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Move the PmeGpuSpecific structure into pme-gpu-types-host-impl.h
2018-05-31
Aleksei Iupinov
Move the
P
meGpuSpecif
i
c struct
u
re int
o
pme-
g
pu-typ
e
s
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei
I
upinov
A
d
ded
t
he bundled clF
F
T in
t
o Op
e
nCL build
s
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
s
e
i
Iup
i
n
o
v
Ga
t
her the PME GPU constants/ma
c
r
o
s in
a single header
commit
|
commitdiff
|
tree
2018-05-28
A
leksei Iupinov
S
u
p
p
ort persi
s
t
e
n
t
device con
t
ex
t
-
derived data in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
Mark
Abraham
Clean u
p
forc
e
.
h and its
u
se
commit
|
commitdiff
|
tree
2018-05-24
M
a
r
k Abraham
Remo
v
e bDomDe
c
from t_for
c
erec
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Fix grompp bug with block
s
of same molecule
s
commit
|
commitdiff
|
tree
2018-05-24
Mark Abra
h
am
Re
f
orm E
w
ald-mod
u
le cmak
e
h
andling
commit
|
commitdiff
|
tree
2018-05-23
R
o
land Schulz
Rename GMX_OCL
_
CLUSTER
_
SIZE to GMX_O
C
L_NB_CLUSTE
R
_
S
I
Z
E
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
S
plit off collect
.
cpp from domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk He
s
s
C
o
nve
r
t nbnxn_search to C
+
+
commit
|
commitdiff
|
tree
2018-05-22
B
erk Hess
C
h
ange nbn
x
n
g
r
i
d reall
o
cation
commit
|
commitdiff
|
tree
2018-05-22
Be
r
k
Hess
Use std::vecto
r
in nbnxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
B
e
r
k He
s
s
Use std::
v
ector in nbn
x
n_grid_t
commit
|
commitdiff
|
tree
2018-05-22
Kevin Boy
d
Cosmetic docume
n
tation changes
commit
|
commitdiff
|
tree
2018-05-22
Kevin B
o
yd
Minor fixes
to mdru
n
performanc
e
documentation
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iu
p
i
nov
pre
p
a
r
eGpuKernelArgument
s
()
a
nd l
a
unchGpuKernel
(
) are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split off d
o
mdec distrib
u
ti
o
n and cellsize
s
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
S
p
l
i
t
atom redistributio
n
off from
dom
d
e
c
.
cp
p
commit
|
commitdiff
|
tree
2018-05-17
Berk H
e
s
s
R
emo
v
e
commr
e
c f
r
om
set
_
d
dbo
x
()
commit
|
commitdiff
|
tree
2018-05-15
Roland Schulz
Use sa
m
e OpenCL kernel for di
f
ferent Vend
o
rs
commit
|
commitdiff
|
tree
2018-05-10
C
a
rsten Kutzner
Introduce helper clas
s
es for forc
e
prov
i
der input and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Pau
l
Baue
r
Fix md -cpi -noappend
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
M
e
rge "Merge branch relea
s
e-201
8
"
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
More con
s
t correctness
commit
|
commitdiff
|
tree
2018-05-03
Ma
r
k Ab
r
a
ham
Merge branch re
l
ea
s
e
-
2018
commit
|
commitdiff
|
tree
2018-05-02
Roland
S
chulz
En
a
ble uncrustify for Open
C
L
commit
|
commitdiff
|
tree
2018-05-02
Roland Sch
u
lz
Support 4 s
i
zed clus
t
e
r
f
o
r
G
PU NBL sear
c
h
commit
|
commitdiff
|
tree
2018-04-27
Berk
Hess
Rem
o
v
e pull MPI
c
ode duplica
t
i
on
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Reorganize
files
for referenc
e
m
a
nual
commit
|
commitdiff
|
tree
2018-04-26
P
a
ul Bauer
S
plit up anal
y
sis chap
t
er i
n
r
e
ference
m
an
u
al
commit
|
commitdiff
|
tree
2018-04-26
Paul Ba
u
er
Split up special to
p
i
c
s section in
m
anual
commit
|
commitdiff
|
tree
2018-04-25
Paul
Baue
r
Add page breaks in
refer
e
nce manual
commit
|
commitdiff
|
tree
2018-04-25
P
a
ul Bauer
Split u
p
Interactio
n
functions manual page
commit
|
commitdiff
|
tree
2018-04-25
Mark Abraham
Refac
t
or SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Change image
c
onvers
i
o
n to
o
nly be build once
commit
|
commitdiff
|
tree
2018-04-23
Al
e
ksei
Iupinov
DeviceB
u
ffer headers are added
commit
|
commitdiff
|
tree
2018-04-23
Szil
á
rd
Páll
Fix icc
warn
i
ng in post-submit
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Pá
l
l
A
d
d pos
t
-submit with A
R
M
H
PC Toolchai
n
commit
|
commitdiff
|
tree
2018-04-21
Szi
l
á
rd Páll
Tweak
PM
E
run mode
ch
e
cks
commit
|
commitdiff
|
tree
2018-04-21
P
a
ul
B
auer
Co
n
vert manual from
LaTeX
to Ma
r
kup
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Seco
n
d c
h
a
n
ge
tracking commit
commit
|
commitdiff
|
tree
2018-04-21
P
aul Bauer
Interme
d
iate commit to track changes to
manua
l
commit
|
commitdiff
|
tree
2018-04-17
Viveca Li
n
dahl
Disa
l
low -sk
i
p val
u
es <= 0 for g
m
x trjconv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul Bauer
Fix legacy
topology
m
e
mo
r
y error
commit
|
commitdiff
|
tree
2018-04-17
Ma
r
k Ab
r
aham
S
h
ift per-
s
t
e
p control logi
c
t
o
d
o
_md
commit
|
commitdiff
|
tree
2018-04-17
Ma
r
k Abraham
Brea
k
apart u
p
date_constraints
commit
|
commitdiff
|
tree
2018-04-16
Sz
i
lárd Páll
Add
p
ost-subm
i
t test wit
h
hwloc off
commit
|
commitdiff
|
tree
2018-04-16
Berk
H
ess
Move natoms_mol out
of g
m
x_m
o
lblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark Abraham
U
pdated md
r
un
c
o
mparison infrastructure
commit
|
commitdiff
|
tree
2018-04-13
Ma
r
k Abra
h
am
C
l
ean
u
p constraints
code
commit
|
commitdiff
|
tree
2018-04-12
M
a
rk Abraha
m
Remove use of where(), if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Ma
r
k
A
b
raham
Reorganiz
e
en
e
rgy evaluat
i
on f
o
r EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iu
p
inov
Pre
v
ent OpenCL timing memory leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
C
onvert gmx_molblock
_
t to C
+
+
commit
|
commitdiff
|
tree
2018-04-05
Mark Ab
r
ah
a
m
Simpl
i
f
ied hand
l
ing
of simu
l
a
t
ion runners
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
C
re
a
te g
r
omacs/mdrun
module and move code th
e
re
commit
|
commitdiff
|
tree
2018-04-05
Szilárd Páll
Refactor cj preload in the nonbonded Ope
n
CL kernels
commit
|
commitdiff
|
tree
2018-04-04
Ma
r
k Abraha
m
Q
uiet
c
h
eckpoint reading
commit
|
commitdiff
|
tree
2018-04-04
Pas
c
al M
e
rz
Move chec
k
NumberOfBo
n
dedInteractions
commit
|
commitdiff
|
tree
2018-04-03
Berk
Hess
Convert gmx_mtop_t to C+
+
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Remo
v
e leftover mention of twin-
r
ange sche
m
e
commit
|
commitdiff
|
tree
2018-04-03
Mark A
b
raham
Merge "Merge branch release
-
2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk H
e
ss
Mov
e
file opening out of ini
t
_pull()
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
Tweak/enable ic
c
18 post
-
submit tests
commit
|
commitdiff
|
tree
2018-03-29
Magnus Lundborg
I
m
proved check
of if only
f
orces are computed
in do
_
pairs()
commit
|
commitdiff
|
tree
2018-03-29
Paul Bauer
Fix cmake Sphin
x
det
e
ction
for versions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilá
r
d Páll
S
witch CUDA 9
.
0
/gcc 5
t
est
t
o
CUD
A
9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modu
l
ari
z
e
pull_co
o
rd_wo
r
k_t
commit
|
commitdiff
|
tree
2018-03-28
Ma
r
k
Abraham
Free more memory in grompp and mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk
H
e
s
s
Remove mols
from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-28
Mark
Abrah
a
m
Merge branch
release-2018
commit
|
commitdiff
|
tree
2018-03-27
Ma
r
k Abr
a
ham
Cla
r
ified mdp options
r
ela
t
ing to bonds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
More gcc-8
f
ixes for P
O
WER
commit
|
commitdiff
|
tree
2018-03-21
David va
n
d
e
r
Spoel
Renam
e
d
e
ntropy
.
*
to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Version 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abrah
a
m
Merg
e
"
Merge branch release-2016 into
release-2
0
18
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Up
d
ate release note
s
for
2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Merge branch rel
e
ase-2016
i
n
t
o r
e
lease
-
2018
commit
|
commitdiff
|
tree
2018-03-20
M
ark Abr
a
h
a
m
Update
u
se of g
p
u_
i
d
i
n Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
D
i
s
a
llow single simu
l
ation with multisim
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
b
r
aham
Updat
e
use of g
p
u_id in Jenki
n
s
commit
|
commitdiff
|
tree
2018-03-20
Mark A
b
raham
Update use of gpu_id in
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
A
dd helper fun
c
tion to make a
vector
f
ro
m
an
A
rrayRef
commit
|
commitdiff
|
tree
2018-03-19
Mark Abra
h
am
Fix VSX SIMD with g
c
c 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only free t
o
pology when all
o
cate
d
commit
|
commitdiff
|
tree
2018-03-16
Berk
Hes
s
C
orrect PMF
s
ign e
r
ror in AWH bia
s
sharing
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
H
ess
Improve inter-simul
a
tio
n
signali
n
g
commit
|
commitdiff
|
tree
2018-03-14
Mark
A
braham
Make a persistent physica
l
node communica
t
or
commit
|
commitdiff
|
tree
2018-03-14
Berk He
s
s
Fix
mdr
u
n s
i
gnalling with AWH bias sh
a
ring
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AWH fix
e
s to release notes
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Require OpenCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensemble chec
k
poi
n
ting
commit
|
commitdiff
|
tree
2018-03-13
Ber
k
Hess
F
i
x AWH dec
o
nv
o
l
ut
i
on when s
h
aring a bias
commit
|
commitdiff
|
tree
2018-03-13
Ma
r
k
Abrah
a
m
Introduce co
n
str
a
in_
s
h
ake
commit
|
commitdiff
|
tree
2018-03-13
Sz
i
lárd Páll
Fix clang
6
.
0 wit
h
C
UDA 9
.
0
commit
|
commitdiff
|
tree
2018-03-13
M
a
r
k Abraham
Merge "Merge bra
n
ch release-20
1
8"
commit
|
commitdiff
|
tree
2018-03-09
B
erk Hess
C
o
rrect pdb2gmx
-
missing option
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Convert t_filenm to C
+
+
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
Merge branc
h
rel
e
ase-2018
commit
|
commitdiff
|
tree
next