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GROMACS version 2019.4
2019-09-27
Mark Abra
h
am
Fix
g
ro file output with in
d
ex gr
o
ups
commit
|
commitdiff
|
tree
2019-08-06
M
a
rk Ab
r
ah
a
m
F
i
x
fo
r
MSVC
+
CUDA
commit
|
commitdiff
|
tree
2019-07-02
Mark Abraham
Clarify wording of r
e
lease
no
t
e
s
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Initialize
a
l
l
o
f g
m
x_domdec_comm_t
commit
|
commitdiff
|
tree
2019-05-23
Mark Abraham
Re
v
ert "Fix
e
d dv
d
lambda for
S
HAKE + FE"
commit
|
commitdiff
|
tree
2019-05-20
Mark Abraham
Fix equatio
n
t
ypo
commit
|
commitdiff
|
tree
2019-05-07
Mark Ab
r
a
h
a
m
A
dd an
e
xample of usi
n
g an M
P
I w
r
apper compiler
commit
|
commitdiff
|
tree
2019-04-13
Mark A
b
raham
F
i
x s
e
lf-consistency tests of hwloc
data structures
commit
|
commitdiff
|
tree
2019-04-12
M
a
rk A
b
raham
I
mprove warning
me
s
sages about
d
u
pli
c
ate definitions
commit
|
commitdiff
|
tree
2019-04-09
Mark Abraham
Fix t
y
po in AVX512
d
e
tectio
n
code
commit
|
commitdiff
|
tree
2019-03-19
Mark
Abraham
Prev
e
nted
FFT
W
bui
l
d e
r
rors
with c
l
ang and AVX-512
commit
|
commitdiff
|
tree
2019-03-13
Mark Abrah
a
m
Provi
d
e remin
d
er
of which
n
vc
c
is
in use
commit
|
commitdiff
|
tree
2019-02-27
Mark
A
br
a
ham
K
e
ep n
i
c
h
e C
M
ake variab
l
es as
a
dvanced
commit
|
commitdiff
|
tree
2019-02-26
Mark Abraham
A
d
d ne
w
l
ine to t
r
jconv
not
i
ce to users
commit
|
commitdiff
|
tree
2019-02-15
Mark Abraham
Im
p
rove
d
diagnostics when PME can
n
ot run on GPUs
commit
|
commitdiff
|
tree
2019-02-14
Mark Abraham
Fix
u
s
e of selections referri
n
g to index gro
u
p
s
commit
|
commitdiff
|
tree
2019-02-14
Ma
r
k Abrah
a
m
Revert changes to impl
e
mentation
of insert
-
molecules
.
.
.
commit
|
commitdiff
|
tree
2019-02-13
Mark Abraham
Improved e
l
ectric-field docs
commit
|
commitdiff
|
tree
2019-01-30
Mark Abr
a
h
am
Me
r
ge
r
emote branch relea
s
e-2018 into re
l
ease
-
20
1
9
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraha
m
Fi
x
releas
e
notes i
s
sue lin
k
s
commit
|
commitdiff
|
tree
2019-01-30
Mark
A
b
r
aham
Fix release notes issue links
commit
|
commitdiff
|
tree
2019-01-28
Mark Ab
r
aham
S
top
t
ry
i
ng to check
n
vcc o
n
Windo
w
s
commit
|
commitdiff
|
tree
2019-01-21
M
ark
Abraham
Fix tr
j
conv -ndec
commit
|
commitdiff
|
tree
2019-01-18
Mark
A
b
r
aham
Disable
d
i
nter
n
al
c
lFFT when us
i
ng MSVC with OpenCL
commit
|
commitdiff
|
tree
2019-01-18
M
ark Abraham
I
m
prove
n
vcc error
r
eporting
commit
|
commitdiff
|
tree
2019-01-16
Mark Abrah
a
m
Migrate
test c
o
nfigu
r
ation off bs_mac
commit
|
commitdiff
|
tree
2019-01-14
Mark
A
braham
Improve portability of
P
ME on GPU code
commit
|
commitdiff
|
tree
2019-01-11
Mark Abraham
Fix typ
o
i
n release notes
commit
|
commitdiff
|
tree
2019-01-10
Mark Ab
r
aham
Add more ch
e
c
ks
for division b
y
z
e
r
o
commit
|
commitdiff
|
tree
2019-01-08
Mark Abraham
Fix trjconv -ndec
commit
|
commitdiff
|
tree
2019-01-08
Mark
A
b
r
aham
S
i
m
plify repor
t
i
ng of
GPU selection
commit
|
commitdiff
|
tree
2018-12-22
Mark Ab
r
a
ham
F
ix unuse
d
par
a
met
e
r warning
commit
|
commitdiff
|
tree
2018-12-10
Mark Abraham
Make only mdrun r
e
port process ID
commit
|
commitdiff
|
tree
2018-12-09
M
a
rk Abraham
Fix PO
W
ER8 and P
O
WER9 build
commit
|
commitdiff
|
tree
2018-12-03
M
ark Abr
a
h
a
m
Move responsibility for PME reduction to its module
commit
|
commitdiff
|
tree
2018-11-29
Mark
Abraham
R
e
mov
e
d
erronous man
u
al va
r
i
a
b
l
e handling
commit
|
commitdiff
|
tree
2018-11-28
Mark Abra
h
a
m
I
ntr
o
d
u
c
e GpuBon
d
ed
commit
|
commitdiff
|
tree
2018-11-26
M
a
rk
A
b
ra
h
am
Cle
a
n up initial log output
commit
|
commitdiff
|
tree
2018-11-22
Mark Ab
r
ah
a
m
I
nt
r
oduce PpForceW
o
rkload
commit
|
commitdiff
|
tree
2018-11-20
Mark Abraham
Partial
revert of "Fix inefficient shell minimization"
commit
|
commitdiff
|
tree
2018-11-19
Mark Abraham
Fix inef
f
i
cient shell mi
n
imization
commit
|
commitdiff
|
tree
2018-11-15
Mark Abraham
F
ix chec
k
poi
n
t restart
o
f
tpr with
i
nfinite step cou
n
t
commit
|
commitdiff
|
tree
2018-11-15
Mark Abraham
Relax arbitrary tolerance on rerun test
commit
|
commitdiff
|
tree
2018-11-14
Mark Abr
a
ham
Fix OpenCL mdrun
from instal
l
ed pat
h
commit
|
commitdiff
|
tree
2018-11-14
Mark Abraham
More warning suppressio
n
s for QMMM cod
e
commit
|
commitdiff
|
tree
2018-11-09
Mark Abraham
Di
s
abled FPE che
c
king for no
n
-release builds
commit
|
commitdiff
|
tree
2018-11-08
M
a
rk A
b
raham
Pragm
a
warning suppress
i
ns for
icc+windows
commit
|
commitdiff
|
tree
2018-11-07
Mark Abraham
Suppress clang w
a
r
nings about
QMMM code
commit
|
commitdiff
|
tree
2018-11-05
Ma
r
k A
b
r
a
ham
Make PME Open
C
L enable
d
only
f
or
AMD devices
commit
|
commitdiff
|
tree
2018-11-05
Mark Abraha
m
Remove s
o
urc
e
f
i
l
e
with no c
o
ntent
commit
|
commitdiff
|
tree
2018-11-02
Mark
Abraha
m
Qui
e
t
unused va
r
iable warnings
commit
|
commitdiff
|
tree
2018-11-01
Mark A
b
raham
Stop using h
w
loc on old ARM slave
commit
|
commitdiff
|
tree
2018-11-01
Mark
A
bra
h
a
m
D
isable ccache by def
a
ult
commit
|
commitdiff
|
tree
2018-10-30
Ma
r
k Abraham
Improve ccach
e
implementa
t
ion
commit
|
commitdiff
|
tree
2018-10-30
M
ark Ab
r
aham
Rename to GMX
_
OPENCL_NB_CLUSTER_SIZ
E
commit
|
commitdiff
|
tree
2018-10-30
Mark Abraham
U
p
dat
e
s
t
o docs for Open
C
L s
u
pport
commit
|
commitdiff
|
tree
2018-10-26
Mark Ab
r
aham
Merge "Merg
e
branch r
e
lease-2018 int
o
release
-
2019
.
.
.
commit
|
commitdiff
|
tree
2018-10-26
Mark Abraha
m
M
erge branch release-2
0
18
into release-2019
commit
|
commitdiff
|
tree
2018-10-25
Mark Abraham
I
nt
r
oduce
A
r
rayRefWithPad
d
ing
commit
|
commitdiff
|
tree
2018-10-16
M
ark Abraham
Eliminated t_
i
func from t_inter
a
ction_function
commit
|
commitdiff
|
tree
2018-10-16
Mark A
b
raham
Ta
s
k assign
m
ent fo
r
bond
e
d
intera
c
tions on CUDA GPUs
commit
|
commitdiff
|
tree
2018-10-16
M
a
rk Abr
a
ham
Fix c
o
mpiler
iss
u
es
commit
|
commitdiff
|
tree
2018-10-16
M
a
rk Abraham
Removed
s
uppor
t
fo
r
NVIDIA
CC 2
.
x device
s
(
codename
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
M
ark A
b
raham
I
mprove robus
t
ness of end-t
o
-
e
nd testin
g
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
C
r
e
a
t
e ExclusionBlocks
commit
|
commitdiff
|
tree
2018-10-15
Mark
A
braham
De-duplica
t
ing m
d
run
s
e
tup
commit
|
commitdiff
|
tree
2018-10-14
Mark Abraham
F
ix compiler war
n
ings
commit
|
commitdiff
|
tree
2018-10-13
Mar
k
Abraham
Q
uiet
c
o
mp
i
l
er
w
arnings
commit
|
commitdiff
|
tree
2018-10-13
Mar
k
Abraham
D
ep
r
ecate various functio
n
ality
i
n
GROMACS 2019
commit
|
commitdiff
|
tree
2018-10-12
M
a
rk Abraham
Exclude gmx
a
pi source fi
l
es from include sorting
commit
|
commitdiff
|
tree
2018-10-11
Mark Abrah
a
m
Fix Padd
e
dV
e
ctor issues
commit
|
commitdiff
|
tree
2018-10-11
Mar
k
Abr
a
ha
m
Open mdr
u
n l
o
g file only on
c
e
commit
|
commitdiff
|
tree
2018-10-09
Mar
k
Abraham
Fix DomdecOp
t
ions default
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
Disable FPE exp
l
icitly for TPI f
o
r
c
e calculati
o
n
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraha
m
Implem
e
n
t
PaddedVector
commit
|
commitdiff
|
tree
2018-10-08
Mark
Abraham
More
u
p
dates to
te
s
t
m
atr
i
x
commit
|
commitdiff
|
tree
2018-10-08
Mar
k
Abraha
m
Fix make test
commit
|
commitdiff
|
tree
2018-10-07
Mark Abra
h
am
Te
s
t with
g
cc 8 and cuda
1
0
commit
|
commitdiff
|
tree
2018-10-05
Mark A
b
ra
h
am
Check log and o
t
her files differently dur
i
n
g
appending
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Mark Ab
r
aham
Change to
te
s
t TSAN wit
h
clan
g
a
n
d libomp
commit
|
commitdiff
|
tree
2018-10-04
M
a
rk Abraham
R
eplace CUDA call deprecat
e
d i
n
CUDA 10
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Extract h
e
lper functions for preparing for a
p
p
ending
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Simplify
E
M
usage of mdebin
commit
|
commitdiff
|
tree
2018-10-03
Mark Abrah
a
m
U
se fast retu
r
ns in md5
c
ompu
t
ation
commit
|
commitdiff
|
tree
2018-10-03
Mar
k
Ab
r
aham
A
dd end-to-end test
s
o
f energy mi
n
im
i
za
t
ion
commit
|
commitdiff
|
tree
2018-10-03
Mark
A
bra
h
am
B
asic moder
n
ization
of md5 handlin
g
commit
|
commitdiff
|
tree
2018-10-02
Mark Abraham
Redu
c
e mdrun tests
u
sin
g
g
r
ou
p
sch
e
me
commit
|
commitdiff
|
tree
2018-10-01
Mar
k
Abraham
Fix gcc-
8
warn
i
ngs about strings
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraham
Add release notes
f
or remov
i
ng
n
on-reproducible aspec
t
s
commit
|
commitdiff
|
tree
2018-10-01
Mark Ab
r
aham
Test
s
for md5 computation on open files
commit
|
commitdiff
|
tree
2018-09-29
Mark
Abr
a
ham
Remove NVML sup
p
or
t
commit
|
commitdiff
|
tree
2018-09-29
Mark Abraham
Stop
I
C
C ICE
commit
|
commitdiff
|
tree
2018-09-28
Mark Ab
r
aham
Use
m
ore default initialization o
f
md
r
un struc
t
s
commit
|
commitdiff
|
tree
2018-09-28
Mark Abraham
Make
s
ome symbols in gmxpre-conf
i
g
.
h
always de
f
i
n
e
d
commit
|
commitdiff
|
tree
2018-09-26
Mark Abraham
Cla
r
ify distinct pat
h
s for mdrun lo
g
file ha
n
dling
commit
|
commitdiff
|
tree
2018-09-24
Mark Abraham
F
ix D
o
xygen links
commit
|
commitdiff
|
tree
2018-09-23
Mar
k
Ab
r
aham
L
e
ak le
s
s f
r
om gro
m
ppp wi
t
h cmap
commit
|
commitdiff
|
tree
2018-09-20
Mark
A
bra
h
am
Update to tes
t
with cla
n
g
-7
commit
|
commitdiff
|
tree
2018-09-19
Ma
r
k Abraham
Fix bug wit
h
s
t
ate natoms
i
n
membed
commit
|
commitdiff
|
tree
2018-09-18
Mark Abra
h
am
Separ
a
ted
p
artitioning and dlb code within domdec
commit
|
commitdiff
|
tree
next