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schwede
ProMod3
Commits
5f3efd5a
Commit
5f3efd5a
authored
8 years ago
by
Gerardo Tauriello
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Use new ost.mol.mm functionality to check for CPU platform.
parent
b6407e14
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modelling/pymod/_pipeline.py
+8
-9
8 additions, 9 deletions
modelling/pymod/_pipeline.py
with
8 additions
and
9 deletions
modelling/pymod/_pipeline.py
+
8
−
9
View file @
5f3efd5a
...
...
@@ -121,23 +121,22 @@ def _SetupMmSimulation(model, force_fields):
if
lig_ent
.
residue_count
>
0
:
_AddLigands
(
ent
,
top
,
lig_ent
,
settings
,
force_fields
)
# finally set up the simulation
try
:
# use fast CPU platform by default
# NOTE: settings.platform only relevant for mm.Simulation!
settings
.
platform
=
mm
.
Platform
.
CPU
# use fast CPU platform by default
# NOTE: settings.platform only relevant for mm.Simulation!
settings
.
platform
=
mm
.
Platform
.
CPU
if
mm
.
Simulation
.
IsPlatformAvailable
(
settings
):
num_cpu_threads
=
os
.
getenv
(
'
PM3_OPENMM_CPU_THREADS
'
)
if
num_cpu_threads
is
None
:
settings
.
cpu_properties
[
"
CpuThreads
"
]
=
"
1
"
else
:
settings
.
cpu_properties
[
"
CpuThreads
"
]
=
num_cpu_threads
sim
=
mm
.
Simulation
(
top
,
ent
,
settings
)
except
RuntimeError
as
ex
:
ost
.
LogWarning
(
"
OpenMM failed to initialize with error: %s
"
%
str
(
ex
))
else
:
# switch to "mm.Platform.Reference" as fallback
settings
.
platform
=
mm
.
Platform
.
Reference
sim
=
mm
.
Simulation
(
top
,
ent
,
settings
)
ost
.
LogWarning
(
"
Switched to slower reference platform of OpenMM!
"
)
# finally set up the simulation
sim
=
mm
.
Simulation
(
top
,
ent
,
settings
)
return
sim
def
_GetSimEntity
(
sim
):
...
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