[slurm-users] Fwd: gres/gpu: count changed for node node002 from 0 to 1
Robert Kudyba
rkudyba at fordham.edu
Sat Mar 14 19:09:52 UTC 2020
I posted this yesterday and this does appear to be related to a specific
job. Note this error: "gres/gpu: count changed for node node002 from 0 to
1" Could it be misleading? What could cause the node to drain? Here are the
contents of the user's SBATCH file. Could the piping having an effect here?
#!/bin/sh
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --mail-type=ALL
#SBATCH --gres=gpu:1
#SBATCH --job-name=$1sequentialBlur_squeezenet_training_imagewoof_crossval
module purge
module load gcc5 cuda10.0
module load openmpi/cuda/64
module load pytorch-py36-cuda10.1-gcc/1.3.1
module load ml-pythondeps-py36-cuda10.1-gcc/3.0.0
python3.6 SequentialBlur_untrained.py squeezenet 100 imagewoof $1 | tee
squeeze_100_imwoof_seq_longtrain_cv_$1.txt
Here is the script contents:
# Banks 1978 paper:
# 1 month: 2.4 cyc/deg
# 2 month: 2.8 cyc/deg
# 3 month: 4 cyc/deg
# 224 pixels:
# 20 deg -> 11 pix in deg; 4.6 pix blur; 4 pix blur; 2.8 pix blur
# 4 deg -> 56 pix in deg; 23 pix blur (1 mo); 20 pix blur (2 mo); 14 pix
blur (3 mo)
import torch
import torchvision
import torchvision.transforms as transforms
from torchvision import models
import torchvision.datasets
import matplotlib.pyplot as plt
import numpy as np
import matplotlib.pyplot as plt
import numpy as np
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import os
import sys
import scipy
from torch.utils.data.sampler import SubsetRandomSampler
import h5py
args = sys.argv
modelType = args[1] # 'alexnet', 'squeezenet', 'vgg16'
numEpochs = args[2] # int
image_set = str(args[3]) # 'imagewoof', 'imagenette'
block_call = args[4] # int {0:4}
# Example call:
# python3 alexnet 100 imagenette 1
def
get_train_valid_loader(data_dir,block,augment=0,random_seed=69420,valid_size=0.2,shuffle=False,
show_sample=False,num_workers=4, pin_memory=False, batch_size=128):
# valid_size gotta be in [0,1]
# block must be an int between 0:(1/valid_size) (0:4 for
valid_size==0.2)
transform = transforms.Compose([
transforms.Resize(256),
transforms.CenterCrop(224),
transforms.ToTensor(),
transforms.Normalize(
mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]
)])
train_dataset =
torchvision.datasets.ImageFolder(root=data_dir,transform=transform)
valid_dataset =
torchvision.datasets.ImageFolder(root=data_dir,transform=transform)
num_train = len(train_dataset)
indices = list(range(num_train))
split = int(np.floor(valid_size * num_train))
split1 = int(np.floor(block*split))
split2 = int(np.floor((block+1)*split))
# if shuffle:
np.random.seed(100)
np.random.shuffle(indices)
valid_idx = indices[split1:split2]
train_idx = np.append(indices[:split1],indices[split2:])
train_idx = train_idx.astype('int32')
if block != 0:
for b in range(block):
indices = [indices[(i + split) % len(indices)] for
i, x in enumerate(indices)]
# train_idx, valid_idx = indices[split:], indices[:split]
train_sampler = SubsetRandomSampler(train_idx)
# train_sampler = torch.utils.data.Subset(dataset, indices)
valid_sampler = SubsetRandomSampler(valid_idx)
train_loader = torch.utils.data.DataLoader(
train_dataset, sampler=train_sampler, batch_size=batch_size,
num_workers=num_workers, pin_memory=pin_memory,
)
valid_loader = torch.utils.data.DataLoader(
valid_dataset, sampler=valid_sampler, batch_size=batch_size,
num_workers=num_workers, pin_memory=pin_memory,
)
return (train_loader, valid_loader)
transform = transforms.Compose([
transforms.Resize(256),
transforms.CenterCrop(224),
transforms.ToTensor(),
transforms.Normalize(
mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]
)])
blurTypes = ['gaussian']
data_dir = "/path/to/dir/" + image_set + "-320_blur/"
classes = []
for directory, subdirectories, files in os.walk(data_dir):
for file in files:
if directory.split("\\")[-1] not in classes:
classes.append(directory.split("\\")[-1])
criterion = nn.CrossEntropyLoss()
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
def train():
for epoch in range(int(numEpochs)):
prev_loss = 100000.0
running_loss = 0.0
for i, data in enumerate(trainloader, 0):
# get the inputs; data is a list of [inputs, labels]
inputs, labels = data
inputs = inputs.to(device)
labels = labels.to(device)
# zero the parameter gradients
optimizer.zero_grad()
# forward + backward + optimize
outputs = net(inputs)
loss = criterion(outputs, labels)
loss.backward()
optimizer.step()
running_loss += loss.item()
if epoch % 10 == 9:
print('[%d, %5d] loss: %.3f' %
(epoch + 1, i + 1, running_loss / 100))
allAccs = []
for blurType in blurTypes: # multiple types of blur
print(blurType)
print('-' * 10)
# for block in range(5):
block = int(block_call)
print("\nFOLD " + str(block+1) + ":")
for i in range(5):
if i == 0:
blurLevels = [23, 11, 5, 3, 1]
elif i == 1:
blurLevels = [11, 5, 3, 1]
elif i == 2:
blurLevels = [5, 3, 1]
elif i == 3:
blurLevels = [3, 1]
elif i == 4:
blurLevels = [1]
if modelType == 'vgg16':
net = torchvision.models.vgg16(pretrained=False)
num_ftrs = net.classifier[6].in_features
net.classifier[6] = nn.Linear(num_ftrs,
len(classes))
elif modelType == 'alexnet':
net = torchvision.models.alexnet(pretrained=False)
num_ftrs = net.classifier[6].in_features
net.classifier[6] = nn.Linear(num_ftrs,
len(classes))
else:
net =
torchvision.models.squeezenet1_1(pretrained=False)
net.classifier[1] = nn.Conv2d(512, len(classes),
kernel_size=(1, 1), stride=(1, 1))
net.num_classes = len(classes)
optimizer = optim.SGD(net.parameters(), lr=0.001,
momentum=0.9)
net = net.to(device)
for i in range(len(blurLevels)): #5 levels of blur: 1, 3,
5, 11, 23
mult = blurLevels[i]
trainloader, validloader =
get_train_valid_loader(data_dir=data_dir + blurType + '/' + image_set +
'-320_' + str(mult) + '/train',
block=block,shuffle=False,num_workers=0,batch_size=128)
print('Start training on blur window of ' +
str(mult))
train()
print('Finished Training on ' + blurType + ' with
blur window of ' + str(mult))
accs = []
permBlurLevels = [23, 11, 5, 3, 1]
for j in range(len(permBlurLevels)):
tempMult = permBlurLevels[j]
correct = 0
total = 0
# newTestSet =
torchvision.datasets.ImageFolder(root=data_dir + blurType + '/' + image_set
+ '-320_' +
# str(tempMult) + '/val',
# transform=transform)
# newTestLoader =
torch.utils.data.DataLoader(newTestSet, batch_size=128,
# shuffle=True, num_workers=0)
t2, validloader2 =
get_train_valid_loader(data_dir=data_dir + blurType + '/' + image_set +
'-320_' + str(mult) + '/train',
block=block,shuffle=False,num_workers=0,batch_size=128)
with torch.no_grad():
for data in validloader2:
images, labels = data
images = images.to(device)
labels = labels.to(device)
outputs = net(images)
_, predicted =
torch.max(outputs.data, 1)
total += labels.size(0)
correct += (predicted ==
labels).sum().item()
acc = 100 * correct / total
print('Accuracy: %f %%' % (acc))
accs.append(acc)
allAccs.append(accs)
---------- Forwarded message ---------
From: Robert Kudyba <rkudyba at fordham.edu>
Date: Fri, Mar 13, 2020 at 11:36 AM
Subject: gres/gpu: count changed for node node002 from 0 to 1
To: Slurm User Community List <slurm-users at lists.schedmd.com>
We're running slurm-17.11.12 on Bright Cluster 8.1 and our node002 keeps
going into a draining state:
sinfo -a
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
defq* up infinite 1 drng node002
info -N -o "%.20N %.15C %.10t %.10m %.15P %.15G %.35E"
NODELIST CPUS(A/I/O/T) STATE MEMORY PARTITION
GRES REASON
node001 9/15/0/24 mix 191800 defq*
gpu:1 none
node002 1/0/23/24 drng 191800 defq*
gpu:1 gres/gpu count changed and jobs are
node003 1/23/0/24 mix 191800 defq*
gpu:1 none
Node of the nodes have a separate slurm.conf file, it's all shared from the
head node. What else could be causing this?
[2020-03-13T08:54:02.269] gres/gpu: count changed for node node002 from 0
to 1
[2020-03-13T08:54:02.269] error: Setting node node002 state to DRAIN
[2020-03-13T08:54:02.269] drain_nodes: node node002 state set to DRAIN
[2020-03-13T08:54:02.269] error: _slurm_rpc_node_registration node=node002:
Invalid argument
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