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Allow empty lines in hdb files
2018-01-02
Mark Abrah
a
m
Fix
me
m
bed by calling the proper mtop finalization
.
.
.
commit
|
commitdiff
|
tree
2017-12-30
Mark Abraham
First release candid
a
te for
vers
i
on 2018
commit
|
commitdiff
|
tree
2017-12-29
Mark Abraham
S
eparate canD
e
tectGp
u
s and findGpus fu
t
h
e
r
, an
d
fix
.
.
.
commit
|
commitdiff
|
tree
2017-12-27
Mar
k
Abraham
Silence POWER8 c
o
mpiler warn
i
ngs
commit
|
commitdiff
|
tree
2017-12-22
Mark Abraham
Me
r
ge branch
r
eleas
e
-
2
016 into release
-
2018
commit
|
commitdiff
|
tree
2017-12-21
Mar
k
A
braham
Merge branc
h
r
elease-5-1 into
r
eleas
e
-201
6
commit
|
commitdiff
|
tree
2017-12-21
Mark Abrah
a
m
Bump min
o
r version for
t
heoretical new r
e
lease
commit
|
commitdiff
|
tree
2017-12-21
M
a
r
k Abraham
Update doub
l
e-precision test
c
onfigurations
commit
|
commitdiff
|
tree
2017-12-21
Mark Abr
a
ham
Vers
i
o
n 5
.
1
.
5
commit
|
commitdiff
|
tree
2017-12-20
Mark Abraham
U
s
e
new def
a
ultRealToler
a
nce()
t
o
s
tabil
i
se some
t
ests
commit
|
commitdiff
|
tree
2017-12-20
Mar
k
Abraham
Merge "Merge branch rel
e
a
se-2016 into release-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-20
Mark
A
braham
M
e
rge b
r
anch release-2016 in
t
o
release
-
201
8
commit
|
commitdiff
|
tree
2017-12-19
Mar
k
A
b
raham
Thi
r
d beta release
o
f
2018
commit
|
commitdiff
|
tree
2017-12-19
Ma
r
k Abraham
Fix
table t
e
sts and
i
m
pr
o
ve table con
s
truction
commit
|
commitdiff
|
tree
2017-12-15
Mark Abraham
Make
O
p
enC
L
i
m
plementati
o
n
o
f gpu
_
utils
t
e
st
s
conform
commit
|
commitdiff
|
tree
2017-12-14
Mar
k
A
b
raham
A
void
c
onfus
i
ng
m
essag
e
at
e
nd
of
non-dy
n
amic
a
l ru
n
s
commit
|
commitdiff
|
tree
2017-12-14
Mark
Ab
r
aham
Fix ret
u
rn val
u
e
s
of frame-re
a
ding
f
u
nc
t
ions
commit
|
commitdiff
|
tree
2017-12-14
Mark Abraham
Ma
k
e AVX
-
512 C
M
a
ke det
c
tio
n
work
commit
|
commitdiff
|
tree
2017-12-14
M
a
rk Abr
a
h
a
m
Mer
g
e "Merge bra
n
ch release-201
6
into re
l
ease-
2
018
.
.
.
commit
|
commitdiff
|
tree
2017-12-12
Mark Abraham
Improve grompp missing-p
a
rameters err
o
r mess
a
ge
commit
|
commitdiff
|
tree
2017-12-12
Mar
k
Abraham
Merge branch release
-
2016 i
n
to release-2018
commit
|
commitdiff
|
tree
2017-12-11
Ma
r
k
Abraham
Se
c
ond beta rel
e
ase of 2018
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraha
m
Leave NVML use off by default
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraham
Check for GPU detection support before de
t
ecting
commit
|
commitdiff
|
tree
2017-12-11
Mark Ab
r
aham
Cons
u
me
a
ny error
p
roduc
e
d dur
i
ng
G
P
U detection
commit
|
commitdiff
|
tree
2017-12-11
Mark Abraham
Av
o
id signed-overfl
o
w warning with
g
cc
7
commit
|
commitdiff
|
tree
2017-12-11
Ma
r
k Abraham
Remove
S
IMD shift operators
commit
|
commitdiff
|
tree
2017-12-08
Mar
k
Ab
r
aham
R
e
f
i
n
e ulp
t
olerances
f
or s
o
m
e more
ewald
t
ests
commit
|
commitdiff
|
tree
2017-12-05
Mar
k
Abrah
a
m
Fix mdrun -nb auto -pme a
u
to
when GPUs are absen
t
commit
|
commitdiff
|
tree
2017-12-05
Mark
A
braham
U
pdate testing to includ
e
cm
a
k
e 3
.
10
.
0
commit
|
commitdiff
|
tree
2017-12-04
Mark Abraham
Fix free_gpu
commit
|
commitdiff
|
tree
2017-12-04
Mark Abraham
Fix u
n
u
s
e
d
var
i
ables in CPU pruning kernels
commit
|
commitdiff
|
tree
2017-12-04
Mark A
b
raham
M
e
r
ge branc
h
release-201
6
i
nto r
e
lease-20
1
8
commit
|
commitdiff
|
tree
2017-12-03
M
a
rk Abra
h
a
m
Fix fft
5
d pin
n
ing
commit
|
commitdiff
|
tree
2017-11-28
Mark A
b
r
a
ham
GR
O
MACS 2
0
18 first
b
eta release
commit
|
commitdiff
|
tree
2017-11-24
Mar
k
Abra
h
am
U
p
da
t
e develope
r
guide
commit
|
commitdiff
|
tree
2017-11-24
Ma
r
k Abra
h
am
Ac
t
ivate
PME on
GPUs
commit
|
commitdiff
|
tree
2017-11-24
Mark Abrah
a
m
Separate manage
m
e
nt o
f
G
P
U contex
t
s from mo
d
ules
commit
|
commitdiff
|
tree
2017-11-24
Mark
A
braham
Add PM
E
integration test
commit
|
commitdiff
|
tree
2017-11-24
Mark Abraham
E
x
t
end task a
s
s
ignme
n
t code
commit
|
commitdiff
|
tree
2017-11-21
Mark Abr
a
h
a
m
Use much less PaddedRVecVector and
m
o
re ArrayRef of
.
.
.
commit
|
commitdiff
|
tree
2017-11-21
Mark Ab
r
aham
Sup
p
ort pinning
in
HostAllocator
commit
|
commitdiff
|
tree
2017-11-20
Mar
k
Abra
h
am
Fix nightly matrix config
commit
|
commitdiff
|
tree
2017-11-19
Mark Abraham
Fix FindCUDA
.
cmak
e
f
o
r
-
Wundef
commit
|
commitdiff
|
tree
2017-11-17
Mark Abrah
a
m
U
s
e HostAllocationP
o
licy for
c
h
arg
e
A
commit
|
commitdiff
|
tree
2017-11-17
M
a
r
k
Abraham
A
dd
checking
fu
n
ction
f
or
w
he
t
her a
bu
f
fer is pinned
commit
|
commitdiff
|
tree
2017-11-17
Mark
A
braham
Improve h
a
n
dl
i
ng
of PME GPU force buffer
commit
|
commitdiff
|
tree
2017-11-10
Mark Abraham
Import cmake Modules/Fi
n
dCUDA
.
cm
a
ke
commit
|
commitdiff
|
tree
2017-11-09
Mark
Abraham
Prepared
t
_mdat
o
m
s fo
r
using
vector
commit
|
commitdiff
|
tree
2017-11-09
M
a
rk Abr
a
ham
I
ntroduce HostAl
l
ocationPolicy
commit
|
commitdiff
|
tree
2017-11-07
Mark
A
b
rah
a
m
R
e
form gmx_pm
e
_pp
a
lloc and us
e
vector
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Introduce g
m
xopen
c
l
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Test clan
g
on ARM i
n
nightly
m
a
t
rix
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
I
m
p
rov
e
PME inc
l
udes
commit
|
commitdiff
|
tree
2017-11-03
Ma
r
k
Abraham
Merge "
M
erge b
r
anch
release-2016"
commit
|
commitdiff
|
tree
2017-11-02
Mark Abraham
Merge b
r
anch
r
elease-2016
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix
t
h
r
ead-MPI ra
n
k choice for
or
i
entation restr
a
int
s
commit
|
commitdiff
|
tree
2017-11-01
Mark
Abra
h
am
Improve han
d
ling of GPU IDs
commit
|
commitdiff
|
tree
2017-10-31
M
a
rk A
b
raham
Up
d
ate treatment of GPU com
p
a
tibility data stru
c
ture
commit
|
commitdiff
|
tree
2017-10-30
M
ark Abraham
Fix
and update hw_info
commit
|
commitdiff
|
tree
2017-10-27
Mar
k
Abraham
F
i
x
h
w de
t
ection m
o
re
commit
|
commitdiff
|
tree
2017-10-26
Mar
k
Abr
a
ham
Make rele
a
se
matr
i
x w
o
rk a
g
ain
commit
|
commitdiff
|
tree
2017-10-26
Mark Abraham
New quote
commit
|
commitdiff
|
tree
2017-10-25
M
a
rk Abraham
Teach the copy
r
ight
c
he
c
ker about template
.
cpp
commit
|
commitdiff
|
tree
2017-10-20
Mark Ab
r
aha
m
Clarify docs for
Fm
a
x in EM
commit
|
commitdiff
|
tree
2017-10-20
Mark Abraham
M
e
rge branch release-2016
commit
|
commitdiff
|
tree
2017-10-16
M
a
rk Abraha
m
Me
r
ge
b
ranch rel
e
ase-2016
commit
|
commitdiff
|
tree
2017-10-13
M
ark A
b
raham
Update test
s
fo
r
C
+
+11 c
o
mpile
r
and standar
d
library
commit
|
commitdiff
|
tree
2017-10-13
M
ark Abraham
F
i
x
cp
u
info on
c
lan
g
+ non
-
x86
commit
|
commitdiff
|
tree
2017-10-11
Mark
Abraham
Introduced header for
c
ommunication to/from PME
r
ank
s
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Cleaned up ewa
l
dcoeff f
o
r PME-only ranks
commit
|
commitdiff
|
tree
2017-10-11
Ma
r
k Abra
h
am
U
s
e c
l
a
ng-5 in
J
enki
n
s
commit
|
commitdiff
|
tree
2017-10-07
Mark Abraha
m
Tell cpp
c
heck that
.
c
pp and
.
cu
files
are
c
++
commit
|
commitdiff
|
tree
2017-10-05
M
a
rk Abraham
C
o
ntinue re
m
ovi
n
g
-
n
b gpu_cpu
commit
|
commitdiff
|
tree
2017-10-04
Ma
r
k A
b
raha
m
Enab
l
e g
r
oup-scheme S
I
MD with GMX_SIMD=AVX2_128
commit
|
commitdiff
|
tree
2017-10-03
Mark Abraham
In
t
ro
d
uce and use Al
i
gnedAllo
c
a
t
io
n
P
olicy
commit
|
commitdiff
|
tree
2017-09-19
Mark Abraham
Update t
e
s
ting matrices
to test wi
t
h (latest)
i
cc-18
commit
|
commitdiff
|
tree
2017-09-17
Mar
k
A
braha
m
Merge branch
r
el
e
ase-2016
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Expre
s
s int
e
nt of matrix release
b
uild typ
e
s
e
xplicitly
commit
|
commitdiff
|
tree
2017-09-15
Mark
A
b
r
aham
Bumped
pa
t
ch v
e
rsi
o
n for next
release
commit
|
commitdiff
|
tree
2017-09-15
Mark Abraham
Ve
r
s
ion 2016
.
4
commit
|
commitdiff
|
tree
2017-09-14
M
ark A
b
raham
F
or
m
ta
s
ka
s
s
i
g
n
ment modu
l
e
commit
|
commitdiff
|
tree
2017-09-14
Mark Abraham
Fix c
o
mpat m
o
du
l
e definition
commit
|
commitdiff
|
tree
2017-09-12
Mark Abraham
Mer
g
e branch release-2016
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraham
I
n
t
roduce t
y
pe-sa
f
e GPU emul
a
tion v
a
riables
commit
|
commitdiff
|
tree
2017-09-07
Mark Abraham
Enable g
r
o
u
p
-
scheme SIMD kernels on recent AVX
extensio
n
s
commit
|
commitdiff
|
tree
2017-09-06
Mark Abraham
Prepar
e
V
e
rl
e
t scheme later in run
n
er
commit
|
commitdiff
|
tree
2017-09-05
Mark Abraham
Fixes for Solaris
commit
|
commitdiff
|
tree
2017-09-05
Ma
r
k Abraham
Fi
x
us
e
of
GPU
in
f
orma
t
ion for thread-MPI setup
commit
|
commitdiff
|
tree
2017-09-03
M
a
rk
A
braham
Fix
compiler f
l
a
gs for
using MKL
commit
|
commitdiff
|
tree
2017-09-03
M
a
rk A
b
r
ah
a
m
Mer
g
e
branch release-5-1 into
r
elease-2016
commit
|
commitdiff
|
tree
2017-08-25
Mar
k
A
b
raham
Fi
x
flat-bot
t
omed pos
i
tion restraints
w
i
th m
u
l
tiple
.
.
.
commit
|
commitdiff
|
tree
2017-08-23
Mark
A
braha
m
Stopp
e
d
c
heckpo
i
n
t
influenc
i
ng paralleli
s
m setup
commit
|
commitdiff
|
tree
2017-08-22
Ma
r
k
Abraham
R
u
n GPU detection even for mdrun
-nb cpu
commit
|
commitdiff
|
tree
2017-08-22
Mark Abraham
Fixed thre
a
d-MPI with non-default -npme
commit
|
commitdiff
|
tree
2017-08-22
Mark
A
b
raham
F
i
x m
i
ssing declarati
o
n
o
f G
M
X_UNUSED_VALUE
commit
|
commitdiff
|
tree
2017-08-22
Mark Ab
r
aha
m
Merge
b
ranch relea
s
e
-
2016
commit
|
commitdiff
|
tree
2017-08-21
Mark
A
braha
m
M
o
v
ed i
n
crease_nstlist()
t
o nbnxn_tun
i
ng
.
h
commit
|
commitdiff
|
tree
2017-08-21
Mark Abra
h
am
Fix c
o
mpilation issues with ARM SIMD
commit
|
commitdiff
|
tree
2017-08-17
Mark Abraham
Replace con
s
i
s
t
ency ch
e
c
k
ing with ass
e
rtion
commit
|
commitdiff
|
tree
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