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Avoid 386 O3 codegen bug
2019-12-06
Mark Abrah
a
m
Avoid
3
86 O3 codeg
e
n b
u
g
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
r
ic Ir
r
gang
Add n
o
tes on MPI with gmxapi Python package
.
commit
|
commitdiff
|
tree
2019-12-06
Artem
Z
hmurov
P
ass a
r
ray
ref
i
n
s
tead
o
f
casting to basi
c
array in
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Mark
A
braham
Provi
d
e more
f
eedba
c
k when listed force
s
te
s
ts fail
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric
Irrgang
gmxapi Pytho
n
pac
k
age usag
e
p
ros
e
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
E
ric Irrga
n
g
Improv
e
py
t
est fixtures for di
r
ectory m
a
nagement
.
commit
|
commitdiff
|
tree
2019-12-05
Chr
i
stian B
l
au
Rel
a
x
c
ros
s
-
corr
e
l
a
t
i
on
te
s
t prec
i
sion
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Third beta relea
s
e of GROMACS 2
0
20
commit
|
commitdiff
|
tree
2019-12-03
Pau
l
Bauer
Revert "Enable
G
PU updat
e
w
i
th DD when G
P
U
c
omm
f
eatures
.
.
.
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Fix nightl
y
build by cor
r
ectly defining several
commit
|
commitdiff
|
tree
2019-12-03
Alan Gr
a
y
E
n
able GPU upd
a
te
with DD when GPU co
m
m features are
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
A
dd
ch
e
ck for c
o
u
p
led constraints for CUDA update
commit
|
commitdiff
|
tree
2019-12-02
Berk Hes
s
Extract LINCS
CUDA h
e
lper functions
commit
|
commitdiff
|
tree
2019-12-01
Paul Bauer
Use
D
O
I
for
c
iti
n
g in reference man
u
a
l s
e
ction
commit
|
commitdiff
|
tree
2019-12-01
Mar
k
Abraham
Further improve
t
askassignment ex
c
ep
t
i
o
n handl
i
ng
commit
|
commitdiff
|
tree
2019-11-29
Paul Bauer
Fix un
a
lig
n
ed
access with AVX512
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmu
r
o
v
Print Open
C
L error
info in case of failed asserti
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Paul Bauer
Fix postsubmit
commit
|
commitdiff
|
tree
2019-11-28
Ch
r
istia
n
Bl
a
u
Fix check
-
po
i
nting fo
r
densi
t
y gui
d
ed simulati
o
ns
commit
|
commitdiff
|
tree
2019-11-26
M
a
rk
Abraham
R
e
lax
tol
e
rance for bd tests
commit
|
commitdiff
|
tree
2019-11-26
Paul
Ba
u
er
Fix unused va
r
iable warnin
g
in e
w
ald code
commit
|
commitdiff
|
tree
2019-11-26
Berk Hess
F
ix issue
s
with AWH
with periodic pulling
commit
|
commitdiff
|
tree
2019-11-25
Chr
i
stian Blau
Fix duplicate CO
N
N
E
CT records in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use same matrix for
Par
r
ine
l
l
o
-Rahman and Beren
d
se
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
C
hristian Bla
u
Re
a
d mrc density map for
m
a
t w
i
th
al
l
endiane
s
ses
.
commit
|
commitdiff
|
tree
2019-11-25
Christian
B
lau
C
he
c
k
m
rc h
e
ader
fo
r
san
i
ty
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhm
u
r
o
v
Fix in
d
ex mapping i
s
s
u
e
w
ith
LINCS on GP
U
commit
|
commitdiff
|
tree
2019-11-20
Pau
l
B
a
uer
M
e
r
ge '
o
rigin/rel
e
ase-
2
019' into release-2020
commit
|
commitdiff
|
tree
2019-11-20
Mark Abraham
Q
uiet u
n
in
i
tialized variab
l
e warning with clang 9
commit
|
commitdiff
|
tree
2019-11-17
S
zil
á
rd Pá
l
l
Trigger ocl_nbnxm
_
kernels tar
g
et wi
t
h cl
a
ng-tidy
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
ri
c
Irrgang
Remove e
x
traneous f
i
le
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
r
ic
Irrga
n
g
Add t
r
ansitional links for online gmxa
p
i Python packag
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
E
r
ic I
r
rgang
Imp
r
ove
g
mxapi
D
ock
e
r
f
iles
.
commit
|
commitdiff
|
tree
2019-11-17
Szilárd Páll
Fix cl
a
ng-tidy 8 wa
r
nings i
n
Open
C
L nbnxm kernels
commit
|
commitdiff
|
tree
2019-11-16
Mark Abraha
m
Stop testing that h
w
loc
cache-si
z
e detection works
.
.
.
commit
|
commitdiff
|
tree
2019-11-14
Paul Bauer
Fix formatting error
commit
|
commitdiff
|
tree
2019-11-13
Erik
Lindahl
Updated phy
s
i
cal
constants to CODATA 2018
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
ric Irrg
a
ng
Achi
e
ve gmxapi f
r
15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
U
p
dates to gmxapi FR15 acceptance test
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
ric Irrgang
U
p
date
n
o
tes and tests regardi
n
g gmxapi ac
c
eptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-09
A
lan
G
ray
Modernize naming in GP
U
buf
f
er ops kern
e
l
s
commit
|
commitdiff
|
tree
2019-11-09
ejj
o
rdan
Fix
m
d
p
p
a
r
ameter ha
n
dling in mdrun tes
t
s
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eri
c
I
rrgang
Fix bug i
n
trod
u
c
e
d b
y
clang-format
reformat
.
commit
|
commitdiff
|
tree
2019-11-07
Paul Bauer
Apply c
l
a
ng-form
a
t to sou
r
c
e tr
e
e
commit
|
commitdiff
|
tree
2019-11-06
Erik Lindahl
Work ar
o
und broken Apple compil
e
rs
in Ma
c
OS 10
.
15
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric Irrgang
Update gmxapi
P
ython d
o
cum
e
ntat
i
o
n
ins
t
r
uct
i
ons
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrgang
Update Sphinx link
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrgang
Fix
typos
.
commit
|
commitdiff
|
tree
2019-11-01
Paul Bauer
S
econd beta rel
e
ase of GROMACS
2
020
commit
|
commitdiff
|
tree
2019-11-01
Christian Blau
Fix cross-correlation c
a
lculation in
s
tability
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Páll
R
e
n
a
me reference
c
h
ec
k
su
m
gener
a
t
i
ng ta
r
get
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Páll
U
se
"-
"
in ch
e
cksum-relate
d
version
s
u
f
fix
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Pál
l
I
m
prove
wo
r
k
l
oad data
s
t
ructures' docs
commit
|
commitdiff
|
tree
2019-11-01
Ala
n
Gr
a
y
Remo
v
e
e
nergy
step dependence on GP
U
force bu
f
fer ops
commit
|
commitdiff
|
tree
2019-11-01
B
erk Hess
A
d
d hav
e
EwaldSurfaceC
o
ntribut
i
o
n
to
S
imulationWorkload
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric Irrga
n
g
Normalize
s
ample_restraint target names
.
commit
|
commitdiff
|
tree
2019-11-01
Paul Bauer
Pre
p
are f
o
r
202
0
bet
a
2
commit
|
commitdiff
|
tree
2019-11-01
Paul Bauer
A
dd
va
l
i
da
t
ion of tarball
builds
commit
|
commitdiff
|
tree
2019-10-31
M
.
Er
i
c Irrgang
Allow validation
of the
g
enera
t
ed
CMa
k
e toolchain file
.
commit
|
commitdiff
|
tree
2019-10-31
Paul Baue
r
Use type
of ex
p
licit si
z
e in inm
e
mor
y
seri
a
lizer
commit
|
commitdiff
|
tree
2019-10-29
P
ascal Merz
Fix compatibility check of mod
u
lar simul
a
tor
commit
|
commitdiff
|
tree
2019-10-29
B
e
rk Hess
Add mdr
u
n GPU
u
pdate docume
n
t
ation
commit
|
commitdiff
|
tree
2019-10-29
Berk
H
ess
Fix Ewald dipole cor
r
ection with GPU
u
p
d
a
te
commit
|
commitdiff
|
tree
2019-10-29
Paul Bauer
M
e
rge "Merge branch 'release-2019' into master"
commit
|
commitdiff
|
tree
2019-10-29
Paul Bauer
M
e
rge
b
r
anch 'release-2
0
1
9
'
i
nto ma
s
ter
commit
|
commitdiff
|
tree
2019-10-29
Alan G
r
ay
Explicit
l
y destroy P
M
E-PP GPU communicat
i
o
n
o
b
ject
commit
|
commitdiff
|
tree
2019-10-28
M
.
E
r
ic Irrgang
Update bundled pyb
i
nd
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric Irrgang
Fi
x
CMake message t
y
po
.
commit
|
commitdiff
|
tree
2019-10-27
P
ascal Mer
z
En
a
ble forc
e
d rotati
o
n
f
or modular si
m
ulato
r
commit
|
commitdiff
|
tree
2019-10-23
M
.
Eric Irrga
n
g
Supp
r
ess some outp
u
t whe
n
sa
m
pl
e
_res
t
raint is built
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pa
s
cal Merz
A
d
apt
e
num to
s
tyle
convention (mo
d
ular simul
a
tor)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Small
i
mprovement
to EnergyElement (modular simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pas
c
al
Merz
F
ix DomDec s
t
ep (m
o
dular si
m
ula
t
or)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fi
x
PmeLoadBalanceHelper initialization (modular sim
u
lat
o
r)
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric Irrgang
Add tra
j
ectory output to mdrun operatio
n
.
commit
|
commitdiff
|
tree
2019-10-18
Be
r
k Hess
U
p
d
a
te grompp cu
t
off-scheme w
a
rnings
commit
|
commitdiff
|
tree
2019-10-16
Szi
l
árd
P
áll
Make the wai
t
o
n
nonbonded
G
P
U
result
s
conditional
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric
Ir
r
ga
n
g
Add generi
c
check for
g
mxapi support library to Pytho
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-09
Ber
k
Hess
Increase spc mi
n
i
miz
a
tion test to
l
erance
commit
|
commitdiff
|
tree
2019-10-09
Berk Hes
s
Fi
x
random e
n
ergy a
n
d vi
r
ial wit
h
PME on GPU on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
M
.
Er
i
c
Irrga
n
g
Buil
d
gmxapi documentati
o
n in m
a
in GROMACS docum
e
ntation
.
commit
|
commitdiff
|
tree
2019-10-02
Paul Bauer
Fix failures i
n
c
l
ang-8
n
ight
l
y build
commit
|
commitdiff
|
tree
2019-10-02
Pa
u
l Ba
u
e
r
P
r
e
pare for 2
0
19
.
5
commit
|
commitdiff
|
tree
2019-10-02
Paul Bau
e
r
GROMACS ve
r
sio
n
201
9
.
4
commit
|
commitdiff
|
tree
2019-10-01
Berk
H
ess
Always output correct kinet
i
c at last step
commit
|
commitdiff
|
tree
2019-10-01
Pasc
a
l Merz
Output correct kinetic at
l
a
s
t
st
e
p (modu
l
ar s
i
mulator)
commit
|
commitdiff
|
tree
2019-09-27
Berk Hes
s
Fix lo
c
ation of angle in vsite
figu
r
e
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Ad
d
te
s
ts
f
or edit
c
onf f
i
le conversion with i
n
dexing
commit
|
commitdiff
|
tree
2019-09-26
Paul Bauer
Revert "Remove update flag
a
gai
n
"
commit
|
commitdiff
|
tree
2019-09-25
Paul
Bauer
GROMACS
2020
first beta release
commit
|
commitdiff
|
tree
2019-09-25
M
a
rk Abr
a
h
am
Fix lo
g
file flag
o
utput
commit
|
commitdiff
|
tree
2019-09-24
Ma
g
nu
s
Lundborg
Add
.
pa
r
t0001
.
to files from the first run with -noappend
.
commit
|
commitdiff
|
tree
2019-09-24
Paul Bauer
Merge br
a
nch release-201
9
into master
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Grompp error for mi
s
matching nst for energy calu
l
a
t
i
on
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Christia
n
Blau
Ame
n
dments to density f
i
tting manu
a
l
section
commit
|
commitdiff
|
tree
2019-09-23
Mark Abraham
Fixes to br
o
ken
CUD
A
compiler flag
s
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
a
l Merz
Make Check
p
oi
n
tHelper safer and easi
e
r to use
commit
|
commitdiff
|
tree
2019-09-18
Chr
i
stian Blau
Add mdp opt
i
on documenta
t
ion for de
n
s
it
y
fitting
.
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Fix todos for update groups
commit
|
commitdiff
|
tree
2019-09-17
Pa
s
ca
l
Merz
F
i
x modul
a
r simulator M
P
I bugs
commit
|
commitdiff
|
tree
next