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optimized generic SIMD invsqrt
2013-09-24
Berk Hess
opt
i
mized generic SIMD in
v
sqrt
commit
|
commitdiff
|
tree
2013-09-21
Berk
H
ess
fixed multip
l
e dist
a
n
ce
r
e
straints with Ope
n
MP
commit
|
commitdiff
|
tree
2013-09-20
Mark Abraham
Described another way
g_tune_pme might
reasonably fa
i
l
commit
|
commitdiff
|
tree
2013-09-20
Mark Abraham
F
i
x total ti
m
e measu
r
eme
n
t with
s
e
parate PME n
o
des
commit
|
commitdiff
|
tree
2013-09-19
Mar
k
Abraham
Fixe
d
r
e
a
d
i
ng h
i
s
t
o
ry_t
f
rom che
c
k
poin
t
commit
|
commitdiff
|
tree
2013-09-19
Mark
A
brah
a
m
Fi
x
ed g_
t
une_pme assumption that MPI is available
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
made
f
ree energy
PME kerne
l
4
0
% faster
commit
|
commitdiff
|
tree
2013-09-16
Mi
c
hael Shirts
Fixing manual f
o
r sc-coul d
e
scription
.
commit
|
commitdiff
|
tree
2013-09-16
Berk Hess
m
d
run without Open
M
P
with thread-M
P
I n
o
w uses all cor
e
s
commit
|
commitdiff
|
tree
2013-09-13
B
e
rk Hess
corrected
grompp constr
a
i
nt/DOF warning with v
s
i
t
es
commit
|
commitdiff
|
tree
2013-08-25
Mar
k
Abraha
m
Split up Verlet SIMD
kernels for fas
t
er compi
l
ati
o
n
commit
|
commitdiff
|
tree
2013-08-25
Mark Abraha
m
Fi
x
detection and suggesti
o
n in gmx
_
c
p
uid for IBM QPX
commit
|
commitdiff
|
tree
2013-08-25
Ber
k
H
ess
introdu
c
e
d nb
n
x
n
data str
u
cture for bounding boxes
commit
|
commitdiff
|
tree
2013-08-25
M
ark
A
braham
Fixes for Blu
e
g
ene/Q
commit
|
commitdiff
|
tree
2013-08-25
Mark Abraham
Consolid
a
t
ed NBNxN SIMD kernel utility routines
commit
|
commitdiff
|
tree
2013-08-25
Mark
Abraham
Fix mino
r
wallcy
c
le output i
s
s
u
es
commit
|
commitdiff
|
tree
2013-08-25
Ma
r
k A
b
raham
F
i
xed GMX_DD_
D
UMP_GRID
commit
|
commitdiff
|
tree
2013-08-20
Ber
k
Hes
s
fi
x
ed parallel nor
m
al m
o
d
e
s with PME
commit
|
commitdiff
|
tree
2013-08-05
Mark Abraham
Fixed reference SIM
D
code to work
with M
S
VC
commit
|
commitdiff
|
tree
2013-08-01
M
a
rk Abr
a
ha
m
Refactored p
r
eparation of buffer f
o
r NBNxN table loads
commit
|
commitdiff
|
tree
2013-08-01
Ca
r
s
t
en Kutzner
Pro
p
erly fi
n
alize MPI
on mdrun -version
.
Fix
e
s
#
1
313
commit
|
commitdiff
|
tree
2013-07-25
J
u
sti
n
Lemkul
Updated
d
list
.
c t
o
recognize more a
t
om names
.
commit
|
commitdiff
|
tree
2013-07-25
Mark
Abraham
Find
mk
l
.
h o
n
more icc versions
commit
|
commitdiff
|
tree
2013-07-25
Mark Abra
h
am
U
p
date management of l
i
near algebr
a
librari
e
s
commit
|
commitdiff
|
tree
2013-07-24
B
erk
Hess
implemente
d
plain-
C
S
I
MD ma
c
ros for re
f
erenc
e
commit
|
commitdiff
|
tree
2013-07-24
Mark
A
braham
Removed bugg
y
-seppot
o
utput
commit
|
commitdiff
|
tree
2013-07-18
Mark Ab
r
aham
Fixe
d
pdb2gmx -vsi
t
e
hydrogen -o
c
onf
.
pdb
commit
|
commitdiff
|
tree
2013-07-14
Mark Abraham
Fi
x
ed p
o
ssib
l
e
der
e
fe
r
ence of null point
e
r
commit
|
commitdiff
|
tree
2013-07-11
M
ark Ab
r
a
ham
Fixed
typo
s
i
n #in
c
lude g
u
ar
d
#def
i
nes
commit
|
commitdiff
|
tree
2013-07-07
Mark Abrah
a
m
Fix
e
d mino
r
admin issues
commit
|
commitdiff
|
tree
2013-07-05
Ma
r
k
Abra
h
am
Bump versio
n
a
fter
4
.
6
.
3 release
commit
|
commitdiff
|
tree
2013-07-01
Mark Abraham
Correct
e
d
d
efinitio
n
o
f EEL_USE
R
commit
|
commitdiff
|
tree
2013-07-01
S
a
n
d
e
r P
r
onk
Co
m
preh
e
nsive hwinfo stru
c
ture concurrency fix
.
commit
|
commitdiff
|
tree
2013-06-28
Justin
L
e
m
k
ul
Minor tweaks to qm_or
c
a
.
c
commit
|
commitdiff
|
tree
2013-06-28
Justin Lemkul
F
i
xes t
o
config
.
h
.
cmakein to
s
et GMX_QMMM_OR
C
A
.
commit
|
commitdiff
|
tree
2013-06-25
Mark Abraha
m
F
i
x
e
d #include of he
a
der for atomics on K-computer
commit
|
commitdiff
|
tree
2013-06-25
Jeff Ham
m
ond
F
i
x declarat
i
on that XLC rej
e
cted
commit
|
commitdiff
|
tree
2013-06-25
Szilard P
a
ll
added CUDA compil
e
r flags to versi
o
n header
commit
|
commitdiff
|
tree
2013-06-20
Berk Hess
fixed SD and
BD integrator OpenM
P
perfor
m
ance
commit
|
commitdiff
|
tree
2013-06-20
Michael Shirt
s
Fix
i
ng a probl
e
m when dhdl and replex
a
re no
t
multiples
commit
|
commitdiff
|
tree
2013-06-20
Berk Hess
f
lops
table
now
r
eport
s
CU
D
A
a
nalytical Ewald
commit
|
commitdiff
|
tree
2013-06-14
Ber
k
Hess
fixed minor g_bar outpu
t
is
s
u
es
commit
|
commitdiff
|
tree
2013-06-13
M
a
rk Abraham
Remo
v
e un
u
s
e
d varia
b
le
s
commit
|
commitdiff
|
tree
2013-06-07
Peter Kasson
Fixes
s
yntax for F
A
HC
O
R
E
in CM
a
keLists
.
txt
.
commit
|
commitdiff
|
tree
2013-06-07
Pedro Lacerda
Add a GMX_
N
O
_CREDITS varia
b
le
t
o not sh
o
w c
r
edits
commit
|
commitdiff
|
tree
2013-06-06
Pedro Lacerda
Var
i
ous fixes for genion
commit
|
commitdiff
|
tree
2013-06-05
Berk Hess
fixed DD i
n
t
ern
a
l state c
o
rrupti
o
n with
e
nergy min
i
m
iza
t
io
n
commit
|
commitdiff
|
tree
2013-06-04
Sander Pro
n
k
Fixed inconsistent loca
l
ity_order ar
r
a
y
f
or
t
hread
.
.
.
commit
|
commitdiff
|
tree
2013-06-04
S
a
nder Pronk
F
i
x
e
d
d
e
adlock on Mac OS X during thread affinit
y
check
.
commit
|
commitdiff
|
tree
2013-06-04
T
e
emu Murtola
S
p
lit
cmake th
r
e
a
d
detectio
n
into core t
h
read and thread_mpi
.
commit
|
commitdiff
|
tree
2013-05-30
S
zilárd Páll
fix unnecessary switch to polling GPU wait
commit
|
commitdiff
|
tree
2013-05-30
S
z
il
a
rd Pall
fix th
r
ead-safety issue in
af
f
inity layout detect
i
on
commit
|
commitdiff
|
tree
2013-05-30
Szilard Pall
add workaround for c
l
ang on AMD with FMA
commit
|
commitdiff
|
tree
2013-05-30
Justin Le
m
kul
Added GROMOS96 54A7 f
o
rce field fil
e
s
.
commit
|
commitdiff
|
tree
2013-05-30
Szilard Pa
l
l
fix thre
a
d of
f
set + stride chec
k
commit
|
commitdiff
|
tree
2013-05-30
Mic
h
ael Sh
i
rts
F
i
xing
t
he
c
o
n
straint dhdl term in s
h
ak
e
commit
|
commitdiff
|
tree
2013-05-30
David van der Spoel
Fixes #1194 error reading 4
.
5
.
5 tpr
files with dihres
commit
|
commitdiff
|
tree
2013-05-30
Mark Abraham
Work around for correct treatment
of all-vs-all
commit
|
commitdiff
|
tree
2013-05-28
Carsten Kutzner
F
i
xed calculation of sla
b
b
uffer size for flexible
.
.
.
commit
|
commitdiff
|
tree
2013-05-28
Teemu
M
urtola
Fix an error in selection
o
nl
i
ne h
e
lp
.
commit
|
commitdiff
|
tree
2013-05-28
Carsten K
u
tzner
F
ix fo
r
a rar
e
con
d
itio
n
in flexi
b
le
r
otati
o
n potentials
.
commit
|
commitdiff
|
tree
2013-05-25
Mark
Abraham
M
a
k
e F
F
T detection quieter
when
nothing is changing
commit
|
commitdiff
|
tree
2013-05-24
San
d
er Pronk
F
i
x
e
d
a potential race
condit
i
on in tMPI_Threa
d
_
c
re
a
te()
commit
|
commitdiff
|
tree
2013-05-22
Mark A
b
raham
Cl
a
r
i
fy g_gyrate -h
commit
|
commitdiff
|
tree
2013-05-22
M
a
rk Abraham
Fix
g_chi -omega
commit
|
commitdiff
|
tree
2013-05-22
Pedro Lace
r
da
Fix genion -nq an
d
-pq w
h
en using -neutral
commit
|
commitdiff
|
tree
2013-05-21
Mark Abr
a
ham
Up
d
ated
g
rom
p
p cut-off and
P
ME-Switch check
s
commit
|
commitdiff
|
tree
2013-05-21
P S L
a
cerda
Fix
-neutral option in genion
commit
|
commitdiff
|
tree
2013-05-21
Mich
a
el Sh
i
rts
F
ixed problem with
b
ond con
s
tr
a
int dhdl
b
eing left
out
commit
|
commitdiff
|
tree
2013-05-21
Erik
L
indahl
F
ujitsu
Sparc64
a
c
cele
r
ation and
g
eneral fixes f
o
r
.
.
.
commit
|
commitdiff
|
tree
2013-05-21
Sa
n
der
P
r
o
nk
New ver
s
ion of thread_mpi with many minor enh
a
nc
e
m
ent
s
commit
|
commitdiff
|
tree
2013-05-21
Mark Ab
r
aham
H
a
c
k compiler flags to silence
w
arnings on g
c
c 4
.
8
commit
|
commitdiff
|
tree
2013-05-17
Mark Abraham
I
ntroduce
fatal error
f
or GB with FE
commit
|
commitdiff
|
tree
2013-05-16
J
us
t
in Lemkul
Fix
e
d g_sgang
l
e legends
.
commit
|
commitdiff
|
tree
2013-05-16
Carsten Kut
z
ner
Choose the PBC
i
m
age of e
a
ch rot
a
tion group a
t
om d
e
pending
commit
|
commitdiff
|
tree
2013-05-15
Christoph Jung
h
ans
M
erg
e
"
fi
x
ed inco
r
r
e
ct scaling
of cos
-
acceleration
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Sander Pron
k
Merge "Fixing hand
l
in
g
of pert
u
r
b
ation ma
s
s changes
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
M
ark Abrah
a
m
Me
r
ge
"
Fixes "Fu
n
c
t
i
on t
y
pe U-B n
o
t implemented in
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Mark Abrah
a
m
Merge "
i
mprove b
u
il
d
with OpenMM, sti
l
l not 100% fixed
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Mark Abraham
Merge "fi
x
ing reru
n
with free ene
r
gy +
.
xt
c
or
.
gro
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Christoph
Junghans
improve b
u
ild with OpenM
M
, still not
1
00% fixed
commit
|
commitdiff
|
tree
2013-04-29
Ca
r
sten Ku
t
zner
Eva
l
uate en
f
orced r
o
tat
i
on potenial with V
e
r
let,
f
ixes
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark
A
braha
m
Merge
"Update li
n
king
t
o MKL an
d
document
s
am
e
" int
o
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark Abraham
M
erge "gen
e
ral SIMD acceleration for
a
ngles+
d
ihedrals
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark
A
braham
Merge
"
PM
E
l
oad
b
alancin
g
now ch
e
cks for
P
M
E grid
r
estrict
i
o
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Ber
k
Hess
ge
n
eral SIMD acceleration f
o
r
a
n
gles+
d
ihedrals
commit
|
commitdiff
|
tree
2013-04-29
Mark Abraham
Merge
"
Fixing a proble
m
with d
h
/dl
1
-
4
i
n
t
e
rac
t
i
o
n
s
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
Mark Abraham
Merge
"
C
UDA PME kernels with analyt
i
c
a
l Ew
a
l
d
corr
e
cti
o
n
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
Mar
k
Abraham
Merge "impro
v
ed load balancing w
i
t
h Verlet
cut-off
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
Christoph
J
unghans
Merge "v
-
rescale works
w
ith tau-t >=
0
" into release-4-6
commit
|
commitdiff
|
tree
2013-04-25
Mark Abraham
M
e
rg
e
"
Merge branch 'release-4-5
-
patches'" into release-4-6
commit
|
commitdiff
|
tree
2013-04-22
Mark
A
b
raham
Merge "Use git snapshots of th
e
tests
if
a
re on git
.
.
.
commit
|
commitdiff
|
tree
2013-04-16
Christoph Junghans
Use git sn
a
pshots
of
the t
e
sts if
are on g
i
t
commit
|
commitdiff
|
tree
2013-04-16
D
a
vid van der
S
p
o
e
l
Merge "cor
r
ected grompp
r
vdw
c
h
arge-group
radii check
.
.
.
commit
|
commitdiff
|
tree
2013-04-13
David va
n
der Spoel
Merge "added mdrun check
for V
e
rlet+pe
r
turbed atoms
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Mark A
b
ra
h
am
Mer
g
e "r
e
moved x86
specifics
from
n
bnxn SIMD kernels
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Mark Abraham
Merg
e
"corrected log file wall time break
d
o
w
n
" into
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
M
a
r
k Abraha
m
Me
r
ge
"
made PME work wi
t
h a mi
x
of
1 and more threa
d
s
.
.
.
commit
|
commitdiff
|
tree
2013-04-10
Te
e
mu Murtola
Merge "Merge relea
s
e-4-5-patches
i
n
to release-4-6"
.
.
.
commit
|
commitdiff
|
tree
2013-03-29
Christoph
J
unghans
Merge
"
A
d
ded install guide section
for BLAS/LAPAC
K
.
.
.
commit
|
commitdiff
|
tree
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