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Clean up PME load balancing struct
2019-01-09
Kevin Boyd
Clea
n
up PME
load
b
alancin
g
struct
commit
|
commitdiff
|
tree
2019-01-07
Mark Abra
h
am
Finish r
e
mov
i
ng group-
s
cheme a
l
l-vs
-
all support
commit
|
commitdiff
|
tree
2019-01-04
Berk Hess
Split nbnxn pairlist types for CPU and GPU
commit
|
commitdiff
|
tree
2019-01-04
Berk He
s
s
Repl
a
ce NBNXN
_
CP
U
_C
L
USTER_I_SIZE by c_nbnxnCpuIClusterSize
commit
|
commitdiff
|
tree
2019-01-04
Paul
B
auer
C
hange gm
x
_localtop_t to C++
commit
|
commitdiff
|
tree
2018-12-30
David van
d
e
r
Spoel
Implem
e
nted
n
ative normal mode analysis tests
.
commit
|
commitdiff
|
tree
2018-12-27
Ke
v
i
n Boyd
R
emove un
u
sed
function declarations in update
.
h
commit
|
commitdiff
|
tree
2018-12-22
Paul Bauer
Fix mdrun -nb GPU
on
non-gpu build
s
commit
|
commitdiff
|
tree
2018-12-22
Mark
Abraham
Fi
x
unused
p
arameter warni
n
g
commit
|
commitdiff
|
tree
2018-12-22
Aleksei Iupinov
Add a sanit
y
ch
e
ck for OpenCL device
s
commit
|
commitdiff
|
tree
2018-12-22
Ji
a
n
n
an Liu
Missing fact
o
r of 2
in c
o
s
-
a
cc
e
leration
commit
|
commitdiff
|
tree
2018-12-11
Paul
Bauer
Properly check for
M
S
VC in build script
commit
|
commitdiff
|
tree
2018-12-11
Szilárd Pál
l
Twe
a
k the bonded GPU energy co
p
y
/
w
ait opera
t
ions
commit
|
commitdiff
|
tree
2018-12-11
Berk H
e
ss
F
ix
updat
e
groups
with 2D/3D DLB
commit
|
commitdiff
|
tree
2018-12-11
B
e
rk H
e
s
s
Ma
k
e lar
g
e PME grid
s
work on
G
P
U
commit
|
commitdiff
|
tree
2018-12-11
B
erk
H
e
ss
Document mdru
n
md
p
option m
o
dification
commit
|
commitdiff
|
tree
2018-12-10
Pasca
l
M
e
rz
Fail
p
roof signal c
o
n
v
ersion
commit
|
commitdiff
|
tree
2018-12-10
Paul
Bauer
Make release notes html only
commit
|
commitdiff
|
tree
2018-12-10
Paul Bauer
Change
t
oct
r
e
e
depth in PDF manual
commit
|
commitdiff
|
tree
2018-12-09
Mark Ab
r
aham
Fix POWER8 and PO
W
ER9 build
commit
|
commitdiff
|
tree
2018-11-29
Paul Bauer
More fixe
s
for ImageMagick test sc
r
ipt
commit
|
commitdiff
|
tree
2018-11-29
Mag
n
us Lund
b
org
Make
p
ull with
COM from
p
rev
i
o
u
s step work
w
ith MPI
commit
|
commitdiff
|
tree
2018-11-29
M
a
r
k Abraham
Removed erronous manual var
i
abl
e
handling
commit
|
commitdiff
|
tree
2018-11-29
Paul Bau
e
r
Fix reference manua
l
ima
g
e sizes
commit
|
commitdiff
|
tree
2018-11-29
Paul Bauer
Fix
reference manual doc build
commit
|
commitdiff
|
tree
2018-11-28
Paul Bauer
Fix gcc-8 warnin
g
s
commit
|
commitdiff
|
tree
2018-11-28
Mark Abraham
I
n
t
r
oduce GpuBonded
commit
|
commitdiff
|
tree
2018-11-27
Szilárd Pál
l
Ad
d
ARMPL support to
a
dm
i
n script
commit
|
commitdiff
|
tree
2018-11-27
Szil
á
rd P
á
ll
Add tweaks to suppor
t
A
R
MPL f
o
r FFTs
commit
|
commitdiff
|
tree
2018-11-26
Pa
u
l
Ba
u
er
Fix ne
w
line printin
g
in -
v
output
commit
|
commitdiff
|
tree
2018-11-22
Mark
A
braham
M
e
r
ge "Merge
b
r
anch 'r
e
l
e
ase-20
1
9'"
commit
|
commitdiff
|
tree
2018-11-20
Mark Abra
h
am
P
a
rtial revert of "Fix ineff
i
cient
shell minimization"
commit
|
commitdiff
|
tree
2018-11-20
Mark Abra
h
am
Merg
e
"Merge rele
a
se-201
9
in
t
o master"
commit
|
commitdiff
|
tree
2018-11-15
Pau
l
Bauer
R
efi
n
e Find
S
phin
x
commit
|
commitdiff
|
tree
2018-11-15
M
.
E
r
i
c I
r
rgan
g
N
ote GMX_ENABLE_CCACHE
in build system
d
ocs
.
commit
|
commitdiff
|
tree
2018-11-15
Mark Abraham
Fix ch
e
c
kpoint restart of
t
pr wi
t
h in
f
inite step count
commit
|
commitdiff
|
tree
2018-11-15
Paul Ba
u
e
r
Rework GMXAPI test
s
commit
|
commitdiff
|
tree
2018-11-15
Ma
r
k
A
braham
Relax arb
i
trary t
o
ler
a
nce on rerun
test
commit
|
commitdiff
|
tree
2018-11-14
Mark Abraham
Fix Op
e
n
C
L
m
drun
from i
n
stalle
d
path
commit
|
commitdiff
|
tree
2018-11-11
Viacheslav Bolny
k
h
F
ixing se
g
f
a
ult in parallel MiMiC Q
M
/MM runs
commit
|
commitdiff
|
tree
2018-11-11
David
van d
e
r Spoel
Fix entropy calc
u
lation in gmx anaeig
commit
|
commitdiff
|
tree
2018-11-09
David
v
an der S
p
oel
Change get_atom_index to allow multiple molecules
.
commit
|
commitdiff
|
tree
2018-11-08
Paul Bauer
Issue fata
l
er
r
or if checkpo
i
nt do
e
s not suit the
.
t
pr
commit
|
commitdiff
|
tree
2018-11-08
Mar
k
Abraham
Pragma
w
arning suppressi
n
s for icc+w
i
n
d
o
ws
commit
|
commitdiff
|
tree
2018-11-07
Paul Bauer
Mark new c
m
ake v
a
ri
a
bles a
d
vanced
commit
|
commitdiff
|
tree
2018-11-07
S
zilárd Páll
Elimin
a
te m
a
cro tha
t
expands to v
a
riable in PME GPU
commit
|
commitdiff
|
tree
2018-11-07
Szilárd Páll
E
n
sure minimum exec
width of the P
M
E OpenCL k
e
rnels
commit
|
commitdiff
|
tree
2018-11-07
Pau
l
Bauer
Add g
l
obal directory f
o
r simulation test inputs
commit
|
commitdiff
|
tree
2018-11-06
P
aul Bauer
Fix wrong branc
h
f
o
r
regression
t
ests
commit
|
commitdiff
|
tree
2018-11-05
Mar
k
A
b
r
a
ham
Make PME
O
penCL e
n
a
b
led o
n
ly for AMD dev
i
c
es
commit
|
commitdiff
|
tree
2018-11-05
Paul Bauer
Make QM/MM code alway
s
c
om
p
ile
commit
|
commitdiff
|
tree
2018-11-05
Ale
x
ey Shvetsov
D
i
s
able
-Wno-
m
issing-pr
o
totypes
commit
|
commitdiff
|
tree
2018-11-05
Paul Bauer
Give mor
e
i
n
f
o whe
n
trying to
b
uild m
a
nu
a
l
commit
|
commitdiff
|
tree
2018-11-01
Mark
A
b
raham
Disa
b
le c
c
ache by default
commit
|
commitdiff
|
tree
2018-10-31
Be
r
k
Hess
Limit auto assignment o
f
bondeds to GPUs
commit
|
commitdiff
|
tree
2018-10-31
Jonath
a
n Vince
n
t
Add C
U
DA bonded kernel
s
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Work around expand
e
d en
s
e
mble issues
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
C
o
rr
e
ct VV inte
g
rator
ns
t
ca
l
cenergy u
s
e
commit
|
commitdiff
|
tree
2018-10-30
Ma
r
k Abraham
I
m
p
r
ove ccache impleme
n
tation
commit
|
commitdiff
|
tree
2018-10-30
P
aul
B
auer
Change T
a
ble of contents depth
commit
|
commitdiff
|
tree
2018-10-30
Mark
A
braham
Re
n
ame to
GMX_OPENCL_NB
_
CLUSTER_SIZE
commit
|
commitdiff
|
tree
2018-10-26
Mark Abraham
Merge "Merge br
a
nch
relea
s
e
-
2
0
18 into release-2
0
19
.
.
.
commit
|
commitdiff
|
tree
2018-10-26
Mark Abrah
a
m
Merge b
r
anch release-2018 i
n
to r
e
lease-2019
commit
|
commitdiff
|
tree
2018-10-26
Be
r
k Hess
Add
m
issi
n
g mass term to delt
a
H
commit
|
commitdiff
|
tree
2018-10-25
Mark Abrah
a
m
Introduce Arra
y
R
e
f
WithPaddin
g
commit
|
commitdiff
|
tree
2018-10-25
Paul Bauer
Cha
n
ge doc
bu
i
ld withou
t
i
m
age
conversion
commit
|
commitdiff
|
tree
2018-10-24
Paul Bauer
Fix MPI w/o M
P
I_I
N
_P
L
AC
E
commit
|
commitdiff
|
tree
2018-10-22
Paul Bauer
Pr
e
pa
r
e master f
o
r 2020
commit
|
commitdiff
|
tree
2018-10-21
Berk Hess
Fix
mdrun start/end
t
ime
print
commit
|
commitdiff
|
tree
2018-10-19
M
.
Eric Irrgang
D
o
cument
a
t
ion bug in gmxapi/c
o
n
t
ext
.
h
commit
|
commitdiff
|
tree
2018-10-18
B
e
rk Hess
Add env
.
v
ar
.
t
o
d
i
sabl
e
update groups
commit
|
commitdiff
|
tree
2018-10-16
M
a
rk Abraham
Eliminated t_ifunc from t_int
e
raction_function
commit
|
commitdiff
|
tree
2018-10-16
Magnu
s
Lun
d
borg
Move gmx_ffparams_t to forcefi
e
l
d
par
a
me
t
ers
commit
|
commitdiff
|
tree
2018-10-16
Mark
Abraham
Task assignment for bonded interactions on CUDA
GPUs
commit
|
commitdiff
|
tree
2018-10-16
Mark Abraham
Fix c
o
m
piler issu
e
s
commit
|
commitdiff
|
tree
2018-10-16
Mark A
b
raham
Removed support
f
o
r
NVIDIA
CC 2
.
x devices (co
d
en
a
m
e
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
Crea
t
e Exclusio
n
Bl
o
cks
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
De-d
u
p
l
icating mdrun setup
commit
|
commitdiff
|
tree
2018-10-15
Magnus Lundborg
Enable output of average pull force and positions
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
E
ric Irrgan
g
Re
s
olve some linte
r
warnings
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric I
r
rgang
Test sig
n
a
l
i
ng facility th
r
ough session resources
.
commit
|
commitdiff
|
tree
2018-10-14
Szilárd Páll
Modernize O
p
e
n
C
L
m
e
m
ory allocation f
l
ag
s
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
Irrgang
Clean u
p
gmxapi testsupport o
u
tput
.
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric
I
rrgang
g
m
x
a
pi::UsageError
commit
|
commitdiff
|
tree
2018-10-14
M
.
Eric Ir
r
gang
Allow API a
c
c
e
s
s to sim
u
lation signals
.
commit
|
commitdiff
|
tree
2018-10-13
Aleksei Iupinov
Add and
e
nable PME Op
e
nCL
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Ir
r
g
a
ng
Add AP
I
for adding MDModules
/ Restrai
n
ts
.
commit
|
commitdiff
|
tree
2018-10-12
Berk
Hess
I
mplemen
t
ass
i
gning b
o
ndeds to
t
he GPU
commit
|
commitdiff
|
tree
2018-10-12
M
.
Eric Irrgang
Add
res
t
r
a
ints frame
w
ork
.
commit
|
commitdiff
|
tree
2018-10-12
Viach
e
s
l
av Bol
n
y
k
h
Implemented QM/MM workflow
in
s
ide core GROMACS
commit
|
commitdiff
|
tree
2018-10-12
Mark Abr
a
h
a
m
Exclud
e
gmxapi source files
from include sorting
commit
|
commitdiff
|
tree
2018-10-11
Dav
i
d
v
an der
S
poel
Reinstated quasiharmonic
entropy calculation in gmx
.
.
.
commit
|
commitdiff
|
tree
2018-10-11
M
.
Eric Irrgang
Add gm
x
api::Session
.
commit
|
commitdiff
|
tree
2018-10-11
Mark
Abraham
Fix Padd
e
dVe
c
tor issues
commit
|
commitdiff
|
tree
2018-10-11
Paul B
a
uer
Add
sho
r
t security
n
o
t
ice
commit
|
commitdiff
|
tree
2018-10-10
Paul Bauer
Include d
o
i string
s
from zenodo du
r
i
n
g releas
e
commit
|
commitdiff
|
tree
2018-10-10
M
.
E
r
ic
Irrga
n
g
g
m
xapi expects p
o
si
t
io
n
i
n
dependent code
.
commit
|
commitdiff
|
tree
2018-10-10
Szilárd
P
á
ll
Swa
p
cu
s
tom
O
p
enCL memset kernel for
c
lEnqueueFillBuffer
commit
|
commitdiff
|
tree
2018-10-09
S
zil
á
r
d
Páll
Update regr
e
ssiont
e
st ref to download
commit
|
commitdiff
|
tree
2018-10-09
Viacheslav Bol
n
yk
h
Implemented chang
e
s t
o
pr
e
pro
c
es
s
or t
o
work wit
h
MiMiC
.
.
.
commit
|
commitdiff
|
tree
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