From 607c21428454f0af11839cb8d72b76cba569a5d6 Mon Sep 17 00:00:00 2001 From: Zhenwen Dai Date: Mon, 7 Sep 2015 16:27:31 +0100 Subject: [PATCH] changed gpu interface for mpi --- GPy/kern/_src/psi_comp/rbf_psi_comp.py | 32 --------------- GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py | 25 ++++++------ GPy/kern/_src/psi_comp/sslinear_psi_comp.py | 2 +- GPy/kern/_src/psi_comp/ssrbf_psi_gpucomp.py | 24 +++++------ GPy/util/__init__.py | 1 - GPy/util/gpu_init.py | 44 +++++++++------------ GPy/util/linalg_gpu.py | 7 ---- 7 files changed, 46 insertions(+), 89 deletions(-) diff --git a/GPy/kern/_src/psi_comp/rbf_psi_comp.py b/GPy/kern/_src/psi_comp/rbf_psi_comp.py index 892eb1a0..735a354d 100644 --- a/GPy/kern/_src/psi_comp/rbf_psi_comp.py +++ b/GPy/kern/_src/psi_comp/rbf_psi_comp.py @@ -6,12 +6,6 @@ import numpy as np from GPy.util.caching import Cacher def psicomputations(variance, lengthscale, Z, variational_posterior, return_psi2_n=False): - """ - Z - MxQ - mu - NxQ - S - NxQ - gamma - NxQ - """ # here are the "statistics" for psi0, psi1 and psi2 # Produced intermediate results: # _psi1 NxM @@ -26,12 +20,6 @@ def psicomputations(variance, lengthscale, Z, variational_posterior, return_psi2 return psi0, psi1, psi2 def __psi1computations(variance, lengthscale, Z, mu, S): - """ - Z - MxQ - mu - NxQ - S - NxQ - gamma - NxQ - """ # here are the "statistics" for psi1 # Produced intermediate results: # _psi1 NxM @@ -46,12 +34,6 @@ def __psi1computations(variance, lengthscale, Z, mu, S): return _psi1 def __psi2computations(variance, lengthscale, Z, mu, S): - """ - Z - MxQ - mu - NxQ - S - NxQ - gamma - NxQ - """ # here are the "statistics" for psi2 # Produced intermediate results: # _psi2 MxM @@ -86,13 +68,6 @@ def psiDerivativecomputations(dL_dpsi0, dL_dpsi1, dL_dpsi2, variance, lengthscal return dL_dvar, dL_dlengscale, dL_dZ, dL_dmu, dL_dS def _psi1compDer(dL_dpsi1, variance, lengthscale, Z, mu, S): - """ - dL_dpsi1 - NxM - Z - MxQ - mu - NxQ - S - NxQ - gamma - NxQ - """ # here are the "statistics" for psi1 # Produced intermediate results: dL_dparams w.r.t. psi1 # _dL_dvariance 1 @@ -118,13 +93,6 @@ def _psi1compDer(dL_dpsi1, variance, lengthscale, Z, mu, S): return _dL_dvar, _dL_dl, _dL_dZ, _dL_dmu, _dL_dS def _psi2compDer(dL_dpsi2, variance, lengthscale, Z, mu, S): - """ - Z - MxQ - mu - NxQ - S - NxQ - gamma - NxQ - dL_dpsi2 - MxM - """ # here are the "statistics" for psi2 # Produced the derivatives w.r.t. psi2: # _dL_dvariance 1 diff --git a/GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py b/GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py index 03c4c8af..b3de8363 100644 --- a/GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py +++ b/GPy/kern/_src/psi_comp/rbf_psi_gpucomp.py @@ -7,13 +7,6 @@ from ....util.caching import Cache_this from . import PSICOMP_RBF from ....util import gpu_init -try: - import pycuda.gpuarray as gpuarray - from pycuda.compiler import SourceModule - from ....util.linalg_gpu import sum_axis -except: - pass - gpu_code = """ // define THREADNUM @@ -242,6 +235,10 @@ gpu_code = """ class PSICOMP_RBF_GPU(PSICOMP_RBF): def __init__(self, threadnum=256, blocknum=30, GPU_direct=False): + from pycuda.compiler import SourceModule + from ....util.gpu_init import initGPU + initGPU() + self.GPU_direct = GPU_direct self.gpuCache = None @@ -264,7 +261,8 @@ class PSICOMP_RBF_GPU(PSICOMP_RBF): memo[id(self)] = s return s - def _initGPUCache(self, N, M, Q): + def _initGPUCache(self, N, M, Q): + import pycuda.gpuarray as gpuarray if self.gpuCache == None: self.gpuCache = { 'l_gpu' :gpuarray.empty((Q,),np.float64,order='F'), @@ -320,13 +318,14 @@ class PSICOMP_RBF_GPU(PSICOMP_RBF): def get_dimensions(self, Z, variational_posterior): return variational_posterior.mean.shape[0], Z.shape[0], Z.shape[1] - @Cache_this(limit=1, ignore_args=(0,)) - def psicomputations(self, variance, lengthscale, Z, variational_posterior): + @Cache_this(limit=5, ignore_args=(0,)) + def psicomputations(self, kern, Z, variational_posterior, return_psi2_n=False): """ Z - MxQ mu - NxQ S - NxQ """ + variance, lengthscale = kern.variance, kern.lengthscale N,M,Q = self.get_dimensions(Z, variational_posterior) self._initGPUCache(N,M,Q) self.sync_params(lengthscale, Z, variational_posterior.mean, variational_posterior.variance) @@ -355,8 +354,10 @@ class PSICOMP_RBF_GPU(PSICOMP_RBF): else: return psi0, psi1_gpu.get(), psi2_gpu.get() - @Cache_this(limit=1, ignore_args=(0,1,2,3)) - def psiDerivativecomputations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, variance, lengthscale, Z, variational_posterior): + @Cache_this(limit=5, ignore_args=(0,2,3,4)) + def psiDerivativecomputations(self, kern, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior): + variance, lengthscale = kern.variance, kern.lengthscale + from ....util.linalg_gpu import sum_axis ARD = (len(lengthscale)!=1) N,M,Q = self.get_dimensions(Z, variational_posterior) diff --git a/GPy/kern/_src/psi_comp/sslinear_psi_comp.py b/GPy/kern/_src/psi_comp/sslinear_psi_comp.py index d431cd61..7e9b4fdc 100644 --- a/GPy/kern/_src/psi_comp/sslinear_psi_comp.py +++ b/GPy/kern/_src/psi_comp/sslinear_psi_comp.py @@ -9,7 +9,7 @@ from ....util.linalg import tdot import numpy as np -def psicomputations(variance, Z, variational_posterior): +def psicomputations(variance, Z, variational_posterior, return_psi2_n=False): """ Compute psi-statistics for ss-linear kernel """ diff --git a/GPy/kern/_src/psi_comp/ssrbf_psi_gpucomp.py b/GPy/kern/_src/psi_comp/ssrbf_psi_gpucomp.py index 1a9d2058..46f4a06e 100644 --- a/GPy/kern/_src/psi_comp/ssrbf_psi_gpucomp.py +++ b/GPy/kern/_src/psi_comp/ssrbf_psi_gpucomp.py @@ -6,14 +6,7 @@ The module for psi-statistics for RBF kernel for Spike-and-Slab GPLVM import numpy as np from ....util.caching import Cache_this from . import PSICOMP_RBF -from ....util import gpu_init -try: - import pycuda.gpuarray as gpuarray - from pycuda.compiler import SourceModule - from ....util.linalg_gpu import sum_axis -except: - pass gpu_code = """ // define THREADNUM @@ -292,6 +285,11 @@ gpu_code = """ class PSICOMP_SSRBF_GPU(PSICOMP_RBF): def __init__(self, threadnum=128, blocknum=15, GPU_direct=False): + + from pycuda.compiler import SourceModule + from ....util.gpu_init import initGPU + initGPU() + self.GPU_direct = GPU_direct self.gpuCache = None @@ -314,7 +312,8 @@ class PSICOMP_SSRBF_GPU(PSICOMP_RBF): memo[id(self)] = s return s - def _initGPUCache(self, N, M, Q): + def _initGPUCache(self, N, M, Q): + import pycuda.gpuarray as gpuarray if self.gpuCache == None: self.gpuCache = { 'l_gpu' :gpuarray.empty((Q,),np.float64,order='F'), @@ -377,12 +376,13 @@ class PSICOMP_SSRBF_GPU(PSICOMP_RBF): return variational_posterior.mean.shape[0], Z.shape[0], Z.shape[1] @Cache_this(limit=1, ignore_args=(0,)) - def psicomputations(self, variance, lengthscale, Z, variational_posterior): + def psicomputations(self, kern, Z, variational_posterior, return_psi2_n=False): """ Z - MxQ mu - NxQ S - NxQ """ + variance, lengthscale = kern.variance, kern.lengthscale N,M,Q = self.get_dimensions(Z, variational_posterior) self._initGPUCache(N,M,Q) self.sync_params(lengthscale, Z, variational_posterior.mean, variational_posterior.variance, variational_posterior.binary_prob) @@ -409,8 +409,10 @@ class PSICOMP_SSRBF_GPU(PSICOMP_RBF): else: return psi0, psi1_gpu.get(), psi2_gpu.get() - @Cache_this(limit=1, ignore_args=(0,1,2,3)) - def psiDerivativecomputations(self, dL_dpsi0, dL_dpsi1, dL_dpsi2, variance, lengthscale, Z, variational_posterior): + @Cache_this(limit=1, ignore_args=(0,2,3,4)) + def psiDerivativecomputations(self, kern, dL_dpsi0, dL_dpsi1, dL_dpsi2, Z, variational_posterior): + variance, lengthscale = kern.variance, kern.lengthscale + from ....util.linalg_gpu import sum_axis ARD = (len(lengthscale)!=1) N,M,Q = self.get_dimensions(Z, variational_posterior) diff --git a/GPy/util/__init__.py b/GPy/util/__init__.py index a21dc84e..6919f1a8 100644 --- a/GPy/util/__init__.py +++ b/GPy/util/__init__.py @@ -15,6 +15,5 @@ from . import caching from . import diag from . import initialization from . import multioutput -from . import linalg_gpu from . import parallel diff --git a/GPy/util/gpu_init.py b/GPy/util/gpu_init.py index 26dff0b3..0c496db3 100644 --- a/GPy/util/gpu_init.py +++ b/GPy/util/gpu_init.py @@ -16,33 +16,27 @@ try: except: pass -try: - if MPI_enabled and MPI.COMM_WORLD.size>1: - from .parallel import get_id_within_node - gpuid = get_id_within_node() - import pycuda.driver - pycuda.driver.init() - if gpuid>=pycuda.driver.Device.count(): - print('['+MPI.Get_processor_name()+'] more processes than the GPU numbers!') - #MPI.COMM_WORLD.Abort() - raise - gpu_device = pycuda.driver.Device(gpuid) - gpu_context = gpu_device.make_context() - gpu_initialized = True - else: - import pycuda.autoinit - gpu_initialized = True -except: - pass -try: - from scikits.cuda import cublas - import scikits.cuda.linalg as culinalg - culinalg.init() - cublas_handle = cublas.cublasCreate() -except: - pass +def initGPU(): + try: + if MPI_enabled and MPI.COMM_WORLD.size>1: + from .parallel import get_id_within_node + gpuid = get_id_within_node() + import pycuda.driver + pycuda.driver.init() + if gpuid>=pycuda.driver.Device.count(): + print('['+MPI.Get_processor_name()+'] more processes than the GPU numbers!') + raise + gpu_device = pycuda.driver.Device(gpuid) + gpu_context = gpu_device.make_context() + gpu_initialized = True + else: + import pycuda.autoinit + gpu_initialized = True + except: + pass + def closeGPU(): if gpu_context is not None: gpu_context.detach() diff --git a/GPy/util/linalg_gpu.py b/GPy/util/linalg_gpu.py index cba09dd3..db1c5317 100644 --- a/GPy/util/linalg_gpu.py +++ b/GPy/util/linalg_gpu.py @@ -61,12 +61,5 @@ try: except: pass -try: - import scikits.cuda.linalg as culinalg - from scikits.cuda import cublas - from scikits.cuda.cula import culaExceptions -except: - pass -