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Merge branch release-5-1 into release-2016
2017-02-15
M
ark
Abr
a
ham
M
e
rge branch release-5-1 into release-2016
commit
|
commitdiff
|
tree
2017-02-10
Mark Abraham
Co
r
r
ected output of gmx do_dssp -sc
commit
|
commitdiff
|
tree
2017-02-07
Ved
r
an Mileti
ć
Document
r
unning Cl
a
ng s
t
atic a
n
alyzer manual
l
y
commit
|
commitdiff
|
tree
2017-02-07
M
a
rk Abraham
Bump
e
d ver
s
ion to prepare for next p
a
t
c
h release
commit
|
commitdiff
|
tree
2017-02-07
Mark Abraham
Versio
n
201
6
.
2
commit
|
commitdiff
|
tree
2017-02-07
Berk Hes
s
Ad
d
mdp option check w
i
th decoupled mo
d
es
commit
|
commitdiff
|
tree
2017-02-05
Mark Abraham
Merge branch r
e
l
e
ase-5-1 i
n
to rele
a
se-2016
commit
|
commitdiff
|
tree
2017-01-31
Mark
A
b
raham
Me
r
g
e branc
h
r
e
lease-5-1 into relea
s
e
-2016
commit
|
commitdiff
|
tree
2017-01-22
Mark
A
braha
m
Fixed gmx rms
f
-q -oq
.
commit
|
commitdiff
|
tree
2017-01-20
Berk Hess
Di
s
allow ov
e
rwriti
n
g of dihedral type 9
commit
|
commitdiff
|
tree
2017-01-04
Mark Abraham
Stop tr
y
ing to use
o
b
jdump --reloc on
Mac
commit
|
commitdiff
|
tree
2017-01-03
Mark Ab
r
a
ham
Merge bran
c
h relea
s
e-5-1 into
release-20
1
6
commit
|
commitdiff
|
tree
2016-12-20
M
a
r
k Ab
r
a
h
a
m
Corrected docume
n
tation
abou
t
eigenvalue
h
andling
commit
|
commitdiff
|
tree
2016-12-10
Teemu Murto
l
a
Bui
l
d scripts fo
r
improv
e
d release workfl
o
w
commit
|
commitdiff
|
tree
2016-12-09
Szilárd Pá
l
l
Turn off hwloc s
u
pport
w
hen sta
t
ic
lib
foun
d
commit
|
commitdiff
|
tree
2016-12-08
Teemu Murtola
Fix possible memory error with
l
o
ng sele
c
tions
commit
|
commitdiff
|
tree
2016-12-07
Teemu Mu
r
tola
Fix use of posi
t
ion variables with plus/merge
commit
|
commitdiff
|
tree
2016-12-07
Mark Ab
r
aham
Fix memor
y
handling in gmx
d
ump of TNG fil
e
s
commit
|
commitdiff
|
tree
2016-12-05
Mark
A
braham
Remove u
n
due narrowing of
integ
e
r i
n
TNG
re
a
ding
commit
|
commitdiff
|
tree
2016-12-01
Mark Abraha
m
Fix minor trjco
n
v b
u
g
commit
|
commitdiff
|
tree
2016-11-16
Carsten Kutzner
Increase
d
the d
e
fault reset step to 1500
in gmx tune_pme
commit
|
commitdiff
|
tree
2016-11-08
Dan Horá
k
Fix
x
86 condition
a
l
commit
|
commitdiff
|
tree
2016-10-28
M
a
r
k Abrah
a
m
B
umped versio
n
to
p
repa
r
e for next patch
r
elease
commit
|
commitdiff
|
tree
2016-10-28
Ma
r
k Abraham
Version 2016
.
1
commit
|
commitdiff
|
tree
2016-10-28
Berk Hess
DLB
c
an
now turn off, when
sl
o
wer
commit
|
commitdiff
|
tree
2016-10-28
Szi
l
árd Páll
GPU
-
relate
d
additions t
o
the install/us
e
r guide
commit
|
commitdiff
|
tree
2016-10-28
B
e
rk Hess
Fix DL
B
timi
n
g
w
ith
CUDA and
Op
e
nC
L
commit
|
commitdiff
|
tree
2016-10-27
S
z
ilár
d
Páll
Make -cl-fast
-
relaxed-math default
commit
|
commitdiff
|
tree
2016-10-21
Mark Abra
h
a
m
Update install guide
commit
|
commitdiff
|
tree
2016-10-18
Mark Abraham
Fix S
I
MD suggesti
o
n
for
V
MX
commit
|
commitdiff
|
tree
2016-10-12
Berk Hess
Fixe
d
p
r
int bug in gmx wham
commit
|
commitdiff
|
tree
2016-10-11
James
W
.
Barnett
fix t
y
po
commit
|
commitdiff
|
tree
2016-10-07
Mark
A
b
r
a
ham
A
d
d
script for
J
enkins regres
s
ionte
s
t
u
p
date job
commit
|
commitdiff
|
tree
2016-10-06
C
a
rlo Cam
i
lloni
Always update mdatoms when
d
o
i
ng energ
y
m
ini
m
i
s
ation
commit
|
commitdiff
|
tree
2016-10-03
M
a
rk Abraham
Merge branch releas
e
-5-1 in
t
o r
e
leas
e
-
2016
commit
|
commitdiff
|
tree
2016-10-03
Mark
A
b
ra
h
am
Replace
use o
f
de
p
recated read
d
ir_r
commit
|
commitdiff
|
tree
2016-09-28
Jo
c
hen Hub
Fixed bug in gmx wha
m
f
o
r r
e
ading
p
ullx f
i
l
e
s
.
commit
|
commitdiff
|
tree
2016-09-27
Dav
i
d van der Spoel
Fixed s
c
ript xpl
o
r
2gmx
.
pl to work with GMXDATA
commit
|
commitdiff
|
tree
2016-09-08
Mark Abraha
m
Merge branch
r
e
lease
-
5-1 into re
l
ease-2016
commit
|
commitdiff
|
tree
2016-09-08
M
a
r
k
A
braha
m
Bumped patch numbe
r
to prep
a
re for future
5
.
1
.
5 relea
s
e
commit
|
commitdiff
|
tree
2016-09-07
Mar
k
Abraham
Versi
o
n 5
.
1
.
4
commit
|
commitdiff
|
tree
2016-09-07
Mark Abraham
Removed HIS1
fr
o
m oplsaa an
d
charmm definitions
commit
|
commitdiff
|
tree
2016-09-06
Mar
k
Abraham
Work
ar
o
und g
l
ibc 2
.
23 wit
h
CUDA
commit
|
commitdiff
|
tree
2016-09-02
Berk Hess
Fix
P
a
rrinel
l
o-Rahm
a
n with n
s
tpcoupl
e
>1
commit
|
commitdiff
|
tree
2016-08-30
Berk
H
ess
M
ak
e
virial re
p
r
oduci
b
le
commit
|
commitdiff
|
tree
2016-08-15
Mark Abraha
m
Fixe
s
fo
r
BG/Q platf
o
r
m
files and instal
l
gu
i
de
commit
|
commitdiff
|
tree
2016-08-15
Berk Hess
Reduce FE pair-list me
m
ory us
a
ge
commit
|
commitdiff
|
tree
2016-08-12
Mark Abraham
B
ump number t
o
prepare for first patch
release
commit
|
commitdiff
|
tree
2016-08-04
Mark A
b
raham
Version
2016
commit
|
commitdiff
|
tree
2016-08-03
David
v
an der Spoel
Three new quotes
.
commit
|
commitdiff
|
tree
2016-08-03
Vedran Milet
i
ć
Use
o
nly legal
c
haract
e
rs i
n
OpenCL cache filena
m
e
commit
|
commitdiff
|
tree
2016-07-29
Mark Abraham
I
mp
r
o
v
e handl
i
n
g
o
f gmock and g
c
c6
commit
|
commitdiff
|
tree
2016-07-29
Mark
Abra
h
a
m
Me
r
g
e
branch
r
elease-5
-
1 into release-
2
016
commit
|
commitdiff
|
tree
2016-07-29
David van
d
er Spoel
F
i
xes incor
r
ect charges in OPL
S
/A
A
-L for HISD a
n
d HI
S
E
commit
|
commitdiff
|
tree
2016-07-28
Mark A
b
raham
Add toolchain flags for SSE2
c
ompi
l
ation
commit
|
commitdiff
|
tree
2016-07-21
Mark Abraham
Bumped patch number to
p
repar
e
for
f
uture
5
.
1
.
4 r
e
lease
commit
|
commitdiff
|
tree
2016-07-14
Mark Abrah
a
m
F
ix issues with using int
for number o
f
s
t
e
ps
commit
|
commitdiff
|
tree
2016-07-13
Mark Abraham
Ve
r
sion 5
.
1
.
3
commit
|
commitdiff
|
tree
2016-07-12
Mark
A
braham
Fix trr
m
a
gic number readin
g
commit
|
commitdiff
|
tree
2016-07-11
M
a
rk A
b
raham
F
i
x
g
m
x mdrun -memb
e
d -ntmpi -1
commit
|
commitdiff
|
tree
2016-07-11
E
r
ik Li
n
da
h
l
Fix m
e
mbed with p
a
r
t
i
a
l
revert
of 29943
f
commit
|
commitdiff
|
tree
2016-07-11
Michael Shi
r
ts
Fix f
o
r
incorrec
t
ly setting expanded e
n
semble
w
h
en
.
.
.
commit
|
commitdiff
|
tree
2016-07-11
Mark Abraham
Fix r
e
g
ressiontes
t
download md5sum
commit
|
commitdiff
|
tree
2016-07-09
Mark Abraham
Fir
s
t
2016
r
elease candidate
commit
|
commitdiff
|
tree
2016-07-09
Erik Lindahl
Hardware de
t
ec
t
i
on clean-up and pre/post-proces
s
i
ng
commit
|
commitdiff
|
tree
2016-07-08
Jochen Hub
U
p
d
a
ted g
_
wham for the
n
ew pull setup
commit
|
commitdiff
|
tree
2016-07-08
Mark Abraham
M
e
rge branch release-5-1 into relea
s
e-20
1
6
commit
|
commitdiff
|
tree
2016-07-08
David
van
d
e
r
Spoel
Introduce fat
a
l e
r
ror for
t
o
o
few frames i
n
gmx dos
.
commit
|
commitdiff
|
tree
2016-07-08
Mark Abraham
Sim
p
lify SIMD c
o
mpiler flag construction
commit
|
commitdiff
|
tree
2016-07-08
Erik Li
n
d
a
hl
Add detection
f
o
r
ARMv7 c
y
cle cou
n
ter support
commit
|
commitdiff
|
tree
2016-07-07
Mark A
b
r
aham
Move
c
onsi
s
tency check for number of th
r
eads
commit
|
commitdiff
|
tree
2016-07-04
M
ark Abraham
Fixe
s
for Power7 big-e
n
dian
commit
|
commitdiff
|
tree
2016-07-04
Szi
l
árd
P
áll
Disable NVIDIA
J
IT ca
c
he
with
O
penCL
commit
|
commitdiff
|
tree
2016-06-30
Mark Abraham
Merge b
r
a
nch
releas
e
-
5
-
1 into
release-2016
commit
|
commitdiff
|
tree
2016-06-29
Mark Abraham
Refactor s
y
s
c
onf checking
commit
|
commitdiff
|
tree
2016-06-29
Mark
A
bra
h
am
W
o
r
k ar
o
und glibc 2
.
23
with CUD
A
commit
|
commitdiff
|
tree
2016-06-28
B
e
rk Hess
Properly reset CUDA applic
a
ti
o
n clocks
commit
|
commitdiff
|
tree
2016-06-28
Ma
r
k Abra
h
am
U
p
date to i
n
cl
u
d
e a
g
cc 6
.
1 configurat
i
on
commit
|
commitdiff
|
tree
2016-06-28
Mark Abrah
a
m
Fix
S
IMD configuration
management
commit
|
commitdiff
|
tree
2016-06-27
Mark A
b
raham
Removed
unneces
s
ary in
t
e
r-sim
u
l
a
t
ion signalling
commit
|
commitdiff
|
tree
2016-06-27
Ber
k
Hess
Use sysconf(_S
C
_
NPR
O
C
E
SSORS_O
N
LN
)
commit
|
commitdiff
|
tree
2016-06-27
Mark Abra
h
am
M
erge br
a
n
ch releas
e
-5
-
1 in
t
o r
e
leas
e
-2016
commit
|
commitdiff
|
tree
2016-06-24
Berk Hess
Fix Ve
r
let buff
e
r c
a
lculation with
nstlist=1
commit
|
commitdiff
|
tree
2016-06-23
Berk He
s
s
More acc
u
r
a
t
e GPU
l
ist
splitting
commit
|
commitdiff
|
tree
2016-06-23
Mar
k
Abraham
Allow use of
e
xternal
l
m
fit package
commit
|
commitdiff
|
tree
2016-06-23
Mark Abraha
m
Pre
v
en
t
use
o
f mdr
u
n -maxh -mult
i
commit
|
commitdiff
|
tree
2016-06-22
Be
r
k Hess
Updated O
p
e
nCLTODOList
.
t
x
t
commit
|
commitdiff
|
tree
2016-06-22
Mark Ab
r
a
ha
m
Fix con
f
igur
a
tion-time cpuinfo code
commit
|
commitdiff
|
tree
2016-06-22
David v
a
n d
e
r Spoel
Removed
s
p
urious r_ij in force for
Morse p
o
t
ential
.
.
.
commit
|
commitdiff
|
tree
2016-06-22
Mar
k
A
b
rah
a
m
M
e
rge
branch release-5-1
i
nto releas
e
-201
6
commit
|
commitdiff
|
tree
2016-06-22
Ber
k
Hess
Add nbnxn pair-list rebalanci
n
g
commit
|
commitdiff
|
tree
2016-06-22
Berk
H
ess
Rem
o
ve OpenMP overhead at high pa
r
allelization
commit
|
commitdiff
|
tree
2016-06-22
B
e
rk Hess
C
o
rre
c
t
G
PU p
a
ir esti
m
ate
f
or l
i
s
t splitting
commit
|
commitdiff
|
tree
2016-06-22
Mark Abraha
m
Adjust an
d
document C++11 compiler tests
commit
|
commitdiff
|
tree
2016-06-20
M
a
r
k
A
br
a
h
am
Update pre
-
submit m
a
trix contents
commit
|
commitdiff
|
tree
2016-06-19
Berk Hess
Remove war
n
ings on ch
e
ckpoi
n
t mismat
c
h
commit
|
commitdiff
|
tree
2016-06-19
Mark Ab
r
aha
m
Improve doc
s
for linking stdlibc++ needed b
y
icc
commit
|
commitdiff
|
tree
2016-06-17
Berk
Hes
s
R
e
mo
v
e std::
t
h
r
ea
d
::hardw
a
re_concurren
c
y()
commit
|
commitdiff
|
tree
2016-06-17
V
e
d
ran Milet
i
ć
Report the filename and the line number on
fa
i
lure
commit
|
commitdiff
|
tree
2016-06-17
Mark Abraham
Merg
e
bra
n
ch release-5-1 into release-2016
commit
|
commitdiff
|
tree
next