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Added the bundled clFFT into OpenCL builds
2018-05-31
Aleksei Iupinov
Ad
d
ed t
h
e bundled clFFT i
n
to OpenCL
b
u
il
d
s
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
se
i
Iup
i
nov
G
a
t
h
er the PM
E
GPU consta
n
ts
/
macr
o
s
in a single h
e
ader
commit
|
commitdiff
|
tree
2018-05-28
Aleksei Iupi
n
ov
Support persistent device contex
t
-derived
d
ata in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
M
ark Abr
a
h
am
Clea
n
up force
.
h
and its use
commit
|
commitdiff
|
tree
2018-05-24
Mark A
b
raham
Re
m
ov
e
b
DomDe
c
from t_
f
orcere
c
commit
|
commitdiff
|
tree
2018-05-24
Berk H
e
ss
Fi
x
grompp bug w
i
th blocks of same molecule
s
commit
|
commitdiff
|
tree
2018-05-24
Mar
k
Abraham
Reform Ewa
l
d-
m
odule cmake ha
n
dling
commit
|
commitdiff
|
tree
2018-05-23
Roland Schulz
Rename
G
MX_OCL
_
CLUSTER_SIZE to
G
M
X
_OCL_NB_CLUSTER_SIZE
commit
|
commitdiff
|
tree
2018-05-23
Ber
k
H
e
ss
Spli
t
off collect
.
cpp
from
do
m
de
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
B
e
rk Hess
Co
n
ver
t
nbn
x
n
_
se
a
r
c
h to
C++
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Chang
e
nbnxn gr
i
d reallocat
i
on
commit
|
commitdiff
|
tree
2018-05-22
B
e
r
k
H
ess
Us
e
std:
:
vector i
n
n
bnxn_
s
earch_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use s
t
d:
:
vect
o
r
i
n
n
b
nxn
_
g
r
id_t
commit
|
commitdiff
|
tree
2018-05-22
K
evin Boyd
Cosmetic d
o
cume
n
tati
o
n changes
commit
|
commitdiff
|
tree
2018-05-22
K
e
vin B
o
yd
M
i
nor
f
i
x
e
s
t
o
mdru
n
performance d
o
cum
e
n
t
at
i
on
commit
|
commitdiff
|
tree
2018-05-18
Aleksei I
u
pinov
prepareGpuKerne
l
A
r
g
uments() and launchGpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
B
erk Hess
Split
o
ff domdec
distribution and ce
l
lsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk H
e
s
s
Split atom red
i
s
tributi
o
n
o
ff from domde
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
R
em
o
ve commrec from s
e
t_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Roland Schul
z
Use sa
m
e O
p
e
n
C
L
kernel for dif
f
e
r
ent Vendors
commit
|
commitdiff
|
tree
2018-05-10
C
arsten Kutzner
Intr
o
duce helper classes for force p
r
ovider input and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
P
a
u
l Bauer
Fix md
-
cpi -noappend
commit
|
commitdiff
|
tree
2018-05-04
Mark
A
b
ra
h
a
m
Merge "Merge br
a
nc
h
release-2018"
commit
|
commitdiff
|
tree
2018-05-04
M
a
rk
Ab
r
ah
a
m
More const correctness
commit
|
commitdiff
|
tree
2018-05-03
M
ark Ab
r
ah
a
m
Merg
e
br
a
nch release-2018
commit
|
commitdiff
|
tree
2018-05-02
R
o
lan
d
Schulz
Enable uncrust
i
fy f
o
r OpenCL
commit
|
commitdiff
|
tree
2018-05-02
Rol
a
nd Schulz
Support 4 sized cluster for
G
P
U NBL search
commit
|
commitdiff
|
tree
2018-04-27
Berk H
e
ss
Re
m
ove pull MPI co
d
e duplication
commit
|
commitdiff
|
tree
2018-04-26
P
aul Bauer
R
eorganize files f
o
r refere
n
ce manu
a
l
commit
|
commitdiff
|
tree
2018-04-26
Paul B
a
uer
Split up a
n
a
lysis
ch
a
pter i
n
referen
c
e manual
commit
|
commitdiff
|
tree
2018-04-26
Pa
u
l B
a
uer
S
plit up spec
i
al
to
p
ics section in ma
n
u
a
l
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Add page br
e
aks
in refe
r
ence
m
anu
a
l
commit
|
commitdiff
|
tree
2018-04-25
Pau
l
Baue
r
Sp
l
it up Interaction functions
man
u
al page
commit
|
commitdiff
|
tree
2018-04-25
Mark Ab
r
aham
Refactor
SD upda
t
e
commit
|
commitdiff
|
tree
2018-04-25
P
a
ul Bauer
Change image conversion to only be
build o
n
ce
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iu
p
inov
D
eviceBuffer header
s
ar
e
added
commit
|
commitdiff
|
tree
2018-04-23
S
zi
l
árd Páll
Fi
x
icc warni
n
g
i
n p
o
st-submit
commit
|
commitdiff
|
tree
2018-04-21
S
z
ilárd Páll
Add post-submit with ARM HPC Tool
c
ha
i
n
commit
|
commitdiff
|
tree
2018-04-21
Szilárd Páll
Tweak PME run mode checks
commit
|
commitdiff
|
tree
2018-04-21
Paul
Ba
u
er
Convert manual fr
o
m LaTeX to Mar
k
up
commit
|
commitdiff
|
tree
2018-04-21
Paul Bau
e
r
Seco
n
d
chan
g
e
tracking commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
I
ntermediate commit to track c
h
anges
t
o manual
commit
|
commitdiff
|
tree
2018-04-17
Viveca
L
indahl
Di
s
a
l
l
o
w
-
s
kip value
s
<= 0 for gmx trj
c
on
v
.
commit
|
commitdiff
|
tree
2018-04-17
Paul Bauer
Fix
legacy
t
opol
o
gy memory e
r
ror
commit
|
commitdiff
|
tree
2018-04-17
M
ark Abraham
Shif
t
per-s
t
ep contr
o
l logic to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mark Ab
r
aham
B
reak
a
part update_constrai
n
ts
commit
|
commitdiff
|
tree
2018-04-16
Szil
á
rd Pá
l
l
Add post-submit te
s
t with h
w
loc off
commit
|
commitdiff
|
tree
2018-04-16
Be
r
k Hess
Move
n
ato
m
s_mo
l
out of gmx_molblock
_
t
commit
|
commitdiff
|
tree
2018-04-16
M
a
r
k Abraham
Update
d
m
d
run co
m
parison
i
nfra
s
t
ru
c
ture
commit
|
commitdiff
|
tree
2018-04-13
Mark Ab
r
ah
a
m
Clean up
c
o
n
stra
i
n
t
s code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Remove
u
se of where(), if DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
M
a
rk Abrah
a
m
Reor
g
anize energ
y
eval
u
ation
f
o
r EM
commit
|
commitdiff
|
tree
2018-04-10
A
l
eksei Iupinov
Prevent OpenCL timi
n
g
memo
r
y leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert gmx_molblo
c
k_t to C++
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
S
implified han
d
ling of sim
u
lation runners
commit
|
commitdiff
|
tree
2018-04-05
M
a
rk Ab
r
aham
Create g
r
omacs/md
r
un mod
u
le and move code t
h
ere
commit
|
commitdiff
|
tree
2018-04-05
Sz
i
l
árd
Páll
Refa
c
tor cj preload in t
h
e nonb
o
nd
e
d OpenCL k
e
r
nels
commit
|
commitdiff
|
tree
2018-04-04
Mark Abraha
m
Quiet checkpoint reading
commit
|
commitdiff
|
tree
2018-04-04
Pas
c
al M
e
rz
Move checkNumberOf
B
ondedInt
e
ractions
commit
|
commitdiff
|
tree
2018-04-03
Berk H
e
ss
Convert gmx_m
t
o
p
_
t
to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark
A
braham
R
e
move
l
e
ftover
m
ention of twin-range sch
e
me
commit
|
commitdiff
|
tree
2018-04-03
Mark
Abraha
m
Mer
g
e "Merge branch
r
e
l
ease-20
1
8
"
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
M
ove file openi
n
g out of init_pu
l
l()
commit
|
commitdiff
|
tree
2018-03-29
S
z
ilárd Páll
Tweak/enable
i
cc 18 post-sub
m
it
t
ests
commit
|
commitdiff
|
tree
2018-03-29
Magn
u
s Lund
b
org
Improved check of if only forces are
compu
t
ed i
n
do_pairs
(
)
commit
|
commitdiff
|
tree
2018-03-29
Pau
l
Bauer
Fi
x
c
m
a
k
e S
p
h
i
n
x detection for versi
o
ns >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd
Pá
l
l
Switch
C
U
DA
9
.
0/gcc 5 test to CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modularize p
u
ll_coord_work
_
t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Free
more memory in gr
o
mp
p
an
d
mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk
H
ess
Rem
o
ve mols fro
m
gmx_
m
top_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
Merge
branch release
-
2018
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Clari
f
ied
mdp options
r
e
l
ating
t
o bonds
commit
|
commitdiff
|
tree
2018-03-27
Mark
A
braham
Mor
e
gcc-8 fixes for
P
O
W
E
R
commit
|
commitdiff
|
tree
2018-03-21
David van d
e
r Spoel
Renamed e
n
tropy
.
* to ther
m
ochemistr
y
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Version 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark
Abraham
Merge "Merge br
a
nch relea
s
e-2016 i
n
to release-
2
0
1
8
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
U
p
date rel
e
ase notes f
o
r 2
0
18
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mark Abra
h
am
Merge bran
c
h releas
e
-2016 into
r
ele
a
se-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update us
e
of gpu_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk
H
ess
Disallow single sim
u
lat
i
on
wit
h
multisim
commit
|
commitdiff
|
tree
2018-03-20
Mark Abrah
a
m
Update u
s
e of gpu_id
i
n Je
n
kins
commit
|
commitdiff
|
tree
2018-03-20
Mark Abra
h
am
U
p
date use of gpu
_
id i
n
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mark
A
bra
h
am
Add helper functio
n
to make
a
v
e
ctor from an Arr
a
yRef
commit
|
commitdiff
|
tree
2018-03-19
Mark Abra
h
a
m
F
i
x V
S
X S
I
M
D
with gcc 8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only free topology
when al
l
o
c
ated
commit
|
commitdiff
|
tree
2018-03-16
Be
r
k H
e
ss
Correct PMF
s
ig
n
error in AWH bias shari
n
g
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk Hess
Improve inter-simulation
signaling
commit
|
commitdiff
|
tree
2018-03-14
Mark Abraha
m
Make a pe
r
sisten
t
physical nod
e
communicator
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fi
x
mdrun signa
l
l
ing wi
t
h AWH bias sha
r
ing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AWH fixes
t
o
release notes
commit
|
commitdiff
|
tree
2018-03-13
S
z
ilárd Páll
Require O
p
enCL 1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ense
m
b
l
e checkpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH deconvolu
t
i
o
n whe
n
s
h
ari
n
g
a
bi
a
s
commit
|
commitdiff
|
tree
2018-03-13
M
ark Abraham
Introduce constrai
n
_shake
commit
|
commitdiff
|
tree
2018-03-13
S
zilárd
Páll
Fi
x
clang 6
.
0 with CUDA 9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark
A
braham
M
erge "M
e
rge
bra
n
ch
release-2018
"
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Corre
c
t pdb2gmx -m
i
ssing o
p
tion
commit
|
commitdiff
|
tree
2018-03-06
Berk Hes
s
Con
v
ert t_filenm t
o
C
+
+
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
M
erge branc
h
releas
e
-2018
commit
|
commitdiff
|
tree
2018-03-06
Mark Abraham
F
i
xed
d
vdlambda
f
o
r
SHAKE + FE
commit
|
commitdiff
|
tree
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