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Remove redundant shell-code fatal errors
2018-06-04
Mark A
b
raham
Remove redun
d
ant
s
hell-code f
a
t
a
l err
o
rs
commit
|
commitdiff
|
tree
2018-05-24
Mark
Abraham
M
o
ve
responsibility
f
or bonded
t
hreading de
c
omp
o
sition
commit
|
commitdiff
|
tree
2018-05-24
Berk H
e
ss
Ch
a
nge nbs in
n
bv
t
o
std::unique
commit
|
commitdiff
|
tree
2018-05-24
B
e
rk
H
ess
Convert gm
x
_domd
e
c_master_t
t
o C++
commit
|
commitdiff
|
tree
2018-05-18
B
erk
Hess
Clean
up in
n
b
nxn_g
r
i
d
.
cp
p
commit
|
commitdiff
|
tree
2018-05-15
Ber
k
Hess
Clean up PME domain count passin
g
commit
|
commitdiff
|
tree
2018-05-03
Berk
He
s
s
Enable SIMD v
e
r
sion of update
commit
|
commitdiff
|
tree
2018-04-24
Berk Hess
Fix indexing iss
u
e in the pull code
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Change w
a
rnin
p
fil
e
nm to std:
:
s
tr
i
ng
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do not
c
alculate COM for
pull group 0
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fi
x
gmx dump AWH fo
r
matti
n
g i
s
sue
commit
|
commitdiff
|
tree
2018-03-20
A
leksei Iupinov
Clarif
y
t
he mdrun
G
PU o
p
tio
n
s d
o
c
s
commit
|
commitdiff
|
tree
2018-03-16
Aleksei Iupinov
Res
t
ore the lost m
c
_temp check in grompp
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
F
i
x virial w
i
th
e
xternal pull potential a
n
d MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk He
s
s
Fix COM p
u
lli
n
g with external potential wit
h
#ranks
>
32
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
ess
Fix pull bug with geometry=direction-pe
r
io
d
i
c
commit
|
commitdiff
|
tree
2018-03-07
Berk H
e
ss
Fix memory l
e
ak in PM
E
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Wor
k
a
round gcc bug with group kernel
tables
commit
|
commitdiff
|
tree
2018-03-05
Berk
Hess
L
e
a
ve
nullptr opt in t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk He
s
s
F
i
x cppcheck war
n
in
g
commit
|
commitdiff
|
tree
2018-03-02
Berk H
e
ss
Fix AWH bias-sharing wit
h
par
a
llel simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk Hess
Fix
mdrun
mu
l
t
isim w
i
th se
p
ara
t
e
PME ranks
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simpli
f
y mdrun
tMPI thread spawning
commit
|
commitdiff
|
tree
2018-02-19
Mark
Abraham
Remove
cycl
e
suppressio
n
commit
|
commitdiff
|
tree
2018-02-19
Mar
k
Abraham
Disallowed change of ensemble for checkpoint re
s
tart
commit
|
commitdiff
|
tree
2018-02-14
Mark Abraha
m
Fix bug in chec
k
point error c
h
ecking
commit
|
commitdiff
|
tree
2018-02-12
Sz
i
l
á
r
d Páll
Remove single/multi com
p
il
a
tion unit swi
t
ch
i
ng l
o
gic
commit
|
commitdiff
|
tree
2018-02-12
Szilá
r
d
Páll
Remove texture reference
s
upport in the CUD
A
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
ess
Al
l
ow b
o
n
ds
with distance=0
commit
|
commitdiff
|
tree
2018-02-06
Al
e
ksei Iup
i
nov
O
n
ly
setu
p
Ewa
l
d in the g
e
n
er
i
c group ke
r
n
e
l
if it
.
.
.
commit
|
commitdiff
|
tree
2018-02-05
Berk
Hess
Set cutoff modifi
e
r
s in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix
assertion fail
u
r
e
i
n
TPI
commit
|
commitdiff
|
tree
2018-01-30
Mark Abraham
Replace macros for mu
l
ti-sim
commit
|
commitdiff
|
tree
2018-01-18
A
leksei I
u
p
i
n
ov
G
o
t rid of manual
m
em
o
ry mana
g
ement in
the PME overlap
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
A
leksei Iupinov
Re-en
a
bl
e
m
u
l
ti-rank PM
E
tests (with the file race
.
.
.
commit
|
commitdiff
|
tree
2018-01-18
Be
r
k Hess
Add check
in
g
rompp to avoid asserti
o
n fai
l
ure
commit
|
commitdiff
|
tree
2018-01-17
Berk H
e
ss
Repl
a
ce stderr prints in filenm
.
c
p
p
by as
s
erts
commit
|
commitdiff
|
tree
2018-01-16
B
e
rk He
s
s
Remov
e
tu
m
bling ice-cube
w
arning with SD
commit
|
commitdiff
|
tree
2018-01-12
Szil
á
rd Páll
Call GPU
p
rof
i
l
e
r
reset on s
e
parat
e
PME
ranks
commit
|
commitdiff
|
tree
2018-01-09
Berk Hess
Reword CPU/GPU imba
l
ance no
t
es
commit
|
commitdiff
|
tree
2018-01-09
M
a
rk Abraha
m
Deactivate
autoselect of PM
E
o
n G
P
U
on se
p
arate rank
commit
|
commitdiff
|
tree
2018-01-08
Be
r
k Hess
Fix t
r
iclinic domain deco
m
position bu
g
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Ma
k
e
a
cc
e
ler
a
tion correct
i
o
n VCM mode work
commit
|
commitdiff
|
tree
2017-12-14
Berk
H
ess
Require -ntmp
i
wi
t
h se
t
ting -ntom
p
wi
t
h GPUs
commit
|
commitdiff
|
tree
2017-12-11
P
a
ul Bauer
Di
s
allow co
m
b
i
nat
i
on of PM
E
-
user and
ve
r
let cutoff
commit
|
commitdiff
|
tree
2017-12-06
A
leksei Iupinov
Provi
d
e d
u
mmy initi
a
lization t
o
silence a warnin
g
commit
|
commitdiff
|
tree
2017-12-04
Berk
Hess
Fi
x
p
m
e gather in double wi
t
h AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Aleksei Iupino
v
Reformulate PM
E
solv
i
ng tests toleranc
e
s
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Merge "
M
erge branch release-2016
i
n
t
o release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Ber
k
He
s
s
F
i
x
e
d initial temperature repo
r
ting
commit
|
commitdiff
|
tree
2017-12-04
Mark Abraham
Fix unused va
r
iables in CP
U
prun
i
ng k
e
r
n
els
commit
|
commitdiff
|
tree
2017-11-30
Viveca Li
n
d
ahl
Cor
r
ect AWH input file name in docum
e
ntation
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
U
pda
t
e documenti
o
n
of Nose-H
o
over outpu
t
commit
|
commitdiff
|
tree
2017-11-28
Be
r
k He
s
s
Extend grompp missing
ene
r
gy term
m
essage
commit
|
commitdiff
|
tree
2017-11-27
Berk H
e
ss
Fix PME GPU with wall
s
commit
|
commitdiff
|
tree
2017-11-25
Berk
H
ess
F
ix compiler warning without MP
I
commit
|
commitdiff
|
tree
2017-11-24
Be
r
k Hess
Speed up
n
bnxn buffe
r
clearing
commit
|
commitdiff
|
tree
2017-11-23
Ber
k
H
e
ss
U
p
date n
o
te in manual on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Cor
r
ect PME GPU
timing naming
commit
|
commitdiff
|
tree
2017-11-21
M
ark
A
brah
a
m
Use muc
h
less
Padd
e
dRVecVector
and more
ArrayRef of
.
.
.
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fi
x
g
e
n
i
on charge summ
a
tio
n
ac
c
ur
a
cy
commit
|
commitdiff
|
tree
2017-11-10
Roland Schulz
Rename load1DualHsi
m
d to
loadU1D
u
al
H
s
i
md
commit
|
commitdiff
|
tree
2017-11-10
R
o
l
a
n
d Schulz
AVX: Improve load1DualHsimd
commit
|
commitdiff
|
tree
2017-11-02
Be
r
k Hess
Fix E
k
in at step 0 with COM removal
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Add missing E
w
ald correctio
n
for
p
me-u
s
er
commit
|
commitdiff
|
tree
2017-10-30
Mark Abraha
m
Fix and up
d
ate
h
w_info
commit
|
commitdiff
|
tree
2017-10-29
Berk H
e
ss
Remove
i
ncorrect
c
o
mment for CHARMM tips3p
commit
|
commitdiff
|
tree
2017-10-26
Szilárd Páll
Reorganize
P
ME GPU l
a
unch
commit
|
commitdiff
|
tree
2017-10-24
Berk Hess
Fix gmx check
f
or tprs with
different
#
atoms
commit
|
commitdiff
|
tree
2017-10-24
Aleksei Iupinov
Move commrec duty checking
into simple getter
s
commit
|
commitdiff
|
tree
2017-10-23
Berk Hes
s
F
i
x
incorrec
t
dV/
d
lambda for walls
commit
|
commitdiff
|
tree
2017-10-23
David van der Spoel
Split of
f
the
N
MR related analyses from
g
m
x
en
e
rg
y
.
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
Merge "Me
r
ge branch rel
e
ase-2016"
commit
|
commitdiff
|
tree
2017-10-18
Berk
Hess
M
a
d
e
CUDA PME texture reference condi
t
ional
commit
|
commitdiff
|
tree
2017-10-13
R
oland Schulz
Replace al
l
C
o
n
s
t
A
rrayRef with Arr
a
yRef<const
T
>
commit
|
commitdiff
|
tree
2017-10-13
Magnus Lundborg
D
o
not in
c
lude headers related to ObservablesH
i
story
commit
|
commitdiff
|
tree
2017-10-13
Mark Abraham
Fix cpui
n
fo on clang
+
n
on-x
8
6
commit
|
commitdiff
|
tree
2017-10-12
Aleksei Iu
p
i
nov
R
eve
r
t "Drop NB_ f
r
om
GMX_CUDA_NB_S
I
NG
L
E_COM
P
ILATIO
N
_UNIT
.
.
.
commit
|
commitdiff
|
tree
2017-10-12
B
e
rk
Hess
Si
m
plify virial ha
n
dling
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Fix max_size()
in allocator
.
h
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Pál
l
Re
f
a
ctor scaled box handling for PME/Ewald
commit
|
commitdiff
|
tree
2017-10-05
Mark Abr
a
h
am
C
ontinue rem
o
ving
-
n
b g
p
u_cpu
commit
|
commitdiff
|
tree
2017-10-04
Rol
a
nd
Schulz
Allo
w
non-cons
t
a
cces
s
f
o
r const A
r
rayRef
commit
|
commitdiff
|
tree
2017-10-04
B
e
rk H
e
ss
Remove a
f
orce buffer
a
rg
u
ment
from
IF
o
rc
e
Pr
o
vider
commit
|
commitdiff
|
tree
2017-10-03
Aleksei Iu
p
inov
Template/move
C
UDA texture
c
leanu
p
code from NB CU
D
A
.
.
.
commit
|
commitdiff
|
tree
2017-09-28
S
z
ilá
r
d Páll
Correct misplaced CUDA timing e
v
en
t
record
commit
|
commitdiff
|
tree
2017-09-28
tomaskubar
QM
/
MM:
r
emove opt
i
mizat
i
on and trans
.
st
a
te se
a
rch
commit
|
commitdiff
|
tree
2017-09-26
S
z
ilárd
Páll
R
e
name GPU launc
h
/w
a
it c
y
cle cou
n
t
e
rs
commit
|
commitdiff
|
tree
2017-09-23
Berk Hess
Fix grompp with Andersen
m
a
s
sive and no
COM remova
l
commit
|
commitdiff
|
tree
2017-09-20
Berk H
e
ss
C
h
ang
e
nbnxn in
d
ex
i
ng to templates
commit
|
commitdiff
|
tree
2017-09-18
Al
e
ksei
I
upinov
Skip
G
PU reall
o
c
a
tion of an empty non-local pairlist
commit
|
commitdiff
|
tree
2017-09-18
Szilárd Páll
Mino
r
refactoring of
CUDA
n
on-bonded
k
e
rnels
commit
|
commitdiff
|
tree
2017-09-14
Berk Hess
Fix nbnxn SIMD
2
xNN P
M
E
tabulated ke
r
n
el
commit
|
commitdiff
|
tree
2017-09-12
S
zilárd Páll
M
e
rge branch 'release-2016'
commit
|
commitdiff
|
tree
2017-09-07
B
erk
H
ess
Fix
F
EP state wit
h
re
r
un
commit
|
commitdiff
|
tree
2017-09-01
Berk
Hess
Fi
x
mdrun -nb option p
o
i
nter
commit
|
commitdiff
|
tree
2017-08-29
Al
e
ksei Iupi
n
ov
Fix
t
ypo
commit
|
commitdiff
|
tree
2017-08-29
Szilárd Pá
l
l
A
vo
i
d
division by ze
r
o is pruning
p
art cal
c
ulat
i
on
commit
|
commitdiff
|
tree
2017-08-29
A
l
eksei
I
upinov
Adjust PME LJ
s
olver test input coefficien
t
commit
|
commitdiff
|
tree
2017-08-23
Mark Abr
a
h
a
m
Stopped
checkpoint influencing para
l
le
l
ism setup
commit
|
commitdiff
|
tree
next