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Support for portable hardware locality (hwloc)
2015-12-11
Mark Abr
a
ham
Stop global communicat
i
on dependi
n
g on integra
t
or
commit
|
commitdiff
|
tree
2015-12-11
T
e
emu Mu
r
to
l
a
Merge
"
Merge br
a
nch 'ori
g
in/releas
e
-5-1'"
commit
|
commitdiff
|
tree
2015-12-09
Robert M
c
Gibbon
Implem
e
nt parse_
d
igi
t
s_fr
o
m_csv_strin
g
commit
|
commitdiff
|
tree
2015-12-09
Mark Abrah
a
m
Update
u
se of preprocessor
in man
a
ging GPU support
commit
|
commitdiff
|
tree
2015-12-08
Roland Schulz
R
e
m
o
ve ol
d
MS
V
C references
commit
|
commitdiff
|
tree
2015-12-07
Berk Hess
Mov
e
d
p
u
l
l
params to mdty
p
e
s/pull-p
a
rams
.
h
commit
|
commitdiff
|
tree
2015-12-02
Teemu Murtola
Split filenm
.
*
commit
|
commitdiff
|
tree
2015-12-02
Berk
H
ess
Refactor
e
d
s
et_pbc_dd
commit
|
commitdiff
|
tree
2015-12-01
Er
i
k
Linda
h
l
Fixed null-d
e
r
e
f
e
r
encing bug in vsites
commit
|
commitdiff
|
tree
2015-11-30
Magn
u
s Lund
b
org
Fixed typos in outpu
t
.
commit
|
commitdiff
|
tree
2015-11-30
Erik Lindahl
C+
+
classes for
cp
u
id and hardwa
r
e topology
commit
|
commitdiff
|
tree
2015-11-30
Teemu Murtola
Cle
a
n up some selec
t
ion cod
e
commit
|
commitdiff
|
tree
2015-11-23
T
e
e
mu Murt
o
la
M
ove precision detect
i
on
s
ymbols to bas
e
v
e
rsion
.
*
commit
|
commitdiff
|
tree
2015-11-22
Ma
r
k
A
b
raham
F
i
x ge
n
er
i
c g
r
oup-sche
m
e ke
r
n
e
l
table
der
e
ferencing
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged genborn
.
h from l
e
gacyheaders/types
i
nto mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Mark Abraham
Remove ewcWA
I
T_GPU_N
B
_L_EST
commit
|
commitdiff
|
tree
2015-11-20
David van
d
e
r Spoel
Mo
v
e
d
legacyhea
d
ers/types/energy
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-19
Mark Abr
a
ham
S
i
m
p
lifie
d
init and
m
dr
u
n
code
commit
|
commitdiff
|
tree
2015-11-16
Mark Abraham
Fix use of
#if vs #ifdef
commit
|
commitdiff
|
tree
2015-11-16
Ma
r
k
Abrah
a
m
Fix
Alig
n
e
dAllocat
o
r wi
t
h MSVC2
0
15 debug mode
commit
|
commitdiff
|
tree
2015-11-16
Erik
L
indahl
Re
m
o
v
e unu
s
ed
c
o
d
e dete
c
ted
b
y PGI compi
l
er
commit
|
commitdiff
|
tree
2015-11-16
Mark
A
braham
Remove "s
u
pport" f
o
r twin-
r
ange with VV inte
g
rato
r
s
commit
|
commitdiff
|
tree
2015-11-15
Teemu Murtola
Add EnumOption with s
u
p
po
r
t for proper enum types
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
Merged lega
c
yheader
s
/type
s
/inputrec
.
h i
n
to
m
dtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Teemu M
u
rtola
Fix reporting of unused
cycle suppressions
commit
|
commitdiff
|
tree
2015-11-14
Mark Abraha
m
Fix wall
t
ime
measurement
with bgclang
commit
|
commitdiff
|
tree
2015-11-14
T
e
emu Murtola
M
ove network
.
h to gmxlib
/
commit
|
commitdiff
|
tree
2015-11-14
Teemu Murtola
M
o
v
e
g
mx_ga2la
.
h to domdec/
commit
|
commitdiff
|
tree
2015-11-13
David van der
S
poel
Replaced
a
tom_id
by in
t
.
commit
|
commitdiff
|
tree
2015-11-13
Teemu Murtol
a
R
e
m
ove
t
_
c
omm
r
ec
d
ependenc
y
from cmd
l
inein
i
t
.
c
p
p
commit
|
commitdiff
|
tree
2015-11-13
Teemu Murtola
Move no
n
bon
d
ed
.
h to gmxlib/nonbonded/
commit
|
commitdiff
|
tree
2015-11-13
Teemu
Murtola
Let use
r
s build
without com
p
iler warnings
commit
|
commitdiff
|
tree
2015-11-13
Tee
m
u Murtol
a
Merge
t
ypes/nsgri
d
.
h into
nsgrid
.
h
commit
|
commitdiff
|
tree
2015-11-13
Mark Abraham
Update
include
s
orter
.
py
commit
|
commitdiff
|
tree
2015-11-13
Teem
u
Murtola
Report unuse
d
cy
c
le
s
u
ppressions
commit
|
commitdiff
|
tree
2015-11-11
D
a
vi
d
van der Spoel
M
o
ved
inputrec
.
* from gmxlib a
n
d lega
c
yheaders to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-11
Teemu Murtola
Remove build sys
t
em for boost
commit
|
commitdiff
|
tree
2015-11-10
David van der Spo
e
l
R
emoved le
g
acyheaders/typedefs
.
h
commit
|
commitdiff
|
tree
2015-11-10
Teemu
M
urtola
R
emov
e
rema
i
ning boost
d
epende
n
cies
commit
|
commitdiff
|
tree
2015-11-06
Teemu Murtola
Move f
o
rce
.
h and vsit
e
.
h
into mdlib
/
commit
|
commitdiff
|
tree
2015-11-05
T
e
em
u
Murtola
M
ove type
s
/rgb
.
h t
o
fileio
/
commit
|
commitdiff
|
tree
2015-11-05
Vedran
Mileti
ć
Document gmx_repl_ex
str
u
ct
commit
|
commitdiff
|
tree
2015-11-05
Mark Abraha
m
Ha
n
dle anoth
e
r
unused var
i
able
commit
|
commitdiff
|
tree
2015-11-05
Erik Lindahl
Av
o
id __vectorcall with
clang
f
or reference b
u
ild
commit
|
commitdiff
|
tree
2015-11-04
Te
e
m
u
M
urt
o
l
a
Merge "Mer
g
e b
r
anch release-5-1"
commit
|
commitdiff
|
tree
2015-11-04
Mark Abra
h
am
Permit matr
i
x build wi
t
h RelW
i
thDebInfo set
commit
|
commitdiff
|
tree
2015-11-04
Mark Abraham
Fix icc 16 issues
commit
|
commitdiff
|
tree
2015-11-04
Mark Abraham
S
t
op
m
oving from unique_
p
tr when copy elisi
o
n works
commit
|
commitdiff
|
tree
2015-11-03
Teemu Murto
l
a
Upd
a
te build scripts to matc
h
r
e
leng refactoring
commit
|
commitdiff
|
tree
2015-11-03
David van der Spoel
Moved
df_history
u
t
ilit
y
r
o
ut
i
nes fr
o
m typedef
s
t
o
.
.
.
commit
|
commitdiff
|
tree
2015-11-03
Mark
Abra
h
am
Quiet warnings with clang-3
.
7
commit
|
commitdiff
|
tree
2015-11-03
B
e
r
k
H
ess
Fix no
w
allcycl
e
support
commit
|
commitdiff
|
tree
2015-11-03
J
ames W
.
Ba
r
nett
Output re
p
lica exchange order
descrip
t
ion to debug
commit
|
commitdiff
|
tree
2015-11-02
Ber
k
Hess
Fix intermol
e
c
u
lar interactions with small mols
commit
|
commitdiff
|
tree
2015-11-02
Teemu Murto
l
a
R
eplace boos
t
::exception_ptr with std::exception_ptr
commit
|
commitdiff
|
tree
2015-11-02
Erik
Linda
h
l
Enable 64-bit
cycle counters
on ARMV7a
commit
|
commitdiff
|
tree
2015-11-02
S
z
ilard Pall
Fix signal
t
ype
commit
|
commitdiff
|
tree
2015-11-02
Er
i
k
Lindahl
S
plit SIMD
im
p
lementations into 4 files
commit
|
commitdiff
|
tree
2015-11-02
Mark Abraham
Replace boost
:
:shared_ptr wi
t
h std::shared_ptr
commit
|
commitdiff
|
tree
2015-11-02
Eri
k
Lin
d
ahl
Moved GM
X
_SIMD_* ma
c
ros fr
o
m i
f
defs to values 0
/
1
commit
|
commitdiff
|
tree
2015-11-01
David van d
e
r
S
poel
Replaced NOTSET from typedefs
.
h by local
s
olutions
.
commit
|
commitdiff
|
tree
2015-10-28
Mark A
b
raham
Use
d
efault ali
g
nment for OpenCL host buffer
commit
|
commitdiff
|
tree
2015-10-28
Teemu Murtola
Remove unused TrajectoryAnalysisM
o
dule code
commit
|
commitdiff
|
tree
2015-10-28
M
a
rk Abraham
S
e
para
t
e wallcycle responsibiliti
e
s
commit
|
commitdiff
|
tree
2015-10-25
Teemu Murtola
Fi
x
miss
i
ng
he
l
p
text for traje
c
tory anal
y
sis tool
s
commit
|
commitdiff
|
tree
2015-10-24
Sz
i
l
a
rd
P
a
l
l
A
v
oid using incompati
b
le NVML v
e
rsion
commit
|
commitdiff
|
tree
2015-10-23
David va
n
der Spoel
Removed e
n
er
g
yhi
s
tory code from typedefs t
o
a separa
t
e
.
.
.
commit
|
commitdiff
|
tree
2015-10-23
M
a
r
k Abraham
Impr
o
ve
implementation of
c
ycle
s
ub
c
ounting
commit
|
commitdiff
|
tree
2015-10-23
Erik Linda
h
l
Added AlignedAl
l
ocator cla
s
s
commit
|
commitdiff
|
tree
2015-10-22
Te
e
mu Murtola
Additional norma
l
ization op
t
i
ons for gmx
rdf
commit
|
commitdiff
|
tree
2015-10-22
Sz
i
lar
d
Pall
Quiet FindN
V
ML
commit
|
commitdiff
|
tree
2015-10-22
Te
e
m
u Murto
l
a
Use
i
nc
l
ude_direc
t
orie
s
(SYS
T
EM
.
.
.
) consistently
commit
|
commitdiff
|
tree
2015-10-22
Erik Lindahl
Merge "Merge rel
e
ase-5-0 into release-5-1" into releas
e
-5-1
commit
|
commitdiff
|
tree
2015-10-22
Teemu Murtola
Cle
a
n up and improve fatal
e
rror han
d
lin
g
commit
|
commitdiff
|
tree
2015-10-19
Mark Abraham
Fix cycle sub
c
ounters
commit
|
commitdiff
|
tree
2015-10-19
Tee
m
u
Murtola
Sp
l
i
t
EnumIntOption
f
rom
StringOption
commit
|
commitdiff
|
tree
2015-10-18
Justin Le
m
kul
R
emoved dihe
d
rals
from G
L
Y
.
r
tp entry
.
commit
|
commitdiff
|
tree
2015-10-16
M
a
r
k
Abraha
m
Add Jenk
i
ns opt
i
ons matrix to source rep
o
commit
|
commitdiff
|
tree
2015-10-15
Szilárd Páll
Correct CUDA version co
m
p
a
risons
commit
|
commitdiff
|
tree
2015-10-14
Erik Linda
h
l
Another quote from Economi
s
t today
commit
|
commitdiff
|
tree
2015-10-14
Alfre
d
o
Metere
Fixed segfault in genconf
u
tility
commit
|
commitdiff
|
tree
2015-10-13
E
rik Lin
d
ahl
Moved no
n
bonded sources
t
o C++
commit
|
commitdiff
|
tree
2015-10-13
Erik Lindahl
Moved last
n
bnxn_kernel
s
o
u
r
c
es to C++
commit
|
commitdiff
|
tree
2015-10-13
T
eemu Murtola
I
mpro
v
e documentation
a
nd tests for refdata
commit
|
commitdiff
|
tree
2015-10-12
Michael
S
hirt
s
Fix
for lack o
f
C
O
M remov
a
l for md-
v
v
commit
|
commitdiff
|
tree
2015-10-12
Ja
m
es W
.
Barnett
gmx wh
a
m: Use mac
r
os for units a
n
d conversio
n
s
.
commit
|
commitdiff
|
tree
2015-10-12
T
eemu Murtola
H
i
de i
m
plementation details from cmdlinerunner
.
h
commit
|
commitdiff
|
tree
2015-10-12
Carsten Kutz
n
er
Described the compu
t
at
i
onal electrophysio
l
ogy
.
mdp
.
.
.
commit
|
commitdiff
|
tree
2015-10-12
Teemu Murtola
Improve
gmx
sa
s
a tests a
n
d clean up
-or
handling
commit
|
commitdiff
|
tree
2015-10-11
J
a
mes W
.
Ba
r
nett
User g
u
ide: Update spelling,
a
dd some
inte
r
nal refs
commit
|
commitdiff
|
tree
2015-10-11
Teemu Mu
r
t
ola
Remove obsolete build scrip
t
s
commit
|
commitdiff
|
tree
2015-10-09
Mark
A
braham
Remove CGLO_RERUNMD
commit
|
commitdiff
|
tree
2015-10-08
Teemu Murtola
Remove unused error handling code
commit
|
commitdiff
|
tree
2015-10-07
C
a
r
s
ten Ku
t
zner
Ex
t
ra options for computational electrophys
i
ology
.
commit
|
commitdiff
|
tree
2015-10-06
Jam
e
s W
.
B
a
r
n
ett
U
pdate
EI_MD to use EI_R
A
NDOM
.
A
l
so use
E
I_M
D
commit
|
commitdiff
|
tree
2015-10-06
James W
.
Barnett
Note when pc
o
upl or tcou
p
l are
a
uto
set to no
commit
|
commitdiff
|
tree
2015-10-05
James W
.
Barnett
Add more i
n
f
o
to
h
eader for p
r
oce
s
se
d
mdp files
commit
|
commitdiff
|
tree
2015-10-05
Jame
s
W
.
Barnett
Remove l
a
mbda fr
o
m print_ebin_header
.
commit
|
commitdiff
|
tree
2015-10-05
James W
.
B
a
rnett
Temporary fil
e
tw
e
aks
.
commit
|
commitdiff
|
tree
2015-10-05
Er
i
k L
i
ndahl
Added
t
r
y/catch statements
in OpenMP reg
i
ons a
n
d tMPI
.
.
.
commit
|
commitdiff
|
tree
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