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Fix pre-submit build matrix and description
2019-07-11
Mark Abr
a
ham
Fix
pre-submit bu
i
ld matrix and descript
i
on
commit
|
commitdiff
|
tree
2019-07-08
Mark
A
br
a
ham
Fix hwloc and sphinx det
e
ction
commit
|
commitdiff
|
tree
2019-07-08
Mark Abraham
T
e
s
t
specific hw
l
oc versions
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraham
Impr
o
ve tests of index block construction
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraham
Modernize Fi
n
dHwloc
.
c
m
ake
commit
|
commitdiff
|
tree
2019-07-04
Mark
Abraham
Fur
t
her clang-tidy-7
f
ix
commit
|
commitdiff
|
tree
2019-07-04
Mark
Abraham
F
i
x clang-t
i
dy-7 issues
commit
|
commitdiff
|
tree
2019-07-03
Mark Abr
a
ham
Reord
e
r
opti
o
ns
commit
|
commitdiff
|
tree
2019-06-18
M
a
r
k
A
b
raham
M
o
ve code handling mdrun -gp
u
_id t
o
taskassignm
e
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mar
k
Abr
a
ham
Fix pygments detecti
o
n
for sphinx
f
or docs buil
d
commit
|
commitdiff
|
tree
2019-06-11
Mar
k
Abraham
Use RA
I
I
approaches f
o
r hardwa
r
e informat
i
on de
t
e
ct
i
o
n
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Cle
a
n up multi
s
im
,
communica
t
ion, and REMD cod
e
commit
|
commitdiff
|
tree
2019-05-24
Mark Abra
h
am
Reorder code before thread-MPI spawns th
r
e
ads
commit
|
commitdiff
|
tree
2019-05-23
Mark
A
b
r
ah
a
m
Teach ArrayR
e
fW
i
thPadd
i
ng to make a const flav
o
ur
commit
|
commitdiff
|
tree
2019-05-22
M
ark Abraham
Rewr
i
te s
t
art
i
ng
b
ehavior
commit
|
commitdiff
|
tree
2019-05-22
M
a
r
k Abraha
m
In
t
ro
d
uce tri-
s
tate enums
f
or restarts
commit
|
commitdiff
|
tree
2019-05-22
Mark Ab
r
a
ham
Move functional
i
ty to mdrunutility
commit
|
commitdiff
|
tree
2019-05-14
Mark Abraham
Update infrastruct
u
r
e needed for r
e
st
a
r
t
re
w
r
i
te
commit
|
commitdiff
|
tree
2019-05-08
Mark Abr
a
ham
Provide hook fo
r
forks of GROMACS to
describe th
e
mselves
commit
|
commitdiff
|
tree
2019-05-07
Mark Abr
a
h
a
m
P
r
ovide be
t
ter
help for
u
s
ing libc
+
+
commit
|
commitdiff
|
tree
2019-05-06
Mark Abraham
Improve how mdrun -noappend nam
e
s outpu
t
files
commit
|
commitdiff
|
tree
2019-05-03
Mar
k
Abraham
M
o
r
e
t
ests for how mdru
n
-cpi restarts handle files
commit
|
commitdiff
|
tree
2019-05-02
Mark Abrah
a
m
E
nhance
p
at
h
search functions
commit
|
commitdiff
|
tree
2019-04-30
Mark Abr
a
ham
T
e
st the outpu
t
of "gmx mdrun help"
commit
|
commitdiff
|
tree
2019-04-25
Mark Abraham
Update style g
u
ide
a
b
out
c
lass
e
nums
commit
|
commitdiff
|
tree
2019-04-23
Mar
k
Abra
h
am
Clarify pu
s
hing of interaction types
commit
|
commitdiff
|
tree
2019-04-23
Mark
A
braham
U
p
date
d
cl
a
n
g -
W
eve
r
yt
h
ing c
h
ecks to
clang
-
7
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Cr
e
ate gmx::com
p
at
:
:o
p
ti
o
nal
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Mov
e
pull
w
ork stru
c
t ou
t
of inputr
e
c
commit
|
commitdiff
|
tree
2019-04-18
M
a
rk Abraham
I
mpr
o
ve sw
a
pcoords session lif
e
time management
commit
|
commitdiff
|
tree
2019-04-17
Mar
k
Abraham
Fix post-sub
m
it
commit
|
commitdiff
|
tree
2019-04-16
Mark Abr
a
ham
Re
m
o
ved mdrun
-
gcom
commit
|
commitdiff
|
tree
2019-04-10
Mark
A
b
ra
h
am
Start
making IMD and sw
a
p m
o
del IMDModule
commit
|
commitdiff
|
tree
2019-04-10
M
a
r
k Abraha
m
Reuse rvecs_differ in I
n
teractiveMD module
commit
|
commitdiff
|
tree
2019-04-10
Mark Abr
a
ham
Make ImdSession into
a Pimpl-ed
c
l
ass with facto
r
y
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Mark
Abrah
a
m
Refor
m
IMD module
commit
|
commitdiff
|
tree
2019-04-03
Mark Abr
a
ham
I
nit
i
al dea
c
tivation of group sch
e
me
.
commit
|
commitdiff
|
tree
2019-04-01
Mark Abraham
Move MDModules
i
nitializatio
n
ear
l
ier
commit
|
commitdiff
|
tree
2019-04-01
Mark Abr
a
ham
Move enerdata
o
wnership t
o
mdr
u
nner
commit
|
commitdiff
|
tree
2019-03-28
Ma
r
k Abraham
Move Do
m
d
e
cOptions
i
nto its own header
commit
|
commitdiff
|
tree
2019-03-25
Mark Abraham
Su
p
p
ort Arr
a
yRef o
f
E
n
umer
a
tionArray
commit
|
commitdiff
|
tree
2019-03-25
M
a
rk Abraham
Conver
t
gmx d
u
m
p
to
modu
l
e
commit
|
commitdiff
|
tree
2019-03-20
Mark A
b
rah
a
m
Clean up mdrun help descr
i
ption
commit
|
commitdiff
|
tree
2019-03-20
M
ark
A
braham
Imp
r
ov
e
m
imic module
commit
|
commitdiff
|
tree
2019-03-19
Mark A
b
rah
a
m
A
d
d suppor
t
for se
r
iali
z
ing 32-bit integers
commit
|
commitdiff
|
tree
2019-03-19
Mark
Abraham
Fix
c
la
n
g warn
i
ng
commit
|
commitdiff
|
tree
2019-03-19
Mark Ab
r
aham
U
p
d
ate
E
l
ectri
c
Field module
commit
|
commitdiff
|
tree
2019-03-12
M
ark
A
braham
Fix memory leak
commit
|
commitdiff
|
tree
2019-03-07
Ma
r
k A
b
raham
Elimin
a
te md
l
ib/
m
drun
.
h
commit
|
commitdiff
|
tree
2019-03-07
Ma
r
k Abraham
R
e
m
o
ve i
n
effect
i
ve code for writing more
T
ER fiel
d
s
.
.
.
commit
|
commitdiff
|
tree
2019-03-07
Mark
Abraham
New t
e
sts for pdb2g
m
x and
e
ditconf
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
C
l
ean up use of
loop in
d
ices
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraha
m
R
e
v
ert "
E
liminate mdlib/
m
drun
.
h"
commit
|
commitdiff
|
tree
2019-03-06
M
ark
Abr
a
ha
m
E
lim
i
nate mdlib/mdrun
.
h
commit
|
commitdiff
|
tree
2019-03-06
Mark
A
braham
M
i
n
o
r mod
e
rnization in gmx_dump
commit
|
commitdiff
|
tree
2019-03-05
Mar
k
Abr
a
ham
Make
p
db2gmx t
e
sts run in Jen
k
in
s
commit
|
commitdiff
|
tree
2019-03-02
Mark
A
braham
Me
r
ge
b
ranch release-2019
commit
|
commitdiff
|
tree
2019-03-02
Mark Abraham
Re
m
ove
defunct mdrun opt
i
ons
commit
|
commitdiff
|
tree
2019-02-27
M
a
rk Abra
h
am
K
eep
niche CMake variables as ad
v
anc
e
d
commit
|
commitdiff
|
tree
2019-02-27
Mark Abraham
Remove minor broken
f
unctionality i
n
gmx
b
ar
commit
|
commitdiff
|
tree
2019-02-26
M
ark Abraham
A
d
d
n
ew line to trjconv
notic
e
to users
commit
|
commitdiff
|
tree
2019-02-25
Mark Abraha
m
Mov
e
code out of sim_util
.
cpp
commit
|
commitdiff
|
tree
2019-02-25
Ma
r
k
Abraham
De-duplicate gmx_tmpnam and gmx_fopen_temp
o
ra
r
y
commit
|
commitdiff
|
tree
2019-02-15
Ma
r
k
Ab
r
aham
Impro
v
ed diagnostics w
h
en PME
c
a
n
not run on GPU
s
commit
|
commitdiff
|
tree
2019-02-14
Mark Abraham
F
i
x us
e
of selections referring t
o
i
n
dex groups
commit
|
commitdiff
|
tree
2019-02-14
M
ark
A
b
raham
R
eve
r
t changes to
im
p
lementation
of insert-mole
c
ules
.
.
.
commit
|
commitdiff
|
tree
2019-02-13
M
ark Abraham
I
mproved el
e
ctric-field
docs
commit
|
commitdiff
|
tree
2019-02-13
Mark Abra
h
a
m
Make EnergyOu
t
put wrapper cl
a
ss
commit
|
commitdiff
|
tree
2019-02-13
Mark A
b
raham
Reduce coupling to paddedvector
.
h
commit
|
commitdiff
|
tree
2019-02-12
Mark Abraha
m
Quiet cl
a
n
g
wa
r
ning
commit
|
commitdiff
|
tree
2019-02-12
Ma
r
k Abra
h
a
m
Remove gm
x
::Re
g
ex
commit
|
commitdiff
|
tree
2019-02-08
M
a
rk A
b
ra
h
am
Fix In
t
el compiler
w
arning
commit
|
commitdiff
|
tree
2019-02-08
M
ark
Abraham
Remove copy_ener
g
y from energy-wri
t
ing
steps
commit
|
commitdiff
|
tree
2019-02-08
M
a
r
k Abraham
Reform
e
nergy o
u
tput tests
commit
|
commitdiff
|
tree
2019-02-04
Mark Abraham
Remove SIMD support from gro
u
p sch
e
me
commit
|
commitdiff
|
tree
2019-01-30
M
ark Abraham
Me
r
ge rem
o
t
e
b
r
anch
r
elease-2018
i
nto release-2019
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraham
F
i
x
r
elea
s
e
n
o
tes
i
ss
u
e
links
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraha
m
Fix r
e
lease n
o
tes issue
l
i
n
ks
commit
|
commitdiff
|
tree
2019-01-28
Mark
Abraham
Stop
t
r
ying to check nvcc on Windows
commit
|
commitdiff
|
tree
2019-01-28
Mark Abraham
Bump CUDA req
u
ire
m
e
n
t to
9
.
0
commit
|
commitdiff
|
tree
2019-01-25
Ma
r
k
Abraham
Re
q
uire cl
a
n
g
3
.
6
commit
|
commitdiff
|
tree
2019-01-25
Ma
r
k Abraham
Fix post-
s
ubmit b
u
ild
commit
|
commitdiff
|
tree
2019-01-25
Mar
k
Abraham
Unify
r
e
gex impl
e
menta
t
ion
commit
|
commitdiff
|
tree
2019-01-25
Mark Abra
h
a
m
Bum
p
requ
i
red gcc
compiler
to 5
.
1
commit
|
commitdiff
|
tree
2019-01-25
Mark
Abraham
Use
native cma
k
e C++11 support
commit
|
commitdiff
|
tree
2019-01-22
Mark Abraham
Rem
o
ve ini
t
_md and impro
v
e ini
t
_em
commit
|
commitdiff
|
tree
2019-01-21
Mark Abraham
Clean up initialize_lambd
a
s
commit
|
commitdiff
|
tree
2019-01-21
Mark
A
braha
m
Fix trjcon
v
-ndec
commit
|
commitdiff
|
tree
2019-01-18
Mark Abraham
Disa
b
led internal clFFT when
u
sing MSV
C
with OpenCL
commit
|
commitdiff
|
tree
2019-01-18
M
a
rk Ab
r
aham
Improve n
v
cc error reporting
commit
|
commitdiff
|
tree
2019-01-18
Mark
A
braham
Remo
v
e ctest se
c
t
ion called simp
l
e
commit
|
commitdiff
|
tree
2019-01-16
Mark Abraha
m
Migrate test conf
i
gu
r
ati
o
n off
b
s
_m
a
c
commit
|
commitdiff
|
tree
2019-01-16
Ma
r
k
Abraham
Remove
s
everal unnecessary things
commit
|
commitdiff
|
tree
2019-01-15
Mar
k
A
braham
Reverted standard ExternalPr
o
ject
f
or FFTW
download
commit
|
commitdiff
|
tree
2019-01-14
Mark
A
b
rah
a
m
I
mp
r
ove portability of PM
E
on
GPU code
commit
|
commitdiff
|
tree
2019-01-14
Ma
r
k
Abraham
Rem
o
ve ctest section
ca
l
le
d
k
e
rnel
commit
|
commitdiff
|
tree
2019-01-14
Mark Abrah
a
m
Migrate TPI
t
esting to Ve
r
l
et scheme
commit
|
commitdiff
|
tree
2019-01-13
M
a
rk Abraham
Impro
v
e
u
s
e
o
f
gmxp
r
epr
o
cess h
e
aders
commit
|
commitdiff
|
tree
2019-01-11
Mark Abraham
Use enum class
f
or
g
rompp dir
e
ctive
s
commit
|
commitdiff
|
tree
2019-01-11
M
a
rk Abraham
Fix typo in
r
elease notes
commit
|
commitdiff
|
tree
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