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Convert nbnxn_search to C++
2018-05-23
Berk
Hess
Convert nbnxn
_
se
a
r
c
h to C++
commit
|
commitdiff
|
tree
2018-05-22
B
e
rk Hess
Change nbnxn grid
reallocation
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
Hess
Use std::vector
in
nbnxn_search_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use st
d
::ve
c
tor
i
n nbnxn_
g
r
id_t
commit
|
commitdiff
|
tree
2018-05-22
Kevi
n
Boy
d
Cosmet
i
c
documentation changes
commit
|
commitdiff
|
tree
2018-05-22
Kevin Boyd
Mino
r
f
i
xe
s
t
o mdr
u
n performance docum
e
ntatio
n
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupi
n
ov
prepareGpuKernelArg
u
ments
(
)
a
n
d
launchGpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk
Hess
Split of
f
d
o
md
e
c distrib
u
tion a
n
d
c
ellsizes
commit
|
commitdiff
|
tree
2018-05-17
B
erk H
e
ss
Split atom redist
r
ibution o
f
f
fr
o
m
d
omd
e
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk He
s
s
R
emove
c
ommrec from set_ddbox()
commit
|
commitdiff
|
tree
2018-05-15
Roland Schulz
Use same OpenCL k
e
rnel for different Ven
d
o
rs
commit
|
commitdiff
|
tree
2018-05-10
Carsten K
u
t
z
n
er
Introd
u
ce helper clas
s
es for
force pro
v
i
d
er inp
u
t and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul Bauer
Fix
m
d -cpi -noappend
commit
|
commitdiff
|
tree
2018-05-04
Mark Abraham
M
e
rge "Merge
b
ranch release-2018"
commit
|
commitdiff
|
tree
2018-05-04
M
a
rk Abra
h
am
More const cor
r
ectness
commit
|
commitdiff
|
tree
2018-05-03
Ma
r
k Abraham
M
e
rge bra
n
ch release
-
2018
commit
|
commitdiff
|
tree
2018-05-02
Ro
l
and Schu
l
z
Ena
b
le uncrustify for OpenCL
commit
|
commitdiff
|
tree
2018-05-02
Roland Schul
z
Sup
p
ort 4 sized cluster for GPU NBL sear
c
h
commit
|
commitdiff
|
tree
2018-04-27
Berk He
s
s
Remov
e
pull MPI c
o
de duplicati
o
n
commit
|
commitdiff
|
tree
2018-04-26
P
a
u
l
B
auer
Reor
g
an
i
ze files fo
r
reference manual
commit
|
commitdiff
|
tree
2018-04-26
P
a
ul Bauer
Split up a
n
alysis cha
p
ter
i
n referenc
e
m
a
nual
commit
|
commitdiff
|
tree
2018-04-26
Pa
u
l Baue
r
Split up specia
l
to
p
ics section
in
m
anu
a
l
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Add p
a
ge b
r
eaks in reference manual
commit
|
commitdiff
|
tree
2018-04-25
P
aul
Bauer
Split up Intera
c
t
ion functions m
a
n
ual page
commit
|
commitdiff
|
tree
2018-04-25
Mark
Abraham
Refactor SD update
commit
|
commitdiff
|
tree
2018-04-25
Paul
B
auer
Change image conver
s
ion
t
o only be build onc
e
commit
|
commitdiff
|
tree
2018-04-23
Al
e
ksei Iupinov
D
eviceBuffer
headers a
r
e add
e
d
commit
|
commitdiff
|
tree
2018-04-23
Szilárd P
á
l
l
Fix
i
cc warning in p
o
st-s
u
bmit
commit
|
commitdiff
|
tree
2018-04-21
S
z
ilárd
P
áll
A
d
d
post-submit w
i
th ARM HPC T
o
olchain
commit
|
commitdiff
|
tree
2018-04-21
S
z
i
lárd
Pá
l
l
Tweak PME
r
un mo
d
e checks
commit
|
commitdiff
|
tree
2018-04-21
P
aul Bauer
Convert manu
a
l from LaTeX to
M
arkup
commit
|
commitdiff
|
tree
2018-04-21
Paul Baue
r
S
e
cond change tracking
c
ommit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
I
n
term
e
dia
t
e
commit to tra
c
k changes to manual
commit
|
commitdiff
|
tree
2018-04-17
V
ive
c
a Lindahl
Disa
l
lo
w
-skip valu
e
s <
=
0 f
o
r gmx trj
c
onv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul
Bauer
Fix legacy topology memor
y
erro
r
commit
|
commitdiff
|
tree
2018-04-17
Mark Abr
a
ham
S
hif
t
per-ste
p
control
logi
c
to do_md
commit
|
commitdiff
|
tree
2018-04-17
Mar
k
Abraham
Brea
k
apart u
p
date_constraints
commit
|
commitdiff
|
tree
2018-04-16
Szilárd P
á
l
l
Add post-submit test with hwloc of
f
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
M
ove na
t
oms_
m
ol out
o
f gmx_molblock_t
commit
|
commitdiff
|
tree
2018-04-16
Mark Abraham
U
p
d
a
t
e
d mdru
n
co
m
parison i
n
frastructure
commit
|
commitdiff
|
tree
2018-04-13
Mark A
b
ra
h
a
m
C
l
ean up constraints code
commit
|
commitdiff
|
tree
2018-04-12
Mark Abraham
Rem
o
ve u
s
e
o
f where(), if
DEBUG etc
.
commit
|
commitdiff
|
tree
2018-04-12
Mark Abra
h
am
R
e
organi
z
e energ
y
e
val
u
ation
for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iu
p
inov
Prevent
Op
e
nC
L
timing
memory leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert g
m
x_
m
olblock_t to C++
commit
|
commitdiff
|
tree
2018-04-05
Mark Ab
r
a
h
am
Simpli
f
ied handl
i
ng of simula
t
io
n
runn
e
rs
commit
|
commitdiff
|
tree
2018-04-05
Mark Abraham
C
reate
g
r
omacs/mdrun module a
n
d
m
o
ve code
t
h
ere
commit
|
commitdiff
|
tree
2018-04-05
Szilárd Páll
Refactor
cj prel
o
ad in the nonbonde
d
OpenCL kernels
commit
|
commitdiff
|
tree
2018-04-04
Mark Abra
h
am
Quiet ch
e
ck
p
oi
n
t
readin
g
commit
|
commitdiff
|
tree
2018-04-04
Pascal Merz
M
ove checkN
u
mbe
r
OfBond
e
dInteractio
n
s
commit
|
commitdiff
|
tree
2018-04-03
B
e
rk
H
ess
Convert gmx_mtop_
t
to C++
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Remov
e
left
o
v
e
r
m
e
n
tion of twin-range scheme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Merge
"Merge branch
r
elease-2
0
1
8"
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
Move file opening o
u
t of init
_
pull()
commit
|
commitdiff
|
tree
2018-03-29
S
z
i
lá
r
d Páll
Tweak/enabl
e
icc 18 po
s
t
-
submi
t
tests
commit
|
commitdiff
|
tree
2018-03-29
Mag
n
us Lundborg
Impr
o
ve
d
che
c
k of if only
f
orc
e
s are computed in
do_pairs()
commit
|
commitdiff
|
tree
2018-03-29
Pau
l
Bauer
Fi
x
cmake
Sp
h
i
n
x detect
i
on for v
e
rsions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szilárd
Páll
Sw
i
tch
C
UDA 9
.
0/gcc 5 te
s
t to CUDA 9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
M
o
dula
r
ize
pull_coo
r
d_
w
ork_t
commit
|
commitdiff
|
tree
2018-03-28
Ma
r
k A
b
raham
Free more memory in grompp
a
nd
mdrun
commit
|
commitdiff
|
tree
2018-03-28
Ber
k
Hess
Re
m
ove mols from gmx_mto
p
_t
commit
|
commitdiff
|
tree
2018-03-28
Mark Abraham
M
e
rge br
a
nch release-201
8
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Clar
i
f
i
ed mdp opti
o
ns relating to bonds
commit
|
commitdiff
|
tree
2018-03-27
Mark Abraham
Mor
e
gcc-8 f
i
xe
s
for POWER
commit
|
commitdiff
|
tree
2018-03-21
David van der
S
p
o
el
R
e
n
amed entropy
.
* t
o
the
r
m
o
che
m
ist
r
y
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mar
k
Abraham
V
e
rsion 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Ab
r
aham
Me
r
g
e
"
Merge branch
r
elease-2
0
16
i
n
to release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abrah
a
m
Update release notes
for 2
0
18
.
1
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk A
b
raham
Mer
g
e
b
ranch
re
l
ease-2016 in
t
o
release-2018
commit
|
commitdiff
|
tree
2018-03-20
M
a
rk Abra
h
a
m
Update use of gpu
_
id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk He
s
s
Disallow
s
i
n
gle simulation
with multisi
m
commit
|
commitdiff
|
tree
2018-03-20
M
ark
Ab
r
a
h
a
m
Update use of g
p
u_id in Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Abraha
m
Updat
e
use o
f
gpu_id in Jenk
i
n
s
commit
|
commitdiff
|
tree
2018-03-20
Mark
Abraham
Add
helper
f
unction to make a vecto
r
f
rom an Array
R
ef
commit
|
commitdiff
|
tree
2018-03-19
Mark
Abraham
Fix VSX SIMD
with gcc
8
commit
|
commitdiff
|
tree
2018-03-16
Paul Bauer
Only free t
o
p
ology when
allocated
commit
|
commitdiff
|
tree
2018-03-16
B
er
k
Hess
Correct
P
MF sign e
r
ro
r
in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Ber
k
H
ess
Im
p
rove
inter-sim
u
lation signal
i
ng
commit
|
commitdiff
|
tree
2018-03-14
Mar
k
Abra
h
a
m
Make a p
e
rsistent physic
a
l node c
o
m
mun
i
cator
commit
|
commitdiff
|
tree
2018-03-14
Be
r
k
Hess
F
i
x md
r
un
s
i
gn
a
lling wi
t
h AWH b
i
a
s
shari
n
g
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
A
dd AWH
fixe
s
t
o r
e
lease notes
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
R
e
quire Ope
n
CL
1
.
2
commit
|
commitdiff
|
tree
2018-03-13
B
e
rk Hess
Fix A
W
H e
n
semble checkpointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hes
s
Fix AWH deconvolu
t
ion when
s
h
aring a b
i
as
commit
|
commitdiff
|
tree
2018-03-13
M
a
rk A
b
ra
h
am
I
n
troduce constr
a
in_sha
k
e
commit
|
commitdiff
|
tree
2018-03-13
Szilárd Páll
Fix clang 6
.
0
with C
U
DA
9
.
0
commit
|
commitdiff
|
tree
2018-03-13
Mark Abraham
Merge "Merge bra
n
ch release-2018"
commit
|
commitdiff
|
tree
2018-03-09
Berk H
e
ss
Correc
t
pdb2g
m
x -m
i
ssing opti
o
n
commit
|
commitdiff
|
tree
2018-03-06
B
e
rk
H
e
s
s
C
o
nver
t
t_filenm to C++
commit
|
commitdiff
|
tree
2018-03-06
Mark Abrah
a
m
M
er
g
e
b
ranch re
l
ease-201
8
commit
|
commitdiff
|
tree
2018-03-06
Mar
k
Abra
h
am
Fixed d
v
d
l
ambda for SHAKE + FE
commit
|
commitdiff
|
tree
2018-03-05
Szilárd Páll
Add to the co
n
t
r
ibu
t
or se
c
tion
commit
|
commitdiff
|
tree
2018-03-01
Berk H
e
s
s
Detect AM
D
SMT
topology
commit
|
commitdiff
|
tree
2018-02-28
Mark Ab
r
aham
Moved and removed
c
ons
t
r
aint code
commit
|
commitdiff
|
tree
2018-02-28
Mark Abraham
Reo
r
g
a
nized
c
on
s
traint cod
e
commit
|
commitdiff
|
tree
2018-02-27
Mark Abraham
F
ix GPU
utils test
commit
|
commitdiff
|
tree
2018-02-26
P
aul
Bauer
Change T
N
G
f
i
le opening
commit
|
commitdiff
|
tree
2018-02-26
Mark A
b
ra
h
am
P
ermit define
.
mdp f
i
el
d
to assig
n
values
commit
|
commitdiff
|
tree
2018-02-26
Aleksei Iupinov
Advice users on infinite o
u
t
p
ut of
T
P
I
commit
|
commitdiff
|
tree
2018-02-26
Mark
A
braha
m
Organ
i
ze for
r
ecording 20
1
6-
e
ra
r
e
l
ease note
s
and add
.
.
.
commit
|
commitdiff
|
tree
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