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Detect incorrect cycle counting
2015-09-15
Berk Hess
Detect incorrect cycle countin
g
commit
|
commitdiff
|
tree
2015-06-30
B
erk Hess
Fi
x
in
c
ons
i
stent
OpenMP
automatio
n
commit
|
commitdiff
|
tree
2015-06-26
Alexey Shve
t
sov
F
i
x recent compilation issu
e
in pullcode
commit
|
commitdiff
|
tree
2015-06-22
B
e
rk Hess
Fix g_energy ave
r
age/RMSD
b
ug
commit
|
commitdiff
|
tree
2015-05-23
Berk H
e
ss
R
e
moved s
t
atic
from vari
a
b
les in gmx_lapack
commit
|
commitdiff
|
tree
2015-05-13
Ber
k
He
s
s
Fixed CUD
A
error
w
ith empt
y
domains
commit
|
commitdiff
|
tree
2015-05-11
Berk Hes
s
Changed FFTW w
a
rn
i
ng from AVX
to
n
o SSE
commit
|
commitdiff
|
tree
2015-05-07
B
e
rk Hess
Removed non-ff at
o
m
typ
e
s
from
oplsaa a
n
d charmm
2
7
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fix
e
d GPU
non-l
o
cal F copy local con
d
i
t
ional
commit
|
commitdiff
|
tree
2015-04-28
Berk Hess
Re-e
n
ab
l
ed
F
MA for AVX-128-FMA
commit
|
commitdiff
|
tree
2015-04-22
B
erk
Hess
Merge branch 're
l
ease-5-0'
commit
|
commitdiff
|
tree
2015-04-17
Berk Hess
Correct -ntmpi auto
f
o
r
intel neha
l
em and older
commit
|
commitdiff
|
tree
2015-03-05
Berk H
e
ss
Mad
e
DD exclu
s
ion p
r
o
c
essing more
e
f
f
i
c
ient
commit
|
commitdiff
|
tree
2015-02-12
B
e
rk Hess
R
e
-fix
e
d PME bug with high
OpenM
P
thread co
u
nt
commit
|
commitdiff
|
tree
2015-01-21
Be
r
k Hess
Corre
c
ted RDTSCP warnin
g
text
commit
|
commitdiff
|
tree
2014-12-11
B
erk H
e
ss
Added
g
ro
m
pp error for pulling to negative distan
c
e
commit
|
commitdiff
|
tree
2014-12-09
B
erk Hess
Fi
x
recent bug with
t
rilinic 1D DD
commit
|
commitdiff
|
tree
2014-11-24
D
avid van der Spo
e
l
A
d
ded warn
i
n
gs f
o
r ewald-
g
eometry
and sur
f
ace-epsi
l
on
commit
|
commitdiff
|
tree
2014-10-07
Berk Hes
s
Fixes issu
e
with
v
siten
and
V
erlet
buffers
commit
|
commitdiff
|
tree
2014-09-09
Berk He
s
s
Fixed DD state collecti
o
n is
s
ue
commit
|
commitdiff
|
tree
2014-09-08
Berk Hess
Check for impli
c
it solvent
+
Verl
e
t
scheme
commit
|
commitdiff
|
tree
2014-08-25
B
e
rk Hess
F
i
xed bugs
in v
s
iteN w
i
th Op
e
nMP
commit
|
commitdiff
|
tree
2014-08-02
B
erk Hess
Fixed
PME bug with high OpenMP thread co
u
nt
commit
|
commitdiff
|
tree
2014-07-31
Berk Hess
Avoid division by 0
in
nbnxn_search
commit
|
commitdiff
|
tree
2014-07-28
Christi
a
n
W
e
nnb
e
rg
Fix
overflow in LJ-PME nb
n
xn kernels
commit
|
commitdiff
|
tree
2014-06-20
Be
r
k Hess
Fixe
d
shells wit
h
p
a
rt
i
cle decomposition
commit
|
commitdiff
|
tree
2014-06-10
Berk Hess
Re
p
l
a
ced gmx_ho
s
tname
_
n
u
m by gmx_physica
l
n
o
de_id_hash
commit
|
commitdiff
|
tree
2014-06-02
Berk
H
e
ss
Fixed g_ene
r
gy Ein
s
t
e
in viscosity
commit
|
commitdiff
|
tree
2014-03-24
Berk
Hess
Adds
cut
-
off checks fo
r
triclinic
domain dec
o
mposition
commit
|
commitdiff
|
tree
2013-12-03
Berk Hes
s
Re
m
o
ved restri
c
tion
o
f on
e
reference p
u
ll group
commit
|
commitdiff
|
tree
2013-11-15
Berk Hess
corre
c
ted p
o
t
e
ntial nbnxn SIM
D
memory issue
commit
|
commitdiff
|
tree
2013-11-08
Berk Hess
f
i
x nbnxn
at
o
m
s
o
r
ting wit
h
distant bondeds
commit
|
commitdiff
|
tree
2013-11-06
S
z
ilard Pa
l
l
en
a
ble GPU shar
i
ng am
o
ng tMPI rank
s
commit
|
commitdiff
|
tree
2013-10-31
B
e
rk Hess
reorganized
G
P
U detection a
n
d selection
commit
|
commitdiff
|
tree
2013-10-22
Ber
k
Hess
fixed re
c
ent bug with
C
UDA texture
objects
commit
|
commitdiff
|
tree
2013-10-22
B
e
rk Hess
fixed O
p
enMP threads being pinned to the same cores
commit
|
commitdiff
|
tree
2013-10-10
B
e
rk
Hess
f
ixed n
b
nxn 4x8 pair search without AVX
commit
|
commitdiff
|
tree
2013-06-03
Ber
k
H
e
ss
fixed de
a
dlock with r
e
plica exchange
a
nd -m
a
x
h
commit
|
commitdiff
|
tree
2013-05-08
Berk Hess
f
ixed incorrect scaling
o
f cos
-
acceleration
viscosit
y
commit
|
commitdiff
|
tree
2013-04-26
Berk Hess
PME load
bal
a
n
c
i
ng now c
h
ecks for PM
E
grid restrictio
n
s
commit
|
commitdiff
|
tree
2013-04-18
Berk Hess
c
hanged mdrun -nsteps to gmx
_
large_
i
nt_t
commit
|
commitdiff
|
tree
2013-04-12
Berk Hes
s
i
mproved
l
oad
b
a
lanc
i
ng w
i
th Verlet cut-off scheme
commit
|
commitdiff
|
tree
2013-03-27
Berk
Hess
removed x86
s
p
ecifics from nbnxn SIMD kernels
commit
|
commitdiff
|
tree
2013-03-27
B
erk He
s
s
correct
e
d log file wall time breakdown
commit
|
commitdiff
|
tree
2013-03-21
Berk Hess
made PME work with a mix of
1
and mor
e
threads
commit
|
commitdiff
|
tree
2013-03-14
Berk Hess
correct
e
d g
r
om
p
p rvdw c
h
arge-g
r
oup radii che
c
k
commit
|
commitdiff
|
tree
2013-02-26
Berk He
s
s
fixed PME t
i
me
p
r
i
nt with -ntomp_pme != -
n
tomp
commit
|
commitdiff
|
tree
2013-02-20
B
erk Hess
added mdrun check for Ve
r
l
et
+
pe
r
turbed
ato
m
s
commit
|
commitdiff
|
tree
2013-02-06
Berk
Hess
fixed bug w
i
th sd integrator a
n
d OpenMP threa
d
ing
commit
|
commitdiff
|
tree
2013-02-05
Berk Hess
i
m
proved
l
o
ad
balancing o
n
th
e
G
PU
commit
|
commitdiff
|
tree
2013-02-04
Ber
k
He
s
s
fixed segv i
n
in
i
t_forcerec with fr->hwi
n
fo=NULL
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
improved
CUDA kernel performanc
e
by pre-l
o
ading cj
commit
|
commitdiff
|
tree
2013-01-16
Carsten
K
utzner
M
a
d
e
g
_tune_pme work cor
r
ectly a
g
ain
with thread-M
P
I
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
B
e
rk Hess
made SHAKE
w
o
rk a
g
ain with particle deco
m
postion
commit
|
commitdiff
|
tree
2013-01-10
Berk H
e
ss
f
i
x
e
d
b
u
g
with Verlet + DD
+
bonded
atom c
o
mmunicati
o
n
commit
|
commitdiff
|
tree
2013-01-10
Erik
L
indahl
R
e
vert
d
efault rlist/r
v
dw/rcou
l
omb t
o
va
l
id
v
a
lues
.
.
.
commit
|
commitdiff
|
tree
2013-01-02
Ber
k
Hess
minor speed
-
u
p and code
clean-up
in nbnxn
kernels
commit
|
commitdiff
|
tree
2012-12-20
B
e
rk Hess
fix
e
d recent bugs in LINCS for d
e
ri
v
a
t
i
v
e
s
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
ren
a
med
g
mx_x86_sim
d
_macro
s
.
h to gmx_simd_macros
.
h
commit
|
commitdiff
|
tree
2012-12-18
B
e
r
k
Hess
implemented nbnxn AVX-2
5
6 2x(N+
N
) ker
n
e
l
s
commit
|
commitdiff
|
tree
2012-12-11
Berk Hes
s
reduc
e
d
PLI
N
CS co
m
mun
i
cation with H-b
o
nd constr
a
i
nts
commit
|
commitdiff
|
tree
2012-12-07
Berk Hess
fi
x
ed GPU pair-search with GMX_CPU_AC
C
E
L
E
RATION=None
commit
|
commitdiff
|
tree
2012-12-05
Berk Hess
fixed incorrect viri
a
l with virtual
s
ites and OpenM
P
commit
|
commitdiff
|
tree
2012-12-05
Berk H
e
ss
fixed s
e
gv
in Ve
r
let pair
-
s
earc
h
with trilinic DD
commit
|
commitdiff
|
tree
2012-11-30
B
erk Hess
fixed issue with -multi and GPUs
commit
|
commitdiff
|
tree
2012-11-28
Berk H
e
ss
f
ixed thread pinni
n
g
with mdru
n
-
multi
commit
|
commitdiff
|
tree
2012-11-28
Szilard Pall
ena
b
l
e
G
PU emulat
i
on without G
P
U
s
upp
o
rt
commit
|
commitdiff
|
tree
2012-11-28
Berk H
e
s
s
exte
n
ded
nbnxn x86
SIMD kernel blendv s
u
pport
commit
|
commitdiff
|
tree
2012-11-27
B
erk Hess
fixed b
u
g i
n
nbnxn
O
penM
P
non-bonded force reducti
o
n
commit
|
commitdiff
|
tree
2012-11-26
Berk Hess
m
a
de nbnxn an
a
lytical Ewa
l
d consiste
n
t
commit
|
commitdiff
|
tree
2012-11-26
Berk Hess
added nb
n
xn anal
y
tic
a
l Ew
a
ld cor
r
ection
k
ern
e
l
s
commit
|
commitdiff
|
tree
2012-11-15
B
e
rk Hess
fixed incorr
e
ct 1-4 energies with OpenMP + energy groups
commit
|
commitdiff
|
tree
2012-11-14
Berk Hess
fixed nbnxn x86 SIM
D
non-
b
o
nded
perform
a
nce regressio
n
commit
|
commitdiff
|
tree
2012-11-12
Berk He
s
s
nbnxn
CPU force bu
f
fer reduc
t
ion now uses SIMD
commit
|
commitdiff
|
tree
2012-11-05
B
e
rk Hess
upd
a
t
ed several things related with OpenMP thread c
o
unt
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
fixe
d
incorrect PME load balancing l
i
mitation
commit
|
commitdiff
|
tree
2012-10-26
B
e
rk Hess
set the default fo
r
nstdh
d
l to 100
commit
|
commitdiff
|
tree
2012-10-26
B
e
rk Hess
f
ixed
i
ncorrect group
energ
i
e
s with nbnxn CPU
k
ernels
commit
|
commitdiff
|
tree
2012-10-22
Roland Schulz
Fix clang 3
.
2 uninti
a
l
ized variabl
e
warnings
commit
|
commitdiff
|
tree
2012-10-18
Berk Hess
renamed
c
o
n
straint variables r
m
dr to vir
_
r_m_dr
commit
|
commitdiff
|
tree
2012-10-17
Berk Hess
ren
a
med pme_switch
.
.
.
to
pme_loadbal
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
B
e
rk Hess
made pair-
s
ear
c
h with GPU 20% faster
commit
|
commitdiff
|
tree
2012-10-08
Berk Hess
made
n
on
-
bonded po
t
ential shif
t
s mdp options
commit
|
commitdiff
|
tree
2012-10-03
B
erk Hess
impr
o
ved the energy c
o
nservation
w
i
th SE
T
TLE
commit
|
commitdiff
|
tree
2012-09-13
B
er
k
Hess
fixed recent bug w
i
th grom
p
p
check for P-R P-coupling
commit
|
commitdiff
|
tree
2012-08-29
Berk Hess
b
ug fix for pme
.
c M
P
I_COMM_NULL fix dcf8
b
67e
commit
|
commitdiff
|
tree
2012-08-09
B
e
r
k
Hess
fixed tr
j
conv no
t
wr
i
t
i
ng velocit
i
es with c
p
t
i
n
put
commit
|
commitdiff
|
tree
2012-08-06
B
e
rk Hess
fixed i
n
corr
e
ct TPI res
u
lts with dynamic
box
commit
|
commitdiff
|
tree
2012-07-18
B
erk Hes
s
fixed D
D
c
h
arge gr
o
up d
i
splacement er
r
or chec
k
commit
|
commitdiff
|
tree
2012-06-25
Ber
k
He
s
s
f
i
xed segv/hang with EM and foreign
l
ambda val
u
e
s
commit
|
commitdiff
|
tree
2012-06-25
Be
r
k
He
s
s
a
d
ded check for log fp!=NULL whe
n
disa
b
li
n
g acc
e
lerat
i
on
commit
|
commitdiff
|
tree
2012-05-24
Berk He
s
s
now m
d
run alway
s
i
n
it
i
alizes MPI
commit
|
commitdiff
|
tree
2012-05-21
Berk Hess
gromp
p
now
r
etains
t
h
e
order
o
f bonds
co
n
verted to
.
.
.
commit
|
commitdiff
|
tree
2012-05-21
Be
r
k
Hess
re-intr
o
d
uced
fix for
r
e
al/doub
l
e issue
in gmx_density
commit
|
commitdiff
|
tree
2012-05-08
B
erk Hess
fixed
m
drun -cpi SD and
pcou
p
l initializa
t
ion
commit
|
commitdiff
|
tree
2012-04-27
B
e
rk Hess
fixed segv i
n
T
P
I with PME, fi
x
es #9
2
7
commit
|
commitdiff
|
tree
2012-04-27
Berk
H
ess
c
h
anged
P
ME
M
PI_Comm comparisi
o
ns to MPI_
C
O
MM_NULL
.
.
.
commit
|
commitdiff
|
tree
2012-04-27
Berk He
s
s
changed number of
iatoms for F_SETTLE
f
r
om
1
t
o 3
commit
|
commitdiff
|
tree
2012-04-26
Ber
k
H
ess
added su
p
por
t
fo
r
graphs not start
i
n
g
a
t 0
commit
|
commitdiff
|
tree
2012-04-26
Ber
k
Hess
Merge release-4-5-pa
t
c
h
es
i
nto
r
elease-
4
-6
commit
|
commitdiff
|
tree
next