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Simplify gmxapi RPATH handling
2019-12-14
M
a
rk
A
braham
S
implify gmxapi RPATH
h
a
ndling
commit
|
commitdiff
|
tree
2019-12-12
Art
e
m
Z
hmurov
Allow usi
n
g
G
P
U update w
i
th DD and upda
t
e groups
commit
|
commitdiff
|
tree
2019-12-11
Mark Abraham
D
ocum
e
nt
DOMAINDECOMP
(
cr) correctly
commit
|
commitdiff
|
tree
2019-12-04
Mark Abraham
Added
O
p
e
nCL build t
o
release ma
t
rix
commit
|
commitdiff
|
tree
2019-12-04
Mark A
b
raham
Removed unnecess
a
ry li
n
k
_directories command f
o
r gtest
commit
|
commitdiff
|
tree
2019-11-29
Pau
l
Bauer
Fix build e
r
ror wi
t
hout thread or re
g
ul
a
r mpi
commit
|
commitdiff
|
tree
2019-11-29
Mark Ab
r
aham
Me
r
ge
branch release-2019 into release-2
0
20
commit
|
commitdiff
|
tree
2019-11-29
Artem
Z
hm
u
r
o
v
Rename some variables in GPU
U
pdate
commit
|
commitdiff
|
tree
2019-11-28
Pa
u
l
B
auer
Che
c
k for
using
c
o
r
re
c
t hwloc head
e
rs and runtime
commit
|
commitdiff
|
tree
2019-11-28
Artem
Z
hmurov
Clear device force
buffer i
f
it was re
a
llocated
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmur
o
v
Add method for coor
d
i
n
ates scal
i
ng into G
P
U
updat
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-27
M
.
Eric Irrgang
A
d
d gmxapi_
e
xtension tests to 'te
s
ts' t
a
rget
.
commit
|
commitdiff
|
tree
2019-11-27
Alan Gra
y
Eve
n
t
-
b
ased Depe
n
d
en
c
y for GPU Force Ha
l
o Exchange
commit
|
commitdiff
|
tree
2019-11-26
Mark Abraham
Improve h
a
nd
l
i
ng of ta
s
k
-assignment exceptions
commit
|
commitdiff
|
tree
2019-11-25
Alan Gray
Fix
race condit
i
on
in GPU X halo exc
h
ange w
i
t
h
GPU
.
.
.
commit
|
commitdiff
|
tree
2019-11-24
Christian Bla
u
InMemorySeri
a
liz
e
r with endianess swap
.
commit
|
commitdiff
|
tree
2019-11-21
Mark Abraha
m
New cool quote
commit
|
commitdiff
|
tree
2019-11-20
A
rt
e
m
Z
h
murov
A
dd D2
H
copies for the ch
e
ck
p
ointing
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmu
r
o
v
Move
the c
o
py of t
h
e velocities for th
e
o
utput closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-20
B
erk He
s
s
Quiet pdb2g
m
x
and use g
m
x_fatal
commit
|
commitdiff
|
tree
2019-11-20
M
.
E
r
ic
Irrgang
R
e
move stub
c
ontent from gm
x
api docs
.
commit
|
commitdiff
|
tree
2019-11-16
M
ark Abraham
Relaxed l
i
sted
forces test tole
r
ances
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
Depr
e
cated s
c
-r-power=48
commit
|
commitdiff
|
tree
2019-11-04
Paul Bauer
Add b
u
ild fo
r
clang-form
a
t
commit
|
commitdiff
|
tree
2019-11-04
Pau
l
Bauer
Spl
i
t up source co
d
e
f
ormatt
i
ng scri
p
ts
commit
|
commitdiff
|
tree
2019-11-04
Teem
u
M
u
rtola
Update cla
n
g-format config
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric I
r
r
g
ang
Improv
e
uniformity
o
f OS
X
CMake configuration
.
commit
|
commitdiff
|
tree
2019-10-31
M
.
Eric Irrgang
Restor
e
CMake convenien
c
e targets for sample_restraint
.
commit
|
commitdiff
|
tree
2019-10-31
Al
a
n Gray
Remove
d
ead code for
nbnxm H2D
c
oordina
t
e copy event
commit
|
commitdiff
|
tree
2019-10-31
Alan Gray
B
ug fix for eve
n
t passed to GPU comm
features
commit
|
commitdiff
|
tree
2019-10-31
Pascal Merz
Ch
e
ck for c
o
ntradicting environment variables (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
M
a
rk Abraham
Tests fo
r
va
l
id periodic actions
commit
|
commitdiff
|
tree
2019-10-29
M
.
E
ri
c
Irrgang
Disable its tests w
h
e
n
sample_
r
estraint is
n
ot the
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
M
.
Eric Irrgang
Decrease the maximum allowed Pytho
n
version for gm
x
api
.
commit
|
commitdiff
|
tree
2019-10-29
Ar
t
em Zh
m
urov
Di
s
able GPU u
p
date when coordinates swapping
is enabl
e
d
commit
|
commitdiff
|
tree
2019-10-24
Berk
He
s
s
Add bool useD
o
main
D
ecomposit
i
on in mdrunn
e
r
commit
|
commitdiff
|
tree
2019-10-24
B
erk Hess
Add gmx_mtop
_
i
nte
r
action_count
(
)
commit
|
commitdiff
|
tree
2019-10-23
ejjordan
Make t_
n
e
xtnb a
n
implementati
o
n deta
i
l
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Correct for skewed box before domain decomposit
i
on
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Alan G
r
ay
Enable GPU Peer Access in GPU Utilities
commit
|
commitdiff
|
tree
2019-10-22
ejjordan
Remove unu
s
ed fu
n
ctio
n
s
f
r
om gmxpreprocess
commit
|
commitdiff
|
tree
2019-10-22
Berk Hess
Requ
i
re -ei
f
or e
s
sentia
l
d
ynamics
commit
|
commitdiff
|
tree
2019-10-22
ej
j
ordan
Remov
e
unused f
u
nction gen
e
ra
t
e_excls an
d
make clean_excls
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Berk
Hess
Const corr
e
ctnes
s
for genhydro
commit
|
commitdiff
|
tree
2019-10-15
P
a
ul Bauer
F
i
x
b
u
g in pr
e
p
r
o
c
essi
n
g
commit
|
commitdiff
|
tree
2019-10-14
M
.
Er
i
c
Irrgang
Fix logic error in g
m
xapi
.
version
.
api
_
i
s
_a
t
_least()
.
commit
|
commitdiff
|
tree
2019-10-13
Mark Abraham
Ensu
r
e env
i
r
o
n
me
n
t vari
a
b
le use does n
o
t g
i
ve
w
arnin
g
s
commit
|
commitdiff
|
tree
2019-10-12
Berk
H
ess
A
dd class
Fixe
d
Capaci
t
yVector
commit
|
commitdiff
|
tree
2019-10-12
Artem Zh
m
u
r
ov
Cen
t
ra
l
iz
e
management of
c
oordinate
s
ready
o
n
GP
U
event
commit
|
commitdiff
|
tree
2019-10-08
Prashanth Kand
u
ri
Fused t
w
o if branches
w
i
th the
s
a
me conditional
commit
|
commitdiff
|
tree
2019-10-02
Cars
t
en Ku
t
zner
Update
t
h
e
www link
to
t
he D
o
xygen
d
o
cumen
t
ation
i
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-02
B
er
k
Hess
Fix harmless OpenMP
writ
e
race
commit
|
commitdiff
|
tree
2019-10-02
Mark Abraham
Improve
PME testing
commit
|
commitdiff
|
tree
2019-10-01
Berk H
e
ss
Use gmx::Range
i
n
domd
e
c
commit
|
commitdiff
|
tree
2019-10-01
Artem Zh
m
urov
StatePropagatorDataGpu
object to m
a
na
g
e
GPU forces
.
.
.
commit
|
commitdiff
|
tree
2019-10-01
Mark
Abra
h
am
F
i
x
ic
c
warnings
commit
|
commitdiff
|
tree
2019-10-01
B
e
rk Hess
Completely remove cha
r
g
e
group
s
commit
|
commitdiff
|
tree
2019-10-01
Paul Bauer
Fix chain ID han
d
ling in make_nd
x
commit
|
commitdiff
|
tree
2019-10-01
Chr
i
stoph J
u
nghans
cmake: add missing heade
r
to legacy ap
i
commit
|
commitdiff
|
tree
2019-10-01
Mark Abraham
Remove
d
dep
e
ndency
o
n commrec of
m
d
run setup
commit
|
commitdiff
|
tree
2019-09-30
C
a
rsten Kutzner
Mov
e
Fo
r
ceProviders class into the gmx namespace
commit
|
commitdiff
|
tree
2019-09-30
Mark Abraham
Make a
b
uilde
r
for DD
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Re
m
ove char
g
e
group code from forcerec
commit
|
commitdiff
|
tree
2019-09-30
Szilárd P
á
ll
Make th
e
wait on PME GPU results condi
t
ional
commit
|
commitdiff
|
tree
2019-09-27
M
a
rk Ab
r
a
h
am
Impr
o
ve MiMiC
t
est implementation
commit
|
commitdiff
|
tree
2019-09-27
Mar
k
Abraham
Fix gro file output with i
n
dex groups
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Fix
g
r
o
file o
u
tput with index
g
roups
commit
|
commitdiff
|
tree
2019-09-27
Mark
A
b
r
aham
Remove
l
eftover support fo
r
p
r
e-9
.
0 CUDA
commit
|
commitdiff
|
tree
2019-09-24
Pau
l
Ba
u
er
Add test for noappend
commit
|
commitdiff
|
tree
2019-09-24
Mark
Abraham
Fix no-MPI CUDA build
commit
|
commitdiff
|
tree
2019-09-24
M
ark Abraham
Merg
e
"M
e
rge branch r
e
lease-2019 in
t
o mast
e
r"
commit
|
commitdiff
|
tree
2019-09-24
Mark Abraham
Fix clang
un
u
s
ed-func
t
ion wa
r
n
i
ngs
commit
|
commitdiff
|
tree
2019-09-24
Pa
u
l Bauer
Ad
d
relea
s
e notes
f
or
m
odular simulat
o
r
commit
|
commitdiff
|
tree
2019-09-23
Paul Ba
u
er
Fix issue
s
w
h
e
n PME
rank request
b
ec
o
mes negative
commit
|
commitdiff
|
tree
2019-09-23
P
a
ul Bauer
Change MPI s
e
t
up to communicate TPR as buffer
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al
Merz
Z
e
ro p
r
essure and
v
ir
i
al tensor
s
at beginnin
g
o
f s
t
ep
commit
|
commitdiff
|
tree
2019-09-23
Pascal
Merz
Introduce FEP
into mo
d
ular
s
imulat
o
r
commit
|
commitdiff
|
tree
2019-09-22
Chr
i
stoph Junghans
workar
o
und for
r
h
el bug #1749463,
cmake
bug #1
8
349
commit
|
commitdiff
|
tree
2019-09-22
Paul Bauer
Remove update
f
lag again
commit
|
commitdiff
|
tree
2019-09-22
Berk He
s
s
Remove cgs_g
l
f
rom g
m
x_domde
c
_co
m
m
_t
commit
|
commitdiff
|
tree
2019-09-20
Ma
r
k
Abraham
Ref
a
ctor to create a GpuTa
s
kAssig
n
ments ob
j
ect
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Remove bLoc
a
lCG from DD
code
commit
|
commitdiff
|
tree
2019-09-19
B
erk Hes
s
Remove obsolete
make_
e
xclusions_zone_cg(
)
commit
|
commitdiff
|
tree
2019-09-19
Chris
t
ian Blau
Che
c
k input record als
o
in tests
commit
|
commitdiff
|
tree
2019-09-19
Mark Abra
h
am
Use
G
PU halo ex
c
h
an
g
e
only when compatib
l
e DD is
a
v
a
ila
b
l
e
commit
|
commitdiff
|
tree
2019-09-19
Mark Abr
a
ham
Fu
r
the
r
improve getDDGri
d
Set
u
p
commit
|
commitdiff
|
tree
2019-09-19
Paul Baue
r
A
d
d bas
i
c int
e
rface to run update on GPU
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Add haveFreeEnerg
y
Work to DomainLifetimeWorkload flags
commit
|
commitdiff
|
tree
2019-09-19
Chr
i
stian Blau
Consistently
c
hange densityfit
t
ing
s
preadi
n
g weight
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
B
e
r
k
Hess
Added free
-
energy
kernel performance note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
F
i
x
incorrect DD ndim asse
r
tion
commit
|
commitdiff
|
tree
2019-09-18
Pascal Merz
v-rescale therm
o
stat for modular simulator
commit
|
commitdiff
|
tree
2019-09-18
Paul Bauer
Read TPR
fil
e
b
ody in
b
uffer
commit
|
commitdiff
|
tree
2019-09-18
Alan Gray
GPU F
o
r
ce Halo
E
xchange
commit
|
commitdiff
|
tree
2019-09-17
Pasc
a
l
M
e
rz
Fix p
o
sition pin
n
i
ng
fo
r
modular simu
l
ator
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Re
m
o
ve
o
b
solete mdp option ns-t
y
pe
commit
|
commitdiff
|
tree
2019-09-16
ejjordan
Add some
co
o
l quotes
commit
|
commitdiff
|
tree
2019-09-16
Paul Bauer
F
o
rmatting fixes
for referen
c
e manual
commit
|
commitdiff
|
tree
2019-09-16
M
.
Eric Irrgang
Add gmxap
i
r
e
lease
note
s
.
commit
|
commitdiff
|
tree
2019-09-16
Al
a
n Gr
a
y
GP
U
halo exch
a
nge
commit
|
commitdiff
|
tree
next