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Simplify CMAP loop
2017-12-14
Rola
n
d Schulz
Sim
p
li
f
y CMAP loo
p
commit
|
commitdiff
|
tree
2017-12-14
Erik Linda
h
l
Work around AVX-512 issu
e
s in gcc-5
.
4
a
n
d
7
.
1
commit
|
commitdiff
|
tree
2017-12-12
Er
i
k
Li
n
dahl
D
o
c
u
mented
p
ower
s
p
ectrum to
g
mx v
e
lacc
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Ch
e
ck fo
r
large ene
r
g
y
at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
A
void y
e
l
lin
g
about t
h
re
a
d pinning
twice
commit
|
commitdiff
|
tree
2017-12-11
M
a
rk Abraham
Leave NVML use off by default
commit
|
commitdiff
|
tree
2017-12-11
Mark Abr
a
ham
Ch
e
ck
for
G
P
U detecti
o
n
s
upport before detecting
commit
|
commitdiff
|
tree
2017-12-11
Mark A
b
rah
a
m
A
v
oid signed-over
f
low warn
i
n
g
w
ith gcc 7
commit
|
commitdiff
|
tree
2017-12-11
M
a
rk
Abraham
R
e
m
ove
S
IMD shift ope
r
ators
commit
|
commitdiff
|
tree
2017-12-10
B
erk Hess
Remove SIMD war
n
ing for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hes
s
Tone down no
t
e about not pinning threads
commit
|
commitdiff
|
tree
2017-12-10
S
z
ilárd Páll
Di
s
able default-on N
V
ML
s
uppo
r
t in CMa
k
e
commit
|
commitdiff
|
tree
2017-12-07
Roland S
c
h
u
l
z
Fix C
+
+11 libr
a
ry ch
e
ck's thread dependency
commit
|
commitdiff
|
tree
2017-12-03
B
e
rk Hess
Clear vsite ve
l
ocitie
s
for si
m
pl
e
in
t
eg
r
ators
commit
|
commitdiff
|
tree
2017-12-03
Mar
k
Ab
r
aham
Fix
fft5d
pinnin
g
commit
|
commitdiff
|
tree
2017-12-02
Berk He
s
s
Avoid
asser
t
ion f
a
ilure in AWH
commit
|
commitdiff
|
tree
2017-11-29
B
e
rk
H
e
s
s
Chan
g
e
the GPU SMT cut-off to qua
d
r
atic
commit
|
commitdiff
|
tree
2017-11-28
Er
i
k
L
indahl
Fix
A
VX-512 SIMD test fo
r
C
commit
|
commitdiff
|
tree
2017-11-27
Al
e
ksei Iupi
n
ov
D
o
not force se
p
arat
e
PME
r
a
nk to re
c
ompute
r
e
c
ipro
c
a
l
.
.
.
commit
|
commitdiff
|
tree
2017-11-27
Eri
k
Linda
h
l
Test more AVX-5
1
2
F
inst
r
uctions bef
o
re enabling support
commit
|
commitdiff
|
tree
2017-11-24
Er
i
k Lind
a
hl
Detect A
V
X-512 FMA
units to choose best
S
IM
D
commit
|
commitdiff
|
tree
2017-11-24
Berk
H
ess
L
i
m
i
t SMT wit
h
PME on G
P
U
commit
|
commitdiff
|
tree
2017-11-20
Viveca Lindah
l
A
d
d re
a
ding a
n
d
w
ritin
g
to
A
W
H
mod
u
l
e
commit
|
commitdiff
|
tree
2017-11-20
Mark
Ab
r
aham
F
ix nightl
y
matrix
confi
g
commit
|
commitdiff
|
tree
2017-11-19
Berk
H
ess
Add SIMD for AWH
commit
|
commitdiff
|
tree
2017-11-18
Magnus
L
u
n
dborg
Ad
d
ed Magnus Lund
b
org as c
o
ntributor
i
n the manual
.
commit
|
commitdiff
|
tree
2017-11-18
Aleksei Iupinov
Asynchronous CU
D
A transfers a
r
e
asser
t
ed to alwa
y
s
.
.
.
commit
|
commitdiff
|
tree
2017-11-10
Rol
a
nd
S
chu
l
z
Revert "U
s
e
-mavx2 -mfma instead of
-m
a
rch with AVX2"
commit
|
commitdiff
|
tree
2017-11-08
Ro
l
and
Sc
h
ulz
Fix sca
l
ar
bl
e
n
d
commit
|
commitdiff
|
tree
2017-11-08
Magn
u
s
L
u
n
db
o
r
g
Updat
e
to T
N
G v 1
.
8
.
1
commit
|
commitdiff
|
tree
2017-09-09
Berk Hess
Avo
i
d inf i
n
SIMD double sqrt()
commit
|
commitdiff
|
tree
2017-07-19
Mar
k
A
b
raham
I
m
pr
o
ve
C
M
ake i
m
p
l
ementa
t
ion for GMX_SIMD
commit
|
commitdiff
|
tree
2017-06-29
Teemu Mur
t
ola
Generalize I
F
orcePr
o
vider
commit
|
commitdiff
|
tree
2017-06-15
Szilárd
P
áll
Allow
d
is
a
bling the explic
i
t use of CUDA textures
commit
|
commitdiff
|
tree
2017-06-14
Mark Abraham
Simplify
reporti
n
g from init_gpu
commit
|
commitdiff
|
tree
2017-06-13
Erik Lindahl
More quotes
commit
|
commitdiff
|
tree
2017-06-07
Vedran
Mi
l
e
t
ić
D
o
c
ument floating-po
i
n
t arithmetic
commit
|
commitdiff
|
tree
2017-05-29
Szi
l
árd Páll
Q
u
o
tes are
cool,
t
ypo-
f
r
e
e on
e
s
a
re eve
n
"
co
o
ler"
commit
|
commitdiff
|
tree
2017-05-27
Mark A
b
r
aham
Quotes from Go
t
t
ingen
worksh
o
p
commit
|
commitdiff
|
tree
2017-05-14
B
erk Hess
Fix
bugs
i
n double Sim
d
4 implementati
o
ns
commit
|
commitdiff
|
tree
2017-03-19
Erik Linda
h
l
Use OpenMP up to 16 threads with AMD Ryz
e
n
commit
|
commitdiff
|
tree
2017-03-19
E
rik Li
n
da
h
l
128-bit AVX2 SIMD for
A
MD Ryz
e
n
commit
|
commitdiff
|
tree
2017-03-19
Mark Abraham
Fi
x
string ha
n
d
ling for g
c
c 7
commit
|
commitdiff
|
tree
2017-03-14
Erik Lin
d
a
h
l
Fix gcc comp
i
les o
f
A
V
X
-
512 SIMD
commit
|
commitdiff
|
tree
2017-02-14
Mark Abraham
Fix h
a
ndling
o
f previous virials
commit
|
commitdiff
|
tree
2017-02-10
Rola
n
d Schulz
Remove duplicate AVX5
1
2
gather definiti
o
ns
commit
|
commitdiff
|
tree
2017-02-09
Erik Lindahl
Work around false
x
lc-13
.
1
.
5 bug in SIMD test
commit
|
commitdiff
|
tree
2017-02-09
Ma
r
k Ab
r
aham
Re
m
ove
EST_DI
S
T
R
fr
o
m stat
e
.
h
commit
|
commitdiff
|
tree
2017-02-09
Mark A
b
r
aham
E
n
h
anc
e
warninp
commit
|
commitdiff
|
tree
2017-02-08
Roland Schulz
AVX512: Use double-si
z
ed gather fo
r
pairs of floats
commit
|
commitdiff
|
tree
2017-02-07
Mark
Abr
a
ham
Introduced
system
prepar
a
tion sect
i
on to user gu
i
d
e
commit
|
commitdiff
|
tree
2017-02-03
David van der
Spoel
Fixes
SEGV in
g
mx order
.
commit
|
commitdiff
|
tree
2017-01-11
R
oland Schulz
Tid
y
: modernize-
u
se
-
n
ullptr
commit
|
commitdiff
|
tree
2016-11-03
Roland Schu
l
z
Supress ICC 1
6
on
W
indows fal
s
e post
i
ves
commit
|
commitdiff
|
tree
2016-10-30
Teemu Murtola
Support normalizing values in KeyValu
e
T
r
ee
commit
|
commitdiff
|
tree
2016-10-30
Roland Schulz
Replace qsort/bsear
c
h with
std::sor
t
/lower_bo
u
nd
commit
|
commitdiff
|
tree
2016-10-11
Mar
k
Abraham
U
p
date for FFTW 3
.
3
.
5
commit
|
commitdiff
|
tree
2016-09-26
David van der S
p
oel
Fixes issue wit
h
Release build i
n
c
o
rrelat
i
on
f
unctions
.
commit
|
commitdiff
|
tree
2016-09-18
R
o
l
and
S
chulz
Fix mat
h
-te
s
t
f
alse p
o
s
i
tive
commit
|
commitdiff
|
tree
2016-09-18
Roland
S
chulz
Better op
t
im
i
zed ICC release fl
a
g
s
commit
|
commitdiff
|
tree
2016-09-12
Mark Abraham
Prelimin
a
ry
c
le
a
n u
p
of NVML code
commit
|
commitdiff
|
tree
2016-09-12
Ber
k
Hess
Add const t
o
thread-M
P
I functi
o
ns
commit
|
commitdiff
|
tree
2016-09-12
Vedran Miletić
Document
w
allc
y
c
l
e counters and subcounters
commit
|
commitdiff
|
tree
2016-09-12
T
e
e
mu Murtola
F
ix various memor
y
le
a
ks
commit
|
commitdiff
|
tree
2016-07-31
James Graham
Avo
i
d blank line in writing index
f
il
e
commit
|
commitdiff
|
tree
2016-07-30
Roland Sc
h
ulz
Update GCC versio
n
for refe
r
ence build
commit
|
commitdiff
|
tree
2016-07-30
V
edr
a
n Mil
e
tić
D
ocument
g
m
x_cgsort_t and gmx
_
d
o
mdec_sort_t st
r
ucts
commit
|
commitdiff
|
tree
2016-07-09
Erik
Lindahl
P
r
event
fragil
e
use
c
a
s
e
s
of checkpoi
n
t appending
commit
|
commitdiff
|
tree
2016-07-08
Erik Lindahl
Update affinity checking for Intel comp
i
le
r
commit
|
commitdiff
|
tree
2016-07-08
Erik Lindah
l
Work around
c
ompiler issue with r
a
n
dom test
commit
|
commitdiff
|
tree
2016-07-08
Szi
l
árd P
á
ll
Add PDF metada
t
a
t
o the manual
commit
|
commitdiff
|
tree
2016-07-07
E
r
i
k Linda
h
l
R
e
duce hwloc & cpuid test requirement
s
commit
|
commitdiff
|
tree
2016-07-07
Teemu Murto
l
a
Change
handling for
m
issing releng docs
commit
|
commitdiff
|
tree
2016-07-07
Szilá
r
d
Páll
Add
u
ser guide info on CUDA
application cl
o
ck
s
commit
|
commitdiff
|
tree
2016-07-07
M
a
rk Abraham
F
i
x build
i
f
l
ibcud
a
i
s
f
o
u
nd bu
t
nvcc is n
o
t
commit
|
commitdiff
|
tree
2016-06-07
Semen Yesy
l
evskyy
Adde
d
manual section about
embedding protei
n
s
to membra
n
es
.
commit
|
commitdiff
|
tree
2016-06-05
Sz
i
lárd
Páll
Ad
d
s
upport for CUD
A
CC 6
.
0/6
.
1
commit
|
commitdiff
|
tree
2016-06-03
Berk Hess
Hand
l
e partiall
y
f
r
ozen a
n
d co
n
str
a
ine
d
atoms
commit
|
commitdiff
|
tree
2016-06-02
S
z
ilárd Páll
Add env
.
var
.
to enable OpenCL c
a
ching
commit
|
commitdiff
|
tree
2016-06-02
Szilá
r
d Páll
Fix
O
p
e
n
C
L binary cach
e
file name generation
commit
|
commitdiff
|
tree
2016-06-02
Rolan
d
S
c
h
ulz
Fi
x
ICC 16u3
build
commit
|
commitdiff
|
tree
2016-06-02
Patrick Welche
Ensure IMD include dependencies work
commit
|
commitdiff
|
tree
2016-05-29
Mark
Abraha
m
Simpli
f
i
e
d and
u
p
dated OpenCL c
o
mpilatio
n
commit
|
commitdiff
|
tree
2016-05-23
Be
r
k
Hes
s
Fix
bug in v-rescale the
r
mostat &
replica exchange
commit
|
commitdiff
|
tree
2016-05-10
Erik L
i
ndahl
Fixed large file is
s
ue on 32-b
i
t pl
a
t
forms
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
Update mdrun t
e
rminati
o
n info
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
C
orrect nrdf for 1D/
2
D systems
commit
|
commitdiff
|
tree
2015-12-24
Er
i
k Lindahl
E
x
tended
S
I
M
D
, imp
l
ement
a
tion for IBM Power7
/
8
VSX
commit
|
commitdiff
|
tree
2015-12-21
Eri
k
Lin
d
ahl
Extended SIMD
,
i
mplementation
fo
r
B
l
ue
G
ene
/
Q
commit
|
commitdiff
|
tree
2015-12-21
E
r
ik Lindahl
E
xten
d
ed S
I
M
D implementation for 256-bit
A
VX
and
A
V
X
2
commit
|
commitdiff
|
tree
2015-12-16
Er
i
k L
i
n
d
ahl
Next-g
e
neration SIMD
m
odule, reference implementation
commit
|
commitdiff
|
tree
2015-10-30
Erik Lindahl
Break dependence
o
f group
k
e
rnels on s
i
m
d modul
e
commit
|
commitdiff
|
tree
2015-09-30
R
ola
n
d Sch
u
lz
Requi
r
e C++
1
1
commit
|
commitdiff
|
tree
2015-08-13
Ma
r
k
Abr
a
ham
Re-enabl
e
m
ulti
-
GPU su
p
port i
n
OpenCL for thread MPI
commit
|
commitdiff
|
tree
2015-08-05
Eri
k
L
indahl
Fix PGI compiler flag
commit
|
commitdiff
|
tree
2015-07-27
Erik L
i
ndahl
Moved
add
i
tio
n
al g
m
xli
b
sour
c
es to C++
commit
|
commitdiff
|
tree
2015-07-26
Mark
A
braham
Co
n
vert some mdrun uti
l
i
ty code to
C
+
+
commit
|
commitdiff
|
tree
2015-07-26
Erik Lindahl
Merg
e
branch r
e
lease-5-1
commit
|
commitdiff
|
tree
2015-07-07
Eri
k
Lindahl
Move QMMM s
o
urce
t
o
C
++
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix DD DLB state issue
commit
|
commitdiff
|
tree
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