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Modernize naming in GPU buffer ops kernels
2019-11-09
Alan Gra
y
Mod
e
rnize n
a
ming in GPU buf
f
er ops
k
e
rnels
commit
|
commitdiff
|
tree
2019-11-09
ejjor
d
an
F
i
x mdp paramete
r
ha
n
dlin
g
in mdrun
te
s
ts
commit
|
commitdiff
|
tree
2019-11-08
M
.
Eric Irrgang
Fix bug introduced
by cla
n
g-format refo
r
mat
.
commit
|
commitdiff
|
tree
2019-11-07
Paul Bauer
Apply clang-form
a
t to
s
our
c
e tree
commit
|
commitdiff
|
tree
2019-11-06
Erik Lindahl
Wo
r
k
around b
r
o
k
en
A
pple compilers
in Mac OS 10
.
1
5
commit
|
commitdiff
|
tree
2019-11-04
M
.
Er
i
c Irr
g
ang
Update g
m
xapi
P
ython docu
m
e
ntat
i
on instru
c
tio
n
s
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric Irrga
n
g
Update Sp
h
i
n
x
link
.
commit
|
commitdiff
|
tree
2019-11-03
M
.
Eric
I
r
rgang
Fix typ
o
s
.
commit
|
commitdiff
|
tree
2019-11-01
P
a
ul Bauer
Seco
n
d bet
a
release of GROMACS 2020
commit
|
commitdiff
|
tree
2019-11-01
C
hristian Blau
Fix
cr
o
ss-correlat
i
on cal
c
ulation inst
a
bili
t
y
commit
|
commitdiff
|
tree
2019-11-01
Szilá
r
d
P
á
ll
Rename r
e
ference checksum
generating t
a
rget
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Páll
Use "-" in checksum-related
v
e
rsion
s
u
ff
i
x
commit
|
commitdiff
|
tree
2019-11-01
Szilár
d
Páll
Imp
r
ove worklo
a
d
d
ata structu
r
es' docs
commit
|
commitdiff
|
tree
2019-11-01
Alan Gray
Remove
e
nergy step
dependence on GPU force
buffer ops
commit
|
commitdiff
|
tree
2019-11-01
Berk H
e
ss
Add ha
v
eEwaldSurfa
c
eContribution to
S
imulationWorkload
commit
|
commitdiff
|
tree
2019-11-01
M
.
Eric
I
r
r
gang
Norma
l
ize sam
p
le_restraint
targe
t
names
.
commit
|
commitdiff
|
tree
2019-11-01
Paul Bauer
Prepare
f
or 2020 beta
2
commit
|
commitdiff
|
tree
2019-11-01
Pa
u
l Bauer
Add validation of
tarball builds
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric
Irrgang
Allow validation
o
f the genera
t
ed CMake toolc
h
ain
f
ile
.
commit
|
commitdiff
|
tree
2019-10-31
P
a
u
l Bauer
Use
type of ex
p
licit size in inmem
o
ryser
i
al
i
z
er
commit
|
commitdiff
|
tree
2019-10-29
Pascal M
e
rz
F
i
x comp
a
tibility check of modular simulator
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Add m
d
run G
P
U
u
pdate docume
n
tation
commit
|
commitdiff
|
tree
2019-10-29
B
erk Hess
Fix Ewald dipole correct
i
o
n with GPU
update
commit
|
commitdiff
|
tree
2019-10-29
Pau
l
Bauer
M
erge "
M
erge
b
ranch 're
l
ea
s
e-2019' into master"
commit
|
commitdiff
|
tree
2019-10-29
Paul Bauer
Merge
b
ranch 'release-2019
'
into master
commit
|
commitdiff
|
tree
2019-10-29
Alan Gray
Explicitly
destroy
PME-PP GPU comm
u
ni
c
ation object
commit
|
commitdiff
|
tree
2019-10-28
M
.
E
r
ic Irrgang
Update b
u
n
d
led
pybin
d
.
commit
|
commitdiff
|
tree
2019-10-27
M
.
Eric Irrga
n
g
F
i
x CMake m
e
ssage ty
p
o
.
commit
|
commitdiff
|
tree
2019-10-27
Pascal Merz
Enable forc
e
d rotation for modula
r
simulator
commit
|
commitdiff
|
tree
2019-10-23
M
.
Er
i
c Irr
g
ang
S
up
p
r
es
s
some output when sample_rest
r
aint is built
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pas
c
al Me
r
z
Adapt enu
m
to sty
l
e conven
t
ion (m
o
d
u
lar simu
l
ator)
commit
|
commitdiff
|
tree
2019-10-23
P
a
scal Merz
Small improvement
t
o E
n
ergyEl
e
ment (mod
u
lar simulat
o
r)
commit
|
commitdiff
|
tree
2019-10-22
Pascal
M
erz
Fix Dom
D
e
c step (m
o
d
ular simulato
r
)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Mer
z
F
ix PmeLoadBalanceHelper in
i
t
i
ali
z
a
tion
(
mod
u
lar sim
u
lat
o
r)
commit
|
commitdiff
|
tree
2019-10-21
M
.
Eric Irrgan
g
A
dd t
r
aject
o
ry
o
utput t
o
mdru
n
o
p
eration
.
commit
|
commitdiff
|
tree
2019-10-18
B
erk Hess
U
p
date grompp cutoff-s
c
heme warnings
commit
|
commitdiff
|
tree
2019-10-16
Szilárd Pál
l
Make
t
h
e wait
o
n non
b
on
d
ed GPU results conditio
n
al
commit
|
commitdiff
|
tree
2019-10-15
M
.
Eric Irr
g
ang
Add generic c
h
eck
f
o
r
gmxapi sup
p
ort lib
r
ary to P
y
th
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Increase
s
pc minimization
t
es
t
tolerance
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Fix rando
m
energy and viria
l
with PME
o
n GPU
on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
M
.
Eric Irrgang
Build g
m
xapi documen
t
ation in main GROM
A
CS docume
n
t
a
t
ion
.
commit
|
commitdiff
|
tree
2019-10-02
P
a
ul Bauer
Fix failures i
n
c
lang-
8
nightly build
commit
|
commitdiff
|
tree
2019-10-02
Pau
l
Baue
r
Prepare for 2
0
1
9
.
5
commit
|
commitdiff
|
tree
2019-10-02
Paul Baue
r
GROMACS
v
er
s
ion
2
0
1
9
.
4
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Always output c
o
rr
e
ct ki
n
eti
c
at las
t
step
commit
|
commitdiff
|
tree
2019-10-01
Pascal
M
erz
O
u
tput c
o
rrect kin
e
tic at last step (modular
s
imul
a
tor)
commit
|
commitdiff
|
tree
2019-09-27
Berk He
s
s
Fix lo
c
ation of ang
l
e in vsite
figure
commit
|
commitdiff
|
tree
2019-09-27
Mar
k
Abraham
Add
tests
f
or editconf fi
l
e conversion
w
i
t
h
i
n
d
e
xing
commit
|
commitdiff
|
tree
2019-09-26
Pa
u
l
B
au
e
r
R
evert "
R
e
move
update flag again
"
commit
|
commitdiff
|
tree
2019-09-25
P
aul
B
auer
G
R
OMACS 2
0
20 f
i
rst beta release
commit
|
commitdiff
|
tree
2019-09-25
Mark Abrah
a
m
Fix log fil
e
flag output
commit
|
commitdiff
|
tree
2019-09-24
Magnus Lundborg
Add
.
par
t
0
0
01
.
t
o files from t
h
e f
i
rst run
w
i
t
h -noapp
e
nd
.
commit
|
commitdiff
|
tree
2019-09-24
Paul
B
au
e
r
Merge branch release-
2
019 into ma
s
te
r
commit
|
commitdiff
|
tree
2019-09-23
Christian Blau
Grompp error for
mismatch
i
ng nst for ene
r
gy calulation
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
C
hristian
Blau
Amendments to
d
ensity fitting
manual section
commit
|
commitdiff
|
tree
2019-09-23
Mark Abra
h
am
F
i
x
es to broken CUDA
comp
i
ler flags
commit
|
commitdiff
|
tree
2019-09-23
Pasc
a
l Merz
M
a
ke CheckpointHe
l
pe
r
sa
f
er
and easier to us
e
commit
|
commitdiff
|
tree
2019-09-18
Chr
i
s
t
i
an Bl
a
u
Add mdp op
t
ion
documentation for density fitting
.
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
Fix todos f
o
r
updat
e
groups
commit
|
commitdiff
|
tree
2019-09-17
Pa
s
ca
l
Merz
F
ix modular
simulator MPI
b
u
g
s
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Make modular simula
t
or
t
he default c
o
de
p
at
h
for
m
d
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pas
c
al Merz
Fix
fo
r
ce
element
commit
|
commitdiff
|
tree
2019-09-17
P
as
c
al Merz
E
n
able checkpointing for modular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-15
M
.
Eric Irrgan
g
I
mpor
t
gmxapi docs to main GROMAC
S
d
o
cs directory
.
commit
|
commitdiff
|
tree
2019-09-13
Paul B
a
u
e
r
Add lis
t
of unsupported functions i
n
20
2
0
commit
|
commitdiff
|
tree
2019-09-13
Berk Hes
s
Add nbnxm kernel benchmark tool
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
U
p
d
ated
mdp docu
m
entation for group scheme
removal
commit
|
commitdiff
|
tree
2019-09-12
Christia
n
Blau
Manual e
n
try for d
e
n
s
i
ty gu
i
ded sim
u
lati
o
ns
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindah
l
Added SIMD
cbrt
and in
v
cbrt functions
commit
|
commitdiff
|
tree
2019-09-11
Paul Bau
e
r
Dis
a
b
le
false positive
w
arni
n
g
in
I
CC and MSVC
commit
|
commitdiff
|
tree
2019-09-10
M
agnus Lundborg
Mo
r
e
templating of
gmx_
n
b_free_energy_k
e
rnel()
commit
|
commitdiff
|
tree
2019-09-10
Szilár
d
Páll
Eliminate raw for
c
e
f
lags in do_for
c
e_low
l
evel()
commit
|
commitdiff
|
tree
2019-09-10
M
a
rk
A
b
raham
Use more RA
I
I semantics wi
t
h t_co
m
mrec
commit
|
commitdiff
|
tree
2019-09-09
Be
r
k Hess
Extract Cartesia
n
d
a
ta fr
o
m DDRank
S
etup
commit
|
commitdiff
|
tree
2019-09-09
Christian Bla
u
Adding eve
r
y N-steps opt
i
on to densit
y
f
itting
commit
|
commitdiff
|
tree
2019-09-04
Szil
á
rd Páll
Centraliz
e
more MD/force shedu
l
e flags
commit
|
commitdiff
|
tree
2019-09-02
Berk
H
ess
F
ix i
n
c
o
r
r
ect r
v
dw on
GPU with rvdw
<
rcoulomb
commit
|
commitdiff
|
tree
2019-08-30
Chri
s
tian Blau
Co
n
structing loc
a
l a
t
o
m sets for densi
t
y fit
t
ing
commit
|
commitdiff
|
tree
2019-08-30
Mark Abraham
Fix bu
i
ld matrices
commit
|
commitdiff
|
tree
2019-08-29
Eri
k
Lindahl
Some quotes
I bumped into last week
commit
|
commitdiff
|
tree
2019-08-28
Paul Bauer
Have sel
e
ct
i
o
n
s
available for mdr
u
n only
commit
|
commitdiff
|
tree
2019-08-28
Mark
Abrah
a
m
Imp
r
o
v
ed us
a
b
ility of grompp b
y
rejecting
m
ore
i
nvali
d
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Ma
r
k Abraham
Make FE
P
reru
n
tests cover
t
he int
e
nded lambda space
commit
|
commitdiff
|
tree
2019-08-26
M
a
rk Ab
r
ah
a
m
Fix
p
airli
s
t bug
commit
|
commitdiff
|
tree
2019-08-23
Erik Lindahl
Default
to AVX2
_
256 SIMD for Zen2
commit
|
commitdiff
|
tree
2019-08-22
Mark Abrah
a
m
Fix release m
a
trix
commit
|
commitdiff
|
tree
2019-08-06
M
.
Eric Irrgang
Conve
r
t t
e
st
i
nfrastr
u
c
ture targets to
s
t
a
tic librar
y
.
.
.
commit
|
commitdiff
|
tree
2019-08-06
M
.
E
ric
I
rrga
n
g
Add libg
r
omacs
d
ependency to g
p
u
_utilst
e
st_cud
a
target
.
commit
|
commitdiff
|
tree
2019-08-06
Mark Abraham
F
i
x
for M
S
VC+CUDA
commit
|
commitdiff
|
tree
2019-08-02
Berk Hess
Made g
m
x disre work with no
n
-consecu
t
ively labeled
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
Pa
s
cal
M
erz
Introduc
e
Simula
t
or ba
s
e
c
l
a
s
s
commit
|
commitdiff
|
tree
2019-08-02
M
.
Eric
Irrgang
R
ed
u
c
e conflict
s
with ext
e
r
n
al googlete
s
t files
.
commit
|
commitdiff
|
tree
2019-07-23
Mark Abraham
Up
d
ate developer guide
commit
|
commitdiff
|
tree
2019-07-11
M
a
rk
A
braham
Fix pre-submi
t
build matrix and
d
es
c
ription
commit
|
commitdiff
|
tree
2019-07-11
Kevin Boyd
Use const
v
i
e
ws in matrix determinant calculation
commit
|
commitdiff
|
tree
2019-07-11
Kevin Boyd
Add trace fu
n
ctionalit
y
to
3
x3 matric
e
s
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
G
et rid of clang-t
i
d
y w
a
rn
i
ng in d
o
_md/rerun/m
i
mic
commit
|
commitdiff
|
tree
2019-07-11
P
a
scal Merz
Remove dependence of
c
o
mpute_globa
l
s
on t_state
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
M
a
k
e relax_shell_fle
x
con i
n
depe
n
d
ent of t_state
commit
|
commitdiff
|
tree
2019-07-11
Kevin Boy
d
Clean up gmx
s
ol
v
ate
commit
|
commitdiff
|
tree
next