scipy 1.9.3 py310hdd6f644_2 conda-forge
setuptools 65.5.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sysroot_linux-aarch64 2.17 h43d7e78_13 conda-forge
threadpoolctl 3.1.0 pypi_0 pypi
tk 8.6.12 hd8af866_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tqdm 4.64.1 pypi_0 pypi
tzdata 2022f h191b570_0 conda-forge
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xtb 6.5.1 h96c2341_0 conda-forge
xz 5.2.6 h9cdd2b7_0 conda-forge
zlib 1.2.13 h4e544f5_4 conda-forge
zstd 1.5.2 hc1e27d5_4 conda-forge
And trying to manually install it leads to this error:
(vlxenv) ubuntu@ubuntu:~/Documents/veloxchem_jobs$ conda install veloxchem
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- veloxchem
Current channels:
- https://repo.anaconda.com/pkgs/main/linux-aarch64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-aarch64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.Hi again! It appears I misunderstood your initial message. The conda environment YAML files that we provide are useful to provide dependencies for compiling VeloxChem from its sources. Indeed, as you note, veloxchem is not listed among the packages installed in you environment. Installing the pre-compiled conda binary for VeloxChem won't work, simply because we don't have an aarch64 binary. This said, with your environment activated, you should be able to configure and compile. Try this:
CMAKE_ARGS="-DVLX_LA_VENDOR=OpenBLAS" python -m pip install .Let me know how this goes.
giammi56
commented
1 year ago I apologize, I was so focussed on the YAML file and on the Jupyter notebook procedure, that I haven't gone through the compilation. Everything is now working properly, the benchmark runs, and I am waiting for the results. Again, sorry for the second request.
robertodr
commented
1 year ago Great to hear that it works without trouble! I'm curious to hear how the benchmark goes. We can close this issue once you're done with that.
giammi56
commented
1 year ago Here the partial results of the benchmark file. The numbers are quite similar to yours. Thank zou for your support!
!========================================================================================================================!
! !
! VELOXCHEM !
! AN ELECTRONIC STRUCTURE CODE !
! !
! Copyright (C) 2018-2022 VeloxChem developers. !
! All rights reserved. !
!========================================================================================================================!
! VeloxChem execution started at Tue Nov 15 13:12:20 2022. !
!========================================================================================================================!
* Info * Using 4 OpenMP threads per compute node.
* Info * Reading input file benchmark.ini...
* Info * @jobs
* Info * task: response
* Info * @end
* Info * @method_settings
* Info * xcfun: b3lyp
* Info * basis: def2-svp
* Info * @end
* Info * @response
* Info * property: ecd
* Info * nstates: 20
* Info * @end
Molecular Geometry (Angstroms)
================================
Atom Coordinate X Coordinate Y Coordinate Z
O 2.859830000000 0.913840000000 -2.066480000000
O 2.917660000000 -0.599670000000 2.311580000000
O 1.610810000000 0.797750000000 -3.952880000000
O -4.582160000000 -0.301470000000 0.129760000000
O 1.622100000000 -0.618590000000 4.169840000000
N -1.110480000000 3.888010000000 0.356830000000
N -0.630920000000 -4.035940000000 -0.155860000000
C 5.007790000000 -0.214190000000 -3.501110000000
H 5.249720000000 0.697450000000 -4.054130000000
H 5.687710000000 -1.000350000000 -3.841640000000
H 5.197640000000 -0.033890000000 -2.442880000000
C 3.552670000000 -0.655410000000 -3.748570000000
C 2.557850000000 0.428710000000 -3.314780000000
C 1.920550000000 1.745310000000 -1.420780000000
C 0.740770000000 1.146960000000 -1.011690000000
H 0.576220000000 0.104090000000 -1.240980000000
C -0.226390000000 1.900650000000 -0.342530000000
C -1.571990000000 1.653260000000 0.125410000000
C -2.458680000000 0.552500000000 0.183470000000
C -2.372320000000 -0.887290000000 0.019860000000
C -1.357110000000 -1.870910000000 0.061950000000
C 0.006060000000 -1.953070000000 0.536260000000
C 0.865860000000 -1.086380000000 1.214040000000
H 0.575790000000 -0.068420000000 1.430140000000
C 2.096780000000 -1.541220000000 1.655650000000
C 2.529700000000 -0.141290000000 3.546600000000
C 3.370210000000 1.064490000000 3.985360000000
C 3.100100000000 1.332080000000 5.474000000000
H 2.037070000000 1.490930000000 5.659020000000
H 3.649370000000 2.221450000000 5.795070000000
H 3.420320000000 0.489840000000 6.092020000000
C 3.335370000000 -0.948410000000 -5.241020000000
H 2.304410000000 -1.244490000000 -5.438640000000
H 3.999920000000 -1.756340000000 -5.559390000000
H 3.548470000000 -0.068160000000 -5.852170000000
C 2.227490000000 3.105590000000 -1.169860000000
C 1.238600000000 3.861350000000 -0.533040000000
H 1.400640000000 4.913440000000 -0.356160000000
C 0.024440000000 3.283880000000 -0.161810000000
C -1.281590000000 5.301800000000 0.661530000000
H -0.290640000000 5.722590000000 0.848500000000
H -1.830860000000 5.378120000000 1.605160000000
C -2.004630000000 6.116770000000 -0.424330000000
H -2.995210000000 5.684580000000 -0.594350000000
H -2.171360000000 7.121530000000 -0.018450000000
C -1.253130000000 6.212720000000 -1.753830000000
H -0.281960000000 6.701120000000 -1.628180000000
H -1.825090000000 6.797200000000 -2.478980000000
H -1.077700000000 5.225510000000 -2.186780000000
C -2.102420000000 2.917520000000 0.478840000000
C -3.451090000000 3.123160000000 0.798780000000
H -3.786520000000 4.112510000000 1.071360000000
C -4.373480000000 2.081880000000 0.701120000000
C -3.827590000000 0.832320000000 0.347480000000
C -3.699940000000 -1.334780000000 -0.106830000000
C 2.562970000000 -2.859180000000 1.427300000000
C 3.958920000000 -3.345620000000 1.874110000000
C 4.225600000000 -4.804720000000 1.450330000000
H 5.233570000000 -5.087570000000 1.764350000000
H 4.171080000000 -4.934000000000 0.366090000000
H 3.529390000000 -5.504740000000 1.920230000000
C 5.057640000000 -2.474690000000 1.219820000000
H 4.948670000000 -1.423490000000 1.478730000000
H 5.018200000000 -2.563890000000 0.130490000000
H 6.046270000000 -2.810510000000 1.548780000000
C 4.081590000000 -3.295260000000 3.415320000000
H 4.011330000000 -2.281700000000 3.803880000000
H 5.048680000000 -3.704660000000 3.724000000000
H 3.294340000000 -3.889330000000 3.886350000000
C 1.684780000000 -3.727690000000 0.771070000000
H 1.979360000000 -4.750160000000 0.591350000000
C 0.419530000000 -3.298250000000 0.370960000000
C -0.670500000000 -5.480910000000 -0.329960000000
H -1.583050000000 -5.858560000000 0.143230000000
H 0.165940000000 -5.906620000000 0.228580000000
C -0.613070000000 -5.942180000000 -1.794290000000
H -1.457480000000 -5.508770000000 -2.339430000000
H -0.762010000000 -7.028140000000 -1.804410000000
C 0.694960000000 -5.588700000000 -2.504520000000
H 0.864700000000 -4.509550000000 -2.505240000000
H 0.677940000000 -5.924400000000 -3.544380000000
H 1.552560000000 -6.062620000000 -2.016780000000
C -1.733730000000 -3.192310000000 -0.278060000000
C -3.054930000000 -3.565670000000 -0.557990000000
H -3.273150000000 -4.590580000000 -0.818090000000
C -4.096450000000 -2.645960000000 -0.435300000000
C -5.567640000000 -3.035690000000 -0.657510000000
C -6.379780000000 -2.787140000000 0.635030000000
H -5.976860000000 -3.375640000000 1.464010000000
H -7.422430000000 -3.083750000000 0.484140000000
H -6.364620000000 -1.737520000000 0.924330000000
C -6.155420000000 -2.200300000000 -1.819310000000
H -6.101830000000 -1.131460000000 -1.614930000000
H -7.205390000000 -2.464730000000 -1.978900000000
H -5.611910000000 -2.395470000000 -2.747920000000
C -5.719410000000 -4.523440000000 -1.026790000000
H -5.191330000000 -4.771950000000 -1.951450000000
H -6.777610000000 -4.748430000000 -1.182710000000
H -5.357280000000 -5.181670000000 -0.232220000000
C 4.872960000000 0.816760000000 3.754510000000
H 5.226310000000 -0.053480000000 4.314270000000
H 5.440740000000 1.686280000000 4.097900000000
H 5.095590000000 0.658900000000 2.699070000000
C 2.906390000000 2.272510000000 3.138800000000
H 3.069520000000 2.097160000000 2.074170000000
H 3.468980000000 3.163180000000 3.433450000000
H 1.843910000000 2.477620000000 3.293960000000
C -5.873740000000 2.284230000000 0.972900000000
C -6.197290000000 3.739940000000 1.358960000000
H -5.673670000000 4.048770000000 2.267850000000
H -7.269470000000 3.830510000000 1.551200000000
H -5.946930000000 4.441490000000 0.558370000000
C -6.690590000000 1.941250000000 -0.294810000000
H -6.392260000000 2.579240000000 -1.131440000000
H -7.756630000000 2.104020000000 -0.107990000000
H -6.553570000000 0.903070000000 -0.593320000000
C -6.314390000000 1.377720000000 2.146420000000
H -6.135160000000 0.324700000000 1.931930000000
H -7.383220000000 1.508790000000 2.341980000000
H -5.768870000000 1.635390000000 3.058430000000
C 3.567950000000 3.754040000000 -1.579340000000
C 3.728480000000 3.739610000000 -3.117750000000
H 2.891800000000 4.252230000000 -3.599180000000
H 3.776260000000 2.730250000000 -3.520210000000
H 4.651880000000 4.255480000000 -3.399490000000
C 3.657340000000 5.228020000000 -1.132990000000
H 4.634280000000 5.626960000000 -1.417740000000
H 3.561660000000 5.335620000000 -0.049230000000
H 2.898510000000 5.851560000000 -1.613460000000
C 4.744600000000 3.005500000000 -0.909280000000
H 4.761310000000 1.951880000000 -1.180110000000
H 4.672410000000 3.076720000000 0.179630000000
H 5.695260000000 3.455290000000 -1.213010000000
C 3.243040000000 -1.917690000000 -2.911450000000
H 3.370670000000 -1.728150000000 -1.844430000000
H 3.919260000000 -2.726290000000 -3.203570000000
H 2.217950000000 -2.258290000000 -3.079230000000
Molecular charge : 0
Spin multiplicity : 1
Number of atoms : 137
Number of alpha electrons : 232
Number of beta electrons : 232
* Info * Reading basis set from file: /home/ubuntu/anaconda3/envs/vlxenv/lib/python3.10/site-packages/veloxchem/basis/DEF2-SVP
Molecular Basis (Atomic Basis)
================================
Basis: DEF2-SVP
Atom Contracted GTOs Primitive GTOs
O (3S,2P,1D) (7S,4P,1D)
H (2S,1P) (4S,1P)
C (3S,2P,1D) (7S,4P,1D)
N (3S,2P,1D) (7S,4P,1D)
Contracted Basis Functions : 1252
Primitive Basis Functions : 2030
Self Consistent Field Driver Setup
====================================
Wave Function Model : Spin-Restricted Kohn-Sham
Initial Guess Model : Superposition of Atomic Densities
Convergence Accelerator : Two Level Direct Inversion of Iterative Subspace
Max. Number of Iterations : 50
Max. Number of Error Vectors : 10
Convergence Threshold : 1.0e-06
ERI Screening Scheme : Cauchy Schwarz + Density
ERI Screening Mode : Dynamic
ERI Screening Threshold : 1.0e-12
Linear Dependence Threshold : 1.0e-06
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
* Info * Nuclear repulsion energy: 10340.6482081689 a.u.
* Info * Molecular grid with 1558984 points generated in 33.80 sec.
* Info * Overlap matrix computed in 0.05 sec.
* Info * Kinetic energy matrix computed in 0.04 sec.
* Info * Nuclear potential matrix computed in 3.34 sec.
* Info * Orthogonalization matrix computed in 0.09 sec.
* Info * SAD initial guess computed in 0.08 sec.
* Info * Starting Reduced Basis SCF calculation...
* Info * ...done. SCF energy in reduced basis set: -2643.778886664870 a.u. Time: 935.94 sec.
* Info * Overlap matrix computed in 0.02 sec.
* Info * Kinetic energy matrix computed in 0.02 sec.
* Info * Nuclear potential matrix computed in 3.32 sec.
* Info * Orthogonalization matrix computed in 0.38 sec.
Iter. | Kohn-Sham Energy | Energy Change | Gradient Norm | Max. Gradient | Density Change
--------------------------------------------------------------------------------------------
1 -2662.242575977534 0.0000000000 0.92638287 0.03265315 0.00000000
2 -2662.226028248417 0.0165477291 1.02213918 0.02906963 0.94002206
3 -2662.338901683315 -0.1128734349 0.31423891 0.00774929 0.52847674
4 -2662.347949700572 -0.0090480173 0.10014039 0.00202751 0.17287238
5 -2662.348971904912 -0.0010222043 0.03417167 0.00052653 0.06063523
6 -2662.349100914054 -0.0001290091 0.00858497 0.00011362 0.02036779
7 -2662.349108126986 -0.0000072129 0.00460381 0.00007065 0.00596992
8 -2662.349110477133 -0.0000023501 0.00121290 0.00002151 0.00247467
9 -2662.349110638779 -0.0000001616 0.00042706 0.00000581 0.00077898
10 -2662.349110659614 -0.0000000208 0.00013542 0.00000164 0.00025880
11 -2662.349110661580 -0.0000000020 0.00005981 0.00000089 0.00009203
12 -2662.349110661993 -0.0000000004 0.00002265 0.00000037 0.00003744
13 -2662.349110662146 -0.0000000002 0.00000686 0.00000011 0.00001432
14 -2662.349110662117 0.0000000000 0.00000318 0.00000007 0.00000507
15 -2662.349110662006 0.0000000001 0.00000183 0.00000004 0.00000227
16 -2662.349110662019 -0.0000000000 0.00000046 0.00000001 0.00000089
* Info * Checkpoint written to file: benchmark.scf.h5
* Info * SCF tensors written to file: benchmark.scf.tensors.h5
*** SCF converged in 16 iterations. Time: 9109.19 sec.
Spin-Restricted Kohn-Sham:
--------------------------
Total Energy : -2662.3491106620 a.u.
Electronic Energy : -13002.9973188309 a.u.
Nuclear Repulsion Energy : 10340.6482081689 a.u.
------------------------------------
Gradient Norm : 0.0000004636 a.u.
Ground State Information
------------------------
Charge of Molecule : 0.0
Multiplicity (2S+1) : 1.0
Magnetic Quantum Number (M_S) : 0.0
Spin Restricted Orbitals
------------------------
Molecular Orbital No. 228:
--------------------------
Occupation: 2.000 Energy: -0.23864 a.u.
( 54 C 1p0 : 0.17) ( 55 C 1p0 : -0.17) ( 84 C 1p0 : 0.15)
Molecular Orbital No. 229:
--------------------------
Occupation: 2.000 Energy: -0.21366 a.u.
( 18 C 1p0 : -0.19) ( 21 C 1p0 : 0.19) ( 36 C 1p0 : -0.15)
( 50 C 1p0 : -0.15)
Molecular Orbital No. 230:
--------------------------
Occupation: 2.000 Energy: -0.21184 a.u.
( 14 C 1p0 : -0.16) ( 25 C 1p0 : -0.17) ( 39 C 1p0 : 0.16)
( 72 C 1p0 : 0.17) ( 86 C 1p0 : 0.16)
Molecular Orbital No. 231:
--------------------------
Occupation: 2.000 Energy: -0.19103 a.u.
( 7 N 1p0 : -0.24) ( 7 N 2p0 : 0.21) ( 20 C 1p0 : 0.17)
( 25 C 1p0 : 0.15) ( 51 C 1p0 : 0.16) ( 55 C 1p0 : 0.21)
( 55 C 2p0 : 0.15) ( 84 C 1p0 : -0.20) ( 84 C 2p0 : -0.16)
Molecular Orbital No. 232:
--------------------------
Occupation: 2.000 Energy: -0.19042 a.u.
( 4 O 1p0 : -0.18) ( 4 O 2p0 : -0.15) ( 6 N 1p0 : -0.24)
( 6 N 2p0 : 0.21) ( 21 C 1p0 : -0.17) ( 54 C 1p0 : 0.19)
Molecular Orbital No. 233:
--------------------------
Occupation: 0.000 Energy: -0.05120 a.u.
( 18 C 1p0 : -0.16) ( 18 C 2p0 : -0.18) ( 19 C 1p0 : 0.16)
( 19 C 2p0 : 0.18) ( 20 C 1p0 : 0.17) ( 20 C 2p0 : 0.19)
( 21 C 1p0 : -0.17) ( 21 C 2p0 : -0.19) ( 51 C 1p0 : 0.20)
( 51 C 2p0 : 0.24) ( 53 C 1p0 : -0.17) ( 53 C 2p0 : -0.21)
( 84 C 1p0 : 0.20) ( 84 C 2p0 : 0.25) ( 86 C 1p0 : -0.18)
( 86 C 2p0 : -0.22)
Molecular Orbital No. 234:
--------------------------
Occupation: 0.000 Energy: -0.02578 a.u.
( 15 C 1p0 : -0.17) ( 15 C 2p0 : -0.22) ( 23 C 1p0 : 0.17)
( 23 C 2p0 : 0.22) ( 36 C 1p0 : 0.16) ( 36 C 2p0 : 0.18)
( 37 C 1p0 : -0.17) ( 37 C 2p0 : -0.22) ( 53 C 1p0 : 0.17)
( 53 C 2p0 : 0.18) ( 56 C 1p0 : -0.15) ( 56 C 2p0 : -0.16)
( 70 C 1p0 : 0.16) ( 70 C 2p0 : 0.23) ( 86 C 1p0 : -0.17)
( 86 C 2p0 : -0.18)
Molecular Orbital No. 235:
--------------------------
Occupation: 0.000 Energy: -0.00042 a.u.
( 8 C 3s : 0.17) ( 13 C 1p+1: -0.15) ( 13 C 1p-1: -0.20)
( 13 C 2p-1: -0.16) ( 14 C 1p0 : -0.17) ( 14 C 2p-1: 0.15)
( 14 C 2p0 : -0.22) ( 25 C 1p0 : 0.16) ( 25 C 2p0 : 0.20)
( 26 C 1p+1: -0.15) ( 26 C 1p-1: 0.16) ( 39 C 1p0 : -0.19)
( 39 C 2p0 : -0.22) ( 62 C 3s : -0.19) ( 66 C 3s : 0.17)
( 72 C 1p0 : 0.18) ( 72 C 2p0 : 0.20) ( 104 C 3s : -0.19)
( 122 C 3s : 0.19) ( 130 C 3s : -0.19) ( 134 C 3s : -0.23)
( 136 H 2s : 0.15)
Molecular Orbital No. 236:
--------------------------
Occupation: 0.000 Energy: 0.00417 a.u.
( 8 C 3s : -0.16) ( 13 C 1p-1: 0.17) ( 15 C 1p0 : -0.15)
( 15 C 2p0 : -0.18) ( 17 C 3s : 0.18) ( 18 C 2p+1: -0.24)
( 19 C 2p-1: -0.27) ( 20 C 2p-1: -0.24) ( 21 C 2p+1: 0.23)
( 22 C 3s : -0.17) ( 23 C 1p0 : -0.16) ( 23 C 2p0 : -0.19)
( 25 C 2p0 : 0.16) ( 26 C 1p+1: -0.17) ( 26 C 1p-1: 0.17)
( 37 C 2p0 : -0.19) ( 50 C 2p0 : -0.17) ( 70 C 2p0 : -0.21)
( 72 C 2p0 : 0.16) ( 83 C 2p0 : -0.17) ( 100 C 3s : 0.18)
( 104 C 3s : -0.23) ( 134 C 3s : 0.20)
Molecular Orbital No. 237:
--------------------------
Occupation: 0.000 Energy: 0.00828 a.u.
( 8 C 3s : 0.21) ( 13 C 1p+1: -0.15) ( 13 C 1p-1: -0.20)
( 13 C 2p+1: -0.16) ( 13 C 2p-1: -0.15) ( 26 C 1p+1: 0.17)
( 26 C 1p-1: -0.17) ( 26 C 2p+1: 0.17) ( 36 C 2p0 : 0.18)
( 50 C 2p0 : -0.16) ( 51 C 2p0 : 0.16) ( 54 C 2p0 : -0.15)
( 56 C 2p0 : 0.17) ( 83 C 2p0 : -0.15) ( 84 C 2p0 : 0.15)
( 100 C 3s : -0.21) ( 104 C 3s : 0.24) ( 134 C 3s : -0.24)
( 136 H 2s : 0.15)
Ground State Dipole Moment
----------------------------
X : 0.308184 a.u. 0.783327 Debye
Y : 0.064665 a.u. 0.164362 Debye
Z : -0.090140 a.u. -0.229112 Debye
Total : 0.327543 a.u. 0.832531 Debye
Linear Response EigenSolver Setup
===================================
Number of States : 20
Max. Number of Iterations : 150
Convergence Threshold : 1.0e-04
ERI Screening Scheme : Cauchy Schwarz + Density
ERI Screening Threshold : 1.0e-12
Exchange-Correlation Functional : B3LYP
Molecular Grid Level : 4
* Info * Molecular grid with 1558984 points generated in 33.73 sec.
* Info * Processing Fock builds... (batch size: 40)
* Info * batch 1/1 Very good! Thanks for reporting!
I am building veloxchem, following the suggested procedure, on an ARM64 platform from Oracle.
Upon
conda env create -f mkl_env.ymlI get the following output:I looked a bit around and the suggested solution is to put the unresolved packages into a
pip:dependency. My final .yml file looks like:but the syntax
blas=*=*mkl*is not recognized inpipgiving the following error:I don't know what that syntax means, is there a way to fix it?