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Prepare for beta 2
2018-10-16
Mark Ab
r
ah
a
m
Eliminated t_ifunc from
t
_interact
i
on
_
fu
n
c
t
i
o
n
commit
|
commitdiff
|
tree
2018-10-16
Ma
r
k
Abraham
Tas
k
ass
i
gnment fo
r
bonded interactions on CUDA GPUs
commit
|
commitdiff
|
tree
2018-10-16
Mark
A
br
a
ham
Fix c
o
mp
i
ler i
s
sue
s
commit
|
commitdiff
|
tree
2018-10-16
Mark Abr
a
ham
Removed supp
o
rt for NVID
I
A CC 2
.
x device
s
(codename
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
Impro
v
e robustn
e
s
s of e
n
d-to-end testing
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
Create
Exclusio
n
Bl
o
c
k
s
commit
|
commitdiff
|
tree
2018-10-15
Mark Abraham
De-duplic
a
ting mdrun
s
etup
commit
|
commitdiff
|
tree
2018-10-14
Mark Ab
r
aham
Fix c
o
m
piler w
a
rnings
commit
|
commitdiff
|
tree
2018-10-13
Mark Abraham
Q
uie
t
compi
l
er warnings
commit
|
commitdiff
|
tree
2018-10-13
Mark A
b
r
a
ham
Deprecate
v
a
r
io
u
s fu
n
c
t
io
n
ality
in GROMACS 201
9
commit
|
commitdiff
|
tree
2018-10-12
M
ark Abraham
E
xclude gmxapi source files from incl
u
d
e
sorting
commit
|
commitdiff
|
tree
2018-10-11
Ma
r
k
Abraham
F
i
x Pa
d
d
edVector issues
commit
|
commitdiff
|
tree
2018-10-11
Mark Abraham
Open
m
d
r
un log file only once
commit
|
commitdiff
|
tree
2018-10-09
Mark Abraham
Fix DomdecOptio
n
s
default
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
D
i
s
a
ble FP
E
explicitl
y
for TPI force calculation
commit
|
commitdiff
|
tree
2018-10-08
Ma
r
k Abraham
Implemen
t
PaddedVe
c
tor
commit
|
commitdiff
|
tree
2018-10-08
M
a
rk Abraham
More updates to
t
est
mat
r
ix
commit
|
commitdiff
|
tree
2018-10-08
Mark Abrah
a
m
F
ix make test
commit
|
commitdiff
|
tree
2018-10-07
M
a
r
k
A
braham
Test with gcc 8 and
cuda
1
0
commit
|
commitdiff
|
tree
2018-10-05
M
a
r
k
Abra
h
a
m
Check log and ot
h
e
r
files different
l
y durin
g
appending
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Mark
Abra
h
a
m
Change to test TSAN wi
t
h clang
a
nd li
b
omp
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Replace CUDA call deprecated in CU
D
A
10
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Ex
t
r
a
ct
h
elpe
r
func
t
ions
f
o
r
p
reparin
g
f
or append
i
n
g
commit
|
commitdiff
|
tree
2018-10-04
Mark Ab
r
aham
Simplif
y
EM u
s
a
ge of mdebin
commit
|
commitdiff
|
tree
2018-10-03
Mark Ab
r
aham
Use
f
a
st returns in md5
c
o
mputation
commit
|
commitdiff
|
tree
2018-10-03
Mark Abraham
Add end
-
to-end
t
ests of energy mini
m
ization
commit
|
commitdiff
|
tree
2018-10-03
Mark Ab
r
a
ham
B
asic mo
d
ern
i
zation of md5 handling
commit
|
commitdiff
|
tree
2018-10-02
Mark
Abra
h
am
Reduce mdru
n
tests
usi
n
g
g
roup scheme
commit
|
commitdiff
|
tree
2018-10-01
M
ark Abraham
Fix gcc-8 w
a
r
n
ings ab
o
ut
s
trings
commit
|
commitdiff
|
tree
2018-10-01
Mark Abraha
m
Add release note
s
for removi
n
g
n
o
n-reproduc
i
ble aspects
commit
|
commitdiff
|
tree
2018-10-01
Ma
r
k
Abraham
Tests
f
or md5 comp
u
t
a
tion
on
o
pen files
commit
|
commitdiff
|
tree
2018-09-29
Mark Abraham
R
emov
e
NVML suppo
r
t
commit
|
commitdiff
|
tree
2018-09-29
Mark
Abraham
Stop
I
CC ICE
commit
|
commitdiff
|
tree
2018-09-28
Mark A
b
ra
h
a
m
Us
e
more defa
u
lt init
i
a
lization of mdrun str
u
cts
commit
|
commitdiff
|
tree
2018-09-28
Mark Abrah
a
m
Make some symbol
s
in gmxpre-con
f
i
g
.
h
a
l
w
a
y
s defined
commit
|
commitdiff
|
tree
2018-09-26
Ma
r
k Ab
r
aham
Clarify distinct paths for mdrun log file handling
commit
|
commitdiff
|
tree
2018-09-24
Mark Abraham
F
ix
D
o
x
y
gen
links
commit
|
commitdiff
|
tree
2018-09-23
M
ar
k
Abra
h
am
Leak less from gromppp with cm
a
p
commit
|
commitdiff
|
tree
2018-09-20
Mark
Ab
r
aham
Update
to test w
i
th clang-7
commit
|
commitdiff
|
tree
2018-09-18
Mark Abraham
Separa
t
e
d
partitioning
a
nd dlb
c
ode within domdec
commit
|
commitdiff
|
tree
2018-09-18
Mark
Abr
a
ham
A
d
d
not
_
n
ull from GSL
commit
|
commitdiff
|
tree
2018-09-13
Mark A
b
raham
El
i
mina
t
e main
.
h
commit
|
commitdiff
|
tree
2018-09-11
Mark Abraham
Replace C-style l
i
brary
f
ile handlin
g
with RAII ap
p
roaches
commit
|
commitdiff
|
tree
2018-09-11
Mark Abraha
m
I
mprove DD lo
g
gi
n
g
commit
|
commitdiff
|
tree
2018-09-11
Mar
k
Ab
r
aham
Repla
c
e
readCon
f
o
rmation with TopologyI
n
format
i
on
commit
|
commitdiff
|
tree
2018-09-09
M
a
rk Abra
h
am
C
h
ange TopologyInform
a
tion implementation
commit
|
commitdiff
|
tree
2018-09-07
Mar
k
Ab
r
aham
F
ix grompp
m
em
o
r
y
leaks
commit
|
commitdiff
|
tree
2018-09-07
Mark
Abra
h
am
Mino
r
f
ixes to GPU build system
commit
|
commitdiff
|
tree
2018-09-07
Mark Abraham
Separate simula
t
ion
da
t
a
base u
s
ed in test
s
commit
|
commitdiff
|
tree
2018-09-05
M
a
rk A
b
ra
h
am
Be quiet
e
r when fail
i
ng to detect GPUs
commit
|
commitdiff
|
tree
2018-08-30
M
a
rk Abraham
Up
d
ate testing matrices for
co
v
erage and
s
pee
d
commit
|
commitdiff
|
tree
2018-08-29
M
ark Abraham
Merg
e
branch release-2018
commit
|
commitdiff
|
tree
2018-08-29
Mark Abrah
a
m
Move
c
lang-tidy bui
l
d
commit
|
commitdiff
|
tree
2018-08-28
Mark
A
braham
Fix more
c
lang-tidy issues
commit
|
commitdiff
|
tree
2018-08-27
Mark Abr
a
h
am
Fix
use of null
p
tr
commit
|
commitdiff
|
tree
2018-08-24
Mar
k
Ab
r
aham
Fix
build
w
ithout TNG
commit
|
commitdiff
|
tree
2018-08-24
M
ark Abraham
M
e
rge branc
h
r
e
lease-201
8
commit
|
commitdiff
|
tree
2018-08-22
M
ark
Ab
r
a
ham
Fix
h
andling
of count
e
r rese
t
s
commit
|
commitdiff
|
tree
2018-08-22
M
ark Abr
a
ham
Pe
r
m
it PME on
G
PUs only for dynamica
l
int
e
gr
a
to
r
s
commit
|
commitdiff
|
tree
2018-08-21
Mark Abra
h
am
Re-implement
e
d
mdrun -re
r
un
t
ests
commit
|
commitdiff
|
tree
2018-08-21
Mark
A
br
a
ham
Fix
assert
i
ons
for
S
D upd
a
te
commit
|
commitdiff
|
tree
2018-08-14
Mark Abraham
Fix enforced r
o
tati
o
n energy output
commit
|
commitdiff
|
tree
2018-08-05
Mark Abrah
a
m
Re
f
or
m
enforce
d
rotat
i
o
n
w
o
rking
d
ata
commit
|
commitdiff
|
tree
2018-07-31
M
ark Abraham
C
l
ea
n
up input
r
ec st
r
uc
t
s
commit
|
commitdiff
|
tree
2018-07-30
Mark
Abraha
m
Fi
x
CG with mul
t
iple domains
commit
|
commitdiff
|
tree
2018-07-18
Mark Abrah
a
m
Fix pre-s
u
b
m
it matrix
commit
|
commitdiff
|
tree
2018-07-17
M
ark Abraham
Update clang static analyzer to ver
s
ion 6
commit
|
commitdiff
|
tree
2018-07-16
Mark Abraha
m
U
p
dat
e
d infrastruct
u
re for
comp
a
ring m
d
r
u
n
o
utput in
.
.
.
commit
|
commitdiff
|
tree
2018-07-16
Mark Ab
r
aham
Replacement
for pdb2gmx t
e
sts
commit
|
commitdiff
|
tree
2018-07-12
Mark Abraham
Bump minimum
MSVC
v
ersio
n
to 2017
commit
|
commitdiff
|
tree
2018-07-11
Ma
r
k Abrah
a
m
Split T
o
p
ologyInformation into
its own head
e
r
commit
|
commitdiff
|
tree
2018-07-10
Mark
Abr
a
ham
A
d
d
infrastructure f
o
r tools cleanup
commit
|
commitdiff
|
tree
2018-07-08
Mark Abraham
Clar
i
fy the im
p
lement
a
tion of selection -of
p
db
o
ut
p
ut
commit
|
commitdiff
|
tree
2018-07-06
Mark Abraham
Us
e
few
e
r gcc-4
.
8 configura
t
ions
commit
|
commitdiff
|
tree
2018-07-06
Mark A
b
raham
F
ix warnings i
n
i
nterna
l
x
dr code
commit
|
commitdiff
|
tree
2018-07-06
Mar
k
Abraham
Merge "Merge
r
e
l
ease-2
0
1
8 into ma
s
ter"
commit
|
commitdiff
|
tree
2018-07-03
Mark Abraham
Fix
c
lang
CUDA build
commit
|
commitdiff
|
tree
2018-07-02
Mark Ab
r
ah
a
m
Re
m
ove
some pieces from forcer
e
c
.
h
commit
|
commitdiff
|
tree
2018-06-29
M
ark Abraham
Ne
w
quote
from ISC2018
commit
|
commitdiff
|
tree
2018-06-25
M
a
rk Abraham
Test
b
o
t
h i
n
t
ernal
and exte
r
nal clFFT build i
n
J
e
nki
n
s
commit
|
commitdiff
|
tree
2018-06-25
M
ark Ab
r
a
h
am
Fi
x
unused v
a
riable warnings
commit
|
commitdiff
|
tree
2018-06-22
Mark A
b
raham
Update energy an
d
traject
o
r
y
fr
a
me types
commit
|
commitdiff
|
tree
2018-06-14
M
a
rk Abraham
Updat
e
d
t
o prepare fo
r
2
0
18
.
3
r
e
lease
commit
|
commitdiff
|
tree
2018-06-14
Mark Abra
h
am
Version 2018
.
2
commit
|
commitdiff
|
tree
2018-06-13
Mark
Abraham
C
all Cons
t
r
a
ints::s
e
tCo
n
straints with other setup code
commit
|
commitdiff
|
tree
2018-06-13
M
a
rk Abraham
Fix premature repo
r
ti
n
g of
a
ction w
h
en
G
P
Us are not
.
.
.
commit
|
commitdiff
|
tree
2018-06-13
Mark
Abraham
Use
initi
a
lizer li
s
ts
f
or Lincs a
n
d Task
commit
|
commitdiff
|
tree
2018-06-13
Mark Abraham
Use more containe
r
s an
d
vie
w
s
for constrain
t
s code
commit
|
commitdiff
|
tree
2018-06-13
Mark Abraham
Up
d
a
t
e top
-
level README
commit
|
commitdiff
|
tree
2018-06-13
Mark Abraham
Fixed do
c
umen
t
at
i
on typo
commit
|
commitdiff
|
tree
2018-06-13
Mar
k
A
braham
Bump lmfi
t
s
u
p
port to version 7
commit
|
commitdiff
|
tree
2018-06-12
M
a
rk Abraha
m
More fixes to suit gcc 8 for d
o
uble
b
uild
commit
|
commitdiff
|
tree
2018-06-12
Mark
Abrah
a
m
Pr
e
p
a
re
f
or GROMACS 2019 relea
s
e notes
commit
|
commitdiff
|
tree
2018-06-06
M
a
r
k
Abraham
Move IMD initialization and
f
use D
D
s
e
tup
commit
|
commitdiff
|
tree
2018-06-05
Ma
r
k Abr
a
ham
Fixed enemat w
h
e
n
.
edr ha
d
no matching energy group
s
commit
|
commitdiff
|
tree
2018-06-05
Ma
r
k
A
braham
Impro
v
ed docs for gmx
mindist -
p
i
commit
|
commitdiff
|
tree
2018-06-05
Mark Abraham
Make proper
BoxDeformat
i
o
n class
commit
|
commitdiff
|
tree
2018-06-05
Mark Abraham
Sep
a
rate flexible const
r
aint c
o
u
nting
commit
|
commitdiff
|
tree
2018-06-05
Mark Abra
h
am
Make Constrain
t
s a pro
p
e
r
class
commit
|
commitdiff
|
tree
2018-06-04
Mark Abraham
Update Awh
i
n
itia
l
ization a
n
d lifetim
e
manage
m
e
nt
commit
|
commitdiff
|
tree
next