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Version 2020.1
2020-03-03
Paul Bau
e
r
V
e
rsi
o
n 2020
.
1
commit
|
commitdiff
|
tree
2020-03-03
Alan Gray
Allow PM
E
c
oordinate send
before
H
2D coordina
t
e trans
f
e
r
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix g
r
o
mpp unbound atom check
commit
|
commitdiff
|
tree
2020-03-02
Berk
H
ess
Fix nrd
f
with part
i
al COMM removal
commit
|
commitdiff
|
tree
2020-03-02
Paul Bau
e
r
Revert "Remo
v
e
f
rozen atoms from VCM groups"
commit
|
commitdiff
|
tree
2020-02-28
P
aul
Ba
u
er
M
erge
b
ranch rel
e
as
e
-2019 into release-
2
020
commit
|
commitdiff
|
tree
2020-02-28
Paul Bauer
Define all CPU NB ke
r
nels
commit
|
commitdiff
|
tree
2020-02-28
Jonath
a
n Vincent
Moves ca
l
l to cho
o
s
e be
s
t perfo
r
maing
k
ernels to pme_gpu_r
e
i
.
.
.
commit
|
commitdiff
|
tree
2020-02-28
Paul Bauer
Versio
n
2
0
19
.
6
commit
|
commitdiff
|
tree
2020-02-27
P
a
scal Merz
Use legacy code pa
t
h
for t_
g
raph (modular
simulat
o
r)
commit
|
commitdiff
|
tree
2020-02-25
Sz
i
lárd Páll
Improve GPU updat
e
t
a
sks
a
ssignment consistenc
y
commit
|
commitdiff
|
tree
2020-02-25
Paul
Ba
u
er
Avoid integer overflow in dispersion cor
r
ection
commit
|
commitdiff
|
tree
2020-02-25
Pa
u
l Ba
u
e
r
R
ever
t
"Expose
vsite counting"
commit
|
commitdiff
|
tree
2020-02-21
M
.
Eric Irrgang
Simplify GitLab
CI Dockerfi
l
es
.
commit
|
commitdiff
|
tree
2020-02-10
Szilárd Pál
l
Avoid dev flags in trig
g
ering
g
p
uupdate
n
igh
t
ly matrix
commit
|
commitdiff
|
tree
2020-02-10
Szilárd Páll
Avoid
(
r
e
)in
i
tia
l
i
z
ing GPU upd
a
te without DD
commit
|
commitdiff
|
tree
2020-02-05
Berk Hess
Actually fix PME forces wi
t
h
F
E witho
u
t pert
u
rb
e
d q/LJ
commit
|
commitdiff
|
tree
2020-01-24
Paul Bauer
U
se utf-8 for pyt
h
on file reading
commit
|
commitdiff
|
tree
2020-01-23
Berk Hess
Fix DD rank c
o
unt
p
rim
e
check
commit
|
commitdiff
|
tree
2020-01-23
A
rtem
Z
h
mur
o
v
Fix a couple of commas
i
n
c
ool
q
uotes
commit
|
commitdiff
|
tree
2020-01-23
G
a
urav Garg
Fix
PME checks in GPU
up
d
ate
assig
n
ment de
c
i
s
i
on
commit
|
commitdiff
|
tree
2020-01-21
Paul Bauer
Fix documenta
t
ion
e
rror with doxygen >1
.
8
.
16
commit
|
commitdiff
|
tree
2020-01-17
P
a
ul Bauer
Actually
f
i
x
G
i
tla
b
doc build
commit
|
commitdiff
|
tree
2020-01-16
Szi
l
árd Páll
Fix
PME run mode without PME
commit
|
commitdiff
|
tree
2020-01-16
Paul Bauer
F
ix nig
h
tly
b
uild
failure on G
i
t
lab
commit
|
commitdiff
|
tree
2020-01-08
Roland S
c
hulz
M
e
rg
e
rele
a
se-2
0
19 into release-2020
commit
|
commitdiff
|
tree
2020-01-01
P
aul Bauer
Prep
a
re for
20
2
0
.
1
commit
|
commitdiff
|
tree
2020-01-01
P
aul
B
a
uer
GRO
M
ACS 2020 release
commit
|
commitdiff
|
tree
2020-01-01
P
a
ul Bauer
Revert "
G
ROMACS 2020 release"
commit
|
commitdiff
|
tree
2019-12-30
Paul Bauer
Fix b
u
i
ld
e
rror with wrong name from ca
c
hed cmak
e
file
commit
|
commitdiff
|
tree
2019-12-29
Erik
Lindahl
Wr
i
te
T
PR
body as
o
paque
XDR data i
n
b
ig-endian format
commit
|
commitdiff
|
tree
2019-12-28
M
.
E
r
ic
Irr
g
a
n
g
R
e
solv
e
CMake amb
i
guiti
e
s for gmxapi Pyth
o
n packa
g
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
P
aul B
a
uer
Change releng to giv
e
information
about Gitla
b
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Extend i
n
formatio
n
for GPU
u
pdate
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Exclude build-syst
e
m files from CPac
k
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Depre
c
a
t
e
s
upport for
A
rmv7
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhm
u
ro
v
A
d
d
a n
o
te
t
o
the log
f
ile when -
u
pda
t
e gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
P
a
ul B
a
u
e
r
Add copyright check and im
p
ro
v
e
c
ache usag
e
commit
|
commitdiff
|
tree
2019-12-27
P
aul Bauer
Merge origin/release-2
0
19 into release
-
2020
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Cle
a
n
b
ad auto-fo
r
mat in
d
ecid
e
gpuusage doxygen com
m
ent
s
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
Add files for
Gitlab
CI
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
Prepare for GRO
M
ACS
2019
.
6
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
GRO
M
ACS versi
o
n 2019
.
5
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
Revert "Fix
that t
e
st
s
intended for multiple ranks
.
.
.
commit
|
commitdiff
|
tree
2019-12-20
Paul Bauer
GROMACS
2
020
r
elease ca
n
didate
commit
|
commitdiff
|
tree
2019-12-19
Ala
n
Gray
F
i
x
PM
E
tun
i
ng issue when
PME-PP communicatio
n
s are
.
.
.
commit
|
commitdiff
|
tree
2019-12-19
S
z
ilá
r
d Páll
PP-PME load balancing improvements
commit
|
commitdiff
|
tree
2019-12-18
S
z
ilár
d
Pá
l
l
A
l
low x D2H to over
l
ap with GPU force comp
u
te
commit
|
commitdiff
|
tree
2019-12-18
Berk
H
ess
Change
grompp decoup
l
i
n
g SD warnin
g
t
o
note
commit
|
commitdiff
|
tree
2019-12-18
Paul
B
auer
A
dd abil
i
ty to set O
M
P
an
d
t
M
P
I
thr
e
ad for ctest
commit
|
commitdiff
|
tree
2019-12-13
Paul Bauer
Che
c
k for usi
n
g
c
orrect hwloc headers an
d
runtime
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhm
u
rov
Cla
r
i
f
y
w
hat setting zero to some
o
u
t
p
u
t mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric I
r
rgang
gmxapi landing page update
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
E
r
ic Irrgang
Finalize gmxapi 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
M
a
r
k Abraham
A
void 386 O3 cod
e
gen bug
commit
|
commitdiff
|
tree
2019-12-06
M
.
Er
i
c
I
r
r
gang
A
dd notes on MPI with gmxapi Python pa
c
kage
.
commit
|
commitdiff
|
tree
2019-12-06
Artem Zhmurov
P
a
ss
array ref
instead of
c
a
s
ting t
o
basic array in
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Chri
s
tian Blau
Change ar
b
it
r
a
r
y
units to
c
o
unts
i
n RMSD distance
distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
M
ark Abraham
P
r
ovide more feedback
w
hen listed for
c
es tests fail
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrg
a
ng
g
m
xapi Python package
usage
p
rose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
ric Irrgang
Improve p
y
t
est fixtures for dir
e
c
tory man
a
g
e
ment
.
commit
|
commitdiff
|
tree
2019-12-05
Christian Blau
Relax cross-c
o
rrelatio
n
t
e
s
t
p
recision
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Thir
d
b
e
t
a release
of
G
ROMACS 2020
commit
|
commitdiff
|
tree
2019-12-03
P
aul Bauer
Re
v
ert
"Enabl
e
GPU update with DD when
G
P
U
c
omm features
.
.
.
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Fix
nightly build
by co
r
rectl
y
defi
n
ing se
v
eral
commit
|
commitdiff
|
tree
2019-12-03
Alan Gray
E
nable GPU upda
t
e with
D
D when GPU comm features a
r
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Berk
H
ess
A
d
d check for
c
oup
l
ed constr
a
i
nts for
C
UDA update
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Extract
L
INCS CUDA h
e
lper functi
o
ns
commit
|
commitdiff
|
tree
2019-12-01
Paul Bau
e
r
Use
DOI for citin
g
in re
f
erence manual sec
t
i
o
n
commit
|
commitdiff
|
tree
2019-12-01
Mark Abraham
Furthe
r
i
m
prove taskassignment exception
h
andling
commit
|
commitdiff
|
tree
2019-11-29
Paul Bauer
F
i
x unal
i
gned access wit
h
AV
X
5
1
2
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Pr
i
nt OpenCL error info
in
c
a
s
e of failed
assert
i
on
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Paul
B
auer
Fix
p
ostsubmit
commit
|
commitdiff
|
tree
2019-11-28
Christian Bl
a
u
Fix check-pointing for densi
t
y guided simulations
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
R
e
la
x
t
o
l
erance for bd tests
commit
|
commitdiff
|
tree
2019-11-26
Pau
l
Bauer
Fix unused variable warni
n
g
in ewald code
commit
|
commitdiff
|
tree
2019-11-26
Berk Hess
Fix issues w
i
th A
W
H wit
h
periodic pulling
commit
|
commitdiff
|
tree
2019-11-25
Christian Bla
u
F
ix duplicate CO
N
NECT
r
ecords in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use same matrix for Parrinello
-
Rahman and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Christi
a
n B
l
au
Read mrc density map format wit
h
all endi
a
nesse
s
.
commit
|
commitdiff
|
tree
2019-11-25
C
hristian Blau
Che
c
k mrc
h
eader for sanity
commit
|
commitdiff
|
tree
2019-11-25
A
rtem Zhmurov
F
ix index m
a
pping
issue w
i
th LINCS on GPU
commit
|
commitdiff
|
tree
2019-11-20
Pau
l
Bauer
M
erge 'origin
/
release
-
2019' into r
e
lease-2020
commit
|
commitdiff
|
tree
2019-11-20
M
a
rk Abraham
Quiet unin
i
tia
l
ized variabl
e
warnin
g
w
ith clan
g
9
commit
|
commitdiff
|
tree
2019-11-17
S
z
ilá
r
d P
á
ll
Trigger ocl_nbnxm_kernels t
a
rget wi
t
h clan
g
-tidy
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
r
i
c
Irrgang
Remov
e
extrane
o
us file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgang
Ad
d
transitional links for online gmxa
p
i Python packa
g
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eri
c
Irrgang
Impro
v
e gmxapi Dock
e
rfiles
.
commit
|
commitdiff
|
tree
2019-11-17
S
z
ilárd Páll
Fix clan
g
-
t
i
d
y 8 war
n
ings in OpenCL nbnxm kernel
s
commit
|
commitdiff
|
tree
2019-11-16
Mar
k
Abr
a
h
am
Stop t
e
s
ting that
hwloc
c
ache-size
d
etectio
n
works
.
.
.
commit
|
commitdiff
|
tree
2019-11-14
P
aul Bauer
Fix f
o
rmatting
error
commit
|
commitdiff
|
tree
2019-11-13
Erik
L
in
d
ahl
Updated ph
y
sic
a
l cons
t
ants to CODATA 2
0
1
8
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrga
n
g
A
chieve gmxapi fr15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
ric
Irrgang
Updates to
g
mxapi
FR15 acce
p
tance t
e
st
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgan
g
U
pdate notes
a
nd tests
r
egarding gmxapi accepta
n
ce
.
.
.
commit
|
commitdiff
|
tree
2019-11-09
A
l
an Gray
Modernize naming in GPU b
u
f
f
er ops kernels
commit
|
commitdiff
|
tree
2019-11-09
ejjordan
Fix
mdp parame
t
er
ha
n
dling in mdrun tests
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eric Irrga
n
g
Fix bug
i
ntroduced b
y
clang-format refor
m
at
.
commit
|
commitdiff
|
tree
2019-11-07
Pau
l
Bauer
Apply clang
-
format to
s
ou
r
ce tree
commit
|
commitdiff
|
tree
2019-11-06
E
r
ik Lind
a
hl
Work around
broke
n
Apple
c
ompilers in Ma
c
OS 10
.
15
commit
|
commitdiff
|
tree
next