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Removed static from variables in gmx_lapack
2015-05-23
Berk
H
ess
Remove
d
static
f
rom variables in gmx_lapack
commit
|
commitdiff
|
tree
2015-05-13
Berk Hess
Fixed CUDA error with em
p
ty domains
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
Change
d
F
FTW warning from
A
VX to no SSE
commit
|
commitdiff
|
tree
2015-05-07
Berk
H
ess
Removed
non-ff at
o
mtypes fr
o
m oplsaa
a
nd ch
a
r
m
m
2
7
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fixed GPU
n
o
n-loca
l
F copy
l
ocal
c
onditional
commit
|
commitdiff
|
tree
2015-04-28
Berk
Hess
Re-
e
nabled FMA for A
V
X-12
8
-FMA
commit
|
commitdiff
|
tree
2015-04-22
Berk
Hess
Merge bran
c
h
'release
-
5-0'
commit
|
commitdiff
|
tree
2015-04-17
B
e
rk H
e
ss
Correct -ntmpi auto
f
o
r
in
t
el nehalem and o
l
der
commit
|
commitdiff
|
tree
2015-03-05
Berk He
s
s
Made D
D
exc
l
usion proces
s
i
n
g more efficient
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
Re-fixed PME bu
g
with high
Ope
n
MP thread
c
ount
commit
|
commitdiff
|
tree
2015-01-21
Berk He
s
s
Corrected
R
D
T
S
C
P
warni
n
g
text
commit
|
commitdiff
|
tree
2014-12-11
B
e
rk Hess
Added grompp
erro
r
f
o
r
pullin
g
to nega
t
ive d
i
stance
commit
|
commitdiff
|
tree
2014-12-09
B
e
rk
H
ess
F
ix recent bug with trilinic 1D
D
D
commit
|
commitdiff
|
tree
2014-11-24
Da
v
i
d van der Spoel
Adde
d
warnings for ewald-
g
eomet
r
y a
n
d surface-epsilon
commit
|
commitdiff
|
tree
2014-10-07
B
erk
Hes
s
Fixes issue with
v
siten
and Ve
r
let
b
uf
f
er
s
commit
|
commitdiff
|
tree
2014-09-09
Be
r
k He
s
s
Fixed DD state c
o
llection issue
commit
|
commitdiff
|
tree
2014-09-08
Be
r
k Hess
Check for implicit solvent + Ver
l
e
t
schem
e
commit
|
commitdiff
|
tree
2014-08-25
Berk
H
e
ss
Fixe
d
bugs in vsit
e
N with
Open
M
P
commit
|
commitdiff
|
tree
2014-08-02
Berk He
s
s
F
i
xed PME b
u
g with hi
g
h OpenMP thread
count
commit
|
commitdiff
|
tree
2014-07-31
Berk Hess
Avoid division by 0 in nbnxn_s
e
arch
commit
|
commitdiff
|
tree
2014-07-28
Chr
i
s
t
ian Wennbe
r
g
Fix ove
r
flow i
n
LJ-PME nbnxn k
e
rnels
commit
|
commitdiff
|
tree
2014-06-20
Be
r
k Hes
s
Fixed shel
l
s
w
ith particle de
c
o
m
posit
i
on
commit
|
commitdiff
|
tree
2014-06-10
B
erk He
s
s
Re
p
laced
g
mx_ho
s
tname
_
num
b
y
gmx_physicalno
d
e_id_ha
s
h
commit
|
commitdiff
|
tree
2014-06-02
Ber
k
Hess
Fixed g_energy Einstein vi
s
cosity
commit
|
commitdiff
|
tree
2014-03-24
Ber
k
Hess
A
d
ds
cut-off ch
e
cks for t
r
iclini
c
d
omain dec
o
mpositio
n
commit
|
commitdiff
|
tree
2013-12-03
Berk Hess
Remo
v
e
d
restr
i
ct
i
on
of one reference pull gr
o
u
p
commit
|
commitdiff
|
tree
2013-11-15
Berk Hess
corr
e
cte
d
potent
i
al nbnxn SIMD me
m
o
r
y i
s
sue
commit
|
commitdiff
|
tree
2013-11-08
B
e
r
k Hess
fix nbn
x
n
atom
sorti
n
g w
i
th dis
t
an
t
bondeds
commit
|
commitdiff
|
tree
2013-11-06
Szila
r
d
Pall
enable GPU
sharing among t
M
PI ranks
commit
|
commitdiff
|
tree
2013-10-31
Be
r
k Hess
r
e
organized GPU detect
i
on and select
i
o
n
commit
|
commitdiff
|
tree
2013-10-22
B
erk Hess
fixed
recent bug wi
t
h
CUDA texture obj
e
cts
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
fixed
OpenMP th
r
eads
b
eing
pin
n
ed
t
o the sa
m
e core
s
commit
|
commitdiff
|
tree
2013-10-10
Berk Hess
fixed
nb
n
xn 4x8 p
a
i
r sea
r
ch without AV
X
commit
|
commitdiff
|
tree
2013-06-03
Berk Hess
fixed dea
d
lo
c
k
with replica exchang
e
and -maxh
commit
|
commitdiff
|
tree
2013-05-08
B
e
rk Hess
fixed
i
ncorrect
s
caling of co
s
-acceleration viscosity
commit
|
commitdiff
|
tree
2013-04-26
Berk Hess
PME load
balan
c
ing now c
h
ec
k
s for PME grid restrictions
commit
|
commitdiff
|
tree
2013-04-18
B
erk
He
s
s
changed md
r
un -nsteps t
o
gmx_large_in
t
_t
commit
|
commitdiff
|
tree
2013-04-12
Ber
k
Hess
improv
e
d
load ba
l
ancing with
V
e
rlet cut-off sche
m
e
commit
|
commitdiff
|
tree
2013-03-27
Berk Hes
s
removed x86 spec
i
fics
from nbn
x
n SIMD kernels
commit
|
commitdiff
|
tree
2013-03-27
B
e
r
k
H
ess
corrected
log file wall time breakdown
commit
|
commitdiff
|
tree
2013-03-21
B
e
rk
Hess
made PME
w
ork with a mix
o
f 1 a
n
d
m
ore threads
commit
|
commitdiff
|
tree
2013-03-14
Berk Hess
corre
c
ted grompp
r
v
dw cha
r
ge-group radii check
commit
|
commitdiff
|
tree
2013-02-26
Berk Hess
fixed
PM
E
time print wi
t
h
-nto
m
p_pme != -ntomp
commit
|
commitdiff
|
tree
2013-02-20
Berk He
s
s
added md
r
un
check for Verle
t
+perturbed atoms
commit
|
commitdiff
|
tree
2013-02-06
Berk H
e
ss
fix
e
d bug with sd
i
ntegrat
o
r
and OpenMP th
r
eadin
g
commit
|
commitdiff
|
tree
2013-02-05
Berk Hess
improv
e
d
l
oad balancing on th
e
GPU
commit
|
commitdiff
|
tree
2013-02-04
Berk Hess
fixe
d
segv in init_forcere
c
with fr->hwi
n
fo=NULL
commit
|
commitdiff
|
tree
2013-01-17
Berk
H
e
s
s
impr
o
ved CUDA kernel performance by pre-loading cj
commit
|
commitdiff
|
tree
2013-01-16
Carsten Kutzner
Made g_tune_pme
w
o
r
k
co
r
rectly aga
i
n with thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Berk Hess
made SHAKE work again with particle decomp
o
stion
commit
|
commitdiff
|
tree
2013-01-10
Berk Hess
f
ixed
b
ug with Verlet + DD + bo
n
d
e
d
a
t
om
comm
u
nication
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Re
v
ert d
e
fault rlist/rvdw/rcou
l
omb
t
o
valid
v
a
lues
.
.
.
commit
|
commitdiff
|
tree
2013-01-02
Berk Hess
mino
r
s
peed-
u
p and code cl
e
an-up i
n
n
bnxn ker
n
els
commit
|
commitdiff
|
tree
2012-12-20
B
e
rk Hess
f
ixed r
e
cent bugs in
L
INCS
f
or derivativ
e
s
commit
|
commitdiff
|
tree
2012-12-18
Ber
k
Hess
ren
a
m
e
d gmx_x86_simd_m
a
c
r
os
.
h
t
o gmx_s
i
md_mac
r
os
.
h
commit
|
commitdiff
|
tree
2012-12-18
B
e
rk He
s
s
implement
e
d
n
b
nxn
A
VX-256 2x(
N
+N)
kerne
l
s
commit
|
commitdiff
|
tree
2012-12-11
Berk H
e
ss
red
u
ced PLIN
C
S com
m
unicatio
n
with H
-
bond constraints
commit
|
commitdiff
|
tree
2012-12-07
Berk
H
ess
fixe
d
GPU pa
i
r-search with GMX_
C
PU_ACCEL
E
RATION=None
commit
|
commitdiff
|
tree
2012-12-05
Berk H
e
ss
fixed
i
nc
o
rrect viria
l
wi
t
h vi
r
tual sites and OpenMP
commit
|
commitdiff
|
tree
2012-12-05
B
e
rk Hess
fixe
d
seg
v
in
V
erlet pair-search with trilinic DD
commit
|
commitdiff
|
tree
2012-11-30
Berk Hes
s
f
ix
e
d is
s
ue w
i
th -m
u
lti and
G
P
U
s
commit
|
commitdiff
|
tree
2012-11-28
Be
r
k Hess
fixed thread pinning with
mdrun -multi
commit
|
commitdiff
|
tree
2012-11-28
Sz
i
lard Pall
enabl
e
GPU em
u
l
at
i
on
w
ithou
t
GPU suppo
r
t
commit
|
commitdiff
|
tree
2012-11-28
Ber
k
Hess
extended
n
b
nxn x86 S
I
MD k
e
rnel b
l
endv support
commit
|
commitdiff
|
tree
2012-11-27
B
e
rk
H
e
s
s
fixed bug in nbnxn OpenMP non-bond
e
d force reducti
o
n
commit
|
commitdiff
|
tree
2012-11-26
Berk H
e
ss
m
a
d
e
nbnxn analytical Ewald
c
onsistent
commit
|
commitdiff
|
tree
2012-11-26
Berk He
s
s
added nbnxn
a
na
l
ytica
l
Ewald corr
e
ction kerne
l
s
commit
|
commitdiff
|
tree
2012-11-15
Berk Hess
fi
x
ed inc
o
rre
c
t
1
-
4
energies
w
i
t
h
OpenMP + energy grou
p
s
commit
|
commitdiff
|
tree
2012-11-14
Berk Hess
fixe
d
nbn
x
n
x86 S
I
MD non-b
o
nded perf
o
rm
a
nce
r
egre
s
sion
commit
|
commitdiff
|
tree
2012-11-12
B
erk Hess
nb
n
xn CPU f
o
rce
b
uffer reduc
t
ion n
o
w uses SIMD
commit
|
commitdiff
|
tree
2012-11-05
B
e
rk
H
e
s
s
updated several things related with OpenMP t
h
r
e
a
d
count
commit
|
commitdiff
|
tree
2012-10-26
Be
r
k Hess
f
i
xed incorrect P
M
E load bala
n
cing limitation
commit
|
commitdiff
|
tree
2012-10-26
Berk
H
es
s
set the
d
efault for
nstdh
d
l
t
o 100
commit
|
commitdiff
|
tree
2012-10-26
B
erk Hess
fixed in
c
orre
c
t group energies
with nbnxn CPU kern
e
ls
commit
|
commitdiff
|
tree
2012-10-22
R
ola
n
d
S
c
hulz
Fix clang 3
.
2 unintialized variable warnings
commit
|
commitdiff
|
tree
2012-10-18
Ber
k
He
s
s
renamed constraint variables rm
d
r
to
v
ir
_
r_m_
d
r
commit
|
commitdiff
|
tree
2012-10-17
Berk
H
e
ss
re
n
amed pme_switch
.
.
.
to
p
me
_
loadbal
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Berk H
e
s
s
made pair-
s
earch
w
ith GPU
2
0% faster
commit
|
commitdiff
|
tree
2012-10-08
Berk Hess
made non-bonded potential shifts
m
dp options
commit
|
commitdiff
|
tree
2012-10-03
Berk H
e
ss
i
mproved
t
h
e e
n
ergy conservation
w
ith SETTLE
commit
|
commitdiff
|
tree
2012-09-13
Berk H
e
ss
f
i
x
ed recen
t
bug
w
ith
g
rompp
check for P
-
R
P
-cou
p
lin
g
commit
|
commitdiff
|
tree
2012-08-29
B
erk Hess
bug
f
ix
f
or pme
.
c
MPI_
C
OMM
_
N
ULL fi
x
dcf8b67e
commit
|
commitdiff
|
tree
2012-08-09
Berk Hess
fixed trjc
o
nv not writi
n
g v
e
loci
t
i
e
s
with cpt input
commit
|
commitdiff
|
tree
2012-08-06
Berk
H
ess
f
ixed incor
r
ect TPI
resu
l
t
s
with dynamic box
commit
|
commitdiff
|
tree
2012-07-18
Be
r
k Hess
fixed DD charge gro
u
p
d
isplacem
e
nt e
r
ror check
commit
|
commitdiff
|
tree
2012-06-25
B
erk
Hess
fixed s
e
gv/hang with EM and foreig
n
lam
b
da values
commit
|
commitdiff
|
tree
2012-06-25
Berk Hes
s
added check f
o
r l
o
g fp
!
=NULL when disabl
i
ng ac
c
eleration
commit
|
commitdiff
|
tree
2012-05-24
Be
r
k Hess
now mdr
u
n always initializes MPI
commit
|
commitdiff
|
tree
2012-05-21
Berk H
e
ss
gro
m
pp
now retains the
o
rder
of
bonds converted to
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
B
e
r
k
He
s
s
re-i
n
tro
d
uced fix for
real/doubl
e
issue in gmx_d
e
nsity
commit
|
commitdiff
|
tree
2012-05-08
B
e
rk H
e
ss
fixed mdrun -cpi
S
D and pcoupl
i
ni
t
ialization
commit
|
commitdiff
|
tree
2012-04-27
Be
r
k H
e
ss
fixe
d
segv
in T
P
I with PME, fixes #927
commit
|
commitdiff
|
tree
2012-04-27
Berk Hess
changed PME MPI_Comm c
o
m
p
arisions to
MPI_
C
OMM_NUL
L
.
.
.
commit
|
commitdiff
|
tree
2012-04-27
Berk Hess
changed number of iatoms for F_SETTLE fr
o
m 1 to 3
commit
|
commitdiff
|
tree
2012-04-26
Be
r
k
Hess
added suppo
r
t for graphs not star
t
ing
a
t 0
commit
|
commitdiff
|
tree
2012-04-26
B
e
rk H
e
ss
M
e
rge release-4-
5
-pa
t
che
s
into re
l
eas
e
-
4
-
6
commit
|
commitdiff
|
tree
2012-04-26
Berk He
s
s
fixed the
reported temperature
w
ith Brown
i
an dynamics
commit
|
commitdiff
|
tree
2012-04-26
Berk Hess
fixed dispersio
n
correction wi
t
h
parallel EM
commit
|
commitdiff
|
tree
2012-04-25
Berk Hess
replaced PPP
M
by
P3M-AD: a
few lines in pme
.
c
commit
|
commitdiff
|
tree
2012-04-25
Berk Hess
fixed
ini
t
ial
CO
M
motion remo
v
al with multiple
g
roups
commit
|
commitdiff
|
tree
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