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Write lambdas and box to TNG at correct intervals
2018-06-04
M
a
g
n
us Lundborg
Write
l
am
b
das and box to
TNG a
t
c
o
r
rect int
e
rvals
commit
|
commitdiff
|
tree
2018-06-01
Kevin Boy
d
C
osm
e
tic
fixes to mdp documentat
i
on
commit
|
commitdiff
|
tree
2018-05-31
A
lekse
i
I
upinov
Merge pm
e
.
cu
into pme-gpu-in
t
ernal
.
c
p
p
commit
|
commitdiff
|
tree
2018-05-31
Ale
k
sei Iupinov
Move pme-
t
imings
.
cu to pme-gpu-t
i
ming
s
.
c
pp
commit
|
commitdiff
|
tree
2018-05-31
Aleksei I
u
pin
o
v
Prefer linking to system clFFT r
a
ther than bundle
d
one
commit
|
commitdiff
|
tree
2018-05-31
Alek
s
ei Iup
i
nov
Mov
e
the PmeGpuSpecifi
c
structure into pme
-
gpu-types
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i Iupinov
Added
the bundle
d
clFFT int
o
Open
C
L builds
commit
|
commitdiff
|
tree
2018-05-31
Aleks
e
i
I
u
pinov
Gather the PME
GPU
c
onstants/macros in a s
i
ngle
h
eade
r
commit
|
commitdiff
|
tree
2018-05-28
Aleksei Iupinov
Support pers
i
stent
devic
e
context-de
r
ived data in PME
.
.
.
commit
|
commitdiff
|
tree
2018-05-25
M
a
r
k Abraham
Clean up force
.
h
a
nd i
t
s use
commit
|
commitdiff
|
tree
2018-05-24
M
a
r
k
A
braham
Remove bDomDec
from t_forcerec
commit
|
commitdiff
|
tree
2018-05-24
Be
r
k He
s
s
Fix grompp bug
w
i
t
h blocks
o
f same molecules
commit
|
commitdiff
|
tree
2018-05-24
Mark A
b
raham
Reform
Ewald-module
c
make handling
commit
|
commitdiff
|
tree
2018-05-23
Rolan
d
Schulz
Rename GMX_
O
C
L
_CLUS
T
ER_SIZE to G
M
X_OCL_NB
_
CLUSTER_
S
IZE
commit
|
commitdiff
|
tree
2018-05-23
B
e
r
k
Hess
Split off coll
e
ct
.
cpp f
r
om domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Convert nbnxn_sear
c
h
to
C
++
commit
|
commitdiff
|
tree
2018-05-22
B
erk He
s
s
Change nbnxn grid re
a
llocation
commit
|
commitdiff
|
tree
2018-05-22
Ber
k
H
e
ss
Use st
d
::ve
c
tor in nbnxn
_
search_t
commit
|
commitdiff
|
tree
2018-05-22
B
e
rk Hess
Use std::vector in nbnx
n
_gr
i
d_t
commit
|
commitdiff
|
tree
2018-05-22
K
evin Boyd
C
o
sme
t
ic
docu
m
enta
t
ion change
s
commit
|
commitdiff
|
tree
2018-05-22
Kevin Boyd
Minor fixes to mdrun p
e
rformance docu
m
enta
t
io
n
commit
|
commitdiff
|
tree
2018-05-18
Aleksei Iupinov
prepareGpuKer
n
el
A
rgume
n
t
s
() and l
a
u
nchGpuKernel() are
.
.
.
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
S
p
lit off domdec di
s
tribution an
d
cellsizes
commit
|
commitdiff
|
tree
2018-05-17
Berk Hess
Split at
o
m r
e
distribution
off from domdec
.
c
pp
commit
|
commitdiff
|
tree
2018-05-17
Berk Hes
s
Remove
c
o
m
mrec from
se
t
_
dd
b
ox(
)
commit
|
commitdiff
|
tree
2018-05-15
Roland Schulz
U
s
e same OpenCL ke
r
nel for diff
e
rent Ven
d
ors
commit
|
commitdiff
|
tree
2018-05-10
C
arsten Kutzn
e
r
Intro
d
uce helper classes
for force pro
v
ider
input and
.
.
.
commit
|
commitdiff
|
tree
2018-05-04
Paul B
a
uer
Fix md -cpi
-
noappe
n
d
commit
|
commitdiff
|
tree
2018-05-04
M
ark Abraham
Merge "Merge
b
ranch relea
s
e-
2
018"
commit
|
commitdiff
|
tree
2018-05-04
Mark Abr
a
h
a
m
More const correct
n
ess
commit
|
commitdiff
|
tree
2018-05-03
Mark Ab
r
aham
Merge bra
n
ch release-2018
commit
|
commitdiff
|
tree
2018-05-02
Roland
Schulz
Enable uncrusti
f
y
for Open
C
L
commit
|
commitdiff
|
tree
2018-05-02
Rol
a
nd Schulz
Support 4 sized
c
luster fo
r
GPU NBL search
commit
|
commitdiff
|
tree
2018-04-27
Berk Hess
Remove pull MPI code
du
p
lication
commit
|
commitdiff
|
tree
2018-04-26
Paul Ba
u
er
Reorga
n
ize f
i
les for
reference manu
a
l
commit
|
commitdiff
|
tree
2018-04-26
P
aul Bauer
Split up analysis
chapter in reference man
u
a
l
commit
|
commitdiff
|
tree
2018-04-26
Paul B
a
uer
Split up specia
l
t
o
pics secti
o
n
in manual
commit
|
commitdiff
|
tree
2018-04-25
Pau
l
Bauer
A
dd page
breaks in ref
e
rence
manua
l
commit
|
commitdiff
|
tree
2018-04-25
Pau
l
Ba
u
er
Split up Interact
i
on fun
c
tions m
a
nual pag
e
commit
|
commitdiff
|
tree
2018-04-25
M
a
rk
A
brah
a
m
Ref
a
ctor SD u
p
dat
e
commit
|
commitdiff
|
tree
2018-04-25
Paul Bauer
Change ima
g
e
c
o
nversion to only be bu
i
ld once
commit
|
commitdiff
|
tree
2018-04-23
Aleksei Iupinov
D
e
vi
c
eBuffe
r
h
e
aders are
ad
d
ed
commit
|
commitdiff
|
tree
2018-04-23
S
zilár
d
Páll
F
ix
icc
warn
i
ng in post-submit
commit
|
commitdiff
|
tree
2018-04-21
Szil
á
rd Páll
Add post-submit wi
t
h ARM
H
PC Toolchain
commit
|
commitdiff
|
tree
2018-04-21
Szilá
r
d Páll
Tw
e
ak PME run mode c
h
ecks
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Convert man
u
al from LaTe
X
to Mar
k
up
commit
|
commitdiff
|
tree
2018-04-21
P
aul Bauer
Se
c
ond change tra
c
king commit
commit
|
commitdiff
|
tree
2018-04-21
Paul Bauer
Interme
d
ia
t
e com
m
it to
tra
c
k changes to
m
anual
commit
|
commitdiff
|
tree
2018-04-17
Viveca
Lindahl
Disallo
w
-skip values <= 0
f
or gmx
t
rjconv
.
commit
|
commitdiff
|
tree
2018-04-17
Paul
Bauer
Fix leg
a
cy topology
m
e
m
o
ry error
commit
|
commitdiff
|
tree
2018-04-17
Mark Abraham
S
h
i
ft
p
er-s
t
ep cont
r
o
l logic to do_
m
d
commit
|
commitdiff
|
tree
2018-04-17
Ma
r
k
A
braham
Break apar
t
updat
e
_const
r
aints
commit
|
commitdiff
|
tree
2018-04-16
Szilárd Páll
Add p
o
st-s
u
bmit test with hwloc off
commit
|
commitdiff
|
tree
2018-04-16
Berk He
s
s
Move
nat
o
m
s_mol out of
g
mx_molb
l
ock_t
commit
|
commitdiff
|
tree
2018-04-16
M
ark Abraha
m
Upda
t
ed mdrun comparison infr
a
st
r
uctur
e
commit
|
commitdiff
|
tree
2018-04-13
Mar
k
Abraham
Clean up constra
i
nts cod
e
commit
|
commitdiff
|
tree
2018-04-12
Mark
Ab
r
ah
a
m
R
emove
u
s
e
of w
h
ere(), if DEBUG e
t
c
.
commit
|
commitdiff
|
tree
2018-04-12
M
a
r
k Abra
h
am
R
eorga
n
ize ene
r
gy eva
l
uation for EM
commit
|
commitdiff
|
tree
2018-04-10
Aleksei Iupinov
Prevent OpenCL ti
m
i
n
g
m
emory leak
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
C
o
nvert gmx_
m
olbl
o
ck_t t
o
C++
commit
|
commitdiff
|
tree
2018-04-05
Mark Ab
r
aham
S
i
mplif
i
ed h
a
ndling of s
i
mulation runners
commit
|
commitdiff
|
tree
2018-04-05
Mark
Abra
h
am
Create gromacs/mdrun
m
od
u
le and move code there
commit
|
commitdiff
|
tree
2018-04-05
Sz
i
lárd Páll
Refact
o
r cj
prel
o
a
d
i
n
th
e
nonbon
d
e
d Ope
n
CL kern
e
ls
commit
|
commitdiff
|
tree
2018-04-04
Mark Abr
a
h
a
m
Quiet chec
k
point reading
commit
|
commitdiff
|
tree
2018-04-04
Pas
c
al Merz
M
o
v
e checkNumberOfBondedInterac
t
ions
commit
|
commitdiff
|
tree
2018-04-03
Berk Hes
s
Convert gmx_mtop_t t
o
C+
+
commit
|
commitdiff
|
tree
2018-04-03
Ma
r
k Abraham
Remove leftover
mention of
twin-r
a
nge scheme
commit
|
commitdiff
|
tree
2018-04-03
Mark Abraham
Merge "Me
r
ge branch rel
e
ase-2
0
18"
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
M
ove
f
ile
o
pening out of init_
p
ull()
commit
|
commitdiff
|
tree
2018-03-29
Szilárd P
á
ll
Twea
k
/enab
l
e icc 18 post-
s
ubmit t
e
sts
commit
|
commitdiff
|
tree
2018-03-29
M
a
gnus Lundb
o
rg
Improved check of
i
f
o
nly forces are computed in do_pairs(
)
commit
|
commitdiff
|
tree
2018-03-29
Pau
l
Bauer
Fi
x
cmak
e
Sp
h
inx det
e
ction
f
or
versions >1
.
6
.
4
commit
|
commitdiff
|
tree
2018-03-29
Szil
á
rd Páll
Switch CU
D
A 9
.
0/gc
c
5 test
t
o CUDA
9
.
1/gcc 6
commit
|
commitdiff
|
tree
2018-03-29
Berk Hes
s
Modul
a
rize pul
l
_coo
r
d_work_t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
braham
Free more memory in gromp
p
a
nd mdrun
commit
|
commitdiff
|
tree
2018-03-28
Berk Hes
s
Re
m
o
v
e
m
ols from gm
x
_
m
top_t
commit
|
commitdiff
|
tree
2018-03-28
Mark
A
b
r
aham
Merge branch release-20
1
8
commit
|
commitdiff
|
tree
2018-03-27
Mar
k
Abr
a
h
am
C
l
a
r
ified mdp
options relating to bonds
commit
|
commitdiff
|
tree
2018-03-27
M
ark Ab
r
aham
M
o
re
gcc-8 fixes for P
O
WER
commit
|
commitdiff
|
tree
2018-03-21
David van der Spoel
R
enamed entropy
.
* to thermochemistry
.
*
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
Version 2018
.
1
commit
|
commitdiff
|
tree
2018-03-21
Mark Abraham
M
e
rge "Merge branch release-2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2018-03-21
Mark Abra
h
am
Upd
a
t
e
rele
a
se notes
f
o
r
2018
.
1
commit
|
commitdiff
|
tree
2018-03-20
Mar
k
Abraham
Merge bran
c
h releas
e
-2016 into releas
e
-2018
commit
|
commitdiff
|
tree
2018-03-20
Mark Ab
r
aham
Upda
t
e
use
o
f
gpu_id in
Jenkins
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disa
l
l
o
w
sing
l
e simula
t
ion
with mu
l
t
i
sim
commit
|
commitdiff
|
tree
2018-03-20
Mark Abraham
Update use of gpu
_
id in Jenk
i
n
s
commit
|
commitdiff
|
tree
2018-03-20
Mark Abra
h
am
Updat
e
use of gpu_i
d
in J
e
nkins
commit
|
commitdiff
|
tree
2018-03-20
Ma
r
k Abraham
Add h
e
lp
e
r
function to ma
k
e a vec
t
or from an A
r
rayRef
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
opolog
y
wh
e
n a
l
located
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct PMF
sign
e
rr
o
r
i
n
AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve inter-simulation si
g
naling
commit
|
commitdiff
|
tree
2018-03-14
Ma
r
k Ab
r
a
h
am
Make a persistent ph
y
sical node communicator
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdrun
sig
n
alli
n
g
with AWH bia
s
sharing
commit
|
commitdiff
|
tree
2018-03-13
Berk
Hess
Add AWH fixes
to
re
l
ease notes
commit
|
commitdiff
|
tree
2018-03-13
Szi
l
ár
d
Páll
Require OpenCL
1
.
2
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH ensembl
e
check
p
ointing
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH dec
o
nvolution when s
h
aring a b
i
as
commit
|
commitdiff
|
tree
2018-03-13
Ma
r
k Abraham
Intro
d
uce constrain_sh
a
k
e
commit
|
commitdiff
|
tree
next