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Fix segmentation fault in do_dssp
2020-01-01
Erik Lindahl
A
dd
li
n
k to paper explaining GROMOS tw
i
n
-range
i
ss
u
es
.
commit
|
commitdiff
|
tree
2019-12-29
Erik
L
i
n
dahl
Write TPR bo
d
y as o
p
aque X
D
R data in big-endian for
m
at
commit
|
commitdiff
|
tree
2019-11-13
E
r
ik
Lindahl
Updated
p
hysical
con
s
t
ant
s
to C
O
D
A
TA 201
8
commit
|
commitdiff
|
tree
2019-11-06
Erik Lindahl
Wo
r
k around broke
n
A
pple com
p
ilers in Mac
OS
10
.
15
commit
|
commitdiff
|
tree
2019-11-06
Eri
k
Lindahl
Wor
k
around broken
A
p
pl
e
compilers i
n
Ma
c
OS
1
0
.
15
commit
|
commitdiff
|
tree
2019-09-13
Erik Lindahl
A
d
d rounding correction to u
n
safe simd exp
te
s
ts
too
commit
|
commitdiff
|
tree
2019-09-13
Erik
Li
n
dahl
F
i
x clan
g
tidy warning
s
in SIMD
c
ode
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindahl
Adju
s
t
t
e
st range and fix singlea
c
curacy tests
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindahl
A
d
ded SIM
D
cbrt
and invcbrt functions
commit
|
commitdiff
|
tree
2019-09-12
Erik Linda
h
l
Added SIMD log2 a
n
d pow math
f
u
n
ctions
commit
|
commitdiff
|
tree
2019-09-12
Erik Lind
a
hl
U
pdat
e
SIMD mat
h
tests and improve accura
c
y
commit
|
commitdiff
|
tree
2019-09-03
Erik Lindahl
F
i
x CP
U
detection an
d
SIMD on modern
M
ac/c
m
a
k
e combos
commit
|
commitdiff
|
tree
2019-08-30
Erik L
i
ndahl
Fix CPU detection and SIMD o
n
m
odern
Mac
/
cmake combos
commit
|
commitdiff
|
tree
2019-08-29
E
r
i
k
L
i
nd
a
hl
Som
e
q
u
otes I bumped
into la
s
t wee
k
commit
|
commitdiff
|
tree
2019-08-23
Erik L
i
ndahl
Default to AVX2_256 S
I
MD for
Z
en2
commit
|
commitdiff
|
tree
2019-08-20
Erik Lindah
l
Avoid using GMX_SIMD macros t
o
detect _mm
_
p
a
use()
commit
|
commitdiff
|
tree
2019-06-09
Erik Lindahl
More quot
e
s
commit
|
commitdiff
|
tree
2019-05-16
Erik
Lindahl
Added mor
e
quot
e
s
commit
|
commitdiff
|
tree
2018-08-14
Erik
L
indahl
Fix SIMD
a
n
yTrue
b
u
g
, an
d
add better unit test
commit
|
commitdiff
|
tree
2018-06-06
Erik L
i
ndahl
Use default CMake p
a
t
h
variables
commit
|
commitdiff
|
tree
2018-06-06
Erik Li
n
dahl
Bump GMX_
B
UILD_OWN_FFTW to 3
.
3
.
8
t
o
a
void bugs
commit
|
commitdiff
|
tree
2018-01-10
Erik Lindahl
Improve pdb2gmx for no
n
standard resid
u
e types
commit
|
commitdiff
|
tree
2018-01-10
E
ri
k
Lind
a
hl
Clarified gm
x
rmsf d
o
c
u
mentation
commit
|
commitdiff
|
tree
2018-01-05
Erik
Lindahl
Test t
h
at
n
vcc/ho
s
t compiler
c
ombo wo
r
ks
commit
|
commitdiff
|
tree
2018-01-05
E
rik L
i
ndahl
Make TNG writing work with multiple id
e
n
t
ical
steps
commit
|
commitdiff
|
tree
2018-01-05
E
r
ik Lindah
l
Add AVX_512 and K
N
C s
y
mbols to FFTW SIMD test
commit
|
commitdiff
|
tree
2018-01-04
Erik Lindahl
I
mpr
o
ve frame time/st
e
p handli
n
g
in
trjconv
commit
|
commitdiff
|
tree
2018-01-04
Erik Li
n
dahl
Implement changes f
o
r CMake policy 006
8
commit
|
commitdiff
|
tree
2018-01-03
Eri
k
L
indahl
F
ix trjconv for tdump<frame timestep
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindah
l
Fix index error
in gm
x
chi
commit
|
commitdiff
|
tree
2018-01-03
Er
i
k
L
i
ndahl
Fix
complexi
t
y
f
or large exclus
i
on orders
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindahl
Don't allow m
u
l
t
i
p
l
e energy groups f
o
r GPU runs
commit
|
commitdiff
|
tree
2018-01-03
Erik Lindahl
Remove duplica
t
ions in GMXL
I
B se
a
r
ch path
s
commit
|
commitdiff
|
tree
2018-01-03
Erik
Lindah
l
Avoid FTZ
t
r
iggering si
m
d test failu
r
e
s
commit
|
commitdiff
|
tree
2018-01-02
Erik Lind
a
hl
D
o
c
umen
t
requir
e
d posi
t
io
n
res
t
raint f
i
le
s
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindahl
A
l
low empty
l
ines in hdb files
commit
|
commitdiff
|
tree
2018-01-02
Erik Lind
a
hl
Fi
x
OpenCL compiles on Mac OS
commit
|
commitdiff
|
tree
2018-01-02
Erik Lindahl
Improve manual from com
m
e
n
ts by Gang Liu
commit
|
commitdiff
|
tree
2018-01-02
E
r
i
k L
i
ndahl
Ma
k
e i
t
explic
i
t that tim
e
u
nits apply
to begin/end
.
.
.
commit
|
commitdiff
|
tree
2018-01-02
Erik
Lindahl
Don't
r
equire
m
atching n
a
me
s
between rtp
a
nd tdb files
commit
|
commitdiff
|
tree
2018-01-02
Erik Lin
d
ahl
Don't writ
e
reference pull group 0 to
log
commit
|
commitdiff
|
tree
2018-01-01
Er
i
k Lindahl
Fix g
m
x density for
non-mass calcula
t
ions
commit
|
commitdiff
|
tree
2018-01-01
Er
i
k
L
indahl
Clarify XTC
e
rror messa
g
e
commit
|
commitdiff
|
tree
2017-12-26
E
r
ik Lindahl
Fix builds on ARM &
c
lari
f
y (ARM) GPU su
p
port
commit
|
commitdiff
|
tree
2017-12-19
Erik Lindahl
Use reduc
e
d
defa
u
lt toleran
c
e
s
fo
r
t
px c
o
mp
a
rison
commit
|
commitdiff
|
tree
2017-12-14
Erik Lind
a
hl
Wor
k
around AVX-5
1
2
i
ssues in gcc-5
.
4 an
d
7
.
1
commit
|
commitdiff
|
tree
2017-12-14
Erik Lindahl
Fix
PBC error in gmx_spatia
l
commit
|
commitdiff
|
tree
2017-12-12
Erik Li
n
dahl
Documented
p
ower spectr
u
m to gmx
velacc
commit
|
commitdiff
|
tree
2017-12-12
Erik Li
n
dahl
Req
u
ire TPR fi
l
e
for gmx cluster
commit
|
commitdiff
|
tree
2017-12-12
Erik L
i
nd
a
hl
Disa
l
low as
c
ii form
a
ts for gmx t
r
jcat
commit
|
commitdiff
|
tree
2017-12-11
Erik Lindahl
Remo
v
e d
u
plicated
l
ines
f
ro
m
OP
L
S ff
b
onded
.
itp
commit
|
commitdiff
|
tree
2017-12-11
Erik Lindahl
Don't
wa
r
n
a
b
o
ut NVML clocks that
a
re at max
commit
|
commitdiff
|
tree
2017-12-10
Eri
k
Lindah
l
Revert "D
i
sable default
-
on NVML su
p
por
t
in CM
a
ke"
commit
|
commitdiff
|
tree
2017-12-07
E
r
ik
L
indahl
Added c
o
o
l quote from Viveca's d
e
fense
commit
|
commitdiff
|
tree
2017-12-04
Erik
Lindahl
Fi
x
compilation issues
for AVX-51
2
commit
|
commitdiff
|
tree
2017-11-28
Erik Lind
a
hl
F
ix AVX-51
2
SI
M
D t
e
st
for C
commit
|
commitdiff
|
tree
2017-11-28
Eri
k
Li
n
dahl
I
m
prov
e
status messages fo
r
SIMD che
c
ks
commit
|
commitdiff
|
tree
2017-11-27
E
r
ik L
i
ndahl
Test more AVX-512F in
s
tructions before enabl
i
ng
support
commit
|
commitdiff
|
tree
2017-11-24
Erik
L
i
ndahl
Detect AVX-512 FMA units to choose best S
I
MD
commit
|
commitdiff
|
tree
2017-11-21
Er
i
k
Lindahl
Separate SIMD flag
detection fro
m
management
commit
|
commitdiff
|
tree
2017-11-12
Eri
k
Lindahl
O
nly issue F
F
T wa
r
ning mes
s
ages on
c
h
anges
commit
|
commitdiff
|
tree
2017-09-12
Erik Linda
h
l
Improve a
c
curacy of
S
IM
D
exp for small arg
s
commit
|
commitdiff
|
tree
2017-09-04
Erik Lindahl
M
ore SIM
D
math argum
e
nt c
h
ecking, added
u
nsafe options
commit
|
commitdiff
|
tree
2017-08-28
Erik Li
n
da
h
l
Im
p
roved SIMD
t
e
st data to us
e
a
l
l bit
s
commit
|
commitdiff
|
tree
2017-06-26
Erik
Lindah
l
Fix
A
RM
NEON simd debug builds
commit
|
commitdiff
|
tree
2017-06-13
Erik Lind
a
hl
More quot
e
s
commit
|
commitdiff
|
tree
2017-05-23
E
rik Lin
d
ahl
U
pd
a
ted
c
ool quotes
commit
|
commitdiff
|
tree
2017-04-17
Erik Lindahl
F
i
xed AVX-512F compiler fl
a
gs
commit
|
commitdiff
|
tree
2017-03-19
Er
i
k
Lindah
l
U
se OpenMP u
p
to
1
6 threads with AM
D
Ryze
n
commit
|
commitdiff
|
tree
2017-03-19
Eri
k
Lind
a
hl
128-bit AV
X
2 SIMD for AMD Ryzen
commit
|
commitdiff
|
tree
2017-03-14
E
ri
k
L
indahl
Fix gcc compiles of AVX-512 SIMD
commit
|
commitdiff
|
tree
2017-02-09
Erik Li
n
da
h
l
W
o
r
k around false x
l
c-13
.
1
.
5
b
ug in
SIMD test
commit
|
commitdiff
|
tree
2016-10-17
Erik Lindah
l
New c
l
a
ss
e
s for
s
pline interpolat
i
o
n
t
a
b
les
commit
|
commitdiff
|
tree
2016-09-07
E
rik Lin
d
ahl
Bump old
e
st cmake, compiler
and CUD
A
versi
o
ns required
commit
|
commitdiff
|
tree
2016-08-05
E
r
i
k Lindahl
Fix pr
o
per relative tolerance checking in testutils
commit
|
commitdiff
|
tree
2016-07-11
E
r
ik Lindahl
Fix mem
b
ed with
partial reve
r
t
o
f 29943f
commit
|
commitdiff
|
tree
2016-07-09
E
r
ik Lindahl
H
a
rdwar
e
dete
c
ti
o
n c
l
ean
-
up and pre/post-pro
c
essing
commit
|
commitdiff
|
tree
2016-07-09
Erik
Li
n
d
a
hl
Pre
v
ent
fragile u
s
e cases of
c
heckpoint
a
ppen
d
ing
commit
|
commitdiff
|
tree
2016-07-08
Erik Lind
a
hl
U
p
d
ate affinity checking for Intel
c
o
mp
i
ler
commit
|
commitdiff
|
tree
2016-07-08
Er
i
k Lindahl
Add detec
t
io
n
f
or ARMv7 cycle counter support
commit
|
commitdiff
|
tree
2016-07-08
Er
i
k Lin
d
ahl
W
o
r
k arou
n
d compi
l
er is
s
ue with random
te
s
t
commit
|
commitdiff
|
tree
2016-07-07
E
rik Linda
h
l
Reduc
e
hwloc & c
p
uid test re
q
uirements
commit
|
commitdiff
|
tree
2016-06-08
E
r
ik Lin
d
ahl
Disable sta
t
i
c
l
i
bcu
d
ar
t
on O
S
X
commit
|
commitdiff
|
tree
2016-06-04
E
r
ik Lindahl
Check
number of items read
in
m
dp st
a
tements
commit
|
commitdiff
|
tree
2016-05-27
Er
i
k
L
indahl
Detect the usage of hwtop XML cachin
g
commit
|
commitdiff
|
tree
2016-05-21
Eri
k
Linda
h
l
Disable a
u
t
omated FFTW3 buil
d
s
on Windows
commit
|
commitdiff
|
tree
2016-05-10
Erik Lindahl
F
i
xed large file issue on
3
2-bi
t
platforms
commit
|
commitdiff
|
tree
2016-05-10
E
r
i
k Lindahl
Fix prec
i
sion loss in tabulated no
r
m
a
l distr
i
but
i
on
commit
|
commitdiff
|
tree
2016-05-10
Erik Li
n
dahl
Flush
s
tream
s
when not wr
i
ting new
l
ine charact
e
r
commit
|
commitdiff
|
tree
2016-05-09
Erik Lind
a
hl
Impro
v
e
d
de
s
cription for GPU/C
P
U time ratio
commit
|
commitdiff
|
tree
2016-05-08
E
rik Lindahl
Fix Luzar/C
h
ander litera
t
ure ref
e
rence
i
n g_hbond
commit
|
commitdiff
|
tree
2016-05-05
Erik
L
indahl
Fix SIMD detection on AMD AVX CPUs w/o fma (master)
commit
|
commitdiff
|
tree
2016-05-05
Erik Linda
h
l
Avoid allo
c
ating heap memory for tabulated
d
istributi
o
n
commit
|
commitdiff
|
tree
2016-04-04
Eri
k
Lindahl
Fix hwloc narrowing w
a
rn
i
ng
on 32-bit a
r
chit
e
ctures
commit
|
commitdiff
|
tree
2016-04-04
Erik
Lin
d
ahl
F
ix
compi
l
e
e
rror for I
B
M
VMX on ppc64
commit
|
commitdiff
|
tree
2016-04-04
Erik Lindahl
Fix
S
IMD dete
c
tion
o
n new AM
D
A
VX CPUs w/o f
m
a
commit
|
commitdiff
|
tree
2016-04-03
E
r
ik Lindahl
Fix
u
nit
t
est se
g
faults with
g
cc
-
6
.
0
commit
|
commitdiff
|
tree
2016-04-03
Erik Lindahl
Fix incorrec
t
retu
r
n t
y
pe
for
s
cala
r
version of simd
.
.
.
commit
|
commitdiff
|
tree
2016-03-09
Erik Lind
a
hl
Random engines & dis
t
ributions as prop
e
r C++11 classes
commit
|
commitdiff
|
tree
2016-03-09
Erik Lindahl
Support for portabl
e
h
ar
d
ware locality
(
h
w
loc)
commit
|
commitdiff
|
tree
next