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Merge branch release-2016
2017-09-12
Mark Abra
h
a
m
Merge bran
c
h r
e
lease-20
1
6
commit
|
commitdiff
|
tree
2017-09-12
Berk Hess
Do
not pass state to init_replica_exchange
commit
|
commitdiff
|
tree
2017-09-11
Szilárd P
á
ll
NVIDIA Vo
l
ta perf
o
rm
a
nce tweaks
commit
|
commitdiff
|
tree
2017-09-11
Berk Hess
Fix PBC bugs in the sw
a
p c
o
d
e
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraha
m
Introduce type
-
safe GPU emul
a
tion v
a
riables
commit
|
commitdiff
|
tree
2017-09-07
Roland Schulz
A
d
d isIntegralConstant type trai
t
commit
|
commitdiff
|
tree
2017-09-07
Mark
A
b
r
aham
E
nable
g
r
o
up-sch
e
m
e SIMD
k
ernels on
r
ecent
A
VX
e
x
t
ensi
o
ns
commit
|
commitdiff
|
tree
2017-09-06
Roland Sch
u
lz
PME-gather: Use templated
func
t
o
r
instead
of preproces
s
or
commit
|
commitdiff
|
tree
2017-09-05
Christop
h
Junghans
Supported quiet trajector
y
-h
a
nd
l
ing I
/
O
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraham
Fixes for Solaris
commit
|
commitdiff
|
tree
2017-09-05
Ma
r
k Abraham
F
i
x use of GPU
info
r
mation for th
r
ead-MPI setup
commit
|
commitdiff
|
tree
2017-09-04
Be
r
k He
s
s
Fix
two nbnxn s
e
arch
i
ndexing bugs
commit
|
commitdiff
|
tree
2017-09-04
Roland
Schulz
Fix accuracy fo
r
cvtDouble2Floa
t
/cprod
commit
|
commitdiff
|
tree
2017-09-04
Ber
k
Hess
Co
n
solid
a
te arch
i
tecture booleans
commit
|
commitdiff
|
tree
2017-09-03
Mark Abraham
Fix compiler fl
a
g
s
for using MKL
commit
|
commitdiff
|
tree
2017-09-03
Mark Abraham
Merge
b
ranch release-5-1 i
n
to releas
e
-2016
commit
|
commitdiff
|
tree
2017-08-25
Mar
k
Abraham
Fix flat-bott
o
med
posi
t
ion re
s
traints
w
ith multiple
.
.
.
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraha
m
Run GPU detectio
n
e
ven for mdrun -nb cpu
commit
|
commitdiff
|
tree
2017-08-22
Mark Abr
a
ham
Fixed
thread-MPI wi
t
h non-default -np
m
e
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraham
F
i
x
m
issing declarati
o
n of GMX_UNU
S
E
D
_V
A
LUE
commit
|
commitdiff
|
tree
2017-08-22
A
l
e
k
s
e
i Iupinov
Separate
P
ME
spread and gather wallcycle
counters
commit
|
commitdiff
|
tree
2017-08-22
Ber
k
Hess
Enab
l
e dynami
c
pai
r
list pruning
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraham
Merg
e
branc
h
r
elea
s
e-2016
commit
|
commitdiff
|
tree
2017-08-21
Teemu Murtola
S
i
m
p
le
union-f
i
nd structure
commit
|
commitdiff
|
tree
2017-08-21
M
a
rk Abrah
a
m
Move
d
i
nc
r
ease_nstlist() to nbnxn
_
tuning
.
h
commit
|
commitdiff
|
tree
2017-08-21
Mar
k
Abr
a
h
a
m
Fix c
o
mpilation is
s
ues with ARM SIM
D
commit
|
commitdiff
|
tree
2017-08-21
Szilárd Pál
l
A
d
d OpenCL pru
n
i
n
g
kernels and launch/t
i
ming l
o
gic
commit
|
commitdiff
|
tree
2017-08-18
Sz
i
lárd Páll
Improve a
w
kward han
d
l
ing of
G
M
X
_
CUDA_TA
R
GET* help
commit
|
commitdiff
|
tree
2017-08-18
Vedran
M
iletić
Improv
e
the "fil
e
s not present" erro
r
me
s
sage
commit
|
commitdiff
|
tree
2017-08-18
Szilá
r
d P
á
ll
A
d
d CUDA p
r
uning kernels and l
a
un
c
h
/timi
n
g
logi
c
commit
|
commitdiff
|
tree
2017-08-18
B
er
k
H
e
ss
Add CPU r
e
feren
c
e
and SIMD pruning kernels
commit
|
commitdiff
|
tree
2017-08-17
Mark Abraham
Replace consistency checking with as
s
ertion
commit
|
commitdiff
|
tree
2017-08-16
Berk Hess
Ad
d
d
y
n
amic
p
air-list pruning framewor
k
commit
|
commitdiff
|
tree
2017-08-16
Berk H
e
ss
Clea
n
u
p
nbnxn cluster pa
i
r addition
code
commit
|
commitdiff
|
tree
2017-08-16
Ma
r
k Abr
a
h
a
m
Par
s
e u
s
er-supplied GPU task
assignment only when n
e
eded
commit
|
commitdiff
|
tree
2017-08-15
David van d
e
r S
p
oel
Worked arou
n
d m
i
ssing OpenMP im
p
lementation in
o
r
ir
e
s
.
commit
|
commitdiff
|
tree
2017-08-15
M
a
rk
A
br
a
ham
M
erge
bra
n
ch re
l
e
a
se-
5
-1 int
o
release-
2
016
commit
|
commitdiff
|
tree
2017-08-15
Jiri Kraus
CU
D
A 9/
V
olta sup
p
ort for the nonbonded mod
u
l
e
commit
|
commitdiff
|
tree
2017-08-15
Mark Ab
r
aham
Fix va
l
ue of Ewald shift
commit
|
commitdiff
|
tree
2017-08-07
Mark Abraham
F
ix include d
e
p
endency for
g
e
t
e
n
v
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraham
Simpl
i
f
y
resource-division
eff
i
ciency check
commit
|
commitdiff
|
tree
2017-08-06
Mark
A
brah
a
m
Dec
o
uple task
assignment from task exec
u
tio
n
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraham
Removed unus
e
d hos
t
-side allocat
i
on cod
e
commit
|
commitdiff
|
tree
2017-08-04
M
a
rk Abraham
Stop using hwinf
o
_g for repo
r
ting
c
od
e
commit
|
commitdiff
|
tree
2017-08-03
Mark Ab
r
aham
Remov
e
d unused
in
c
l
ude
s
t
a
t
e
m
ents
commit
|
commitdiff
|
tree
2017-08-03
Berk Hes
s
Add c
h
eck fo
r
n
r of orientat
i
o
n restrain
t
s
commit
|
commitdiff
|
tree
2017-08-03
Berk Hess
Fix bugs wi
t
h orientation restraints
commit
|
commitdiff
|
tree
2017-08-03
Carsten Kutzn
e
r
Ad
d
ed mi
s
s
ing
.
m
dp file documentation for the enforced
.
.
.
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
C
l
e
an up matr
i
x
inversion
commit
|
commitdiff
|
tree
2017-08-02
Berk He
s
s
Fix orien
t
ation
r
estrain
t
refere
n
ce
commit
|
commitdiff
|
tree
2017-08-02
David van
d
er Spoel
W
orked around missi
n
g Open
M
P imp
l
e
mentation in o
r
ires
.
commit
|
commitdiff
|
tree
2017-08-01
Mark A
b
raham
In
t
roduced
M
drunner
h
igh-leve
l
class
commit
|
commitdiff
|
tree
2017-07-28
Davi
d
van
d
er Spoel
A
dded unit-test for orientation restraints output
.
commit
|
commitdiff
|
tree
2017-07-27
Mark
Abrah
a
m
Enhance cmake and relen
g
handling o
f
G
M
X
_USE_R
D
TSC
P
commit
|
commitdiff
|
tree
2017-07-27
Szil
á
r
d
P
ál
l
Inform users about t
h
e end
o
f run D
L
B sta
t
e
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Remove
d
u
n
n
e
c
essary s
t
atic declarations f
o
r
co
m
mand
.
.
.
commit
|
commitdiff
|
tree
2017-07-14
Mark Abraham
I
mplem
e
nted grompp
-po for opt
i
ons-style mdp handling
commit
|
commitdiff
|
tree
2017-07-14
Ma
r
k
A
braham
Clean u
p
cmake buil
d
host detection
commit
|
commitdiff
|
tree
2017-07-13
Mark Abraham
Clean
u
p g
m
x_mdrun()
commit
|
commitdiff
|
tree
2017-07-13
Mar
k
Abrah
a
m
Cleaned up mdrunner_start_threads
commit
|
commitdiff
|
tree
2017-07-11
Rola
n
d Schulz
PME-gather:
make va
r
i
ables local and const
commit
|
commitdiff
|
tree
2017-07-11
Teemu
Murtola
Sup
p
ort
s
coped
k
ey
-
value tre
e
t
r
ansform
r
ules
commit
|
commitdiff
|
tree
2017-07-07
Mark Abraham
Refa
c
tor error handling in i
n
it_gp
u
commit
|
commitdiff
|
tree
2017-07-04
Mark Abraham
Clean up pick_
n
b
n
xn
_
r
e
sources
commit
|
commitdiff
|
tree
2017-07-01
Ma
r
k Ab
r
aham
C
leaned
u
p GPU emulation logic
commit
|
commitdiff
|
tree
2017-06-30
Teemu
Murtola
Fix boolean serialization
commit
|
commitdiff
|
tree
2017-06-30
Teem
u
Murtola
Ex
t
e
nd key-value tre
e
comparison a
n
d
t
e
sts
commit
|
commitdiff
|
tree
2017-06-28
Mark Abraham
C
l
eaned up
h
igh-l
e
v
e
l
boolea
n
v
a
riabl
e
na
m
ing
commit
|
commitdiff
|
tree
2017-06-28
Mark Abraham
Fix specifi
c
a
tion for gcc-6
commit
|
commitdiff
|
tree
2017-06-28
Ma
r
k A
b
raham
Mer
g
e
b
r
a
n
c
h
r
elease-
2
016
commit
|
commitdiff
|
tree
2017-06-27
Teemu Mur
t
ola
Do not u
s
e conf
-
man
.
py for non-
m
a
n
page doc
b
uilds
commit
|
commitdiff
|
tree
2017-06-27
Mar
k
A
b
raham
Minor improvements to test
c
o
nf
i
g
s
commit
|
commitdiff
|
tree
2017-06-26
Erik
L
indahl
F
ix ARM
N
EON s
i
md debug builds
commit
|
commitdiff
|
tree
2017-06-26
Szilárd Páll
Add
A
RM_
N
E
ON_ASIMD
p
ost-submit test
commit
|
commitdiff
|
tree
2017-06-26
Jiri K
r
aus
Updated application cloc
k
handling on Pascal+ GPUs
commit
|
commitdiff
|
tree
2017-06-22
M
a
r
k
A
b
raham
Consolida
t
ed log
i
c
f
o
r
choosing nu
m
b
er of thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2017-06-22
Mark Abraham
Rep
l
ace misn
a
med nb
n
xn
_
gpu_accele
r
a
t
ion_supported
commit
|
commitdiff
|
tree
2017-06-22
Mark Abr
a
ham
C
o
ns
o
lidate and fix logic for mdrun -n
b
and
-
g
p
u
i
d
commit
|
commitdiff
|
tree
2017-06-21
Szilárd Pá
l
l
R
e-enable lost DD war
n
ing + minor
code m
o
dernization
commit
|
commitdiff
|
tree
2017-06-21
Mark Abraham
Refor
m
ngpu variable
commit
|
commitdiff
|
tree
2017-06-21
Mark Ab
r
aham
Re
m
ov
e
bUserSetGpuIds field
commit
|
commitdiff
|
tree
2017-06-12
Be
r
k Hess
Disable PME tuning with the group sche
m
e
commit
|
commitdiff
|
tree
2017-06-12
Mar
k
Abra
h
am
Mov
e
gmx_p
a
rse_gpu_id out
of ch
e
c
k
ing function
commit
|
commitdiff
|
tree
2017-06-12
A
le
k
sei Iu
p
i
n
o
v
S
tore a physical
node commun
i
c
a
tor
in t_commrec
commit
|
commitdiff
|
tree
2017-06-11
Magnus Lundborg
Updated TNG
to
version 1
.
8
commit
|
commitdiff
|
tree
2017-05-31
M
ark A
b
raham
New qu
o
t
e
commit
|
commitdiff
|
tree
2017-05-29
Teem
u
Mu
r
tola
A
void some incorrect b
e
havior wit
h
g
m
x solvate
commit
|
commitdiff
|
tree
2017-05-29
Teemu Murtola
Remov
e
p
bcutil <-> md
t
yp
e
s cyclic dependency
commit
|
commitdiff
|
tree
2017-05-29
V
e
dran
M
iletić
Standardize us
e
of |Gromacs|
in reST docs
commit
|
commitdiff
|
tree
2017-05-26
Mark Abraham
Test
invsixth
r
oot function as intended
commit
|
commitdiff
|
tree
2017-05-15
Mark Ab
r
a
ham
Updated use of
c
o
m
piler
spec
i
fier
s
in testing
commit
|
commitdiff
|
tree
2017-05-15
Mark Abraham
Up
d
ated us
e
o
f
gcc-5 specifiers
commit
|
commitdiff
|
tree
2017-05-15
Mark Abraham
Update
cla
n
g static an
a
lyzer slave to use version 4
commit
|
commitdiff
|
tree
2017-05-14
Mark Abraham
Up
d
ate c
l
ang
-
4
commit
|
commitdiff
|
tree
2017-05-14
Justin Lemkul
Clarifications t
o
e
d
itconf hel
p
t
e
x
t
.
commit
|
commitdiff
|
tree
2017-05-14
J
u
stin
Lem
k
ul
Clar
i
fi
c
ations to editconf help text
.
commit
|
commitdiff
|
tree
2017-05-09
M
a
rk Abraham
Fix
f
orm
a
t
ting
of MKL cmake
d
ocs
commit
|
commitdiff
|
tree
2017-05-09
M
a
rk Abraham
Merge bra
n
c
h
re
l
ease-2016
commit
|
commitdiff
|
tree
2017-05-09
Ma
r
k Abra
h
am
Clea
n
ed
u
p
memo
r
y usage in gmx tr
a
j and trjconv
commit
|
commitdiff
|
tree
2017-04-19
B
e
r
k
Hess
Fix un
u
sed SIMD PME table
k
er
n
el
commit
|
commitdiff
|
tree
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