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jeffhammondjeffhammond
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Merge branch 'master' into remove-bgj-crap
2 parents e069175 + 54362d3 commit 14098a2

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‎.github/workflows/github_actions.yml

+121-27
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ jobs:
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strategy:
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matrix:
2020
blas: [build_openblas]
21-
os: [ubuntu-18.04, macos-10.15]
21+
os: [ubuntu-20.04, macos-10.15]
2222
experimental: [false]
2323
mpi_impl:
2424
- openmpi
@@ -32,7 +32,7 @@ jobs:
3232
- "qmandpw qmd"
3333
- "tce"
3434
fc:
35-
- gfortran-9
35+
- gfortran
3636
exclude:
3737
- os: macos-10.15
3838
mpi_impl: mpich
@@ -44,121 +44,201 @@ jobs:
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- os: ubuntu-20.04
4545
experimental: true
4646
mpi_impl: mpich
47-
armci_network: mpi-ts
47+
armci_network: MPI-TS
4848
nwchem_modules: "tinyqmpw python"
4949
fc: flang
5050
cc: clang
51+
- os: ubuntu-18.04
52+
experimental: true
53+
mpi_impl: mpich
54+
armci_network: MPI-TS
55+
nwchem_modules: "tinyqmpw python"
56+
fc: amdflang
57+
cc: amdclang
58+
- os: ubuntu-18.04
59+
experimental: true
60+
mpi_impl: mpich
61+
armci_network: MPI-TS
62+
nwchem_modules: "tce"
63+
fc: amdflang
64+
cc: amdclang
5165
- os: ubuntu-20.04
5266
experimental: true
5367
mpi_impl: intel
54-
armci_network: mpi-pr
68+
armci_network: MPI-PR
5569
nwchem_modules: "tinyqmpw python"
5670
fc: ifort
5771
- os: ubuntu-20.04
5872
experimental: true
5973
mpi_impl: mpich
60-
armci_network: mpi-ts
74+
armci_network: MPI-TS
6175
nwchem_modules: "tinyqmpw python"
6276
fc: nvfortran
6377
cc: gcc
6478
- os: ubuntu-20.04
6579
experimental: true
6680
mpi_impl: intel
67-
armci_network: sockets
81+
armci_network: SOCKETS
6882
nwchem_modules: "tce"
6983
fc: ifort
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- os: ubuntu-20.04
7185
experimental: true
7286
mpi_impl: mpich
73-
armci_network: mpi-ts
87+
armci_network: MPI-TS
7488
nwchem_modules: "tce"
7589
fc: flang
7690
cc: clang
7791
- os: ubuntu-20.04
7892
experimental: true
7993
mpi_impl: intel
80-
armci_network: mpi-pr
94+
armci_network: MPI-PR
8195
nwchem_modules: "tinyqmpw python"
8296
fc: ifort
8397
- os: ubuntu-20.04
8498
experimental: true
8599
mpi_impl: intel
86-
armci_network: sockets
100+
armci_network: SOCKETS
87101
nwchem_modules: "tce"
88102
fc: ifort
89-
- os: ubuntu-20.04
103+
- os: ubuntu-18.04
104+
experimental: true
105+
mpi_impl: intel
106+
armci_network: MPI-PR
107+
nwchem_modules: "tinyqmpw python"
108+
fc: ifx
109+
- os: ubuntu-18.04
110+
experimental: true
111+
mpi_impl: intel
112+
armci_network: SOCKETS
113+
nwchem_modules: "tce"
114+
fc: ifx
115+
- os: ubuntu-18.04
116+
experimental: true
117+
mpi_impl: openmpi
118+
armci_network: MPI-TS
119+
nwchem_modules: "tinyqmpw"
120+
fc: gfortran
121+
cc: gcc
122+
use_libxc: 1
123+
- os: ubuntu-18.04
124+
experimental: true
125+
mpi_impl: intel
126+
armci_network: MPI-TS
127+
nwchem_modules: "tinyqmpw"
128+
fc: ifort
129+
cc: icc
130+
use_libxc: 1
131+
- os: macos-10.15
132+
experimental: true
133+
mpi_impl: openmpi
134+
armci_network: MPI-TS
135+
nwchem_modules: "tinyqmpw"
136+
fc: gfortran-10
137+
cc: gcc
138+
xcode_version: 12.4
139+
use_libxc: 1
140+
- os: ubuntu-18.04
90141
experimental: true
91142
mpi_impl: mpich
92-
armci_network: mpi-pt
143+
armci_network: MPI-PT
93144
nwchem_modules: "nwdft solvation driver"
94145
fc: gfortran-10
146+
cc: gcc-10
95147
use_simint: 1
96148
- os: ubuntu-20.04
97149
experimental: true
98150
mpi_impl: mpich
99-
armci_network: mpi-ts
151+
armci_network: MPI-TS
100152
nwchem_modules: "nwdft solvation driver"
101153
fc: nvfortran
102154
cc: gcc
103155
use_simint: 1
104156
- os: ubuntu-20.04
105157
experimental: true
106158
mpi_impl: intel
107-
armci_network: mpi-ts
159+
armci_network: MPI-TS
108160
nwchem_modules: "nwdft solvation driver"
109161
fc: ifort
110162
cc: icc
111163
use_simint: 1
112-
- os: ubuntu-20.04
164+
- os: ubuntu-18.04
113165
experimental: true
114166
mpi_impl: mpich
115-
armci_network: mpi-pr
167+
armci_network: MPI-PR
116168
nwchem_modules: "tinyqmpw python"
117169
fc: gfortran-10
170+
cc: gcc-10
171+
use_libxc: 1
118172
- os: macos-10.15
119173
experimental: true
120174
mpi_impl: openmpi
121-
armci_network: mpi-pr
175+
armci_network: MPI-PR
122176
nwchem_modules: "qmandpw qmd"
123177
fc: gfortran-10
178+
cc: gcc-10
124179
xcode_version: 12.3
125180
- os: macos-11.0
126181
experimental: true
127182
mpi_impl: openmpi
128-
armci_network: mpi-pr
183+
armci_network: MPI-PR
129184
nwchem_modules: "tce"
130185
fc: gfortran-10
131-
xcode_version: 12.3
186+
cc: gcc-10
187+
xcode_version: 12.5.1
188+
- os: macos-11.0
189+
experimental: true
190+
mpi_impl: openmpi
191+
armci_network: MPI-TS
192+
nwchem_modules: "tinyqmpw"
193+
fc: gfortran-11
194+
xcode_version: 13.2.1
132195
- os: macos-10.15
133196
experimental: true
134197
mpi_impl: openmpi
135-
armci_network: mpi-ts
198+
armci_network: MPI-TS
136199
nwchem_modules: "tinyqmpw"
137200
fc: gfortran-9
138201
blas: "accelerate"
139-
xcode_version: 12.1
140-
- os: ubuntu-20.04
202+
xcode_version: 12.1.1
203+
- os: macos-10.15
141204
experimental: true
142205
mpi_impl: mpich
143-
armci_network: mpi-ts
206+
armci_network: SOCKETS
207+
nwchem_modules: "tinyqmpw"
208+
fc: ifort
209+
xcode_version: 12.4
210+
- os: ubuntu-18.04
211+
experimental: true
212+
mpi_impl: mpich
213+
armci_network: MPI-TS
144214
nwchem_modules: "qmandpw qmd"
145215
fc: gfortran-10
216+
cc: gcc-10
146217
use_openmp: 2
147218
blas: "build_openblas"
148219
- os: ubuntu-20.04
149220
experimental: true
150221
mpi_impl: intel
151-
armci_network: mpi-ts
222+
armci_network: MPI-TS
152223
nwchem_modules: "qmandpw qmd"
153224
fc: ifort
154225
use_openmp: 2
226+
- os: ubuntu-latest
227+
experimental: true
228+
mpi_impl: mpich
229+
armci_network: MPI-TS
230+
nwchem_modules: "tinyqmpw"
231+
fc: gfortran
232+
blas: "internal"
155233
fail-fast: false
156234
env:
157235
MPI_IMPL: ${{ matrix.mpi_impl }}
158236
ARMCI_NETWORK: ${{ matrix.armci_network }}
159237
NWCHEM_MODULES: ${{ matrix.nwchem_modules }}
160238
USE_SIMINT: ${{ matrix.use_simint }}
239+
USE_LIBXC: ${{ matrix.use_libxc }}
161240
FC: ${{ matrix.fc }}
241+
CC: ${{ matrix.cc }}
162242
COMEX_MAX_NB_OUTSTANDING: 4
163243
SIMINT_MAXAM: 3
164244
SIMINT_VECTOR: avx2
@@ -182,7 +262,14 @@ jobs:
182262
with:
183263
path: |
184264
~/cache
185-
key: ${{ matrix.os }}-${{ matrix.mpi_impl}}-${{ matrix.fc}}-xcode${{ matrix.xcode_version}}-simint${{ matrix.use_simint}}-blas${{ matrix.blas}}-simd${{ steps.get-simd.outputs.simd }}-nwchemcache-v005
265+
~/apps
266+
key: ${{ matrix.os }}-${{ matrix.mpi_impl}}-${{ matrix.fc}}-xcode${{ matrix.xcode_version}}-simint${{ matrix.use_simint}}-blas${{ matrix.blas}}-simd${{ steps.get-simd.outputs.simd }}-nwchemcache-v014
267+
- name: fetch apps cache
268+
if: steps.setup-cache.outputs.cache-hit == 'true'
269+
run: |
270+
if [[ -f ~/apps/oneapi/setvars.sh ]]; then \
271+
echo "apps oneapi cache fetched" ; \
272+
export GOT_APPSCACHE="Y" ; fi
186273
- name: build environment
187274
run: |
188275
pwd
@@ -191,11 +278,12 @@ jobs:
191278
- name: fetch cache
192279
if: steps.setup-cache.outputs.cache-hit == 'true'
193280
run: |
194-
[ -d ~/cache/libext ] && mkdir -p ~/cache/libext/mpich/mpich && \
195-
rsync -av ~/cache/libext/* src/libext/.
281+
ls -Rla ~/cache
282+
[ -d ~/cache/libext ] && rsync -av ~/cache/libext/* src/libext/.
196283
[ -d ~/cache/simint/simint_install/lib ] && \
197284
mkdir -p src/NWints/simint/libsimint_source/simint_install && \
198285
rsync -av ~/cache/simint/simint_install/* src/NWints/simint/libsimint_source/simint_install/. || true
286+
[ -f ~/cache/tarballs/dftd3.tgz ] && rsync -av ~/cache/tarballs/dftd3.tgz src/nwpw/nwpwlib/nwpwxc/dftd3.tgz || true
199287
echo "cache fetched"
200288
- name: compile
201289
id: compile
@@ -210,13 +298,17 @@ jobs:
210298
cat src/tools/build/comex/config.log || true
211299
- name: store cache
212300
run: |
301+
mkdir -p ~/apps || true
213302
mkdir -p ~/cache/libext/lib ~/cache/libext/bin ~/cache/libext/include ~/cache/libext/mpich || true
303+
mkdir -p ~/cache/libext/mpich/mpich || true
214304
mkdir -p ~/cache/simint/simint_install || true
305+
mkdir -p ~/cache/tarballs || true
306+
ls -la src/libext ||true
215307
[ -d "src/libext/lib" ] && rsync -av src/libext/lib/* ~/cache/libext/lib/. || true
216308
[ -d "src/libext/bin" ] && rsync -av src/libext/bin/* ~/cache/libext/bin/. || true
217309
[ -d "src/libext/include" ] && rsync -av src/libext/include/* ~/cache/libext/include/. || true
218310
[ -d "src/NWints/simint/libsimint_source/simint_install/lib" ] && rsync -av src/NWints/simint/libsimint_source/simint_install/* ~/cache/simint/simint_install/. || true
219-
mkdir -p ~/cache/libext/mpich/mpich || true
311+
[ -f "src/nwpw/nwpwlib/nwpwxc/dftd3.tgz" ] && rsync -av src/nwpw/nwpwlib/nwpwxc/dftd3.tgz ~/cache/tarballs/dftd3.tgz || true
220312
echo "cache stored"
221313
ls -Rla ~/cache
222314
- name: qa_test
@@ -247,6 +339,8 @@ jobs:
247339
egrep d= QA/testoutputs/dft_smear.out || true; fi
248340
if [[ -f QA/testoutputs/dft_smear.out ]]; then \
249341
tail -2000 QA/testoutputs/dft_smear.out || true; fi
342+
if [[ -f QA/testoutputs/pspw_md.out ]]; then \
343+
grep 'PSPW energy' QA/testoutputs/pspw_md.out || true; fi
250344
251345

252346

‎.github/workflows/github_actions_archs.yml

+2-2
Original file line numberDiff line numberDiff line change
@@ -54,7 +54,7 @@ jobs:
5454
with:
5555
path: |
5656
~/cache
57-
key: ${{ runner.os }}-${{ matrix.mpi_impl}}-${{ matrix.distro}}-${{ matrix.arch}}-nwchem-v006
57+
key: ${{ runner.os }}-${{ matrix.mpi_impl}}-${{ matrix.distro}}-${{ matrix.arch}}-nwchem-v009
5858
- uses: actions/checkout@v2
5959
name: Checkout
6060
with:
@@ -110,7 +110,7 @@ jobs:
110110
export DEBIAN_FRONTEND=noninteractive
111111
apt-get install -y tzdata apt-utils
112112
dpkg-reconfigure --frontend noninteractive tzdata
113-
DEBIAN_FRONTEND=noninteractive apt-get install -q -y sudo git gfortran curl wget unzip perl rsync python3-dev python-dev cmake
113+
DEBIAN_FRONTEND=noninteractive apt-get install -q -y sudo git gfortran curl wget unzip perl rsync python3-dev python-dev cmake libnuma1
114114
;;
115115
fedora*)
116116
dnf -y update

‎.github/workflows/lint_python.yml

+27
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,27 @@
1+
name: lint_python
2+
on: [pull_request, push]
3+
jobs:
4+
lint_python:
5+
runs-on: ubuntu-latest
6+
steps:
7+
- uses: actions/checkout@v2
8+
- uses: actions/setup-python@v2
9+
- run: pip install --upgrade pip wheel
10+
- run: pip install bandit black codespell flake8 flake8-2020 flake8-bugbear
11+
flake8-comprehensions isort mypy pytest pyupgrade safety
12+
- run: bandit --recursive --skip B101,B110,B306,B307,B311,B605,B607 .
13+
- run: black --check . || true
14+
- run: codespell --count
15+
--ignore-words-list=aline,asociated,auxilliary,ba,ficticious,hist,iinclude,iself,ist,ket,mapp,nd,numer,ser,te
16+
--skip="*/graveyard,*.dtx,*.F,*.f,*.f90,*.fh,*.frg,*.orig,*.out,*.par,*.pdb,*.pl,*.tex,*.txt" || true
17+
- run: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
18+
- run: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88
19+
--show-source --statistics
20+
- run: isort --check-only --profile black . || true
21+
- run: pip install -r requirements.txt || pip install --editable . || true
22+
- run: mkdir --parents --verbose .mypy_cache
23+
- run: mypy --ignore-missing-imports --install-types --non-interactive . || true
24+
- run: pytest . || true
25+
- run: pytest --doctest-modules . || true
26+
- run: shopt -s globstar && pyupgrade --py36-plus **/*.py || true
27+
- run: safety check

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