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Add grompp check for usage of "define" field in mdp
2019-01-11
Mark
A
b
raham
Use enum clas
s
for
g
rompp directives
commit
|
commitdiff
|
tree
2019-01-11
Mark Abraham
Add he
l
per
f
u
nctionality for safer
enumerations
commit
|
commitdiff
|
tree
2019-01-10
Mark Abr
a
ham
Add
m
o
re
c
h
ecks for di
v
i
s
i
o
n by zero
commit
|
commitdiff
|
tree
2019-01-09
Mark Abraham
F
ix eioNam
e
s
commit
|
commitdiff
|
tree
2019-01-07
Mark Abraham
Finish
r
e
m
ovi
n
g group-scheme all-vs-all support
commit
|
commitdiff
|
tree
2019-01-02
Mark Abraham
Merge bra
n
ch rele
a
se-2019
commit
|
commitdiff
|
tree
2018-12-22
M
a
rk
A
braham
Fix unused para
m
ete
r
war
n
in
g
commit
|
commitdiff
|
tree
2018-12-10
Mark
Abra
h
am
Mak
e
only mdrun repor
t
p
ro
c
ess ID
commit
|
commitdiff
|
tree
2018-12-09
Mark Abraham
Fi
x
P
OWER
8
a
nd POWER9
b
uild
commit
|
commitdiff
|
tree
2018-12-03
Mar
k
Abraham
Move responsibility
f
or PME r
e
duction to i
t
s module
commit
|
commitdiff
|
tree
2018-11-29
Mark
A
br
a
ham
R
emove
d
erronous manual variab
l
e handling
commit
|
commitdiff
|
tree
2018-11-28
M
a
rk Abr
a
ham
Introduce GpuBonded
commit
|
commitdiff
|
tree
2018-11-26
M
a
r
k
Abraha
m
C
l
ean up initial log
ou
t
put
commit
|
commitdiff
|
tree
2018-11-22
Mark Abraham
Introduce Pp
F
orce
W
orkload
commit
|
commitdiff
|
tree
2018-11-22
M
ark Abraham
Merge "Mer
g
e br
a
nch 're
l
e
ase-2019'"
commit
|
commitdiff
|
tree
2018-11-20
Mark Abra
h
a
m
Partial revert of "Fix ineffi
c
ien
t
shell min
i
mi
z
ation"
commit
|
commitdiff
|
tree
2018-11-20
Mark Ab
r
aham
M
e
rge "Merge release-2
0
1
9
into master"
commit
|
commitdiff
|
tree
2018-11-19
Mark Abra
h
am
Fix ineffi
c
i
ent shell minimizati
o
n
commit
|
commitdiff
|
tree
2018-11-15
Mark Ab
r
a
ham
Fi
x
c
h
eck
p
oi
n
t resta
r
t
of t
p
r with infinite step count
commit
|
commitdiff
|
tree
2018-11-15
Mark Abraham
Relax
arbitrary toler
a
nce o
n
r
erun te
s
t
commit
|
commitdiff
|
tree
2018-11-14
Mar
k
Abr
a
h
a
m
F
i
x Open
C
L mdrun from installed
p
a
th
commit
|
commitdiff
|
tree
2018-11-14
Mark Abr
a
ham
M
ore wa
r
nin
g
suppr
e
ssions f
o
r
QMMM code
commit
|
commitdiff
|
tree
2018-11-09
Mark Abraham
Disabled FPE
checking for no
n
-release b
u
ilds
commit
|
commitdiff
|
tree
2018-11-08
Mar
k
Abraham
Pragma warning sup
p
ressins
f
or i
c
c+windows
commit
|
commitdiff
|
tree
2018-11-07
Mark Abraham
Suppr
e
ss cla
n
g warnings about QM
M
M co
d
e
commit
|
commitdiff
|
tree
2018-11-05
Mark Abrah
a
m
Make PME O
p
enCL enabled onl
y
fo
r
AMD devi
c
es
commit
|
commitdiff
|
tree
2018-11-05
M
ark Abraham
Remove source
file
with
n
o conte
n
t
commit
|
commitdiff
|
tree
2018-11-02
Mark Abraha
m
Quiet
u
n
u
se
d
variable warning
s
commit
|
commitdiff
|
tree
2018-11-01
M
a
rk
A
braha
m
S
top
u
sing hwloc
o
n o
l
d AR
M
s
lave
commit
|
commitdiff
|
tree
2018-11-01
Mark
Abraha
m
Disabl
e
cca
c
he b
y
def
a
ult
commit
|
commitdiff
|
tree
2018-10-30
Mark Abrah
a
m
Improve
ccache impl
e
mentation
commit
|
commitdiff
|
tree
2018-10-30
Mark
Abr
a
ha
m
Ren
a
me to GMX_O
P
E
NCL
_
NB_CLUSTER_SIZE
commit
|
commitdiff
|
tree
2018-10-30
M
a
rk Abraham
Upda
t
es to
docs for OpenCL
s
upport
commit
|
commitdiff
|
tree
2018-10-26
Mark Abra
h
a
m
Merge
"Merge
b
ranch release-2018 into release-20
1
9
.
.
.
commit
|
commitdiff
|
tree
2018-10-26
M
ark
A
braham
Merge b
r
anch release-20
1
8 int
o
release-2019
commit
|
commitdiff
|
tree
2018-10-25
M
a
rk Ab
r
aham
Introdu
c
e
A
rrayRefWithPadding
commit
|
commitdiff
|
tree
2018-10-22
Mark Abraham
F
ix clang CUDA warni
n
gs
commit
|
commitdiff
|
tree
2018-10-16
Mark A
b
raham
Eliminated t_ifunc from t_interact
i
on_function
commit
|
commitdiff
|
tree
2018-10-16
Mark Abraham
Task assi
g
nment
f
o
r b
o
nd
e
d
interactions on CUDA GP
U
s
commit
|
commitdiff
|
tree
2018-10-16
Ma
r
k
Abraham
Fix
c
o
mpiler issues
commit
|
commitdiff
|
tree
2018-10-16
Mark Abraham
Removed support for N
V
I
D
IA CC 2
.
x devices (codename
.
.
.
commit
|
commitdiff
|
tree
2018-10-15
Mar
k
Abraham
Improve
r
obustness of
end-to-end te
s
tin
g
commit
|
commitdiff
|
tree
2018-10-15
Mark A
b
rah
a
m
Crea
t
e Excl
u
sionB
l
ocks
commit
|
commitdiff
|
tree
2018-10-15
Mark Abrah
a
m
De-
d
uplicating mdrun s
e
tu
p
commit
|
commitdiff
|
tree
2018-10-14
Ma
r
k Abrah
a
m
Fix comp
i
ler
war
n
ings
commit
|
commitdiff
|
tree
2018-10-13
M
a
rk Abraham
Qui
e
t compiler warnings
commit
|
commitdiff
|
tree
2018-10-13
Mark Abrah
a
m
Deprecate various functional
i
t
y
i
n GROMACS 2019
commit
|
commitdiff
|
tree
2018-10-12
Mark Abraham
E
x
clude g
m
xapi source files from i
n
clude
sorti
n
g
commit
|
commitdiff
|
tree
2018-10-11
Ma
r
k A
b
rah
a
m
F
i
x Pa
d
dedV
e
ctor issues
commit
|
commitdiff
|
tree
2018-10-11
Mark Abraham
Op
e
n md
r
u
n
log file only on
c
e
commit
|
commitdiff
|
tree
2018-10-09
M
ark Abraham
Fix
D
omdecOptions default
commit
|
commitdiff
|
tree
2018-10-08
Mark
Abraham
Disable
F
PE expl
i
c
itly fo
r
TPI
force
calculation
commit
|
commitdiff
|
tree
2018-10-08
Ma
r
k Abr
a
ham
Implemen
t
Pad
d
edVector
commit
|
commitdiff
|
tree
2018-10-08
Mark Abraham
More updates
t
o
test matrix
commit
|
commitdiff
|
tree
2018-10-08
Mark A
b
raham
Fix m
a
ke test
commit
|
commitdiff
|
tree
2018-10-07
Mark Abraha
m
Test with gcc 8 a
n
d cuda 10
commit
|
commitdiff
|
tree
2018-10-05
Mark Abraham
C
h
ec
k
log
a
nd other files diff
e
re
n
t
ly during appe
n
ding
.
.
.
commit
|
commitdiff
|
tree
2018-10-05
Mark Abraham
Change
to
t
est T
S
AN w
i
th
c
l
ang and libomp
commit
|
commitdiff
|
tree
2018-10-04
Mark Ab
r
aham
Rep
l
ace CUDA c
a
ll
deprecated
i
n
CU
D
A 10
commit
|
commitdiff
|
tree
2018-10-04
Mark Abraham
Extract he
l
per functi
o
ns for p
r
eparing fo
r
a
p
pending
commit
|
commitdiff
|
tree
2018-10-04
Mark
A
braham
S
i
mplify EM
u
sage of mdebin
commit
|
commitdiff
|
tree
2018-10-03
Mark Ab
r
aham
Use fast returns in md5 co
m
putation
commit
|
commitdiff
|
tree
2018-10-03
Mark Abr
a
ham
Add
e
n
d
-to-e
n
d te
s
ts o
f
ene
r
gy minimizat
i
on
commit
|
commitdiff
|
tree
2018-10-03
Mark Abraham
Basic
mod
e
rniza
t
i
on of md5 han
d
ling
commit
|
commitdiff
|
tree
2018-10-02
Mar
k
Abraham
Reduc
e
m
d
run tests
u
sing group
sc
h
eme
commit
|
commitdiff
|
tree
2018-10-01
M
a
r
k
Abr
a
ham
Fix
g
cc-8 war
n
in
g
s about
strings
commit
|
commitdiff
|
tree
2018-10-01
M
ark Abr
a
ham
Add release no
t
e
s
f
or removing non-reproducible
aspe
c
ts
commit
|
commitdiff
|
tree
2018-10-01
M
a
rk Abr
a
ham
Tests for
md5 co
m
putation on
op
e
n
files
commit
|
commitdiff
|
tree
2018-09-29
Mark Abr
a
ham
Rem
o
v
e
NVML
support
commit
|
commitdiff
|
tree
2018-09-29
Mark Abraham
Stop
ICC ICE
commit
|
commitdiff
|
tree
2018-09-28
Mark Abraham
Use more default initialization
o
f
mdrun s
t
r
u
c
t
s
commit
|
commitdiff
|
tree
2018-09-28
M
ark Abraha
m
Make some
s
ymbols in
gmxpre-config
.
h
always defined
commit
|
commitdiff
|
tree
2018-09-26
M
a
r
k
A
braham
Clari
f
y distinct p
a
ths for mdrun log fi
l
e han
d
l
i
ng
commit
|
commitdiff
|
tree
2018-09-24
Mark
Abraham
Fix Doxygen links
commit
|
commitdiff
|
tree
2018-09-23
Mark
A
braham
Leak less
from gromppp with cmap
commit
|
commitdiff
|
tree
2018-09-20
Mark Abraham
Update to test with
c
l
ang-7
commit
|
commitdiff
|
tree
2018-09-19
Mark
Abrah
a
m
Fix bug
with
state
natoms
in mem
b
ed
commit
|
commitdiff
|
tree
2018-09-18
Mark Abraham
S
e
para
t
e
d partitioni
n
g an
d
dlb code within domdec
commit
|
commitdiff
|
tree
2018-09-18
Mark Abraha
m
Add not
_
null from
GSL
commit
|
commitdiff
|
tree
2018-09-13
Mar
k
A
br
a
ham
E
l
im
i
nate main
.
h
commit
|
commitdiff
|
tree
2018-09-11
Mark
Abraham
Replace
C
-style librar
y
file
h
andling with RAII approaches
commit
|
commitdiff
|
tree
2018-09-11
Mark Abraham
I
m
p
r
ov
e
DD logging
commit
|
commitdiff
|
tree
2018-09-11
Mark
Abraham
Repla
c
e readC
o
n
fo
r
mation with TopologyInformation
commit
|
commitdiff
|
tree
2018-09-09
Mar
k
Ab
r
aham
Change TopologyInformati
o
n
imple
m
entation
commit
|
commitdiff
|
tree
2018-09-07
Mark Abraham
F
i
x grompp memory
l
e
aks
commit
|
commitdiff
|
tree
2018-09-07
M
a
r
k
Abraham
Mi
n
or fixes to GPU
b
u
ild system
commit
|
commitdiff
|
tree
2018-09-07
Mark Abra
h
am
Sepa
r
ate simu
l
a
tion
d
atabase used
in tests
commit
|
commitdiff
|
tree
2018-09-05
Mark
A
bra
h
am
Be quieter when f
a
iling to detect GPU
s
commit
|
commitdiff
|
tree
2018-09-04
Mark
Ab
r
aham
Cl
a
rify initial DD
c
e
l
l choice with pre
s
su
r
e
c
oupling
commit
|
commitdiff
|
tree
2018-08-30
Mark Abraham
Up
d
ate testing matrices f
o
r coverage and
s
pee
d
commit
|
commitdiff
|
tree
2018-08-29
Mark Abraham
Merge b
r
a
n
ch release-2018
commit
|
commitdiff
|
tree
2018-08-29
Mark Abraham
Move
c
lan
g
-tid
y
buil
d
commit
|
commitdiff
|
tree
2018-08-28
Mark
A
braham
Fix more c
l
a
n
g-
t
idy issues
commit
|
commitdiff
|
tree
2018-08-27
M
ark Abraham
Fix use of
nullptr
commit
|
commitdiff
|
tree
2018-08-24
M
a
rk
Abraham
Fix bu
i
ld with
o
ut TNG
commit
|
commitdiff
|
tree
2018-08-24
M
a
rk
Abraha
m
Merge branch release-20
1
8
commit
|
commitdiff
|
tree
2018-08-22
M
a
r
k
Abraha
m
Fix handlin
g
of counter resets
commit
|
commitdiff
|
tree
2018-08-22
Ma
r
k Abraham
Pe
r
mit P
M
E
on GPUs only
f
o
r
dyn
a
m
i
cal integrators
commit
|
commitdiff
|
tree
2018-08-21
Mar
k
A
bra
h
am
R
e
-impl
e
mented mdrun -rerun
t
ests
commit
|
commitdiff
|
tree
2018-08-21
Mark
Ab
r
aham
Fix
a
ss
e
rt
i
ons
f
or SD update
commit
|
commitdiff
|
tree
next