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Revert "GROMACS 2020 release"
2020-01-01
Paul Bauer
Revert
"
GROMACS 2020 r
e
lease"
commit
|
commitdiff
|
tree
2019-12-30
Paul
Bauer
F
i
x
build
error wi
t
h
w
rong name from cached c
m
a
k
e file
commit
|
commitdiff
|
tree
2019-12-29
Erik
Lindahl
W
rite TPR body a
s
opaque XDR data in
b
i
g-endian format
commit
|
commitdiff
|
tree
2019-12-28
M
.
Eric Irrgang
Resolve CMak
e
ambig
u
ities for
g
m
xapi Pyth
o
n package
.
.
.
commit
|
commitdiff
|
tree
2019-12-28
Paul Bauer
Change releng to give i
n
formation about Gitlab
commit
|
commitdiff
|
tree
2019-12-28
Paul B
a
uer
E
xtend
informatio
n
for G
P
U u
p
date
commit
|
commitdiff
|
tree
2019-12-28
P
a
ul Baue
r
Exclude build-system
f
il
e
s from
C
P
a
ck
commit
|
commitdiff
|
tree
2019-12-28
Paul
B
auer
Deprecate support for
A
rmv7
commit
|
commitdiff
|
tree
2019-12-27
Arte
m
Zhmuro
v
Add a note to the log file wh
e
n -u
p
date gpu was
s
et
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Paul Bauer
A
d
d
copyr
i
ght check a
n
d
improve c
a
che
u
sage
commit
|
commitdiff
|
tree
2019-12-27
Paul
Bauer
Merge origin/release-2019 into release-2020
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmur
o
v
Clean bad a
u
to-form
a
t in decidegpuusag
e
do
x
yge
n
comments
commit
|
commitdiff
|
tree
2019-12-23
Pau
l
Bauer
A
d
d
files for Gitlab CI
commit
|
commitdiff
|
tree
2019-12-23
P
a
ul Bauer
Pr
e
p
a
re for GROMACS 2019
.
6
commit
|
commitdiff
|
tree
2019-12-23
Paul Bauer
GROMA
C
S version 20
1
9
.
5
commit
|
commitdiff
|
tree
2019-12-23
P
aul Bauer
Revert "Fix that tests
i
ntended for multiple ra
n
ks
.
.
.
commit
|
commitdiff
|
tree
2019-12-20
P
aul Bauer
GR
O
MACS
2020 release candidate
commit
|
commitdiff
|
tree
2019-12-19
Alan Gray
Fix PME
tuning issue when PME-PP communications are
.
.
.
commit
|
commitdiff
|
tree
2019-12-19
Szilárd Páll
PP-P
M
E load bala
n
cing
impr
o
vem
e
nt
s
commit
|
commitdiff
|
tree
2019-12-18
Sz
i
l
árd Pál
l
Allow x
D2
H
to
o
verlap
w
ith GPU force compute
commit
|
commitdiff
|
tree
2019-12-18
B
e
rk Hess
Change gr
o
mpp
d
ecoupling
S
D w
a
rning
t
o note
commit
|
commitdiff
|
tree
2019-12-18
P
a
ul
B
auer
A
d
d ab
i
lity t
o
s
e
t
OMP and tMPI threa
d
fo
r
c
t
est
commit
|
commitdiff
|
tree
2019-12-13
P
au
l
Bauer
Check for u
s
ing corre
c
t hwloc hea
d
ers and
runtim
e
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Cla
r
ify what setting zero to some
o
utput mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric Irrgang
gmxapi landing page update
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Eric I
r
rg
a
ng
F
i
nalize gmxap
i
0
.
1
commit
|
commitdiff
|
tree
2019-12-06
Mark Abraham
Avoid 386 O3 codegen bug
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrg
a
ng
Add
note
s
o
n
MPI with g
m
xapi Pyth
o
n
p
ackag
e
.
commit
|
commitdiff
|
tree
2019-12-06
Artem Zhmurov
P
a
s
s array ref instead of c
a
s
t
ing to basic
array in
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Christian Bla
u
Change
a
r
b
itrary
u
nits to
counts in R
M
SD
d
istance distributi
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
Mar
k
Abraham
Provide m
o
re fee
d
back when listed force
s
tests f
a
il
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric
I
r
r
gang
g
m
xap
i
P
y
thon p
a
cka
g
e usage prose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric I
r
rga
n
g
Impr
o
ve pytest fixtur
e
s
for directory mana
g
ement
.
commit
|
commitdiff
|
tree
2019-12-05
Ch
r
is
t
ian Bla
u
Re
l
a
x
cro
s
s
-correlat
i
on
t
es
t
precisio
n
commit
|
commitdiff
|
tree
2019-12-03
Paul Bauer
Third beta re
l
ease of
G
ROMACS 2020
commit
|
commitdiff
|
tree
2019-12-03
Pau
l
Bauer
Revert "En
a
ble
G
PU update with DD when GPU c
o
mm features
.
.
.
commit
|
commitdiff
|
tree
2019-12-03
Pa
u
l
B
a
u
e
r
F
i
x night
l
y build by correctly defining sever
a
l
commit
|
commitdiff
|
tree
2019-12-03
Alan Gray
En
a
ble GP
U
up
d
ate
w
ith
D
D whe
n
GPU
c
omm f
e
ature
s
are
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Be
r
k
H
ess
Add
check for coupled constraints
f
or CUDA update
commit
|
commitdiff
|
tree
2019-12-02
Ber
k
Hess
Extract L
I
NC
S
CUD
A
helper func
t
io
n
s
commit
|
commitdiff
|
tree
2019-12-01
Paul
B
a
uer
Use DOI fo
r
citing in re
f
erence manua
l
se
c
tion
commit
|
commitdiff
|
tree
2019-12-01
Ma
r
k Abr
a
ham
Further im
p
rove tas
k
assignment exception handling
commit
|
commitdiff
|
tree
2019-11-29
Paul Bau
e
r
Fix una
l
igned access with AVX5
1
2
commit
|
commitdiff
|
tree
2019-11-29
A
rtem Zhmurov
Print Op
e
nCL error
info
i
n
case
o
f failed assert
i
on
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Paul B
a
u
e
r
F
i
x
p
ostsubmit
commit
|
commitdiff
|
tree
2019-11-28
Christia
n
Blau
Fix check-p
o
i
nting for
dens
i
ty guided simu
l
ations
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
Relax tolerance
for bd tes
t
s
commit
|
commitdiff
|
tree
2019-11-26
P
aul Bauer
Fix unused v
a
riab
l
e
w
ar
n
ing
in e
w
a
l
d
c
ode
commit
|
commitdiff
|
tree
2019-11-26
Berk
Hess
Fix issues w
i
th
A
WH with
p
eri
o
dic pulli
n
g
commit
|
commitdiff
|
tree
2019-11-25
Chris
t
ian Blau
Fix duplicate
CON
N
EC
T
records in pd
b
fi
l
e
s
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use
s
ame
m
a
tri
x
fo
r
Parrinell
o
-Rahman an
d
Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
C
hri
s
tian
Blau
Read mrc density map
format with all end
i
ane
s
s
es
.
commit
|
commitdiff
|
tree
2019-11-25
C
h
risti
a
n Blau
C
heck
m
r
c
header
f
or sanity
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Fix index mapping issue wi
t
h L
I
NCS on GPU
commit
|
commitdiff
|
tree
2019-11-20
P
a
u
l
Bauer
Merge '
o
rig
i
n/release
-
2019' into release-2020
commit
|
commitdiff
|
tree
2019-11-20
M
ark Abr
a
ham
Quiet unini
t
ialized
variable
w
arning w
i
t
h clang
9
commit
|
commitdiff
|
tree
2019-11-17
S
zil
á
rd Páll
Tri
g
ger ocl_nbnxm_k
e
r
nel
s
t
ar
g
et wi
t
h
clan
g
-tidy
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgang
Remov
e
extraneous fi
l
e
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrg
a
n
g
Add transitiona
l
links for online gmxapi Py
t
hon p
a
ckage
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgang
Improve g
m
xapi Do
c
kerfile
s
.
commit
|
commitdiff
|
tree
2019-11-17
Sz
i
lárd Páll
Fix cla
n
g-
t
idy 8 warnings in
Open
C
L nb
n
xm kernels
commit
|
commitdiff
|
tree
2019-11-16
M
ark Abraham
Stop testin
g
that hwloc ca
c
he-size dete
c
tion works
.
.
.
commit
|
commitdiff
|
tree
2019-11-14
P
aul Bauer
Fix formatting error
commit
|
commitdiff
|
tree
2019-11-13
Erik Li
n
dahl
Up
d
ated p
h
ysical c
o
nstants to CODATA
2
01
8
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
Ac
h
ie
v
e gm
x
api fr15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgan
g
Updates to gmx
a
pi FR15 acceptance test
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
r
ic I
r
rgang
Upda
t
e
n
otes and tests r
e
garding gm
x
api ac
c
e
ptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-09
Alan Gray
Modernize
naming in
G
PU buffer ops ke
r
n
e
l
s
commit
|
commitdiff
|
tree
2019-11-09
ejjordan
Fix mdp paramet
e
r handling i
n
mdrun test
s
commit
|
commitdiff
|
tree
2019-11-08
M
.
E
r
ic Ir
r
g
ang
F
i
x bug i
n
troduced by cla
n
g
-
format r
e
format
.
commit
|
commitdiff
|
tree
2019-11-07
P
aul Bauer
A
pply clang-format to source tree
commit
|
commitdiff
|
tree
2019-11-06
Erik Lindahl
Wo
r
k around broken Appl
e
compilers in
Mac OS 10
.
15
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric Irrgang
Update gmxapi Python doc
u
mentatio
n
instructio
n
s
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrg
a
ng
Upda
t
e Sp
h
inx
link
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
E
r
ic
I
r
rgang
F
i
x typo
s
.
commit
|
commitdiff
|
tree
2019-11-01
Paul B
a
uer
S
econd be
t
a rele
a
se of
GROMACS 2020
commit
|
commitdiff
|
tree
2019-11-01
Christian Blau
Fix cros
s
-
correlation c
a
lculat
i
on instability
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Páll
Rename
r
efe
r
ence
c
hec
k
sum genera
t
i
ng target
commit
|
commitdiff
|
tree
2019-11-01
Szi
l
árd Páll
Use
"-" i
n
ch
e
cksum-related
v
ersion suffix
commit
|
commitdiff
|
tree
2019-11-01
Szilárd
P
áll
Im
p
rove wor
k
load data structures
'
docs
commit
|
commitdiff
|
tree
2019-11-01
Alan G
r
ay
Re
m
o
v
e energy step d
e
pendence on GPU force buffer ops
commit
|
commitdiff
|
tree
2019-11-01
B
erk Hess
A
d
d haveEw
a
l
d
SurfaceContribu
t
i
on t
o
S
i
m
ulationWorkload
commit
|
commitdiff
|
tree
2019-11-01
M
.
E
r
ic
Irrgang
Norma
l
ize sample_restraint target n
a
mes
.
commit
|
commitdiff
|
tree
2019-11-01
Pa
u
l Bauer
Prepa
r
e for 2020 be
t
a 2
commit
|
commitdiff
|
tree
2019-11-01
Pa
u
l Baue
r
Add validation
o
f tarball builds
commit
|
commitdiff
|
tree
2019-10-31
M
.
E
r
i
c
I
rrgang
All
o
w validation of th
e
gen
e
rat
e
d CMake toolchai
n
file
.
commit
|
commitdiff
|
tree
2019-10-31
Paul
B
a
ue
r
U
se type of explicit size
in inmemoryserializer
commit
|
commitdiff
|
tree
2019-10-29
Pascal Mer
z
Fix compa
t
ibility check of modular simula
t
o
r
commit
|
commitdiff
|
tree
2019-10-29
B
erk Hess
Add mdrun GPU up
d
ate documentation
commit
|
commitdiff
|
tree
2019-10-29
Ber
k
Hess
Fix Ewald d
i
pole correc
t
ion
w
ith GPU update
commit
|
commitdiff
|
tree
2019-10-29
P
a
u
l
Bauer
Merge "Merge br
a
nch 'rele
a
se-2019'
into master"
commit
|
commitdiff
|
tree
2019-10-29
P
a
u
l Ba
u
er
Mer
g
e
b
r
anch 'release-20
1
9' into master
commit
|
commitdiff
|
tree
2019-10-29
Alan Gray
Explicit
l
y destro
y
PME-PP GP
U
communication o
b
ject
commit
|
commitdiff
|
tree
2019-10-28
M
.
Eric Irrgang
Update bundled pybind
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric
I
rrgan
g
F
i
x CMake
m
essage typo
.
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
Enable
f
or
c
ed rotat
i
on for
modular sim
u
l
a
t
o
r
commit
|
commitdiff
|
tree
2019-10-23
M
.
E
r
ic Irrgan
g
S
u
pp
r
ess some o
u
tput
when
s
ample_res
t
r
a
int is
b
u
il
t
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
A
d
a
pt enum
t
o style conventio
n
(
m
odula
r
simula
t
or)
commit
|
commitdiff
|
tree
2019-10-23
P
a
s
ca
l
Merz
Small im
p
rovement to En
e
rgyE
l
em
e
nt (modul
a
r simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pa
s
cal Mer
z
Fi
x
Do
m
Dec
s
t
ep (modular simulator)
commit
|
commitdiff
|
tree
next