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Fix include dependency for getenv
2017-08-07
Mark Abraham
Fix incl
u
de depen
d
en
c
y for getenv
commit
|
commitdiff
|
tree
2017-08-06
Mark Abraham
Simplify resource-divisio
n
efficienc
y
che
c
k
commit
|
commitdiff
|
tree
2017-08-06
Mar
k
Abrah
a
m
Decouple task assignment from
t
ask
e
xec
u
tion
commit
|
commitdiff
|
tree
2017-08-04
Ma
r
k Abra
h
am
Sto
p
u
s
i
n
g
h
winf
o
_g for repo
r
ting code
commit
|
commitdiff
|
tree
2017-08-03
Mark
Ab
r
aham
Remove
d
unuse
d
i
nc
l
ude
s
tatements
commit
|
commitdiff
|
tree
2017-08-02
Berk
Hess
Clean up mat
r
ix inversion
commit
|
commitdiff
|
tree
2017-08-02
Berk Hess
Fix
o
rientation restraint r
e
ference
commit
|
commitdiff
|
tree
2017-08-02
Davi
d
v
a
n der Spoel
Worked
a
round missing Ope
n
MP imp
l
ement
a
tion
in or
i
res
.
commit
|
commitdiff
|
tree
2017-08-01
Mark Abrah
a
m
Introduced Mdru
n
ner
h
igh-level
c
l
a
ss
commit
|
commitdiff
|
tree
2017-07-28
Da
v
i
d
van de
r
Spoel
A
d
d
ed unit
-
test for ori
e
ntation rest
r
aints outpu
t
.
commit
|
commitdiff
|
tree
2017-07-27
Mark Ab
r
aham
E
n
h
ance cma
k
e
a
n
d re
l
eng hand
l
ing of
GM
X
_USE_RDTS
C
P
commit
|
commitdiff
|
tree
2017-07-27
Szil
á
r
d
Pá
l
l
I
n
form
user
s
about t
h
e
e
nd of run
DLB st
a
te
commit
|
commitdiff
|
tree
2017-07-19
Da
v
id van der Spoel
Removed unne
c
essary
s
t
atic declar
a
t
i
ons
f
or command
.
.
.
commit
|
commitdiff
|
tree
2017-07-14
Mark Abrah
a
m
Implemented grompp -po for
o
ptions-style mdp han
d
lin
g
commit
|
commitdiff
|
tree
2017-07-14
M
a
rk Abrah
a
m
C
l
ean
u
p cmake build host detectio
n
commit
|
commitdiff
|
tree
2017-07-13
Mark Abraham
Clean u
p
gmx_mdru
n
()
commit
|
commitdiff
|
tree
2017-07-13
Mar
k
A
braham
C
l
eaned up mdrunner_start_threads
commit
|
commitdiff
|
tree
2017-07-11
Ro
l
and Sch
u
lz
PME-gather: make
v
a
r
iables local and const
commit
|
commitdiff
|
tree
2017-07-11
Teemu Mu
r
tola
Support scoped key-value
t
ree transform rules
commit
|
commitdiff
|
tree
2017-07-07
Mark Abraham
Refa
c
tor error
h
andling in in
i
t_gpu
commit
|
commitdiff
|
tree
2017-07-04
M
ark Abraham
Clean up pick_nbnx
n
_resou
r
ces
commit
|
commitdiff
|
tree
2017-07-01
Mark
Abraham
C
l
eaned up
GPU emulat
i
on logic
commit
|
commitdiff
|
tree
2017-06-30
T
e
emu Murtola
Fix boolea
n
s
e
rialization
commit
|
commitdiff
|
tree
2017-06-30
Teem
u
Murtol
a
Extend k
e
y-value t
r
ee compari
s
on and t
e
sts
commit
|
commitdiff
|
tree
2017-06-28
Mark Abraham
Cleaned
u
p
h
i
gh-level boolean variable naming
commit
|
commitdiff
|
tree
2017-06-28
M
a
rk Abraham
Merge bran
c
h release-2016
commit
|
commitdiff
|
tree
2017-06-27
Te
e
m
u
Murto
l
a
D
o not use conf-man
.
py for non
-
manpage doc builds
commit
|
commitdiff
|
tree
2017-06-27
Ma
r
k Abraham
Minor improvements to test
configs
commit
|
commitdiff
|
tree
2017-06-26
Eri
k
Lindahl
Fix ARM NEON simd debug builds
commit
|
commitdiff
|
tree
2017-06-26
Szilárd Páll
Add ARM
_
NEON_AS
I
MD post-s
u
bmit test
commit
|
commitdiff
|
tree
2017-06-26
Jiri Kraus
U
p
dated app
l
ication cloc
k
handling
o
n Pascal+ GPUs
commit
|
commitdiff
|
tree
2017-06-22
M
a
rk Abra
h
am
Consolidated lo
g
i
c for
c
hoosing numbe
r
of thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2017-06-22
Mark Abraham
Replace mi
s
n
amed
n
bnx
n
_gpu_acc
e
l
eration
_
supported
commit
|
commitdiff
|
tree
2017-06-22
M
ark Abraham
Consolidate and fix logic for mdrun -nb an
d
-g
p
uid
commit
|
commitdiff
|
tree
2017-06-21
Szi
l
árd
Páll
Re-en
a
ble l
o
st
DD warn
i
n
g
+ mi
n
o
r
code modern
i
za
t
ion
commit
|
commitdiff
|
tree
2017-06-21
Mark
A
b
r
ah
a
m
Refo
r
m ngp
u
va
r
iable
commit
|
commitdiff
|
tree
2017-06-21
Mark Ab
r
a
ham
Remove bUserSetGpuIds fie
l
d
commit
|
commitdiff
|
tree
2017-06-12
Mark Abraham
Move g
m
x_p
a
rse_gpu_i
d
out of checki
n
g function
commit
|
commitdiff
|
tree
2017-06-12
A
l
e
ksei
I
u
pinov
Store a
p
hysica
l
n
o
d
e comm
u
nicator in t_commrec
commit
|
commitdiff
|
tree
2017-06-11
M
agnus Lundb
o
rg
Update
d
TNG to version 1
.
8
commit
|
commitdiff
|
tree
2017-05-31
Mark
Abra
h
am
New quote
commit
|
commitdiff
|
tree
2017-05-29
T
e
emu Murtola
Avoi
d
some incorr
e
ct b
e
hav
i
or
w
i
th gmx solvate
commit
|
commitdiff
|
tree
2017-05-29
Teem
u
M
urtol
a
R
e
mo
v
e
p
bcutil
<-> md
t
ypes cycli
c
de
p
endency
commit
|
commitdiff
|
tree
2017-05-29
Vedran Miletić
St
a
ndardize use of |
G
rom
a
cs| in reST
docs
commit
|
commitdiff
|
tree
2017-05-26
Mark Abraham
Test
inv
s
ixthroot functi
o
n a
s
int
e
nded
commit
|
commitdiff
|
tree
2017-05-15
M
ark A
b
raham
Updated use of compiler specifiers in testin
g
commit
|
commitdiff
|
tree
2017-05-15
Mark Abra
h
a
m
Update
d
use of gcc
-
5 specifiers
commit
|
commitdiff
|
tree
2017-05-15
Mark A
b
r
a
ham
Update cl
a
ng s
t
atic analyze
r
slave to use versi
o
n 4
commit
|
commitdiff
|
tree
2017-05-14
M
ar
k
A
braham
Updat
e
clan
g
-4
commit
|
commitdiff
|
tree
2017-05-14
J
ustin Lemkul
Cla
r
ifications to
editcon
f
help
text
.
commit
|
commitdiff
|
tree
2017-05-14
Justin
L
emku
l
Cl
a
rificati
o
ns to editconf hel
p
text
.
commit
|
commitdiff
|
tree
2017-05-09
M
ark Abraham
F
ix formatting of MKL
cmake d
o
cs
commit
|
commitdiff
|
tree
2017-05-09
M
ark Abr
a
ham
Merge bra
n
ch
r
elease-2016
commit
|
commitdiff
|
tree
2017-05-09
Mark A
b
r
a
ham
Cle
a
ned up
m
emory usage in gmx traj
a
nd trjconv
commit
|
commitdiff
|
tree
2017-04-19
Ber
k
Hess
F
i
x unused
S
IMD P
M
E table kerne
l
commit
|
commitdiff
|
tree
2017-04-17
M
a
rk Abrah
a
m
Minor chan
g
e to GPU compati
b
ility
r
ep
o
rting handling
commit
|
commitdiff
|
tree
2017-04-17
M
a
rk Abraham
Propose a post-
s
u
b
m
i
t matrix
commit
|
commitdiff
|
tree
2017-04-17
Tee
m
u
Murtola
Consist
e
nt approach
for wh
o
le-program tests
commit
|
commitdiff
|
tree
2017-03-31
M
ar
k
Abra
h
am
M
e
r
g
e
b
ranch release-2016
commit
|
commitdiff
|
tree
2017-03-22
Mark A
b
r
a
ham
Add
s
ectio
n
t
o
u
ser gu
i
de
f
or managing simulations
commit
|
commitdiff
|
tree
2017-03-17
M
.
Eric Irrgang
Add an extra verbose ta
r
get
for d
o
c
s
commit
|
commitdiff
|
tree
2017-03-16
Szi
l
árd Páll
Print code of unknown OpenCL er
r
or
commit
|
commitdiff
|
tree
2017-03-14
Mar
k
A
b
r
aham
Merge
b
r
anch release-2016
commit
|
commitdiff
|
tree
2017-03-14
Ma
r
k
Ab
r
aham
Bum
p
ed vers
i
on to
p
repare for next p
a
tch relea
s
e
commit
|
commitdiff
|
tree
2017-03-13
Mark Abr
a
ham
Version
20
1
6
.
3
commit
|
commitdiff
|
tree
2017-03-13
Mark A
b
raha
m
Modernize wri
t
e_inpfi
l
e
commit
|
commitdiff
|
tree
2017-03-13
Mark
A
brah
a
m
Modernize
read_inpfile
commit
|
commitdiff
|
tree
2017-03-13
Ake Sandgren
Fix tune_pme detection of
G
PU su
p
port
commit
|
commitdiff
|
tree
2017-03-13
Ake S
a
n
dgren
Fix spa
c
ing in tune_pm
e
call to thread-
m
pi m
d
run
commit
|
commitdiff
|
tree
2017-03-09
Szi
l
árd Páll
Fi
x
m
drun hangin
g
up
o
n e
x
it with
s
ep PME
r
anks
commit
|
commitdiff
|
tree
2017-03-07
Mark Ab
r
aham
Fix minor issue
s
i
n gmx traj -av -a
f
commit
|
commitdiff
|
tree
2017-03-04
Teem
u
Murtol
a
Remove MDMo
d
ules u
s
e from mdlib
commit
|
commitdiff
|
tree
2017-03-04
D
a
vid van der Spoel
Removes rogue p
r
inting to xv
g
fil
e
in gmx
m
i
n
dist
commit
|
commitdiff
|
tree
2017-03-04
Teem
u
Murtola
S
plit
md module facet
s
to different i
n
terfa
c
es
commit
|
commitdiff
|
tree
2017-03-04
Mar
k
Abraham
Fixes for xl comp
i
lers 13
.
1
.
5 on Powe
r
8
commit
|
commitdiff
|
tree
2017-02-20
M
a
r
k
Abr
a
h
a
m
A
dd
t
ests
f
o
r
o
ld gmx energy
fun
c
tional
i
ty
commit
|
commitdiff
|
tree
2017-02-17
Mark Abraham
Use gmx::Mutex and gmx::lock
_
guard to fix som
e
issue
s
commit
|
commitdiff
|
tree
2017-02-15
Ma
r
k Abraham
Merge bran
c
h relea
s
e-5-1 into
r
e
lease-2016
commit
|
commitdiff
|
tree
2017-02-14
Mark Abraham
Re
d
u
c
e
compi
l
a
t
ion c
o
upl
i
ng
commit
|
commitdiff
|
tree
2017-02-10
Mark Abraham
Corrected output of gmx do_dssp -sc
commit
|
commitdiff
|
tree
2017-02-09
Teemu Mur
t
ola
Mult
i
-ran
k
thr
e
a
d affinity tests
commit
|
commitdiff
|
tree
2017-02-09
M
a
r
k Ab
r
ah
a
m
Complete the removal of stat
e
ful
RNG
commit
|
commitdiff
|
tree
2017-02-09
Ma
r
k Abraham
Improved state
_
c
hange_na
t
oms and used it mo
r
e
commit
|
commitdiff
|
tree
2017-02-09
Teemu Murto
l
a
Do
c
ume
n
t key-value tree transforms and improve checks
commit
|
commitdiff
|
tree
2017-02-08
Mark
A
braham
E
x
t
end
s
erialization to gm
x
_int
6
4_t
commit
|
commitdiff
|
tree
2017-02-08
T
e
emu Murtola
Generic KeyValueTree broad
c
ast
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
Generic
g
mx ch
e
ck implementation with KeyValueTree
commit
|
commitdiff
|
tree
2017-02-08
Teemu Murtola
G
e
neric gmx dump imple
m
entation fo
r
KeyVal
u
eTree
commit
|
commitdiff
|
tree
2017-02-08
Teemu
Murtola
Generic tpr
handling for
e
l
ectric field
commit
|
commitdiff
|
tree
2017-02-08
A
leksei Iupinov
PME fo
r
ce
g
athering tests
commit
|
commitdiff
|
tree
2017-02-08
Aleksei Iupinov
Fix invalid triclinic box in the PME tes
t
data
commit
|
commitdiff
|
tree
2017-02-08
Mark Abraham
Give
MDModules responsibility for o
p
t
ion
h
andl
i
ng
commit
|
commitdiff
|
tree
2017-02-07
Ve
d
ran Miletić
Document running
C
lang static a
n
alyzer
m
anually
commit
|
commitdiff
|
tree
2017-02-07
Mar
k
Abraham
M
e
rge branch rel
e
ase-2016
commit
|
commitdiff
|
tree
2017-02-07
Mark Abraham
Bumped ve
r
si
o
n to prepare for next patch release
commit
|
commitdiff
|
tree
2017-02-07
Mark Abraha
m
V
e
rsion 2016
.
2
commit
|
commitdiff
|
tree
2017-02-07
Berk Hess
Add mdp opt
i
on
chec
k
with decouple
d
modes
commit
|
commitdiff
|
tree
2017-02-05
Mark Abra
h
am
Merge branch release-5-1 into release-2016
commit
|
commitdiff
|
tree
2017-02-03
Mark Abraha
m
Remove typede
f
struct in some mdtypes
f
i
l
e
s
commit
|
commitdiff
|
tree
2017-01-31
Mark Abraha
m
Me
r
ge branch
r
el
e
a
s
e
-5-1
i
nto release-2016
commit
|
commitdiff
|
tree
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