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Compile most of PME GPU host code with OpenCL
2018-06-07
Aleks
e
i Iupinov
C
ompile
most of
P
ME G
P
U host code w
i
th
O
p
e
nCL
commit
|
commitdiff
|
tree
2018-06-06
Berk Hess
C
lean up make_at2con
commit
|
commitdiff
|
tree
2018-06-06
Mark Abraham
M
ove IMD
i
nitializa
t
io
n
and f
u
se
DD setup
commit
|
commitdiff
|
tree
2018-06-05
Mark Abra
h
am
M
a
ke pro
p
er BoxDeformat
i
on class
commit
|
commitdiff
|
tree
2018-06-05
Berk Hess
Mak
e
nbnxn_grid_t counts and sizes a
r
ra
y
s
commit
|
commitdiff
|
tree
2018-06-05
M
ark Abr
a
h
a
m
Make Constraints
a
proper class
commit
|
commitdiff
|
tree
2018-06-04
Mark
A
braham
Update Awh ini
t
i
a
lization
and lifetim
e
management
commit
|
commitdiff
|
tree
2018-06-04
S
z
ilárd Pá
l
l
Fix timing of clFFT ker
n
els
commit
|
commitdiff
|
tree
2018-06-04
Ma
g
n
u
s Lundborg
Wr
i
te lambd
a
s
and box
to
TNG at
c
orrect interv
a
ls
commit
|
commitdiff
|
tree
2018-06-01
K
e
vin Boyd
C
o
smetic fixes
t
o mdp documentation
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
Merge pme
.
cu i
n
t
o
p
me-
g
pu
-
internal
.
cp
p
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupino
v
Move pme-timings
.
cu
t
o
p
m
e-
g
pu-timings
.
cpp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei Iupinov
P
refer li
n
king to sys
t
em clFFT
ra
t
her than
bundled
o
ne
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
u
pino
v
Move the PmeGpuSpecific structure into
pme-gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
A
l
eksei
Iu
p
inov
A
dded the bundled clFFT into O
p
enCL b
u
ilds
commit
|
commitdiff
|
tree
2018-05-31
A
l
e
k
sei Iupinov
Ga
t
her the
PME GPU consta
n
ts/macros in
a
s
ingle header
commit
|
commitdiff
|
tree
2018-05-28
A
leksei
I
upinov
Support persistent d
e
vi
c
e context-
d
erived
da
t
a in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
M
a
rk Abraham
Clean
up force
.
h
a
nd
i
ts use
commit
|
commitdiff
|
tree
2018-05-24
Mark
Abrah
a
m
Remov
e
bD
o
m
Dec from t_force
r
e
c
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Fix gr
o
mpp bu
g
w
i
t
h blocks of s
a
me molecules
commit
|
commitdiff
|
tree
2018-05-24
Mark A
b
raham
R
eform Ewal
d
-
m
o
d
u
le cmak
e
handling
commit
|
commitdiff
|
tree
2018-05-23
Rolan
d
Schulz
Rena
m
e GMX_OCL_CLUSTER_SIZE to GMX_OCL_NB_
C
LUSTER_SIZE
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Split o
f
f col
l
ect
.
cpp from domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Convert nbnxn_searc
h
t
o C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Ch
a
n
g
e nbnxn
g
rid rea
l
l
ocation
commit
|
commitdiff
|
tree
2018-05-22
Berk
Hess
Use std::vecto
r
in nb
n
xn_
s
ear
c
h_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hes
s
Use std:
:
vector
i
n nb
n
xn_grid_t
commit
|
commitdiff
|
tree
2018-05-22
K
e
v
i
n Bo
y
d
Co
s
metic documentation cha
n
ges
commit
|
commitdiff
|
tree
2018-05-22
K
e
vin
Boyd
Min
o
r fixes to mdrun p
e
rforman
c
e documentatio
n
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupinov
prepar
e
GpuKernelArgumen
t
s() and launchG
p
uKe
r
n
e
l() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
S
plit off domdec distr
i
bution and cel
l
sizes
commit
|
commitdiff
|
tree
2018-05-17
Berk H
e
s
s
Sp
l
it
atom redistri
b
ution off from
d
omdec
.
c
pp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
R
e
m
o
ve
commrec fr
o
m set_
d
dbox()
commit
|
commitdiff
|
tree
2018-05-15
Rol
a
nd Schulz
Use same OpenCL
kernel for dif
f
eren
t
Vendors
commit
|
commitdiff
|
tree
2018-05-10
Carsten Kutzner
In
t
rod
u
ce he
l
per classes for for
c
e pr
o
vider input a
n
d
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul Bauer
Fix md -
c
pi -n
o
app
e
nd
commit
|
commitdiff
|
tree
2018-05-04
Mark Ab
r
aham
Merge "Merge
branch r
e
lease-2018"
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
More const correctness
commit
|
commitdiff
|
tree
2018-05-03
M
ark Abraham
Merge branch re
l
ease-2018
commit
|
commitdiff
|
tree
2018-05-02
Rol
a
nd Schulz
Enab
l
e
un
c
rustify f
o
r OpenC
L
commit
|
commitdiff
|
tree
2018-05-02
R
ola
n
d Schulz
Support
4
sized clust
e
r
for GPU NBL search
commit
|
commitdiff
|
tree
2018-04-27
B
e
rk Hess
Remove pul
l
MPI c
o
de duplication
commit
|
commitdiff
|
tree
2018-04-26
P
a
u
l
Bauer
R
e
or
g
aniz
e
files fo
r
reference
m
anual
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Split up analysis chapter in refer
e
nce
m
anual
commit
|
commitdiff
|
tree
2018-04-26
Paul Bauer
Split up sp
e
c
ial topics se
c
t
i
o
n in man
u
al
commit
|
commitdiff
|
tree
2018-04-25
P
a
u
l Ba
u
e
r
Ad
d
page
b
r
e
a
ks i
n
reference man
u
a
l
commit
|
commitdiff
|
tree
2018-04-25
Pau
l
Bauer
S
p
lit up Inte
r
action functions m
a
nual page
commit
|
commitdiff
|
tree
2018-04-25
Mark Abraham
Refactor
S
D u
p
date
commit
|
commitdiff
|
tree
2018-04-25
P
aul Bauer
Change image conversion t
o
only be build
o
n
c
e
commit
|
commitdiff
|
tree
2018-04-23
A
l
eks
e
i
Iupinov
Devic
e
Buffer hea
d
ers
are added
commit
|
commitdiff
|
tree
2018-04-23
Szilárd
Páll
F
i
x icc warn
i
ng
i
n post-su
b
m
i
t
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
A
dd post
-
submit with
A
RM HPC Toolchain
commit
|
commitdiff
|
tree
2018-04-21
Szi
l
á
rd Páll
T
w
eak PME r
u
n mode checks
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
C
o
nve
r
t manual from L
a
TeX t
o
Markup
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Second change track
i
ng commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Intermediate commit to
t
r
a
ck changes to manual
commit
|
commitdiff
|
tree
2018-04-17
Viveca L
i
ndahl
Di
s
a
l
low
-
skip values <=
0
for gmx trjc
o
n
v
.
commit
|
commitdiff
|
tree
2018-04-17
Paul
B
auer
Fix legacy
top
o
lo
g
y memor
y
e
r
r
o
r
commit
|
commitdiff
|
tree
2018-04-17
M
a
rk
A
braham
Shift pe
r
-step con
t
rol
l
ogic
t
o do_m
d
commit
|
commitdiff
|
tree
2018-04-17
Mar
k
Abraham
Break ap
a
rt
up
d
ate_
c
onstraints
commit
|
commitdiff
|
tree
2018-04-16
Szilárd Páll
Add post-submit test with hwloc off
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Move natoms_mol out of g
m
x_molblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark
A
braham
Upd
a
t
e
d mdrun comp
a
rison in
f
rastructure
commit
|
commitdiff
|
tree
2018-04-13
M
a
rk
A
b
r
aham
Clean up constraints code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Remov
e
use
o
f where(),
if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
R
eorganize energy
evalu
a
tion for
E
M
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iu
p
inov
Prevent OpenCL timing me
m
or
y
leak
commit
|
commitdiff
|
tree
2018-04-09
Berk
H
ess
C
o
nver
t
gmx_m
o
lblock_t to C++
commit
|
commitdiff
|
tree
2018-04-05
M
ar
k
Abraham
Simp
l
ified
h
andling of simulation runners
commit
|
commitdiff
|
tree
2018-04-05
M
a
rk Abra
h
am
Cr
e
a
te gromacs/mdr
u
n
m
od
u
le
and
move code there
commit
|
commitdiff
|
tree
2018-04-05
S
zilárd
Páll
Ref
a
ctor
c
j preload in
t
he nonb
o
n
ded Op
e
n
CL
k
e
r
n
els
commit
|
commitdiff
|
tree
2018-04-04
Mark Abraha
m
Quiet checkpoi
n
t re
a
ding
commit
|
commitdiff
|
tree
2018-04-04
Pa
s
cal Merz
Mov
e
checkNumberOfBondedInte
r
actions
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Convert gmx_mtop_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abra
h
am
Remove leftover ment
i
o
n
of twin-ra
n
g
e
sc
h
eme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Mer
g
e "Merge bran
c
h release-2018"
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
M
ove file o
p
ening out of init_pull()
commit
|
commitdiff
|
tree
2018-03-29
Szilárd Páll
Tweak/
e
nable icc 18 p
o
st-su
b
mit tests
commit
|
commitdiff
|
tree
2018-03-29
Magnus L
u
n
d
borg
I
m
pr
o
ved chec
k
of
i
f
o
nly forces are com
p
uted in
d
o_pairs()
commit
|
commitdiff
|
tree
2018-03-29
P
a
ul
B
auer
F
ix
c
m
a
ke Sphinx det
e
c
tion for ve
r
sions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Sz
i
lár
d
Páll
Switch CUDA 9
.
0/gcc 5 t
e
st to CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modularize pull_coord
_
work
_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
F
ree more me
m
ory in grompp and mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk
H
e
s
s
Remo
v
e mo
l
s from gmx
_
mtop
_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
braham
M
e
rge branch release-2018
commit
|
commitdiff
|
tree
2018-03-27
M
a
rk Abraha
m
Clarifi
e
d mdp options
r
elati
n
g
t
o
bo
n
ds
commit
|
commitdiff
|
tree
2018-03-27
Mark A
b
r
a
ham
Mor
e
gcc-8 fixes for POWER
commit
|
commitdiff
|
tree
2018-03-21
David van der Sp
o
el
Renamed
e
ntr
o
py
.
*
t
o
t
hermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abrah
a
m
Versio
n
2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Merge
"Merge branch release-201
6
into releas
e
-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
M
a
rk Abraham
U
pdate r
e
l
e
ase notes fo
r
2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abrah
a
m
Merge br
a
n
ch r
e
lease-2016 int
o
rel
e
ase-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abrah
a
m
Updat
e
use of
gp
u
_id i
n
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow single simulation with multisim
commit
|
commitdiff
|
tree
2018-03-20
M
a
r
k
Abraham
Update use of
g
pu_id in
J
enk
i
ns
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Upda
t
e use
of gpu_
i
d in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Add helper function to make a vector
from an
ArrayRef
commit
|
commitdiff
|
tree
2018-03-19
Ma
r
k Abrah
a
m
Fix VSX
S
I
M
D wit
h
gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only fre
e
t
o
pology wh
e
n allocated
commit
|
commitdiff
|
tree
2018-03-16
Ber
k
Hess
Correct
P
MF sign error i
n
AWH
b
ias s
h
arin
g
commit
|
commitdiff
|
tree
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