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GROMACS 2020 release candidate
2019-12-20
P
aul Bauer
GROMACS 2020 re
l
e
ase candi
d
ate
commit
|
commitdiff
|
tree
2019-12-19
A
l
an Gray
Fix
PME tuning issue w
h
en P
M
E-PP
commu
n
i
c
a
tions
a
re
.
.
.
commit
|
commitdiff
|
tree
2019-12-19
Szilárd Páll
PP-PME load
b
alanc
i
ng
i
mprovements
commit
|
commitdiff
|
tree
2019-12-18
Szilárd Pá
l
l
All
o
w x D2H to overlap with GPU force compute
commit
|
commitdiff
|
tree
2019-12-18
Berk Hess
Change gro
m
pp de
c
oupl
i
ng SD warning to note
commit
|
commitdiff
|
tree
2019-12-18
Pa
u
l Bau
e
r
Add
ability to set
OMP and t
M
PI thread for ct
e
s
t
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmu
r
ov
Clarify what settin
g
zero to
some
output mdp
o
p
tion
s
.
.
.
commit
|
commitdiff
|
tree
2019-12-11
M
.
Eric
I
r
rgang
gmxapi landing pa
g
e up
d
a
te
.
commit
|
commitdiff
|
tree
2019-12-07
M
.
Eric
I
rrgang
F
inalize gmxapi 0
.
1
commit
|
commitdiff
|
tree
2019-12-06
Ma
r
k Abraham
A
v
oid 386 O3 codegen bug
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric
I
rrgang
Add no
t
es on
MPI w
i
th
gmx
a
pi
P
y
t
h
on p
a
c
kage
.
commit
|
commitdiff
|
tree
2019-12-06
Ar
t
em Zhmurov
Pass array ref instead of casting to ba
s
ic ar
r
ay in
.
.
.
commit
|
commitdiff
|
tree
2019-12-06
M
a
rk Abraham
Provide
m
ore fe
e
dba
c
k w
h
en listed
f
orc
e
s
test
s
fail
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
gmxapi Pyth
o
n pa
c
kage
usage
prose
.
commit
|
commitdiff
|
tree
2019-12-06
M
.
Eric Irrgang
Impro
v
e pyt
e
st fixt
u
res for directo
r
y management
.
commit
|
commitdiff
|
tree
2019-12-05
Christian Blau
Re
l
ax cross-correlation test precision
commit
|
commitdiff
|
tree
2019-12-03
P
au
l
B
auer
Third beta releas
e
of GROMACS 2020
commit
|
commitdiff
|
tree
2019-12-03
Paul B
a
uer
Revert "E
n
able GPU update w
i
th
D
D
w
hen GPU comm features
.
.
.
commit
|
commitdiff
|
tree
2019-12-03
P
a
ul Bau
e
r
Fix nightl
y
build by correctly
d
efining several
commit
|
commitdiff
|
tree
2019-12-03
Al
a
n Gray
Enable GPU update with DD when GPU comm features are
.
.
.
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Add check for couple
d
constraints
for
C
U
D
A upd
a
t
e
commit
|
commitdiff
|
tree
2019-12-02
Berk H
e
ss
Extract
L
I
NCS CUDA helper functions
commit
|
commitdiff
|
tree
2019-12-01
Paul B
a
u
e
r
U
se DOI for citing in
r
e
f
e
rence m
a
n
u
a
l se
c
ti
o
n
commit
|
commitdiff
|
tree
2019-12-01
Mar
k
Abrah
a
m
F
urther
i
mprove taskas
s
i
gnment exception h
a
ndling
commit
|
commitdiff
|
tree
2019-11-29
Paul
B
a
uer
Fix unaligned access with AVX512
commit
|
commitdiff
|
tree
2019-11-29
A
rt
e
m
Z
hmu
r
ov
Prin
t
Ope
n
CL
error in
f
o i
n
cas
e
of
f
ai
l
ed assertio
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Paul Ba
u
er
F
i
x postsubmit
commit
|
commitdiff
|
tree
2019-11-28
C
h
ri
s
tian Blau
Fix
check-point
i
ng for density guid
e
d simulati
o
ns
commit
|
commitdiff
|
tree
2019-11-26
M
a
rk Abraham
Relax tolerance
for bd tests
commit
|
commitdiff
|
tree
2019-11-26
Paul
B
auer
Fix unu
s
ed va
r
iable warning in
ewald
code
commit
|
commitdiff
|
tree
2019-11-26
Berk Hess
F
ix issues with AWH
w
i
th periodic pulling
commit
|
commitdiff
|
tree
2019-11-25
Chr
i
s
t
ian Blau
Fix d
u
plicate CONNECT records
in pdb files
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmu
r
o
v
Us
e
same matr
i
x for Parrinello-Rahman and B
e
r
e
ndsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
C
h
ristian
B
lau
Read mrc densit
y
m
a
p for
m
at with
a
l
l
en
d
iane
s
s
es
.
commit
|
commitdiff
|
tree
2019-11-25
Chr
i
stian Blau
C
heck mrc h
e
ader for
sanity
commit
|
commitdiff
|
tree
2019-11-25
Ar
t
em Zhmurov
Fi
x
index ma
p
ping issue
w
ith L
I
NCS on GPU
commit
|
commitdiff
|
tree
2019-11-20
Paul Bauer
M
e
rge 'origin/release-2019' into release-2020
commit
|
commitdiff
|
tree
2019-11-20
Ma
r
k
A
braham
Quiet uniniti
a
liz
e
d
var
i
able
w
ar
n
i
n
g with clang 9
commit
|
commitdiff
|
tree
2019-11-17
S
zilár
d
Páll
Trigge
r
ocl_nbnxm_k
e
rnels tar
g
et
w
it
h
clang-
t
idy
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrgang
Remove extraneous file
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Ir
r
gang
Add transitional
lin
k
s for online gmxapi Py
t
ho
n
package
.
.
.
commit
|
commitdiff
|
tree
2019-11-17
M
.
Eric Irrg
a
n
g
Improve g
m
x
api
Do
c
kerf
i
les
.
commit
|
commitdiff
|
tree
2019-11-17
Szilárd
P
á
l
l
Fix c
l
ang-tid
y
8 warnings in
O
penCL nbnxm kernels
commit
|
commitdiff
|
tree
2019-11-16
Ma
r
k Abraham
St
o
p tes
t
ing that hwloc c
a
che-size detection works
.
.
.
commit
|
commitdiff
|
tree
2019-11-14
Paul
B
a
u
e
r
Fix formatti
n
g er
r
or
commit
|
commitdiff
|
tree
2019-11-13
Erik Li
n
d
a
h
l
Up
d
ated ph
y
sical const
a
nts to CODATA 2018
commit
|
commitdiff
|
tree
2019-11-11
M
.
E
r
ic Irrgang
Achiev
e
g
mxapi fr15
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
Update
s
to gmxa
p
i FR15 acceptance test
.
commit
|
commitdiff
|
tree
2019-11-11
M
.
Eric Irrgang
Update notes and tests regarding
g
m
x
api acceptance
.
.
.
commit
|
commitdiff
|
tree
2019-11-09
Alan Gray
M
oder
n
i
z
e naming in GPU buffer ops kernels
commit
|
commitdiff
|
tree
2019-11-09
e
j
jo
r
dan
Fix mdp
p
arame
t
er handlin
g
in md
r
u
n
t
e
sts
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eric Irrgang
Fix
bug i
n
troduced b
y
clang-format reforma
t
.
commit
|
commitdiff
|
tree
2019-11-07
P
a
ul Bauer
Apply cl
a
ng-for
m
at to source t
r
ee
commit
|
commitdiff
|
tree
2019-11-06
Erik Li
n
d
ahl
Work around broken Apple compi
l
e
rs in Ma
c
OS 10
.
15
commit
|
commitdiff
|
tree
2019-11-04
M
.
Eric Ir
r
gang
Update gmxapi Python doc
u
mentati
o
n instr
u
ctions
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Er
i
c Irrgang
Update S
p
hin
x
li
n
k
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
E
r
ic Ir
r
gang
F
i
x t
y
pos
.
commit
|
commitdiff
|
tree
2019-11-01
Paul B
a
uer
Seco
n
d beta release of GROMACS 2020
commit
|
commitdiff
|
tree
2019-11-01
Chri
s
t
ian
Blau
Fix cross-correlation c
a
lculation instab
i
l
ity
commit
|
commitdiff
|
tree
2019-11-01
Szilár
d
Pá
l
l
Rename reference checksum gen
e
rating
target
commit
|
commitdiff
|
tree
2019-11-01
S
z
ilárd Páll
U
se "
-
" in che
c
k
s
u
m
-r
e
l
at
e
d version su
f
f
i
x
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Pál
l
Improve workload da
t
a st
r
uctures' docs
commit
|
commitdiff
|
tree
2019-11-01
Alan Gray
Remove e
n
ergy step dependence on GPU fo
r
ce bu
f
fer ops
commit
|
commitdiff
|
tree
2019-11-01
Berk H
e
ss
Add have
E
w
a
ldSurfaceCont
r
ibut
i
on t
o
SimulationW
o
rkload
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric I
r
rgan
g
Norma
l
ize s
a
mp
l
e
_
re
s
traint tar
g
et n
a
mes
.
commit
|
commitdiff
|
tree
2019-11-01
Pa
u
l
Bau
e
r
P
r
e
pare for 2020 beta 2
commit
|
commitdiff
|
tree
2019-11-01
Paul B
a
uer
Add validatio
n
o
f tarball
bui
l
ds
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
A
llow validation
of the ge
n
e
r
ated
CMake toolch
a
in file
.
commit
|
commitdiff
|
tree
2019-10-31
Paul
B
auer
Use
type of
explicit size in in
m
e
m
oryseria
l
izer
commit
|
commitdiff
|
tree
2019-10-29
Pascal Merz
Fix c
o
m
patib
i
li
t
y
c
heck of mod
u
lar simulato
r
commit
|
commitdiff
|
tree
2019-10-29
Be
r
k Hess
Add mdrun GPU update docu
m
entation
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Fix E
w
ald dipole correctio
n
w
ith GPU update
commit
|
commitdiff
|
tree
2019-10-29
Paul Baue
r
Merge "
M
erge
b
r
a
n
ch 'release-2019' into ma
s
ter"
commit
|
commitdiff
|
tree
2019-10-29
Paul
Bauer
Mer
g
e bra
n
ch 'release
-
2019' into master
commit
|
commitdiff
|
tree
2019-10-29
Alan Gray
Explicitly destroy PME-PP GPU communication
object
commit
|
commitdiff
|
tree
2019-10-28
M
.
E
r
ic
I
rr
g
an
g
Update bundled pybind
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric Irr
g
ang
Fix CMake m
e
ssage typo
.
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
En
a
ble forced rotation for modul
a
r simulator
commit
|
commitdiff
|
tree
2019-10-23
M
.
Eric Irrga
n
g
S
uppre
s
s some output
whe
n
s
ample_re
s
t
r
ai
n
t i
s
built
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
P
ascal Merz
A
d
apt enum to
s
tyle convention (m
o
du
l
ar simulator)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Small improvement to EnergyEl
e
ment (modular simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Me
r
z
Fix Do
m
Dec step (modular simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pa
s
cal
Merz
Fix PmeLoadBalanceHelper
i
nitializ
a
t
ion (m
o
dular s
i
mula
t
or)
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric Irrgan
g
A
dd trajectory ou
t
put to mdrun operat
i
on
.
commit
|
commitdiff
|
tree
2019-10-18
Berk Hess
Update gro
m
pp
c
utoff-s
c
hem
e
war
n
ings
commit
|
commitdiff
|
tree
2019-10-16
Szilárd Páll
Make
t
h
e wait
on nonbonded GPU results cond
i
tion
a
l
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric Ir
r
gang
Add ge
n
eric check for gmxap
i
su
p
port libr
a
ry to Python
.
.
.
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Increase
s
pc mi
n
imiz
a
t
i
on
test toleran
c
e
commit
|
commitdiff
|
tree
2019-10-09
Berk
H
ess
Fix r
a
n
dom energy and virial with PME on GPU o
n
a
P
ME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
M
.
Er
i
c Irrgang
B
u
ild gmx
a
pi docume
n
tation in m
a
in GROMACS docu
m
e
n
tation
.
commit
|
commitdiff
|
tree
2019-10-02
Paul Bau
e
r
Fix fai
l
ure
s
in clang-8 nightly buil
d
commit
|
commitdiff
|
tree
2019-10-02
P
au
l
B
a
u
er
Prep
a
r
e
for 2019
.
5
commit
|
commitdiff
|
tree
2019-10-02
Pa
u
l
B
a
uer
GROMACS vers
i
on 2019
.
4
commit
|
commitdiff
|
tree
2019-10-01
Berk H
e
ss
Alway
s
o
u
tput
c
o
r
rect
kinetic a
t
last s
t
ep
commit
|
commitdiff
|
tree
2019-10-01
Pas
c
al Merz
Outp
u
t correc
t
k
inetic at last step (mod
u
la
r
simulato
r
)
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Fix
location o
f
angle in vsite figure
commit
|
commitdiff
|
tree
2019-09-27
Mark Abrah
a
m
A
d
d tests
for editconf file conversion with indexing
commit
|
commitdiff
|
tree
2019-09-26
Pau
l
Bau
e
r
Revert "
R
emove update flag again"
commit
|
commitdiff
|
tree
2019-09-25
Paul
B
aue
r
GRO
M
AC
S
2020 first beta release
commit
|
commitdiff
|
tree
2019-09-25
Ma
r
k A
b
r
aham
Fix log file
flag output
commit
|
commitdiff
|
tree
next