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Make loop variables in orires.cpp local
2017-08-01
M
a
rk Abraha
m
Introd
u
ced Mdrun
n
er high-level class
commit
|
commitdiff
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tree
2017-07-27
M
a
rk Abraham
E
n
hance cmake a
n
d r
e
leng hand
l
in
g
of
G
M
X_USE_RD
T
SCP
commit
|
commitdiff
|
tree
2017-07-24
Mark
Abraham
Separated
responsib
i
lit
y
for consistenc
y
check
i
ng
commit
|
commitdiff
|
tree
2017-07-24
Mark Abr
a
ham
Rem
o
ve
unne
c
e
s
sary GPU
c
hecking code
commit
|
commitdiff
|
tree
2017-07-20
M
a
rk Abrah
a
m
Cleaned up
bUseGp
u
in runner
commit
|
commitdiff
|
tree
2017-07-20
Mark
A
braha
m
Stop duplicate printing o
f
detecte
d
GPUs
commit
|
commitdiff
|
tree
2017-07-20
Mark Abraham
Fix use of GMX_SIMD in own-fftw build
commit
|
commitdiff
|
tree
2017-07-19
Mark
A
braham
Made p
o
st-submit config to test
c
l
ang+
o
penmp
.
commit
|
commitdiff
|
tree
2017-07-19
Mark Abraham
Improve CMake imple
m
en
t
ation fo
r
GMX_SIMD
commit
|
commitdiff
|
tree
2017-07-18
Mar
k
Abraham
Converted some const
p
ointers into const references
.
.
.
commit
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commitdiff
|
tree
2017-07-18
Mark A
b
r
a
ham
Eliminated pick_nbnxn_resourc
e
s
commit
|
commitdiff
|
tree
2017-07-14
M
a
rk Abraham
Implemented grompp -po for options-s
t
yle mdp
handl
i
ng
commit
|
commitdiff
|
tree
2017-07-14
M
a
rk Abraham
Clean up cmake build ho
s
t
detection
commit
|
commitdiff
|
tree
2017-07-13
Ma
r
k A
b
raham
C
l
e
an up gmx_mdrun()
commit
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commitdiff
|
tree
2017-07-13
Mark
Abraham
Clea
n
ed
u
p
md
r
unn
e
r_star
t
_threads
commit
|
commitdiff
|
tree
2017-07-13
M
a
rk Abr
a
ham
Mo
r
e
updates to testing matr
i
x
commit
|
commitdiff
|
tree
2017-07-07
Mar
k
Abraham
Refactor e
r
r
o
r han
d
ling in init_gpu
commit
|
commitdiff
|
tree
2017-07-06
M
a
rk Abraham
Simplify gmx_gpu_opt_t
commit
|
commitdiff
|
tree
2017-07-04
Mark Ab
r
a
ham
Cle
a
n up pick_nbnxn_resources
commit
|
commitdiff
|
tree
2017-07-01
Ma
r
k Abraham
Clea
n
ed up GPU em
u
lation logic
commit
|
commitdiff
|
tree
2017-06-28
Mark Abraham
Cleaned up
h
igh-level boolean variable naming
commit
|
commitdiff
|
tree
2017-06-28
Mark Abraham
Merge
b
ranch
r
el
e
as
e
-2
0
16
commit
|
commitdiff
|
tree
2017-06-27
M
ark Abra
h
am
Min
o
r
improvemen
t
s t
o
test configs
commit
|
commitdiff
|
tree
2017-06-22
M
ark Abraham
Conso
l
i
dated logic for
c
hoosing number of thread-MPI
.
.
.
commit
|
commitdiff
|
tree
2017-06-22
Mark
Abrah
a
m
Replac
e
misnamed nbnxn_gpu_a
c
celeration_
s
upported
commit
|
commitdiff
|
tree
2017-06-22
Ma
r
k A
b
raham
Consolidate
a
n
d fi
x
logic for mdrun
-
n
b
and -gpuid
commit
|
commitdiff
|
tree
2017-06-21
M
ark Abraham
R
eform ngpu v
a
riable
commit
|
commitdiff
|
tree
2017-06-21
Mark
Abra
h
am
Remove bUserSetGpuIds f
i
el
d
commit
|
commitdiff
|
tree
2017-06-14
Mark A
b
rah
a
m
Simplify repo
r
ting
from init_
g
p
u
commit
|
commitdiff
|
tree
2017-06-12
Mar
k
Ab
r
aham
Move gmx_
p
arse_gpu_i
d
out o
f
checki
n
g
f
u
n
ction
commit
|
commitdiff
|
tree
2017-05-31
M
a
rk Abraham
New quote
commit
|
commitdiff
|
tree
2017-05-30
Mark A
b
raham
Fi
x
N
V
ML er
r
o
r
messages
commit
|
commitdiff
|
tree
2017-05-27
M
a
rk
A
b
r
a
ham
Q
u
o
tes from Gottingen wor
k
s
h
op
commit
|
commitdiff
|
tree
2017-05-26
Mark Abraha
m
T
est i
n
vsixthroot func
t
ion
a
s
intended
commit
|
commitdiff
|
tree
2017-05-15
Mark
A
braham
Upda
t
ed us
e
of compil
e
r spe
c
ifi
e
r
s in test
i
ng
commit
|
commitdiff
|
tree
2017-05-15
M
a
rk
Abr
a
h
am
Update
d
u
s
e o
f
gcc-5
s
pecifiers
commit
|
commitdiff
|
tree
2017-05-15
Mark
Abra
h
a
m
Updat
e
cl
a
ng
s
t
at
i
c ana
l
yzer
s
lave t
o
use version 4
commit
|
commitdiff
|
tree
2017-05-14
Mark Abrah
a
m
Up
d
ate
c
l
a
ng-4
commit
|
commitdiff
|
tree
2017-05-09
Mark Abraham
Fix for
m
attin
g
o
f
MKL cmak
e
do
c
s
commit
|
commitdiff
|
tree
2017-05-09
Mark Abra
h
am
Merg
e
branch
r
elea
s
e-
2
016
commit
|
commitdiff
|
tree
2017-05-09
Ma
r
k
Abraham
C
leaned u
p
mem
o
r
y usage in gmx tra
j
an
d
trjconv
commit
|
commitdiff
|
tree
2017-04-22
Mark Abr
a
h
a
m
Clean up memory usage
w
ith oe
n
v and x
v
g writing
commit
|
commitdiff
|
tree
2017-04-17
M
a
rk Abraham
Minor change to
GPU comp
a
tib
i
lity
r
eporting handling
commit
|
commitdiff
|
tree
2017-04-17
Mark Abraham
Propose a pos
t
-s
u
bmit matri
x
commit
|
commitdiff
|
tree
2017-04-03
M
a
rk Abraham
Remo
v
e
d
o_pbc_first
commit
|
commitdiff
|
tree
2017-03-31
M
a
rk Ab
r
a
ham
Merge
branch rele
a
se-201
6
commit
|
commitdiff
|
tree
2017-03-29
Mark
A
b
r
a
ham
Fix parameter description for dihed
r
al_restrain
t
s
commit
|
commitdiff
|
tree
2017-03-22
Mark Abr
a
ham
Add section
t
o user guide f
o
r ma
n
aging simul
a
ti
o
ns
commit
|
commitdiff
|
tree
2017-03-19
M
a
rk Abr
a
h
a
m
Fix string handling for gcc 7
commit
|
commitdiff
|
tree
2017-03-14
Mark Abr
a
ham
Merge branch rele
a
se-2016
commit
|
commitdiff
|
tree
2017-03-14
Mark Abraham
Bumped versi
o
n to p
r
epare
f
or n
e
xt patch releas
e
commit
|
commitdiff
|
tree
2017-03-13
Mark Abraham
Vers
i
on 20
1
6
.
3
commit
|
commitdiff
|
tree
2017-03-13
Mark Abraham
Modernize write_in
p
file
commit
|
commitdiff
|
tree
2017-03-13
Mark Abraham
Moder
n
ize read_inp
f
ile
commit
|
commitdiff
|
tree
2017-03-13
M
a
rk A
b
raham
Tests for gr
o
mpp -f -p
o
commit
|
commitdiff
|
tree
2017-03-09
Mark Abrah
a
m
R
efactor
G
PU
s
e
lection handl
i
ng
commit
|
commitdiff
|
tree
2017-03-07
Mark Abraham
F
ix minor
issues
in
g
mx
t
ra
j
-av -af
commit
|
commitdiff
|
tree
2017-03-04
Mark Abr
a
ham
Fixes for xl
compilers
1
3
.
1
.
5 on Power8
commit
|
commitdiff
|
tree
2017-02-20
M
ark Abr
a
ham
Add
tests for old
g
mx ener
g
y functionality
commit
|
commitdiff
|
tree
2017-02-17
Mark Abr
a
h
am
Us
e
gmx::Mu
t
ex and gmx::lock_gu
a
r
d
to fix some is
s
ues
commit
|
commitdiff
|
tree
2017-02-15
Mark
A
b
rah
a
m
Merge branch
r
e
l
ease-5-
1
into release-2016
commit
|
commitdiff
|
tree
2017-02-14
M
a
rk Abraham
Fix ha
n
dl
i
n
g
o
f previous virials
commit
|
commitdiff
|
tree
2017-02-14
Ma
r
k Abraham
Reduc
e
com
p
ilation coup
l
i
n
g
commit
|
commitdiff
|
tree
2017-02-10
Mark
Abraham
Corrected
output of gmx do_dss
p
-sc
commit
|
commitdiff
|
tree
2017-02-09
Mark Abraham
C
om
p
lete the
removal of state
f
ul RNG
commit
|
commitdiff
|
tree
2017-02-09
Ma
r
k Abraham
I
m
proved st
a
te_change_natoms and us
e
d it
m
ore
commit
|
commitdiff
|
tree
2017-02-09
M
ark
Abraham
Remove
E
ST_DISTR
f
rom
state
.
h
commit
|
commitdiff
|
tree
2017-02-09
Mark Abraha
m
Enhance warninp
commit
|
commitdiff
|
tree
2017-02-08
M
ark Abra
h
am
E
x
tend
s
e
rializ
a
tion
to gmx_int64_t
commit
|
commitdiff
|
tree
2017-02-08
Mark Abra
h
am
Remo
v
e
do
c
s
f
or
u
nimplemented
trj
c
onv -cl
u
stercenter
commit
|
commitdiff
|
tree
2017-02-08
Mark A
b
r
a
ham
Cre
a
te appl
i
ed-forces mo
d
ule gro
u
p
commit
|
commitdiff
|
tree
2017-02-08
Mark Abraham
Give MDModu
l
es responsibility for opti
o
n handlin
g
commit
|
commitdiff
|
tree
2017-02-07
Mark Abraham
Merge br
a
nch
r
elease-2016
commit
|
commitdiff
|
tree
2017-02-07
Mark Ab
r
aha
m
Bump
e
d version to
p
repare for
next pat
c
h rele
a
se
commit
|
commitdiff
|
tree
2017-02-07
Mark
A
braham
Introduced system prep
a
ration s
e
ction to user g
u
ide
commit
|
commitdiff
|
tree
2017-02-07
Mark
Abraham
Ve
r
si
o
n
2016
.
2
commit
|
commitdiff
|
tree
2017-02-05
Mark Abraham
M
e
rge
branch releas
e
-5-1 into release
-
2016
commit
|
commitdiff
|
tree
2017-02-03
Ma
r
k Abraham
Remove typedef
struct in some
m
dtypes files
commit
|
commitdiff
|
tree
2017-02-02
Mark Abrah
a
m
C
l
arify use of ta
u
-p and pcoupltype
commit
|
commitdiff
|
tree
2017-01-31
M
ark Ab
r
a
ham
Merge branch releas
e
-5-1 into release-2016
commit
|
commitdiff
|
tree
2017-01-30
Mark Abraham
F
i
x multi
-
doma
i
n reruns
commit
|
commitdiff
|
tree
2017-01-30
Mar
k
A
braham
Don'
t
print invali
d
perfo
r
mance
d
ata
commit
|
commitdiff
|
tree
2017-01-23
M
ark
Abrah
a
m
S
topp
e
d hea
d
er files including st
a
te
.
h
commit
|
commitdiff
|
tree
2017-01-22
Ma
r
k Abra
h
am
F
i
xed
gmx rmsf -q
-
oq
.
commit
|
commitdiff
|
tree
2017-01-21
Ma
r
k Abraham
Re
m
ov
e
d
init
_
state
commit
|
commitdiff
|
tree
2017-01-20
Mar
k
Ab
r
a
h
a
m
Initi
a
li
z
e
GMX_*_
L
IBRARI
E
S
cmake
v
a
riables earlier
commit
|
commitdiff
|
tree
2017-01-14
Mark Abraham
Merge branch releas
e
-2016
commit
|
commitdiff
|
tree
2017-01-06
Mark Abraham
Document ISeriali
z
er
c
lass
commit
|
commitdiff
|
tree
2017-01-04
Mark
Abr
a
ha
m
S
top trying
to use objdump --reloc on
Mac
commit
|
commitdiff
|
tree
2017-01-04
Ma
r
k Abraham
Fix docum
e
ntation of Opt
i
onsV
i
sit
o
r
commit
|
commitdiff
|
tree
2017-01-03
Mark A
b
raham
Merge
br
a
n
c
h release
-
5-1 into
r
e
lea
s
e-20
1
6
commit
|
commitdiff
|
tree
2016-12-20
Mark
A
brah
a
m
C
orrec
t
ed docu
m
entation about eigenva
l
u
e
handling
commit
|
commitdiff
|
tree
2016-12-20
Mark Abraham
Improve build system for plugin su
p
port
commit
|
commitdiff
|
tree
2016-12-20
M
ark A
b
raham
Sanitize some incl
u
de heade
r
s
commit
|
commitdiff
|
tree
2016-12-20
Mark Abraham
Merge branch release
-
201
6
commit
|
commitdiff
|
tree
2016-12-15
Mark Abraham
Rem
o
ved support for multiple entrie
s
i
n mdp fi
l
es
commit
|
commitdiff
|
tree
2016-12-15
M
a
rk Abraham
Ha
n
d
le warninp correctl
y
in xpm2ps an
d
membe
d
commit
|
commitdiff
|
tree
2016-12-14
Ma
r
k Abr
a
ham
Fix mis
l
ead
i
ng pa
r
allelization doc
s
f
o
r gmx wham
commit
|
commitdiff
|
tree
2016-12-09
Mark Abraham
Fi
x
logi
c
of TR
R
read
i
ng
commit
|
commitdiff
|
tree
2016-12-09
Mark Abraha
m
R
e
mov
e
n
xframe fr
o
m t_
t
r
xstatus
commit
|
commitdiff
|
tree
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