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Fix memory leak in PME
2018-03-07
Berk Hess
F
ix
memory lea
k
in PME
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leav
e
nullptr o
p
t
in t
_
filen
m
commit
|
commitdiff
|
tree
2018-03-02
Berk
H
ess
F
i
x cppch
e
ck w
a
rn
i
n
g
commit
|
commitdiff
|
tree
2018-02-22
Berk He
s
s
Simplify mdr
u
n tMPI thread
spawning
commit
|
commitdiff
|
tree
2018-02-19
Mark Abr
a
h
a
m
Remove cycle sup
p
re
s
sion
commit
|
commitdiff
|
tree
2018-02-19
Mark Abraham
Disallow
e
d
c
h
a
n
g
e o
f
ensemble for check
p
oi
n
t restart
commit
|
commitdiff
|
tree
2018-02-14
Mark
Abraham
Fix bug in checkpoint e
r
ror
checking
commit
|
commitdiff
|
tree
2018-02-12
Sz
i
lá
r
d Páll
R
e
mov
e
single/multi c
o
m
pilat
i
on unit switchin
g
logic
commit
|
commitdiff
|
tree
2018-02-12
S
zilárd Páll
Remov
e
t
e
xture
r
eference s
u
pp
o
rt in
t
he CUDA
commit
|
commitdiff
|
tree
2018-02-08
Be
r
k Hess
Allow bonds with distance=0
commit
|
commitdiff
|
tree
2018-02-06
Alek
s
e
i
I
upino
v
O
nly setup Ewald in the
g
e
ner
i
c group kernel if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Berk H
e
ss
S
et
c
ut
o
f
f
m
odifiers in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix assertion
f
ailure in TPI
commit
|
commitdiff
|
tree
2018-01-30
Mark Abraham
Re
p
lace macro
s
for mul
t
i
-sim
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iu
p
inov
Got rid of manual
m
emory mana
g
ement in
t
he PME overla
p
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Aleksei Iupinov
R
e
-enabl
e
multi-rank PME tests
(
w
i
t
h the file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Ber
k
Hess
Add
c
he
c
k in g
r
ompp to avoid assertion
f
ailure
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Rep
l
a
ce stderr
pr
i
nts in
f
ilenm
.
cpp by as
s
erts
commit
|
commitdiff
|
tree
2018-01-16
Berk
H
e
s
s
Remo
v
e
t
umbling ice-cube wa
r
ning with SD
commit
|
commitdiff
|
tree
2018-01-12
Szilárd Páll
Ca
l
l GPU
profiler reset on
s
eparat
e
PME ranks
commit
|
commitdiff
|
tree
2018-01-09
Be
r
k Hess
Re
w
ord CPU/GPU
imbal
a
nce notes
commit
|
commitdiff
|
tree
2018-01-09
Mark Abraham
D
e
act
i
vate auto
s
e
l
ect of PM
E
on
G
P
U
on separate ran
k
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
Fix triclinic doma
i
n
decompos
i
tion bug
commit
|
commitdiff
|
tree
2017-12-19
Be
r
k Hess
Make
a
cceleration
c
orr
e
ction VCM mode
w
ork
commit
|
commitdiff
|
tree
2017-12-14
Berk H
e
s
s
Require -ntm
p
i with settin
g
-ntomp with GPUs
commit
|
commitdiff
|
tree
2017-12-11
P
a
ul Bauer
Disallow c
o
m
b
ination
o
f
PME-user and verle
t
c
u
toff
commit
|
commitdiff
|
tree
2017-12-06
A
l
eksei Iupinov
Provide dummy init
i
alization to sil
e
nce
a
warning
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fix
pme gather
i
n double w
i
th AV
X
(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Alekse
i
Iupino
v
R
e
f
o
rmulat
e
PME sol
v
ing test
s
tolerances
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k
H
ess
Mer
g
e "Merge branch release-2
0
16 into
r
e
lease-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fixed ini
t
ial temperature repor
t
ing
commit
|
commitdiff
|
tree
2017-12-04
Mark Abraham
Fix
u
nused variables
i
n CPU p
r
uning kern
e
ls
commit
|
commitdiff
|
tree
2017-11-30
V
iveca Lindahl
Correct AWH in
p
ut fi
l
e name i
n
do
c
ume
n
tati
o
n
commit
|
commitdiff
|
tree
2017-11-28
B
erk Hess
Update documention of N
o
se-Hoo
v
er output
commit
|
commitdiff
|
tree
2017-11-28
B
e
r
k H
e
ss
Extend grompp missing energy term
m
essage
commit
|
commitdiff
|
tree
2017-11-27
B
er
k
H
ess
Fix PME GPU with wal
l
s
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
F
ix compiler war
n
ing withou
t
MP
I
commit
|
commitdiff
|
tree
2017-11-24
B
er
k
H
e
ss
Speed
up nbnxn buffer clearing
commit
|
commitdiff
|
tree
2017-11-23
B
e
rk H
e
ss
Upd
a
te
no
t
e in
manual on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Cor
r
ect PME
G
PU t
i
m
i
ng naming
commit
|
commitdiff
|
tree
2017-11-21
Mark Abraham
Use much less PaddedRVec
V
ec
t
o
r
and more Arr
a
yRef of
.
.
.
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
F
i
x
g
e
ni
o
n cha
r
ge sum
m
a
t
i
on accuracy
commit
|
commitdiff
|
tree
2017-11-10
R
o
lan
d
Sc
h
ulz
Rename load1D
u
alHsimd to loa
d
U1
D
ua
l
Hsimd
commit
|
commitdiff
|
tree
2017-11-10
Rolan
d
S
c
hulz
A
VX:
I
m
p
rov
e
lo
a
d1DualHsimd
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix Ekin at step 0 wit
h
COM
r
emoval
commit
|
commitdiff
|
tree
2017-11-02
Berk
Hess
Add m
i
ssing Ewald co
r
rection for p
m
e-user
commit
|
commitdiff
|
tree
2017-10-30
Mark Abra
h
am
Fix a
n
d up
d
ate hw_in
f
o
commit
|
commitdiff
|
tree
2017-10-29
Berk Hess
Remove
i
nc
o
rre
c
t comment for
CHARMM tip
s
3p
commit
|
commitdiff
|
tree
2017-10-26
Szilá
r
d Páll
R
eorganize PME G
P
U launc
h
commit
|
commitdiff
|
tree
2017-10-24
Be
r
k H
e
ss
Fix g
m
x
c
heck f
o
r tprs with d
i
fferent #atoms
commit
|
commitdiff
|
tree
2017-10-24
Alek
s
ei Iupinov
Move
c
ommrec duty
c
hecking into simple getters
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
F
i
x incorrect dV/dlam
b
d
a for walls
commit
|
commitdiff
|
tree
2017-10-23
David van der
S
poel
S
plit of
f
t
h
e NMR re
l
ated analyses from gmx energy
.
commit
|
commitdiff
|
tree
2017-10-21
Berk
H
e
s
s
Merge "Merge b
r
anch release-2016"
commit
|
commitdiff
|
tree
2017-10-18
B
erk Hess
Mad
e
CUDA PME textu
r
e r
e
ference condition
a
l
commit
|
commitdiff
|
tree
2017-10-13
Roland Schulz
Replace al
l
Cons
t
ArrayRef with ArrayRe
f
<
c
onst T
>
commit
|
commitdiff
|
tree
2017-10-13
Magn
u
s
L
undborg
Do
not include he
a
ders
r
el
a
ted to ObservablesHistory
commit
|
commitdiff
|
tree
2017-10-13
Ma
r
k A
b
raham
Fix cpui
n
fo
o
n cl
a
ng
+
non-x86
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iupin
o
v
Re
v
ert "
D
r
o
p
NB_ from GMX_CUDA_NB_SINGLE_
C
O
M
P
I
LAT
I
ON_UNIT
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
Berk He
s
s
S
i
mplify viri
a
l ha
n
d
l
ing
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Fix
max_size()
i
n
a
llocator
.
h
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
Refacto
r
sc
a
led box handli
n
g for PME/Ewald
commit
|
commitdiff
|
tree
2017-10-05
Mark Abraham
Conti
n
u
e remov
i
ng -nb gpu_cpu
commit
|
commitdiff
|
tree
2017-10-04
Roland Schulz
All
o
w
n
o
n-con
s
t access for con
s
t ArrayRe
f
commit
|
commitdiff
|
tree
2017-10-04
B
erk Hess
R
e
move a
f
orce buffer arg
u
ment
f
rom IForc
e
Provider
commit
|
commitdiff
|
tree
2017-10-03
Aleksei Iupinov
Template/move C
U
DA texture cle
a
nup code from
NB CUDA
.
.
.
commit
|
commitdiff
|
tree
2017-09-28
Szilárd P
á
ll
Correct
misplaced CUDA timing event
re
c
or
d
commit
|
commitdiff
|
tree
2017-09-28
t
om
a
skubar
QM/
M
M: remove optimization
and trans
.
state search
commit
|
commitdiff
|
tree
2017-09-26
Szil
á
rd Páll
Re
n
ame GPU launch/wai
t
cy
c
le counters
commit
|
commitdiff
|
tree
2017-09-23
Berk H
e
ss
Fix gromp
p
with Andersen massive and no
C
OM
remo
v
al
commit
|
commitdiff
|
tree
2017-09-20
Berk Hess
Change nbnxn indexing to templates
commit
|
commitdiff
|
tree
2017-09-18
Aleksei Iup
i
nov
Skip GPU reallocation of a
n
e
mpty
non
-
local pairlist
commit
|
commitdiff
|
tree
2017-09-18
Szilárd P
á
ll
Minor ref
a
ctoring of CUDA non
-
bo
n
ded kernels
commit
|
commitdiff
|
tree
2017-09-14
B
e
rk
Hess
Fix nbnxn SIMD 2xNN PME tabul
a
ted kernel
commit
|
commitdiff
|
tree
2017-09-12
S
z
i
l
á
rd Páll
Merge branch 'release-2016'
commit
|
commitdiff
|
tree
2017-09-07
Berk Hess
Fix FEP state with rerun
commit
|
commitdiff
|
tree
2017-09-01
Berk Hess
Fix mdrun -n
b
option
p
ointe
r
commit
|
commitdiff
|
tree
2017-08-29
Aleksei Iupinov
Fix
t
ypo
commit
|
commitdiff
|
tree
2017-08-29
Szilárd
P
á
l
l
Avoid divisio
n
by z
e
ro is pruning part
c
al
c
ul
a
t
ion
commit
|
commitdiff
|
tree
2017-08-29
A
l
ekse
i
Iupi
n
o
v
Adju
s
t PME LJ solver test input coef
f
i
cie
n
t
commit
|
commitdiff
|
tree
2017-08-23
Mark Ab
r
aham
S
topped c
h
eck
p
oint influe
n
cing
p
a
rallelism setup
commit
|
commitdiff
|
tree
2017-08-12
Berk Hess
Rem
o
v
e
loop
o
ver
a
ll atom
s
i
n
in
i
t_mdatoms
commit
|
commitdiff
|
tree
2017-07-25
Berk H
e
ss
F
i
x
b
ugs wi
t
h
o
r
ien
t
atio
n
rest
r
aints
commit
|
commitdiff
|
tree
2017-07-04
B
e
r
k
Hess
Unify nbnxn k
e
r
n
el
d
ispatchers
commit
|
commitdiff
|
tree
2017-06-20
Szilárd Páll
Re-enab
l
e accidentally
lost DD
w
arning
commit
|
commitdiff
|
tree
2017-06-20
Szilárd P
á
ll
Refactoring + clarification
o
f DLB state handling
commit
|
commitdiff
|
tree
2017-06-17
Be
r
k Hess
A
d
d toleranc
e
to
calc_ver
l
etbuf
t
e
st
commit
|
commitdiff
|
tree
2017-06-12
Berk Hess
Fix
null p
o
i
nter print i
n
D
D
commit
|
commitdiff
|
tree
2017-06-10
Ber
k
Hess
P
ut replica
exchang
e
p
a
rameters in a str
u
c
t
commit
|
commitdiff
|
tree
2017-06-02
Ber
k
H
e
ss
Fix in
i
tia
l
t
e
m
per
a
ture
r
eporting
commit
|
commitdiff
|
tree
2017-05-26
B
e
rk Hess
Improve Ver
l
e
t
buffer
c
onstraint
e
stim
a
te
commit
|
commitdiff
|
tree
2017-05-16
Berk Hess
Fix
c
onfout
.
gro wit
h
e
n
ergy min
i
mizatio
n
commit
|
commitdiff
|
tree
2017-05-15
Berk
H
e
ss
Fix LJPME + switch grompp
error
commit
|
commitdiff
|
tree
2017-04-21
Berk He
s
s
Fix bugs
in doubl
e
A
VX(
2
)_256 Simd
4
commit
|
commitdiff
|
tree
2017-04-03
Ma
r
k Ab
r
aham
Remove
d
o_pbc_fi
r
st
commit
|
commitdiff
|
tree
2017-03-16
Berk Hess
Replace instance of group by coord in pull mdp docs
commit
|
commitdiff
|
tree
2017-03-14
Berk Hess
Make g
r
ompp -r o
b
ligatory wit
h
posres
commit
|
commitdiff
|
tree
2017-03-13
Mark Abraham
Tests for grompp
-f
-po
commit
|
commitdiff
|
tree
2017-03-03
Alekse
i
Iupino
v
R
e
mo
v
e
o
utdated CUDA version
check
commit
|
commitdiff
|
tree
2017-02-02
Berk
H
ess
Reall
y
fi
x
array
o
f complex in
cross_corr
commit
|
commitdiff
|
tree
next