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Compile most of PME GPU host code with OpenCL
2018-06-07
Aleksei Iu
p
ino
v
Compile most of PME
GPU host code with Ope
n
CL
commit
|
commitdiff
|
tree
2018-06-06
B
erk
H
ess
Clea
n
up make_at
2
con
commit
|
commitdiff
|
tree
2018-06-06
Mar
k
Abraha
m
Move IM
D
initial
i
za
t
ion
a
nd f
u
se D
D
setup
commit
|
commitdiff
|
tree
2018-06-05
M
a
rk Ab
r
aham
M
ake
p
r
op
e
r B
o
x
Deformati
o
n class
commit
|
commitdiff
|
tree
2018-06-05
Ber
k
H
ess
Ma
k
e nbnxn_grid
_
t counts and sizes arr
a
ys
commit
|
commitdiff
|
tree
2018-06-05
M
a
r
k
A
br
a
ha
m
Make Con
s
traints a proper c
l
ass
commit
|
commitdiff
|
tree
2018-06-04
Mark Abraham
Upd
a
te Awh initialization an
d
lifetime management
commit
|
commitdiff
|
tree
2018-06-04
Szil
á
rd Páll
F
ix timin
g
of clFFT
kernels
commit
|
commitdiff
|
tree
2018-06-04
Magnus Lundborg
W
r
i
te lambda
s
and
b
ox
to TNG at correct
i
nterv
a
ls
commit
|
commitdiff
|
tree
2018-06-01
Kevin Bo
y
d
C
o
smetic fixe
s
to mdp document
a
t
ion
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
se
i
Iupinov
Merge pme
.
cu into pme
-
gpu-internal
.
cp
p
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupi
n
ov
Move
pme-timings
.
cu
to p
m
e-gpu
-
timi
n
g
s
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iupinov
Prefer link
i
ng to
sys
t
em c
l
FFT rather than b
u
ndled o
n
e
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iu
p
inov
M
ove
the P
m
eGpuSp
e
cific structure
i
n
t
o pme-
g
pu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Added the bu
n
dled clFFT into Op
e
nCL bui
l
ds
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupino
v
G
a
ther th
e
PME GPU constants/macros
in a
s
i
n
gle head
e
r
commit
|
commitdiff
|
tree
2018-05-28
Alekse
i
Iupi
n
ov
Support persistent dev
i
ce
contex
t
-derived d
a
ta in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
Mark
A
braham
Clean up fo
r
ce
.
h and
i
ts use
commit
|
commitdiff
|
tree
2018-05-24
M
a
rk A
b
raham
Remove bDom
D
ec from t_forcerec
commit
|
commitdiff
|
tree
2018-05-24
B
e
rk Hes
s
Fix grom
p
p bug with blocks of
s
ame mo
l
ecules
commit
|
commitdiff
|
tree
2018-05-24
Mark
Abraham
Re
f
orm
E
w
ald-modu
l
e
cmake handling
commit
|
commitdiff
|
tree
2018-05-23
Rol
a
nd Schulz
Rename GMX_OCL_C
L
USTER_S
I
Z
E to GMX_OC
L
_NB_CLUSTER_SIZE
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Split off collect
.
cpp
f
rom domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
C
o
nv
e
rt nbnxn_sear
c
h t
o
C
+
+
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
C
h
ange n
b
nxn grid reallocation
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use st
d
::vector in nbnxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
U
s
e
s
td::v
e
cto
r
in nbnxn_grid_t
commit
|
commitdiff
|
tree
2018-05-22
K
evin Boyd
Cosme
t
ic
d
ocumentation
changes
commit
|
commitdiff
|
tree
2018-05-22
Kevin
Boyd
Minor fixes to
mdrun perform
a
nce docume
n
tation
commit
|
commitdiff
|
tree
2018-05-18
Alekse
i
I
u
p
inov
prepareGpuKerne
l
A
rguments() and launchGpuKer
n
el
(
) are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
Hess
Sp
l
i
t
o
ff
domdec dist
r
i
bution and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
S
p
lit atom redistribution off from
domde
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hes
s
Rem
o
v
e commrec from set_
d
db
o
x()
commit
|
commitdiff
|
tree
2018-05-15
Roland Schulz
Us
e
s
ame OpenCL kernel for different Vendors
commit
|
commitdiff
|
tree
2018-05-10
C
a
rsten Kut
z
n
e
r
Introduc
e
h
e
lper c
l
asse
s
for force p
r
ovider in
p
ut a
n
d
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul Bau
e
r
Fix
m
d -cpi -noap
p
end
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
M
erge "Merge
b
ranch
r
elease-2018"
commit
|
commitdiff
|
tree
2018-05-04
Mark
Abraham
M
ore
c
onst correctness
commit
|
commitdiff
|
tree
2018-05-03
Mark Abra
h
am
Mer
g
e bra
n
c
h release-2
0
18
commit
|
commitdiff
|
tree
2018-05-02
Roland
S
chulz
E
n
able uncrust
i
fy for OpenCL
commit
|
commitdiff
|
tree
2018-05-02
Roland Schulz
Support 4 sized cluste
r
for GPU NBL search
commit
|
commitdiff
|
tree
2018-04-27
B
e
rk H
e
ss
Remove pul
l
MPI code duplicat
i
o
n
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Re
o
rg
a
nize files for reference manual
commit
|
commitdiff
|
tree
2018-04-26
P
aul Bau
e
r
Spli
t
up a
n
alysi
s
chapter
in refe
r
ence manual
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Split up speci
a
l topics section in manual
commit
|
commitdiff
|
tree
2018-04-25
P
a
u
l Bauer
Add
p
age brea
k
s in reference manual
commit
|
commitdiff
|
tree
2018-04-25
Paul Ba
u
e
r
Split up Interac
t
ion funct
i
ons manu
a
l pa
g
e
commit
|
commitdiff
|
tree
2018-04-25
M
a
rk
A
braham
Re
f
actor SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Chan
g
e image co
n
versio
n
to only be
build once
commit
|
commitdiff
|
tree
2018-04-23
Aleksei
I
up
i
nov
Dev
i
ce
B
uffer headers
a
re
a
dded
commit
|
commitdiff
|
tree
2018-04-23
Sz
i
lárd Páll
F
ix icc warnin
g
in post-
s
ubmit
commit
|
commitdiff
|
tree
2018-04-21
S
z
i
l
árd Páll
Ad
d
p
o
s
t-submit with
A
RM HPC Toolch
a
in
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Twe
a
k PME run mode c
h
ecks
commit
|
commitdiff
|
tree
2018-04-21
Paul
Ba
u
er
Convert manual
from LaTeX to Mar
k
up
commit
|
commitdiff
|
tree
2018-04-21
Paul
B
aue
r
S
econd change
t
rac
k
ing
commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Interm
e
diate commit to track cha
n
g
es to
m
anual
commit
|
commitdiff
|
tree
2018-04-17
Viveca Lindahl
Disallow -skip values
<
= 0 for gmx trjcon
v
.
commit
|
commitdiff
|
tree
2018-04-17
Paul
Ba
u
er
Fix legacy topology memory er
r
o
r
commit
|
commitdiff
|
tree
2018-04-17
M
a
rk Abraham
Shift per-st
e
p control
l
ogic t
o
do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark
A
b
r
aham
Break ap
a
rt
u
pdate_constraints
commit
|
commitdiff
|
tree
2018-04-16
Szilárd Páll
Add post-submit
t
est with hwloc
o
f
f
commit
|
commitdiff
|
tree
2018-04-16
Be
r
k
Hess
Move natoms_mol out of gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark Abraham
Upda
t
ed mdru
n
c
om
p
a
rison i
n
fra
s
tructure
commit
|
commitdiff
|
tree
2018-04-13
Mark
A
b
raham
C
le
a
n
up
c
onstra
i
nts code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abra
h
am
Remove
u
se of where(), if D
E
B
UG
etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Reorgan
i
ze energ
y
evaluation for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupin
o
v
Prevent OpenCL
t
i
ming
memo
r
y
leak
commit
|
commitdiff
|
tree
2018-04-09
Berk
H
ess
Conv
e
r
t gmx_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
Simp
l
ified handling of simulation runne
r
s
commit
|
commitdiff
|
tree
2018-04-05
M
a
rk Abraham
Cr
e
ate gr
o
macs/mdrun
mod
u
le and move c
o
d
e
there
commit
|
commitdiff
|
tree
2018-04-05
Szilárd Páll
R
e
factor cj prel
o
ad in the nonbonded O
p
enC
L
k
e
r
n
els
commit
|
commitdiff
|
tree
2018-04-04
Mark Abra
h
a
m
Quie
t
checkpoint reading
commit
|
commitdiff
|
tree
2018-04-04
Pascal Me
r
z
Move c
h
eckNumberOfBondedInteracti
o
ns
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
C
o
nvert
g
m
x
_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
R
e
mov
e
le
f
t
o
ve
r
mention of t
w
in-range scheme
commit
|
commitdiff
|
tree
2018-04-03
Mark
A
b
raham
Merge "Merge bran
c
h releas
e
-2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
Move fi
l
e opening ou
t
of in
i
t_pull()
commit
|
commitdiff
|
tree
2018-03-29
Szilá
r
d
Páll
Tweak/e
n
able
i
c
c 18 post-subm
i
t tests
commit
|
commitdiff
|
tree
2018-03-29
Magnus Lundborg
I
m
proved check of if o
n
ly forces are comput
e
d i
n
do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
P
a
ul Bauer
Fix cmake Sphi
n
x d
e
tection for
versions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
Switch CUDA 9
.
0
/
gcc 5 test t
o
CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk
Hess
Modu
l
ari
z
e pull_coor
d
_
w
ork_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Free m
o
re
memory in gro
m
pp and
m
d
run
commit
|
commitdiff
|
tree
2018-03-28
Berk
He
s
s
Remove mols f
r
o
m
gmx_
m
t
op_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abr
a
ham
Merge
b
ra
n
ch release-2018
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
C
l
a
rified mdp options relating to bond
s
commit
|
commitdiff
|
tree
2018-03-27
Mar
k
A
braham
More gcc
-
8 fix
e
s for POWER
commit
|
commitdiff
|
tree
2018-03-21
D
avid van
d
e
r
Spoel
Renamed
entropy
.
*
t
o th
e
r
moch
e
mis
t
ry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abr
a
ham
Version 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mar
k
Abraha
m
M
e
r
g
e "Merge
b
r
an
c
h
release
-
2016 i
n
t
o
release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
M
ark Abraham
Update release n
o
te
s
for 2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abr
a
ham
Merge branch
release-2016 into release-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
a
h
am
Update use o
f
gpu_id in Jenkin
s
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallo
w
s
i
ngle
s
imulation wit
h
mul
t
is
i
m
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update use of gpu_id in Je
n
kins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update use of
gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
b
raham
Add hel
p
er f
u
nction
t
o make a
vector f
r
om an ArrayR
e
f
commit
|
commitdiff
|
tree
2018-03-19
Mark Abraha
m
Fix VSX SIMD with gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Ba
u
er
O
n
ly f
r
ee topology
w
hen a
l
loca
t
e
d
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct
PMF sign e
r
ro
r
in
A
WH
bias sharing
commit
|
commitdiff
|
tree
next