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Clarified grompp pull error messages
2014-12-05
B
erk Hess
Clarified
g
rom
p
p pull error me
s
sages
commit
|
commitdiff
|
tree
2014-12-05
Berk
H
ess
A
void race
on
d
v
dl with Verl
e
t+OpenMP+LINCS+FE+VV
commit
|
commitdiff
|
tree
2014-12-01
Berk Hess
Added war
n
i
n
g
for unnecessar
y
sof
t
-core
commit
|
commitdiff
|
tree
2014-11-26
Berk Hes
s
Fixed triclinic 1xN
x
1 domain deco
m
pos
i
tion
commit
|
commitdiff
|
tree
2014-11-25
B
e
rk
H
ess
Fixed twin-range
+
freeze + constraints
commit
|
commitdiff
|
tree
2014-11-24
Berk Hess
Avoid NaN in
rlist buffer calculation
commit
|
commitdiff
|
tree
2014-11-12
Berk H
e
ss
Corrected parameter for sorting
on search grid
commit
|
commitdiff
|
tree
2014-11-12
Berk Hes
s
Fix D
D
bonded interacti
o
n rang
e
pri
n
t
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
Removed f_nov
i
rsum reduction in Verle
t
scheme
commit
|
commitdiff
|
tree
2014-10-07
Berk Hess
F
i
xes issue with vsiten and Verlet buffers
commit
|
commitdiff
|
tree
2014-09-30
Berk H
e
ss
Avoid
DLB with overl
o
a
ded PME ra
n
ks
commit
|
commitdiff
|
tree
2014-09-30
Berk
H
ess
A
dded GPU local wait to load balancing
commit
|
commitdiff
|
tree
2014-09-29
Berk
H
e
s
s
Domain decomposition
now checks the rlist buffe
r
commit
|
commitdiff
|
tree
2014-09-29
B
e
rk
He
s
s
S
I
MD a
c
celeratio
n
for RB
dihedrals
commit
|
commitdiff
|
tree
2014-09-29
Berk
He
s
s
Avoid PME tuning decreasing rcoulomb
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
Fix c
a
lc_grid a
v
o
i
ding PME grid factor 84
commit
|
commitdiff
|
tree
2014-09-09
Berk
H
ess
Fixed DD
state
c
o
l
lection issue
commit
|
commitdiff
|
tree
2014-09-08
Be
r
k
Hess
Ch
e
ck f
o
r implicit
s
olvent + Verlet
scheme
commit
|
commitdiff
|
tree
2014-08-28
Be
r
k Hess
F
i
xed
t
wo PME iss
u
es with
M
PI+OpenMP
commit
|
commitdiff
|
tree
2014-08-25
Berk He
s
s
Fixed
b
u
g
s in vsi
t
eN wit
h
OpenMP
commit
|
commitdiff
|
tree
2014-08-24
Berk H
e
ss
I
n
itial
i
ze unused veloc
i
ty constr
a
int
com
p
onen
t
s
commit
|
commitdiff
|
tree
2014-08-17
Berk Hess
H
a
lved the cost
of the pull
c
ommunication
commit
|
commitdiff
|
tree
2014-08-14
B
e
r
k
He
s
s
Corrected SIMD math o
v
erfl
o
w documen
t
ation
commit
|
commitdiff
|
tree
2014-08-10
Berk Hess
A
d
ded check
s
for TPI
+
Verlet scheme
commit
|
commitdiff
|
tree
2014-08-05
Ber
k
Hess
Fix
hang with LJ-PME and empty domains
commit
|
commitdiff
|
tree
2014-08-02
B
erk H
e
ss
Fixed PME bu
g
w
it
h
high O
p
e
nMP thread co
u
n
t
commit
|
commitdiff
|
tree
2014-07-31
Berk H
e
ss
Avoid division by 0 in nbnxn_search
commit
|
commitdiff
|
tree
2014-06-29
Berk Hess
Take LJ-PME into account fo
r
table spa
c
ing
commit
|
commitdiff
|
tree
2014-06-29
Berk Hess
Update
d
LJ-PME
d
ocumentation
commit
|
commitdiff
|
tree
2014-06-24
Be
r
k
H
ess
Fixed the si
g
n o
f
mass
perturb
e
d con
t
ribution
commit
|
commitdiff
|
tree
2014-06-20
Berk
H
ess
Fix g_
m
i
n
dist wi
t
h
pbc=XY
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
F
ix
e
d s
h
ells w
i
th par
t
icle dec
o
mposition
commit
|
commitdiff
|
tree
2014-06-18
B
e
rk He
s
s
Fixed sign error in posres dvdl
commit
|
commitdiff
|
tree
2014-06-17
Ber
k
He
s
s
Updated
m
drun -npme
d
ocumentati
o
n
commit
|
commitdiff
|
tree
2014-06-17
B
e
rk H
e
ss
Rem
o
ved
roun
d
ing iss
u
e i
n
nb
n
xn Ewald
table
commit
|
commitdiff
|
tree
2014-06-14
Berk Hess
Fixed PME bug
w
ith
#OpenMP-thr
e
a
d
s a large prime
commit
|
commitdiff
|
tree
2014-06-13
Be
r
k Hess
Changed appending file name error message
commit
|
commitdiff
|
tree
2014-06-13
Ber
k
Hess
Made shell
s
work
w
i
t
h the Verlet scheme
commit
|
commitdiff
|
tree
2014-06-12
Berk He
s
s
F
ixed perturbed wall interactio
n
s
commit
|
commitdiff
|
tree
2014-06-12
Berk Hes
s
Mad
e
gmxcheck -
r
ms
d
w
o
r
k a
g
a
i
n with f
o
rces
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Decoupled repl_ex_nst fro
m
nstcalcener
g
y
commit
|
commitdiff
|
tree
2014-06-11
Berk Hess
Made
repl_ex ti
m
e step
m
o
r
e readab
l
e
commit
|
commitdiff
|
tree
2014-06-10
B
e
rk
Hess
R
eplaced
g
m
x
_
hostn
a
me_num by
g
mx_physic
a
lnode_
i
d_has
h
commit
|
commitdiff
|
tree
2014-06-09
Berk Hess
Set ma
k
e_n
d
x
max name length a
n
d c
o
unt to 1024
commit
|
commitdiff
|
tree
2014-06-05
Berk H
e
ss
Fi
x
e
d shi
f
t and switc
h
modifiers, parti
c
ularly for
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
B
e
rk Hess
F
i
x
c
on
s
traint viria
l
with mu
l
ti
p
le ti
m
e ste
p
ping
commit
|
commitdiff
|
tree
2014-06-02
Berk Hess
Fixed g_e
n
ergy
E
instein viscosi
t
y
commit
|
commitdiff
|
tree
2014-05-22
Berk Hess
Avoid e
n
ergy drift with v
e
rlet-buf
f
er-tolerance
commit
|
commitdiff
|
tree
2014-05-09
Berk Hess
Minor tweaks to the DD setup
commit
|
commitdiff
|
tree
2014-04-29
B
er
k
Hess
Remove
d
truncation
o
f
nrdf
in
v
-rescale
ther
m
ostat
commit
|
commitdiff
|
tree
2014-04-23
Berk Hess
Fixed n
b
nxn FE lis
t
alloc
a
tion issue
commit
|
commitdiff
|
tree
2014-04-02
Be
r
k Hess
Added LJ-PME
and LJ Pot-switch to PME load estimate
commit
|
commitdiff
|
tree
2014-03-24
Be
r
k
Hess
A
d
ds cut-
o
f
f
check
s
f
o
r
t
ricli
n
ic doma
i
n decompositi
o
n
commit
|
commitdiff
|
tree
2014-03-23
Berk Hess
Fixed bug in paral
l
el v/f co
n
straining
commit
|
commitdiff
|
tree
2014-03-23
Be
r
k Hess
CUDA cut
-
off kernels now shift exclusion energies
commit
|
commitdiff
|
tree
2014-03-11
Berk Hess
PME load b
a
l
ancing now work
s
wi
t
h
L
J-PME
commit
|
commitdiff
|
tree
2014-03-06
B
e
rk Hes
s
Fix
e
d exit wi
t
h
F
E
P
with PME node
s
wit
h
out LJ-PME
commit
|
commitdiff
|
tree
2014-03-05
Ber
k
Hess
Bu
f
fer estimate now works with rvd-switch=0
commit
|
commitdiff
|
tree
2014-02-26
Berk Hess
F
ree-energy now works with the Verlet sc
h
eme
commit
|
commitdiff
|
tree
2014-02-25
Berk H
e
ss
Fixes sep
e
rate PME
node
s
w
i
thout LJ-PME
commit
|
commitdiff
|
tree
2014-02-24
Be
r
k Hess
Implemented LJ-
P
M
E nbn
x
n
kernels
commit
|
commitdiff
|
tree
2014-02-24
B
e
rk
H
e
s
s
Fixed bug with LJ
pot-switch
in
4xN
kernels
commit
|
commitdiff
|
tree
2014-02-19
B
er
k
Hes
s
Imple
m
ented nbnxn L
J
switch functions
commit
|
commitdiff
|
tree
2014-01-30
Berk Hes
s
M
a
de reference SIMD
w
or
k
again
commit
|
commitdiff
|
tree
2014-01-29
Berk Hes
s
Automated Ve
r
l
e
t
rlist
for NVE simulat
i
ons
commit
|
commitdiff
|
tree
2013-12-03
Berk
Hess
R
e
moved
r
estricti
o
n o
f
one refe
r
ence
p
ull group
commit
|
commitdiff
|
tree
2013-12-02
B
e
r
k Hess
M
ade
cuto
f
f-sch
e
m
e=
V
erlet the defa
u
lt
commit
|
commitdiff
|
tree
2013-12-02
Berk Hess
Renam
e
d
verl
e
t-bu
f
f
e
r-drift
t
o
v
e
rlet-b
u
ffer
-
toleranc
e
commit
|
commitdiff
|
tree
2013-12-01
Berk Hess
Fixed zero
hardwa
r
e thread count
commit
|
commitdiff
|
tree
2013-11-29
Berk Hess
C
r
ea
t
ed SIMD modu
l
e
commit
|
commitdiff
|
tree
2013-11-26
Berk Hess
Fixed return
v
alue o
f
gm
x
_
m
t
o
p_b
o
ndeds_
f
re
e
_ener
g
y
commit
|
commitdiff
|
tree
2013-11-15
Berk Hess
c
o
rrected potential nbnxn
S
IMD memory
issue
commit
|
commitdiff
|
tree
2013-11-08
Ber
k
He
s
s
fix nbnxn atom sort
i
ng with distant bondeds
commit
|
commitdiff
|
tree
2013-11-07
Berk Hess
corrected dy
n
am
i
c load balancing when sha
r
ing GP
U
s
commit
|
commitdiff
|
tree
2013-11-05
Berk Hess
GPU
d
etection is
done o
n
ce per physical node
commit
|
commitdiff
|
tree
2013-11-05
Be
r
k
Hess
removed (h
a
rmless) left-over in nbnxn SIMD kernels
commit
|
commitdiff
|
tree
2013-10-31
Berk Hess
reorganized G
P
U detection and selection
commit
|
commitdiff
|
tree
2013-10-29
Berk
Hess
correct
e
d volume wi
t
h seri
a
l NP
T
replica exchange
commit
|
commitdiff
|
tree
2013-10-28
Be
r
k Hes
s
improved the
n
bnxn buffer size estimate with GPUs
commit
|
commitdiff
|
tree
2013-10-22
B
erk Hess
fixed recen
t
bug wi
t
h CUDA texture objects
commit
|
commitdiff
|
tree
2013-10-22
Berk
H
ess
f
ixed OpenMP
thre
a
ds
b
e
ing pinned to the same cores
commit
|
commitdiff
|
tree
2013-10-16
Be
r
k H
e
s
s
avoid division by zero in SIMD
a
ng
l
es and dihed
r
a
ls
commit
|
commitdiff
|
tree
2013-10-16
Berk
H
e
s
s
fixed a
h
a
lf
bin mis
a
lignment in gmx_vanhove -or
commit
|
commitdiff
|
tree
2013-10-11
Berk Hess
i
n
trodu
c
e
d
general 4-w
i
de SIMD su
p
port
commit
|
commitdiff
|
tree
2013-10-10
Ber
k
Hess
fixed
nbnxn 4
x
8 pair se
a
rch wit
h
out
A
V
X
commit
|
commitdiff
|
tree
2013-10-02
Ber
k
H
e
ss
Fi
x
es reactio
n
fie
l
d
fre
e
e
n
ergy bu
g
commit
|
commitdiff
|
tree
2013-09-24
Berk H
e
ss
o
ptimized generi
c
SI
M
D invsq
r
t
commit
|
commitdiff
|
tree
2013-09-21
Berk Hess
fixed
m
ultiple distance
restraints with OpenMP
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
ma
d
e free
energy PME kernel 40% fast
e
r
commit
|
commitdiff
|
tree
2013-09-16
Berk Hess
mdrun without Op
e
nMP with threa
d
-MPI no
w
uses all
c
ores
commit
|
commitdiff
|
tree
2013-09-13
B
erk Hess
corrected grom
p
p
constraint/DOF wa
r
ni
n
g
with vsites
commit
|
commitdiff
|
tree
2013-08-25
Ber
k
Hess
i
n
troduced nbnxn data s
t
ructure
for boundin
g
boxe
s
commit
|
commitdiff
|
tree
2013-08-20
Be
r
k Hess
fixed parallel normal m
o
des wi
t
h PME
commit
|
commitdiff
|
tree
2013-07-24
B
e
rk Hess
i
m
pl
e
m
e
n
ted plain-C SI
M
D macros for reference
commit
|
commitdiff
|
tree
2013-06-20
Be
r
k
Hess
fixe
d
S
D
and BD integrator Ope
n
MP perf
o
rmance
commit
|
commitdiff
|
tree
2013-06-20
B
erk Hess
flops t
a
b
l
e now repo
r
ts CUDA ana
l
ytical Ewald
commit
|
commitdiff
|
tree
2013-06-14
Berk Hess
f
ixed minor g
_
bar out
p
ut issues
commit
|
commitdiff
|
tree
2013-06-05
B
e
r
k H
e
ss
fixed DD
i
nter
n
al state cor
r
uption w
i
th energy mi
n
imiz
a
tion
commit
|
commitdiff
|
tree
2013-06-03
B
erk Hess
fi
x
ed d
e
adlock with
r
e
plica exch
a
nge and
-
maxh
commit
|
commitdiff
|
tree
2013-05-08
Berk Hess
fix
e
d incor
r
ect scali
n
g of c
o
s
-
acce
l
eration viscos
i
t
y
commit
|
commitdiff
|
tree
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