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Move documentation on tool changes from wiki
2015-06-25
Teemu M
u
rtola
Mo
v
e documentation on tool chan
g
es from
wiki
commit
|
commitdiff
|
tree
2015-06-25
Ma
r
k
Abraha
m
M
er
g
e "Merge rel
e
ase-5-0
i
nto
master"
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Reenabled
S
IMD kernels withou
t
cut-offs
commit
|
commitdiff
|
tree
2015-06-24
Erik Lindahl
Avoi
d
access
i
ng hackb
l
ocks f
o
r
x
2top
commit
|
commitdiff
|
tree
2015-06-24
Magnu
s
Lundborg
Upd
a
te header when
appen
d
ing to TNG file
.
commit
|
commitdiff
|
tree
2015-06-24
Berk
H
e
ss
GPU
Ewald
table k
e
rn
e
l now uses CPU spacing
commit
|
commitdiff
|
tree
2015-06-24
B
e
rk Hess
Avoid
G
PU selection
w
i
th GPU emulation
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Minor reformatting of SIMD mi
s
match
message
commit
|
commitdiff
|
tree
2015-06-24
Be
r
k
H
e
ss
Add sugar t
o
print empty line in prin
t
BinaryInformation
commit
|
commitdiff
|
tree
2015-06-23
Erik Lindahl
Updat
e
d physi
c
al constant
s
from N
I
ST 20
1
0 CODAT
A
commit
|
commitdiff
|
tree
2015-06-23
Er
i
k Lin
d
ahl
Removed
bu
g
gy -
s
moot
h
ha
c
k i
n
hbo
n
d
module
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Update launch config
u
rat
i
on for physical nod
e
s
commit
|
commitdiff
|
tree
2015-06-22
Rolan
d
Sc
h
ulz
Fix
GMX_ALIGNMENT for MSVC 20
1
2 and
2
013
commit
|
commitdiff
|
tree
2015-06-22
B
erk Hes
s
Av
o
id fp
e
xcep
t
ions in pair
s
ear
c
h debug
commit
|
commitdiff
|
tree
2015-06-22
Erik
L
indahl
Fix compiler warning
s
in cmake tests
commit
|
commitdiff
|
tree
2015-06-22
Erik Lin
d
ahl
Use
MPI_THREAD_FUNNELED
w
h
e
n available
commit
|
commitdiff
|
tree
2015-06-22
Roland
S
chulz
Fix cmak
e
3
.
1 war
n
ings with MSVC
commit
|
commitdiff
|
tree
2015-06-22
Erik
L
indahl
Fix segfault
in random acc
e
ss
XTC searching
commit
|
commitdiff
|
tree
2015-06-22
Er
i
k Linda
h
l
F
ix argument or
d
er
er
r
o
r
for g_
r
msdist
commit
|
commitdiff
|
tree
2015-06-22
Erik Lindahl
F
ix
g
ro errors
w
ith PDB in
s
er
t
ion c
o
des
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Replaced hardware threads b
y
logical c
o
res in ou
t
put
commit
|
commitdiff
|
tree
2015-06-21
Szilard Pall
fix CPU core oversu
b
scription d
e
tection
commit
|
commitdiff
|
tree
2015-06-20
Erik Linda
h
l
Updated docs for g_g
y
rate
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
Fix po
t
ential
buffer overflo
w
in
pdb2gmx
commit
|
commitdiff
|
tree
2015-06-20
Eri
k
Linda
h
l
Dis
a
llow infini
t
e ep
s
il
o
n with P
M
E or GB
.
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
Remove GMX_MA
X
_M
P
I_THREADS
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
Fix
reproducibility bug in fft
5
d
commit
|
commitdiff
|
tree
2015-06-20
Erik Lindahl
H
andl
e
multidir/multisim wi
t
h singl
e
argument correctly
commit
|
commitdiff
|
tree
2015-06-18
B
erk Hess
Reduced
the
cost of the pull com
m
unication
commit
|
commitdiff
|
tree
2015-06-18
Mark Ab
r
aham
Fix typ
o
in GMX_BUILD
_
OWN_FFTW
m
es
s
ag
e
commit
|
commitdiff
|
tree
2015-06-17
Teemu Murtol
a
Minor clean up fo
r
refdata
.
*
commit
|
commitdiff
|
tree
2015-06-17
Teemu
Mur
t
ola
Impr
o
ve log
i
c for automatic s
e
l
ection names
commit
|
commitdiff
|
tree
2015-06-17
Berk Hes
s
R
e
factored pu
l
l data structures
commit
|
commitdiff
|
tree
2015-06-16
Mark Abraham
Stop pe
o
ple installing
i
nto the bu
i
ld tre
e
commit
|
commitdiff
|
tree
2015-06-16
Erik
Lindahl
F
ix CUDA version info in NVML applica
t
ion cloc
k
warni
n
g
commit
|
commitdiff
|
tree
2015-06-16
Erik Li
n
dahl
Add membrane embedding docs
commit
|
commitdiff
|
tree
2015-06-16
Berk
H
ess
Added missing DD
c
ycle countin
g
commit
|
commitdiff
|
tree
2015-06-16
Er
i
k Lin
d
ahl
Upd
a
ted FFTW
r
ecommendation
s
in install-g
u
ide
.
commit
|
commitdiff
|
tree
2015-06-16
Mark Abraham
Move cod
e
for managing
mdrun
-
cpi
a
nd -app
e
nd
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Automated the -g
p
u_id op
t
i
o
n
commit
|
commitdiff
|
tree
2015-06-16
E
r
ik Lind
a
hl
Fix segfault with timer reset and -
n
b
cpu
commit
|
commitdiff
|
tree
2015-06-16
Erik Li
n
dahl
Avoid warning about affinity on Blu
e
Gene, reduce warnings
commit
|
commitdiff
|
tree
2015-06-16
Mark
A
braham
F
i
x pa
i
r
s_nb not
recognized as
part of
m
oleculetype
commit
|
commitdiff
|
tree
2015-06-16
Mark Abraham
Ad
d
un
i
t t
e
sts for Arra
y
Ref
commit
|
commitdiff
|
tree
2015-06-16
Roland Schulz
Fix warning in uncru
s
tify
commit
|
commitdiff
|
tree
2015-06-15
Erik Lindahl
Fix
O
S
X
FF
T
W
build f
a
ilures introduc
e
d 86
a
7
7
2
commit
|
commitdiff
|
tree
2015-06-15
Erik Linda
h
l
F
i
x
e
d SIMD detection
and
f
la
g
s c
o
mmon for IBM
archs
commit
|
commitdiff
|
tree
2015-06-13
B
erk H
e
ss
Hardwa
r
e repor
t
ing now covers
a
ll nodes
commit
|
commitdiff
|
tree
2015-06-12
Teemu
Murtola
Update help
output
commit
|
commitdiff
|
tree
2015-06-12
Teemu
M
urtola
Ini
t
ial docs
for J
e
nki
n
s integr
a
tion
commit
|
commitdiff
|
tree
2015-06-12
Teemu M
u
r
t
ola
In
i
tial build
system
d
ocumentation
i
n dev guid
e
commit
|
commitdiff
|
tree
2015-06-12
Teemu
M
urtol
a
Improve Jenki
n
s docs build
commit
|
commitdiff
|
tree
2015-06-11
Ma
r
k
Abraham
Merge "Merge branch release-4-
6
i
n
to rele
a
se-5-0" into
.
.
.
commit
|
commitdiff
|
tree
2015-06-11
Mark Abraham
Handle
timing better in Jen
k
i
n
s
commit
|
commitdiff
|
tree
2015-06-11
Teemu Murtola
Sc
r
i
pt f
o
r J
e
nkin
s
docume
n
tation build
commit
|
commitdiff
|
tree
2015-06-11
M
ar
k
Abraham
Clean up
vsit
e
interaction clean-up c
o
de
commit
|
commitdiff
|
tree
2015-06-09
Mark Abraham
Do
c
ument li
m
itatio
n
s
of t
r
jconv -dump
commit
|
commitdiff
|
tree
2015-06-09
Te
e
mu Mur
t
ola
Misc
.
im
p
rovem
e
nts t
o
docs build system
commit
|
commitdiff
|
tree
2015-06-09
Te
e
m
u Murtola
Improve us
e
r guide text for
c
o
mma
n
d
line inte
r
f
a
ce
commit
|
commitdiff
|
tree
2015-06-07
Erik Lindahl
Fix out-of-range integ
e
r literals for threefry
commit
|
commitdiff
|
tree
2015-06-06
Sz
i
l
ard P
a
l
l
Op
t
imize atomic accum
u
l
atio
n
in
C
UDA
N
B
kern
e
l
commit
|
commitdiff
|
tree
2015-06-06
Roland Schu
l
z
Us
e
stat t
o
check tha
t
pat
h
s
are equ
i
valent
commit
|
commitdiff
|
tree
2015-06-05
R
o
land
Schulz
Reenab
l
e lin
c
s/bonded SI
M
D for ICC on Windows
commit
|
commitdiff
|
tree
2015-06-05
Mark Abraham
R
e
move gmx_simd_che
c
k_an
d
_rese
t
_
overflow
commit
|
commitdiff
|
tree
2015-06-05
Berk Hess
D
on
'
t use PM
E
ranks with GPUs and
-npme=-1
commit
|
commitdiff
|
tree
2015-06-04
Mark Abrah
a
m
Fix na
m
ing from "Gromacs" to "
G
ROMA
C
S"
commit
|
commitdiff
|
tree
2015-06-04
E
rik Lind
a
hl
Mo
r
e
new quotes
commit
|
commitdiff
|
tree
2015-06-04
Teemu
Murtola
Fix
pote
n
tial FP
E
in sel
e
ction tests
commit
|
commitdiff
|
tree
2015-06-04
Teemu Murtola
Suppor
t
r
s
t tables in tool he
l
p
texts
commit
|
commitdiff
|
tree
2015-06-03
Roland Schulz
Use
stack buffer for LINCS&
b
ond
e
d
gather/scatt
e
r
commit
|
commitdiff
|
tree
2015-06-02
Ros
s
e
n Apostolov
Conve
r
ted ran
d
o
m mod
u
l
e
to C++
.
commit
|
commitdiff
|
tree
2015-05-28
T
eemu Murtola
Add
i
t
i
on
a
l sel
e
ction
e
xa
m
ples
commit
|
commitdiff
|
tree
2015-05-27
B
e
r
k Hess
R
efac
t
oring of PME load b
a
lanci
n
g
commit
|
commitdiff
|
tree
2015-05-27
Rossen Apo
s
tolov
C
o
n
verted
p
ulling code to
C
++
.
commit
|
commitdiff
|
tree
2015-05-26
M
ark
A
b
raham
A
void po
s
sible flo
a
t
ing-poin
t
exception
commit
|
commitdiff
|
tree
2015-05-24
Teemu Murtola
I
n
cl
u
de selec
t
ion keyword details i
n
us
e
r gui
d
e
commit
|
commitdiff
|
tree
2015-05-23
Mark Abraha
m
Fix misuse of gmx_
s
imd_check_and_reset_overflo
w
commit
|
commitdiff
|
tree
2015-05-22
Teemu M
u
rtola
Bas
e
to get all 'gm
x
help'
c
ontents to user guide
commit
|
commitdiff
|
tree
2015-05-22
Teemu M
u
rtola
Avoid crash
w
i
th e
m
p
t
y
r
e
fer
e
nce for 'sam
e
as' select
i
o
n
commit
|
commitdiff
|
tree
2015-05-22
Teemu M
u
rtola
Add subsection depth to HelpWriter
C
ontext
commit
|
commitdiff
|
tree
2015-05-22
Teem
u
Mu
r
tola
Add note about
a
tom
order in selections
commit
|
commitdiff
|
tree
2015-05-21
Teemu
Murtol
a
Restructure CommandLineM
o
duleManager tests
commit
|
commitdiff
|
tree
2015-05-21
Mark Abraham
Add i
n
t
e
gration test for empty
domain
commit
|
commitdiff
|
tree
2015-05-20
Teemu Murt
o
la
F
ix depende
n
cies for regression test cust
o
m
target
commit
|
commitdiff
|
tree
2015-05-20
Teemu Mur
t
ola
S
o
me
t
ests for
'gmx
h
elp -
e
x
port
rst
'
commit
|
commitdiff
|
tree
2015-05-19
Mark
Abra
h
am
Refactor FFTW setup
commit
|
commitdiff
|
tree
2015-05-18
Teem
u
M
u
rtol
a
M
erge "Merge
b
r
a
n
c
h
origin/
r
e
l
ease-5-0"
commit
|
commitdiff
|
tree
2015-05-17
Er
i
k
Lindahl
Added
h
acks for SIMD
rvec/load store in lincs & bo
n
deds
commit
|
commitdiff
|
tree
2015-05-17
Teemu Mu
r
tola
Move a few de
f
ines
t
o bu
i
ldinfo
.
h
commit
|
commitdiff
|
tree
2015-05-16
Be
r
k Hess
LINCS thread tas
k
s
c
an now be
independent
commit
|
commitdiff
|
tree
2015-05-16
Mark Abraham
Sup
p
ress GCC5 warnings with interna
l
B
o
os
t
commit
|
commitdiff
|
tree
2015-05-16
Magnus Lundborg
TNG version 1
.
7
.
5
commit
|
commitdiff
|
tree
2015-05-16
Alexey Shvetsov
Make b
o
nd-a
t
omtypes
c
a
se sensiti
v
e
commit
|
commitdiff
|
tree
2015-05-14
Mark Abraham
F
i
x
own-FFTW
b
u
i
ld
commit
|
commitdiff
|
tree
2015-05-13
Teemu Murtola
R
e
mo
v
e r
e
ma
i
n
i
ng old-html content
commit
|
commitdiff
|
tree
2015-05-13
Be
r
k Hess
Fix
segv in g_covar
commit
|
commitdiff
|
tree
2015-05-13
Szilard
P
a
l
l
Fix
auto-downloa
d
ed regression tes
t
execution
commit
|
commitdiff
|
tree
2015-05-13
Ro
l
and Sc
h
u
lz
Facili
t
ate linkin
g
of
s
ta
t
ic binaries
commit
|
commitdiff
|
tree
2015-05-12
Mark Abrah
a
m
Fix uninitialized
f
ields in gromp
p
t_state
commit
|
commitdiff
|
tree
2015-05-11
Mark Abraham
Work ar
o
und
g
cc 5 warn
i
ngs
w
ith Google
Te
s
t
commit
|
commitdiff
|
tree
next