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Merge branch 'origin/release-2020' into merge-2020-into-2021
2020-11-24
Paul Baue
r
Me
r
ge bran
c
h
'origin/release-2020' into m
e
rge-2020
.
.
.
commit
|
commitdiff
|
tree
2020-11-24
Erik Lin
d
ahl
M
a
ke sure
f
rexp()
returns
c
or
r
ect for argume
n
t 0
.
0
commit
|
commitdiff
|
tree
2020-11-24
Art
e
m Zhmurov
Improve ha
n
d
l
ing of CUD
A
A
PI
e
rro
r
s
commit
|
commitdiff
|
tree
2020-11-23
M
.
Eric Ir
r
ga
n
g
Look
for t
h
e
v
arious
pos
s
ible n
a
mes of the gr
o
macs
.
.
.
commit
|
commitdiff
|
tree
2020-11-17
J
oe Jordan
Remov
e
som
e
extraneous
compiler
flags from nblib
commit
|
commitdiff
|
tree
2020-11-13
Gi
l
les
G
o
u
aillarde
t
Detect AR
M
SVE
Vector length if pos
s
i
b
le
commit
|
commitdiff
|
tree
2020-11-12
Pau
l
Bauer
Fix
t
hread mpi linking for m
d
ru
n
onl
y
build
commit
|
commitdiff
|
tree
2020-11-12
Paul Bauer
Restore correct dyna
m
ics linking behaviour
commit
|
commitdiff
|
tree
2020-11-11
Paul Ba
u
er
Fix gmx do_dssp CHARMM s
u
pp
o
r
t
commit
|
commitdiff
|
tree
2020-11-11
Pa
u
l
B
auer
Fix segmen
t
ation f
a
ult in gmx pa
i
rdist
commit
|
commitdiff
|
tree
2020-11-10
Berk H
e
ss
Fix dHdl a
n
d foreig
n
energy clearing at chec
k
pointing
commit
|
commitdiff
|
tree
2020-11-09
Andrey Alek
s
een
k
o
Add
SY
C
L implementati
o
n of LeapFrogGp
u
commit
|
commitdiff
|
tree
2020-11-09
Joe Jor
d
an
Add backend for n
b
lib
l
isted forces API
commit
|
commitdiff
|
tree
2020-11-09
Artem Zh
m
urov
Remove
source
file t
h
at is no longer
i
n use
commit
|
commitdiff
|
tree
2020-11-09
Berk
H
ess
M
ove implemen
t
a
t
ion t
o
cpp file
commit
|
commitdiff
|
tree
2020-11-09
A
lan
G
ray
Use dynamic
a
l
ly allocated uniqu
e
poi
n
ters for
G
P
U halo
.
.
.
commit
|
commitdiff
|
tree
2020-11-05
Paul Bauer
Al
l
ow pdb2gmx to handle cyclic mol
e
cules
commit
|
commitdiff
|
tree
2020-11-05
Paul Bauer
A
l
low
C
UDA build tests to succeed without
G
PU
commit
|
commitdiff
|
tree
2020-11-05
Mark Abraham
Sto
p
sh
o
wing wr
o
n
g RE
A
DME on GitHu
b
front page
commit
|
commitdiff
|
tree
2020-11-05
Paul B
a
u
e
r
Limit pa
r
allelism in Github CI
commit
|
commitdiff
|
tree
2020-11-05
B
er
k
Hess
Disable MTS
with SD integrator
commit
|
commitdiff
|
tree
2020-11-05
Mar
k
Abraham
Improve issue
s
wit
h
CUDA interacting
with std
flags
commit
|
commitdiff
|
tree
2020-11-03
A
l
an Gra
y
Extend halo e
x
chang
e
uni
t
te
s
t to GPU
codepa
t
h
commit
|
commitdiff
|
tree
2020-11-03
Gille
s
Gouaillardet
timing: try
to dire
c
tly r
e
trieve gmx_cycles_calibrate
.
.
.
commit
|
commitdiff
|
tree
2020-11-03
Ar
t
em Zh
m
ur
o
v
Make the message why GP
U
bo
n
deds ar
e
not availa
b
le
.
.
.
commit
|
commitdiff
|
tree
2020-11-03
Pa
u
l Bauer
Add Clang
C
U
D
A build to CI
commit
|
commitdiff
|
tree
2020-11-02
M
.
Eri
c
Irrgang
Re
m
ove an u
n
n
e
cessar
y
t
r
ansit
i
ve
dep
e
ndency
o
f imported
.
.
.
commit
|
commitdiff
|
tree
2020-10-30
P
a
ul B
a
u
er
Ad
d
mi
s
sing fix f
o
r
Clang CUDA
commit
|
commitdiff
|
tree
2020-10-30
J
oe J
o
rdan
Int
r
oduce nbl
i
b versioning
commit
|
commitdiff
|
tree
2020-10-30
A
n
d
re
y
A
leks
e
en
k
o
Rework handl
i
ng of PATH-
l
ike variables in G
M
XRC
.
bash/zsh
commit
|
commitdiff
|
tree
2020-10-29
P
aul Bauer
Fix C
U
DA code issues
commit
|
commitdiff
|
tree
2020-10-29
Pau
l
B
a
uer
Defa
u
l
t
i
nitialize pull d
a
tastructures
commit
|
commitdiff
|
tree
2020-10-28
Berk H
e
ss
Correct AW
H
i
n
iti
a
l h
i
stogram
s
ize
commit
|
commitdiff
|
tree
2020-10-28
Gilles Goua
i
llardet
o
p
tions:
a
d
d the e
f
tCSV OptionFileTy
p
e
commit
|
commitdiff
|
tree
2020-10-27
Paul Bauer
Mix minor clang
-
tid
y
warning in d
o
uble
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric Ir
r
gang
Use the
correct CI
script for s
a
mple_restraint job
s
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Eric
Irrgang
N
o
rmalize FindM
P
I
hin
t
s
.
commit
|
commitdiff
|
tree
2020-10-27
M
.
Er
i
c
I
rrgang
Cla
r
ify behav
i
or of LegacyMdrunOptions
.
commit
|
commitdiff
|
tree
2020-10-26
Roland Schulz
M
a
k
e inst
a
ll
-
guid
e
MP
I
c
o
nsistent
commit
|
commitdiff
|
tree
2020-10-26
Artem Zhmurov
Cl
e
ar constr
a
ints RMSD v
a
l
u
es up
o
n domai
n
s reset
commit
|
commitdiff
|
tree
2020-10-22
M
.
Eric Irrgang
Use u
p
dated C
I
pipelin
e
rules for Python package
tes
t
s
.
commit
|
commitdiff
|
tree
2020-10-22
Artem Zhmurov
Fix formatting of
t
h
e
authors list
commit
|
commitdiff
|
tree
2020-10-21
C
hristian Blau
Ensure that gmx covar does not access
in
d
ices out of
.
.
.
commit
|
commitdiff
|
tree
2020-10-21
Szil
á
rd Páll
Add
missi
n
g cycle countin
g
fo
r
GPU h
a
lo exch
a
ng
e
calls
commit
|
commitdiff
|
tree
2020-10-21
Chr
i
stian Bl
a
u
Clar
i
fy
t
hat mdtutorials are not
pro
v
ided by the
gro
m
ac
s
.
.
.
commit
|
commitdiff
|
tree
2020-10-20
M
.
Eric Irrgang
Update
gmxapi versi
o
n details
.
commit
|
commitdiff
|
tree
2020-10-20
P
au
l
Bauer
M
e
rg
e
branch 'origin/
r
e
l
eas
e
-
2
020' in
t
o m
e
rge-release
.
.
.
commit
|
commitdiff
|
tree
2020-10-20
Szi
l
árd Páll
A
l
lo
w
gcc-9 on Power 9
commit
|
commitdiff
|
tree
2020-10-20
Paul Bauer
U
pdate CI rules for release-
2
0
21
commit
|
commitdiff
|
tree
2020-10-20
Paul
Bau
e
r
GROMA
C
S 2021 first be
t
a release
commit
|
commitdiff
|
tree
2020-10-20
Pa
u
l Bauer
Revert "
G
R
O
MACS
2021
first beta relea
s
e"
commit
|
commitdiff
|
tree
2020-10-20
Paul Ba
u
er
GROMACS 2021 first be
t
a r
e
l
e
ase
commit
|
commitdiff
|
tree
2020-10-19
P
aul Bauer
Add
r
elea
s
e highlight
s
commit
|
commitdiff
|
tree
2020-10-19
Paul
B
auer
Revert "Add muparser and CMake
h
andling"
commit
|
commitdiff
|
tree
2020-10-19
Erik Linda
h
l
New Twitter-b
a
sed quote
commit
|
commitdiff
|
tree
2020-10-19
Alan G
r
ay
H
alo
e
x
c
hange unit t
e
st for pre-exis
t
ing CPU co
d
e
p
ath
commit
|
commitdiff
|
tree
2020-10-16
Magnus Lundbo
r
g
When loading AWH user data
d
o
not c
o
n
v
olve the bia
s
.
.
.
commit
|
commitdiff
|
tree
2020-10-16
Mark
Abraham
Fixe
s
for clang 11
commit
|
commitdiff
|
tree
2020-10-15
Andrey
Aleks
e
enko
I
ncrease to
l
e
r
an
c
es for NBlibTest
.
S
p
cMetha
n
olForcesAreCorrec
.
.
.
commit
|
commitdiff
|
tree
2020-10-14
Ma
r
k
A
braham
Fix bon
d
ed
t
e
s
ts
commit
|
commitdiff
|
tree
2020-10-14
Andrey Aleksee
n
ko
R
evert "C
U
DA nightl
y
fail: D
i
rty hack"
commit
|
commitdiff
|
tree
2020-10-13
Paul Ba
u
er
Fix mi
s
sing copyright and release n
o
tes
commit
|
commitdiff
|
tree
2020-10-13
J
o
e Jord
a
n
F
i
x
se
g
fault in
pull readi
n
g
commit
|
commitdiff
|
tree
2020-10-09
Andrey Alek
s
eenko
a
p
i/nblib/tests/integr
a
t
or
.
cpp:
M
in
o
r changes
suggested by
Paul Bauer
.
commit
|
commitdiff
|
tree
2020-10-09
Ar
t
em Zhmurov
Cool quote
p
icking can freez
e
whe
n
hardwa
r
e
r
ando
m
.
.
.
commit
|
commitdiff
|
tree
2020-10-09
C
hristian Blau
Remove
d
ysfunctional QMMM i
n
terface
pt
5
commit
|
commitdiff
|
tree
2020-10-09
Paul B
a
ue
r
R
e
m
o
ve under th
e
hood
editing of pdb fi
l
es
commit
|
commitdiff
|
tree
2020-10-07
Paul
B
aue
r
Fix d
o
w
nlo
a
d location for regressiontests
commit
|
commitdiff
|
tree
2020-10-07
Andrey Ale
k
seenko
md
l
ib/te
s
ts/leapf
r
og
:
Make GPU tests more platform
.
.
.
commit
|
commitdiff
|
tree
2020-10-07
Paul Bauer
Fix SYCL compilation
commit
|
commitdiff
|
tree
2020-10-07
Paul
Baue
r
Merge
branc
h
'
origin/release-2
0
2
0'
into merge-release
.
.
.
commit
|
commitdiff
|
tree
2020-10-06
Paul Bauer
Pre
p
are for GROMACS
2
0
2
0
.
5
commit
|
commitdiff
|
tree
2020-10-05
M
.
E
ric
Irrgang
D
on
'
t override us
e
r provided CMAKE_O
S
X_DEPLOYMENT_TARG
E
T
.
commit
|
commitdiff
|
tree
2020-10-05
Pascal M
e
rz
Fi
x
F
orceBuffers compiler warning
commit
|
commitdiff
|
tree
2020-10-02
Mark Ab
r
aham
Cleaned up CUDA compilatio
n
commit
|
commitdiff
|
tree
2020-10-02
Paul B
a
uer
Work-around for RDRAND returning -1 on Ryzen
commit
|
commitdiff
|
tree
2020-10-02
M
.
Eric Irrg
a
n
g
Let
gmxapi installati
o
n r
e
cord the
G
ROMAC
S
library
.
.
.
commit
|
commitdiff
|
tree
2020-10-02
Paul Bauer
Remov
e
anonymo
u
s namespace
i
n ARM SVE header
commit
|
commitdiff
|
tree
2020-10-02
Mark Abraha
m
Update G
o
ogleTest to v1
.
8
.
1
commit
|
commitdiff
|
tree
2020-10-01
Paul Bauer
Fix pos
t
merge acceptance pipeline
fo
r
release-2020
commit
|
commitdiff
|
tree
2020-10-01
Berk
H
e
ss
Move co
m
p
u
teSlowForces in
t
o stepWork
commit
|
commitdiff
|
tree
2020-09-30
Paul Bauer
Revert "Add new GROMACS logo and use
i
t in the
m
a
n
ual
.
"
commit
|
commitdiff
|
tree
2020-09-30
Pa
s
cal M
e
rz
Fix bug r
e
sett
i
ng
m
datoms masse
s
to
lambd
a
=
0 sta
t
e
commit
|
commitdiff
|
tree
2020-09-30
Pasca
l
Merz
F
i
x
#
3694
commit
|
commitdiff
|
tree
2020-09-30
Art
e
m
Zhmurov
Restore destructor for GpuTest
and gmx_hw_info_t
commit
|
commitdiff
|
tree
2020-09-29
Artem Zhmurov
D
o
n'
t
use fa
h
_fsync
commit
|
commitdiff
|
tree
2020-09-29
Artem Zhmurov
R
emove two-stage in
i
tial
i
zation in Device
S
t
ream
commit
|
commitdiff
|
tree
2020-09-29
Alan Gr
a
y
Redevelopment of GP
U
Force Redu
c
tion
/
Buf
f
er Ops
commit
|
commitdiff
|
tree
2020-09-28
P
a
u
l Ba
u
er
Change downl
o
ad for r
e
gress
i
ontest aw
a
y from
gerrit
commit
|
commitdiff
|
tree
2020-09-28
Giovanni
B
ussi
F
ix
e
d
in
c
orrect enum
commit
|
commitdiff
|
tree
2020-09-28
Art
e
m
Zhmu
r
ov
add detection o
f
CP
X
5300 w/
2
FMAs
commit
|
commitdiff
|
tree
2020-09-25
Pa
u
l
B
auer
Fix
bad lo
g
ic i
n
regressionte
s
t
b
ranch selection
commit
|
commitdiff
|
tree
2020-09-24
Paul Bauer
Allow deployment of
nightly web
p
age to serve
r
commit
|
commitdiff
|
tree
2020-09-23
Alan
G
ray
Add
r
egr
e
ssion tes
t
s
f
or gpucomm paths
commit
|
commitdiff
|
tree
2020-09-22
Christian Blau
Nelder-Mea
d
d
ownhill simplex optimisation
commit
|
commitdiff
|
tree
2020-09-21
Pascal
Merz
Ch
e
c
kp
o
intd
a
ta DD followup
commit
|
commitdiff
|
tree
2020-09-21
Gille
s
Gouail
l
ardet
sim
d
/impl_none: add missing macros
commit
|
commitdiff
|
tree
2020-09-21
M
a
gnus L
u
nd
b
o
r
g
AWH avo
i
d constructors
o
nly di
f
fering in parameter
.
.
.
commit
|
commitdiff
|
tree
2020-09-21
A
rtem Z
h
murov
D
o not
r
u
n Pinn
e
dMe
m
oryCheckerTest when ther
e
are
no
.
.
.
commit
|
commitdiff
|
tree
2020-09-20
Andrey Alekseenko
Add NVIDI
A
GPU
c
ompatibility chec
k
, followin
g
issue
.
.
.
commit
|
commitdiff
|
tree
next