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Fix ocl_kernel target
2019-08-12
Mark Ab
r
a
h
am
Fix ocl_kern
e
l target
commit
|
commitdiff
|
tree
2019-08-08
M
a
r
k
Abraham
Fi
x
e
s
timat
e
of
t
he size of a j list
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraha
m
Initializ
e
g
m
x_
e
kin
d
ata_t and
t
_
vcm proper
l
y
commit
|
commitdiff
|
tree
2019-08-08
Mark
A
braham
Stop
t
e
s
tin
g
ICC on Windo
w
s
commit
|
commitdiff
|
tree
2019-08-05
Ma
r
k
Abraham
Add
quote
commit
|
commitdiff
|
tree
2019-08-05
Mark Abraham
Rem
o
ve libgromacs_generated contributions
f
rom F
i
nd
C
UDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark A
b
raham
Manage
c
ompiler flags and
s
ome incl
u
de options per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
M
ark Abraham
Im
p
rove u
s
e
of object librarie
s
in libgromacs
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Merge
"Mer
g
e
release-2019 into maste
r
"
commit
|
commitdiff
|
tree
2019-07-24
Mark Ab
r
ah
a
m
R
e
m
ove t
e
sts
o
f make_u
n
ique
commit
|
commitdiff
|
tree
2019-07-23
Mark Abraham
Update d
e
veloper guide
commit
|
commitdiff
|
tree
2019-07-16
Mark Abraha
m
A
d
d g
p
ubu
f
ferops t
e
st matrix
commit
|
commitdiff
|
tree
2019-07-11
Mark Abra
h
am
Fix
p
re-submit build matrix an
d
desc
r
iption
commit
|
commitdiff
|
tree
2019-07-08
Mark
Abraham
Fi
x
hwloc and s
p
hi
n
x de
t
e
c
tion
commit
|
commitdiff
|
tree
2019-07-08
Ma
r
k A
b
r
aham
Test speci
f
i
c hwloc versi
o
ns
commit
|
commitdiff
|
tree
2019-07-05
Mark
Abraha
m
Impr
o
ve t
e
s
ts
o
f
index b
l
ock co
n
struc
t
ion
commit
|
commitdiff
|
tree
2019-07-05
M
a
rk Abraham
Mod
e
r
nize FindH
w
loc
.
cmake
commit
|
commitdiff
|
tree
2019-07-04
Mark Abraham
Furt
h
e
r
clang-t
i
dy-7 fi
x
commit
|
commitdiff
|
tree
2019-07-04
Mark Abraham
Fi
x
clang-
t
i
dy-7 issues
commit
|
commitdiff
|
tree
2019-07-03
Mark Abraham
R
eorder options
commit
|
commitdiff
|
tree
2019-07-02
Mark Abr
a
ham
Clarify
word
i
ng of release
n
otes
commit
|
commitdiff
|
tree
2019-06-18
Mark Ab
r
aham
Move code handling mdrun -gpu_
i
d to
taskas
s
ignment
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark Abraham
Fix pygments detection for
sphinx f
o
r do
c
s
build
commit
|
commitdiff
|
tree
2019-06-11
Mark
Abra
h
am
Use RAII
approaches
f
or
hardware information detect
i
on
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraha
m
C
l
ea
n
up multisim,
c
o
mmunication, and REMD code
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Initialize all of g
m
x_do
m
de
c
_com
m
_t
commit
|
commitdiff
|
tree
2019-05-24
Mark Abraham
Reorder code before thread-MPI spawns threads
commit
|
commitdiff
|
tree
2019-05-23
M
a
rk
A
braha
m
T
ea
c
h
ArrayRefWithPadding to make a co
n
st flavour
commit
|
commitdiff
|
tree
2019-05-23
Mar
k
Abraham
R
evert "Fi
x
ed d
v
d
l
ambda for SHA
K
E
+ FE"
commit
|
commitdiff
|
tree
2019-05-22
Mark
A
b
raham
R
e
write start
i
ng be
h
av
i
or
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Int
r
oduce tri-state enu
m
s for
r
e
starts
commit
|
commitdiff
|
tree
2019-05-22
M
ark Abrah
a
m
Move functionality to m
d
runuti
l
ity
commit
|
commitdiff
|
tree
2019-05-20
Mark Abraham
F
i
x equation typo
commit
|
commitdiff
|
tree
2019-05-14
Mark Abraham
U
p
d
at
e
infrastr
u
c
t
ure neede
d
for
r
e
s
tart rewrite
commit
|
commitdiff
|
tree
2019-05-08
Mark Abraham
Prov
i
de hook for fork
s
of G
R
OMACS to
de
s
cribe the
m
selves
commit
|
commitdiff
|
tree
2019-05-07
Mark Abr
a
ham
Prov
i
d
e
bett
e
r
h
elp for using libc++
commit
|
commitdiff
|
tree
2019-05-07
Mark
A
b
r
a
ham
Add an example of
us
i
n
g an MPI wrapper
compiler
commit
|
commitdiff
|
tree
2019-05-06
M
ark Abraham
I
m
p
rove h
o
w
mdrun -noappend names output f
i
l
es
commit
|
commitdiff
|
tree
2019-05-03
M
a
rk
Ab
r
aham
More tests for how mdrun -c
p
i restarts
handle files
commit
|
commitdiff
|
tree
2019-05-02
Mark Abraham
Enhance path searc
h
funct
i
on
s
commit
|
commitdiff
|
tree
2019-04-30
M
a
rk Abraham
Test the o
u
tput of
"
gmx m
d
run
help"
commit
|
commitdiff
|
tree
2019-04-25
M
ark Abraham
Update style guide about
c
l
ass enums
commit
|
commitdiff
|
tree
2019-04-23
Mark Abraham
Clarif
y
push
i
ng of interaction
t
y
pe
s
commit
|
commitdiff
|
tree
2019-04-23
Mark Abraham
Updated clang
-Weverythi
n
g c
h
eck
s
to clang-7
commit
|
commitdiff
|
tree
2019-04-18
Ma
r
k Ab
r
aham
Create gmx::
c
o
m
pat::optional
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Move p
u
l
l w
o
r
k
struct ou
t
o
f
inputrec
commit
|
commitdiff
|
tree
2019-04-18
M
ark
A
b
raham
I
m
prove sw
a
p
c
oords session
l
if
e
time man
a
gement
commit
|
commitdiff
|
tree
2019-04-17
Mark Abraham
Fix
p
o
st-sub
m
it
commit
|
commitdiff
|
tree
2019-04-16
Mark Abr
a
ha
m
Removed mdr
u
n
-
g
com
commit
|
commitdiff
|
tree
2019-04-13
Mark
Abraham
Fi
x
self-
c
onsistency tests of hw
l
oc data structures
commit
|
commitdiff
|
tree
2019-04-12
Mark Abraham
Improve
warning
m
essages a
b
out duplicate de
f
init
i
ons
commit
|
commitdiff
|
tree
2019-04-10
Mark Abraham
Start m
a
king IMD and swap mod
e
l
I
MDModule
commit
|
commitdiff
|
tree
2019-04-10
Mark Abraham
R
euse rve
c
s
_differ in InteractiveMD mod
u
le
commit
|
commitdiff
|
tree
2019-04-10
Mark A
b
raham
M
a
k
e ImdSession into a Pimpl-ed
cla
s
s wi
t
h factory
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Mark Abraha
m
Reform IMD module
commit
|
commitdiff
|
tree
2019-04-09
Mark
Abrah
a
m
Fix typo in AVX5
1
2 detection code
commit
|
commitdiff
|
tree
2019-04-03
Mar
k
Abraham
I
n
itial
d
e
a
ctivation of gro
u
p
s
cheme
.
commit
|
commitdiff
|
tree
2019-04-01
Mark Abraham
Move
M
DModules
initial
i
zation earlier
commit
|
commitdiff
|
tree
2019-04-01
Mark Abraham
Move enerdata owne
r
ship to mdrunner
commit
|
commitdiff
|
tree
2019-03-28
M
ark Abraham
Move Dom
d
ec
O
ptions into its own he
a
der
commit
|
commitdiff
|
tree
2019-03-25
Mark
Abra
h
a
m
Supp
o
rt
Array
R
ef
o
f Enumera
t
i
o
n
Array
commit
|
commitdiff
|
tree
2019-03-25
Mark Abraham
Convert gmx dump
t
o module
commit
|
commitdiff
|
tree
2019-03-20
Mark Abraham
Clean up mdrun he
l
p descripti
o
n
commit
|
commitdiff
|
tree
2019-03-20
Ma
r
k Abraham
Improv
e
m
i
mic module
commit
|
commitdiff
|
tree
2019-03-19
Mark Abraha
m
Add support for serializing 32-bit integ
e
rs
commit
|
commitdiff
|
tree
2019-03-19
Mark
A
braham
Fix cla
n
g
w
a
r
n
ing
commit
|
commitdiff
|
tree
2019-03-19
Mark
A
b
raha
m
Update Elec
t
ricField module
commit
|
commitdiff
|
tree
2019-03-19
Mark Ab
r
a
ham
Preve
n
ted F
F
TW bui
l
d errors with
clang and AVX-512
commit
|
commitdiff
|
tree
2019-03-13
M
a
rk Abraham
Pr
o
vid
e
remi
n
d
er of which nvcc is in use
commit
|
commitdiff
|
tree
2019-03-12
M
a
rk Abraha
m
Fix memory leak
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
E
limi
n
a
t
e mdlib/mdr
u
n
.
h
commit
|
commitdiff
|
tree
2019-03-07
Mark Abra
h
am
Remove ineffective
c
ode for writing more TER fields
.
.
.
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
New
tests for pdb2gmx a
n
d
editconf
commit
|
commitdiff
|
tree
2019-03-06
Mark
A
braha
m
C
lean
up
u
se of
l
o
o
p
indices
commit
|
commitdiff
|
tree
2019-03-06
Ma
r
k
Abr
a
ham
Reve
r
t
"El
i
m
i
nate mdlib/mdrun
.
h"
commit
|
commitdiff
|
tree
2019-03-06
Ma
r
k Abraham
Eliminate mdlib/md
r
un
.
h
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
Minor modernization in gmx_dump
commit
|
commitdiff
|
tree
2019-03-05
Mark Abraham
M
a
ke pdb2gmx te
s
ts run in Jenkins
commit
|
commitdiff
|
tree
2019-03-02
Mark Abraham
M
e
rge branch release-2
0
19
commit
|
commitdiff
|
tree
2019-03-02
Mark
A
braham
Remove defunct
mdrun options
commit
|
commitdiff
|
tree
2019-02-27
Mark Abr
a
ham
Keep niche
C
Make varia
b
le
s
as advanced
commit
|
commitdiff
|
tree
2019-02-27
Mark Abraha
m
Remove
minor br
o
ken func
t
io
n
a
l
i
ty in gmx bar
commit
|
commitdiff
|
tree
2019-02-26
Mark Abraham
Add new li
n
e to trjconv n
o
t
i
ce to users
commit
|
commitdiff
|
tree
2019-02-25
Mar
k
A
b
raham
Move code out
o
f sim_util
.
c
p
p
commit
|
commitdiff
|
tree
2019-02-25
Mark A
b
raham
De-
d
uplicate gmx_tm
p
n
a
m
an
d
gm
x
_fop
e
n_temp
o
r
a
ry
commit
|
commitdiff
|
tree
2019-02-15
Mark A
b
r
aham
Im
p
rove
d
diagnostics w
h
en P
M
E
ca
n
n
ot run
o
n GPUs
commit
|
commitdiff
|
tree
2019-02-14
Mark Abraham
Fix u
s
e
o
f select
i
ons
r
eferring to
index group
s
commit
|
commitdiff
|
tree
2019-02-14
Ma
r
k Abrah
a
m
Revert c
h
a
n
ges to implementation of insert-molecu
l
es
.
.
.
commit
|
commitdiff
|
tree
2019-02-13
Mar
k
Abraham
Improved
electric-field
d
ocs
commit
|
commitdiff
|
tree
2019-02-13
Mark Abraha
m
Make E
n
ergyOutput wrapp
e
r class
commit
|
commitdiff
|
tree
2019-02-13
Mark A
b
r
a
h
am
Reduce co
u
p
li
n
g to paddedvect
o
r
.
h
commit
|
commitdiff
|
tree
2019-02-12
Mark Abraham
Quiet clang warning
commit
|
commitdiff
|
tree
2019-02-12
Mark Ab
r
aha
m
Remov
e
gmx::Regex
commit
|
commitdiff
|
tree
2019-02-08
Mark Abraham
Fix In
t
el
compiler
warning
commit
|
commitdiff
|
tree
2019-02-08
M
a
rk Ab
r
a
h
am
Re
m
ove copy_energy
from energy-w
r
iting
steps
commit
|
commitdiff
|
tree
2019-02-08
Mark Abraham
Reform en
e
rgy
o
utput tests
commit
|
commitdiff
|
tree
2019-02-04
Mark Abraham
Remove SIMD suppo
r
t from group scheme
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraha
m
M
erge
r
emote
b
r
anch r
e
lease-2
0
18 into release-2019
commit
|
commitdiff
|
tree
2019-01-30
Ma
r
k Abraham
Fix re
l
ease notes issue links
commit
|
commitdiff
|
tree
2019-01-30
Mark Ab
r
a
h
am
Fix
r
elease notes issue links
commit
|
commitdiff
|
tree
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