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Fix bug in v-rescale thermostat & replica exchange
2015-06-24
Berk Hess
GPU Ewal
d
ta
b
le kern
e
l now
u
ses CP
U
spacing
commit
|
commitdiff
|
tree
2015-06-24
B
e
r
k
Hess
Avoid GPU
s
election
with GP
U
e
mulation
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Mi
n
or reformatti
n
g o
f
SIM
D
mis
m
atch
m
essage
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Add
sug
a
r to print
e
mpt
y
line
i
n
printBinary
I
nformation
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
H
ess
Fix g_ene
r
gy average
/
RMSD bug
commit
|
commitdiff
|
tree
2015-06-22
Berk He
s
s
Upd
a
t
e
launch c
o
nfigur
a
tion fo
r
ph
y
si
c
al
n
ode
s
commit
|
commitdiff
|
tree
2015-06-22
Ber
k
Hess
Avoid fp
e
x
ceptio
n
s
i
n p
a
ir se
a
rch de
b
u
g
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Repl
a
ced
h
ard
w
are threads by logical cores i
n
outp
u
t
commit
|
commitdiff
|
tree
2015-06-18
Berk Hes
s
Reduced
th
e
cost
of the pu
l
l communication
commit
|
commitdiff
|
tree
2015-06-17
Be
r
k H
e
ss
Refac
t
ored pull d
a
t
a
stru
c
tures
commit
|
commitdiff
|
tree
2015-06-16
B
e
rk Hess
A
d
ded
m
issing
DD cycle
c
ountin
g
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Automated t
h
e -gp
u
_
id o
p
tion
commit
|
commitdiff
|
tree
2015-06-14
Berk Hess
Refactored mdrun resource d
i
vis
i
on
commit
|
commitdiff
|
tree
2015-06-13
Berk Hess
Hardwar
e
reportin
g
now covers
a
ll
node
s
commit
|
commitdiff
|
tree
2015-06-05
Be
r
k
H
e
s
s
Do
n
't use PME ranks
with GPUs
and -npme=-1
commit
|
commitdiff
|
tree
2015-05-27
Berk
H
ess
R
efactoring o
f
PME l
o
ad b
a
l
a
ncing
commit
|
commitdiff
|
tree
2015-05-23
Berk He
s
s
R
emov
e
d s
t
a
t
ic from variables
i
n gmx_lapack
commit
|
commitdiff
|
tree
2015-05-16
Berk
H
ess
LINCS thread
task
s
can now b
e
independent
commit
|
commitdiff
|
tree
2015-05-13
Berk H
e
ss
Fix
e
d CUDA error
w
i
t
h empty domains
commit
|
commitdiff
|
tree
2015-05-13
Berk He
s
s
Fix segv in g_covar
commit
|
commitdiff
|
tree
2015-05-11
Berk He
s
s
Changed FFTW w
a
rning from
A
V
X
to no
SSE
commit
|
commitdiff
|
tree
2015-05-07
Berk Hess
Re
m
o
ved non-ff atomty
p
e
s f
r
om
o
pls
a
a
and charmm27
commit
|
commitdiff
|
tree
2015-05-04
Berk H
e
s
s
Fixed GPU non-local F copy l
o
cal conditional
commit
|
commitdiff
|
tree
2015-04-28
Berk Hess
Re-enabled FMA for AVX-128-FMA
commit
|
commitdiff
|
tree
2015-04-22
Berk Hess
Mer
g
e branch
'
r
e
l
ease-5-0'
commit
|
commitdiff
|
tree
2015-04-17
B
e
rk Hess
Add
value
_
re
f
and va
l
ue to pull_
c
o
o
rd_t
commit
|
commitdiff
|
tree
2015-04-17
Berk Hes
s
Correct -ntmpi au
t
o f
o
r inte
l
nehale
m
and older
commit
|
commitdiff
|
tree
2015-04-08
B
erk Hess
Added pull ge
o
metry direction-relative
commit
|
commitdiff
|
tree
2015-04-01
Berk Hess
C
o
r
rected
f
orce-swit
c
h man
u
al s
e
c
tion
commit
|
commitdiff
|
tree
2015-03-19
Berk Hess
Rem
o
ved reductio
n
of dH/dl witho
u
t FE
commit
|
commitdiff
|
tree
2015-03-12
Ber
k
Hess
Fixed mdrun
fp exc
e
p
tion wit
h
-debug
commit
|
commitdiff
|
tree
2015-03-11
B
erk
H
ess
Added up
d
ate
x copy-back to u
p
date
t
imer
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Reduced cost of Beren
d
sen
p
ressur
e
co
u
pling
commit
|
commitdiff
|
tree
2015-03-06
Be
r
k Hess
Improve threadi
n
g of
b
ondeds
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
M
a
de DD e
x
c
lusion processing more
e
ffic
i
ent
commit
|
commitdiff
|
tree
2015-03-05
B
erk Hess
SIMD acc
e
ler
a
ti
o
n for LIN
C
S
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
A
l
l
o
w pull groups
of 1 atom with mas
s
0
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
COM pul
l
ing options per coo
r
d, improved cylinder
commit
|
commitdiff
|
tree
2015-03-03
Berk
H
ess
F
ix div by zero in
P
P/
P
ME ratio
commit
|
commitdiff
|
tree
2015-03-02
Ber
k
H
e
s
s
A
d
d
e
d parentheses for cas
t
s in
SIM
D
macros
commit
|
commitdiff
|
tree
2015-02-24
B
e
r
k Hess
F
i
xed parallel
d
is
t
ributi
o
n and
t
hre
a
d count r
e
porting
commit
|
commitdiff
|
tree
2015-02-12
Berk
Hess
R
e
-f
i
xed PME
b
ug wi
t
h high Op
e
nMP thread count
commit
|
commitdiff
|
tree
2015-02-06
B
er
k
Hess
Re
-
enabled SIMD for angles
a
nd dihedrals
commit
|
commitdiff
|
tree
2015-02-04
Ber
k
Hess
Corre
c
t CUD
A
ker
n
el energy flag
commit
|
commitdiff
|
tree
2015-01-21
Berk
H
ess
Co
r
rected RD
T
SCP warning text
commit
|
commitdiff
|
tree
2015-01-15
Berk Hess
Fix al
l
o
c
ation
issu
e
with VV integrat
o
r
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fixed pbc=xy + 2 walls + Ve
r
let
sch
e
me
commit
|
commitdiff
|
tree
2014-12-22
Berk
H
ess
Fix bug FE + GPU + 2/3D doma
i
n d
e
comp
o
siti
o
n
commit
|
commitdiff
|
tree
2014-12-11
B
e
rk Hess
Added grompp error fo
r
pulling to
neg
a
tive distance
commit
|
commitdiff
|
tree
2014-12-09
Berk
Hes
s
Fix recent bug with trilinic 1D DD
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
F
i
x
e
d pull c
o
ord in
i
t with ra
t
e!=0, t
_
start!=
0
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Ad
d
e
d PBC note to
c
om
m
-m
o
de=angula
r
w
arni
n
g
commit
|
commitdiff
|
tree
2014-12-05
Berk H
e
ss
Ma
k
e domdec a pro
p
er modu
l
e
commit
|
commitdiff
|
tree
2014-12-05
Berk
Hess
C
la
r
ified grompp p
u
ll
error messages
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Avoid race on dvdl
wi
t
h
Verlet+Ope
n
MP+LI
N
CS+FE+VV
commit
|
commitdiff
|
tree
2014-12-01
Berk
He
s
s
Added wa
r
ning for unne
c
essary soft-core
commit
|
commitdiff
|
tree
2014-11-26
Berk H
e
ss
Fixed triclinic 1xNx1 d
o
m
ain deco
m
position
commit
|
commitdiff
|
tree
2014-11-25
Berk
Hess
F
ixed
twin-range + freeze +
constraints
commit
|
commitdiff
|
tree
2014-11-24
Be
r
k Hes
s
Avoid Na
N
in
r
l
i
st buffer
calculation
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Corre
c
ted pa
r
ameter
f
o
r
sorting
on search grid
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Fix D
D
b
onded inte
r
action range
p
r
in
t
commit
|
commitdiff
|
tree
2014-10-20
Be
r
k He
s
s
Re
m
oved
f
_nov
i
rsum reduction in Verlet sc
h
e
m
e
commit
|
commitdiff
|
tree
2014-10-07
Berk He
s
s
Fixes i
s
sue w
i
th vsiten a
n
d
Verlet
buf
f
ers
commit
|
commitdiff
|
tree
2014-09-30
Ber
k
Hes
s
A
void D
L
B
with overloaded PME ranks
commit
|
commitdiff
|
tree
2014-09-30
Be
r
k
He
s
s
A
d
d
ed GPU local wait
t
o
load b
a
lanci
n
g
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
Domai
n
decomp
o
sition
now c
h
ecks the r
l
ist buffer
commit
|
commitdiff
|
tree
2014-09-29
B
erk Hess
SIMD acceleratio
n
f
o
r RB dihedrals
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
Av
o
id PME tuning decrea
s
i
n
g rcou
l
omb
commit
|
commitdiff
|
tree
2014-09-29
Berk Hess
Fix calc_g
r
id
a
voiding PME gr
i
d
f
actor
8
4
commit
|
commitdiff
|
tree
2014-09-09
Berk Hess
Fixed DD state col
l
ection issue
commit
|
commitdiff
|
tree
2014-09-08
Berk Hess
Check
for implicit solvent + Verlet scheme
commit
|
commitdiff
|
tree
2014-08-28
B
e
rk Hess
Fixed two PM
E
issues with
M
PI+OpenM
P
commit
|
commitdiff
|
tree
2014-08-25
Ber
k
Hess
Fix
e
d bugs in vsit
e
N
with OpenMP
commit
|
commitdiff
|
tree
2014-08-24
Berk H
e
ss
Initialize unused velocity c
o
nst
r
aint components
commit
|
commitdiff
|
tree
2014-08-17
B
e
rk Hess
Halved the c
o
st
o
f
the pull
c
ommunic
a
ti
o
n
commit
|
commitdiff
|
tree
2014-08-14
Ber
k
Hes
s
Correc
t
e
d
SIM
D
math overflow documenta
t
i
on
commit
|
commitdiff
|
tree
2014-08-10
Berk He
s
s
Added checks f
o
r TPI + Verlet scheme
commit
|
commitdiff
|
tree
2014-08-05
Berk Hess
Fix
hang with LJ-
P
ME and empty domains
commit
|
commitdiff
|
tree
2014-08-02
Berk Hess
Fixed PME bug wit
h
high OpenMP
t
hread count
commit
|
commitdiff
|
tree
2014-07-31
Berk Hess
Av
o
id divi
s
ion by 0
in nbnxn_s
e
arch
commit
|
commitdiff
|
tree
2014-06-29
Berk
H
ess
Take
LJ-
P
M
E
into
account fo
r
t
a
ble spacing
commit
|
commitdiff
|
tree
2014-06-29
Berk
H
ess
U
p
dated LJ-PME documentation
commit
|
commitdiff
|
tree
2014-06-24
Berk Hess
Fi
x
ed
the sign of mass perturbed cont
r
ibuti
o
n
commit
|
commitdiff
|
tree
2014-06-20
Berk Hess
Fix g_mi
n
d
i
st with pbc=
X
Y
commit
|
commitdiff
|
tree
2014-06-20
Berk
H
ess
Fi
x
e
d shells with
p
article deco
m
posit
i
on
commit
|
commitdiff
|
tree
2014-06-18
Berk H
e
ss
Fixed sign error in posres dv
d
l
commit
|
commitdiff
|
tree
2014-06-17
B
erk Hes
s
Updat
e
d mdrun -np
m
e
d
ocumentation
commit
|
commitdiff
|
tree
2014-06-17
Berk Hess
Re
m
oved round
i
ng
i
s
s
ue in nbnxn Ewal
d
tab
l
e
commit
|
commitdiff
|
tree
2014-06-14
Berk Hess
Fixed PME
bu
g
w
i
th #OpenMP-threads a l
a
rge
pr
i
me
commit
|
commitdiff
|
tree
2014-06-13
Berk
Hess
Change
d
a
p
pending file name
e
rror message
commit
|
commitdiff
|
tree
2014-06-13
B
erk
H
ess
Made shells work with the Verlet scheme
commit
|
commitdiff
|
tree
2014-06-12
Be
r
k Hess
Fixed perturbed wall interact
i
ons
commit
|
commitdiff
|
tree
2014-06-12
Berk He
s
s
Made
g
mxcheck -rmsd
work again with forces
commit
|
commitdiff
|
tree
2014-06-11
B
e
rk Hess
Dec
o
upled repl_ex_nst from nstcalce
n
e
r
g
y
commit
|
commitdiff
|
tree
2014-06-11
Berk He
s
s
M
a
de
repl_ex t
i
me step more
reada
b
l
e
commit
|
commitdiff
|
tree
2014-06-10
Berk Hess
Replaced
g
mx_h
o
stnam
e
_num by gmx
_
physicalnode_id_hash
commit
|
commitdiff
|
tree
2014-06-09
B
erk Hess
Set make_n
d
x max n
a
me lengt
h
and
count
t
o 10
2
4
commit
|
commitdiff
|
tree
2014-06-05
Be
r
k
H
e
s
s
Fixed
shift and switch modif
i
ers, par
t
icularly fo
r
.
.
.
commit
|
commitdiff
|
tree
2014-06-05
Ber
k
Hess
Fi
x
constraint v
i
rial wi
t
h m
u
ltip
l
e
t
ime stepping
commit
|
commitdiff
|
tree
2014-06-02
Berk Hess
Fi
x
e
d g_e
n
erg
y
Einstein viscosity
commit
|
commitdiff
|
tree
next