I am running a pipeline on multiple images. The pipeline consist of reading the images from file system, doing so processing on each of them, then saving the images to file system. However the dask worker fails due to MemoryError.
Is there a way to assure the dask workers don't load too many images in memory? i.e. Wait until there is enough space on a worker before starting the processing pipeline on a new image.
I have one scheduler and 40 workers with 4 cores, 15GB ram and running Centos7. I am trying to process 125 images in a batch; each image is fairly large but small enough to fit on a worker; around 3GB require for the whole process.
I tried to process a smaller amount of images and it works great.
EDITED
from dask.distributed import Client, LocalCluster
# LocalCluster is used to show the config of the workers on the actual cluster
client = Client(LocalCluster(n_workers=2, resources={'process': 1}))
paths = ['list', 'of', 'paths']
# Read the file data from each path
data = client.map(read, path, resources={'process': 1)
# Apply foo to the data n times
for _ in range(n):
data = client.map(foo, x, resources={'process': 1)
# Save the processed data
data.map(save, x, resources={'process': 1)
# Retrieve results
client.gather(data)
I expected the images to be process as space was available on the workers but it seems like the images are all loaded simultaneously on the different workers.
EDIT:
My issues is that all task get assigned to workers and they don't have enough memory. I found how to limit the number of task a worker handle at a single moment [https://distributed.readthedocs.io/en/latest/resources.html#resources-are-applied-separately-to-each-worker-process](see here).
However, with that limit, when I execute my task they all finish the read step, then the process step and finally the save step. This is an issues since the image are spilled to disk.
Would there be a way to make every task finish before starting a new one?
e.g. on Worker-1: read(img1)->process(img1)->save(img1)->read(img2)->...
Dask does not generally know how much memory a task will need, it can only know the size of the outputs, and that, only once they are finished. This is because Dask simply executes a pthon function and then waits for it to complete; but all osrts of things can happen within a python function. You should generally expect as many tasks to begin as you have available worker cores - as you are finding.
If you want a smaller total memory load, then your solution should be simple: have a small enough number of workers, so that if all of them are using the maximum memory that you can expect, you still have some spare in the system to cope.
To EDIT: you may want to try running optimize on the graph before submission (although this should happen anyway, I think), as it sounds like your linear chains of tasks should be "fused". http://docs.dask.org/en/latest/optimize.html
Related
I have some function which uses image processing functions which are itself multithreaded. I distribute many of those function calls on a dask cluster.
First, I started a scheduler on a host: dask-scheduler. The I started the workers: dask-worker --nthreads 1 --memory-limit 0.9 tcp://scheduler:8786.
The python code looks similar to this:
import SimpleITK as sitk
def func(filename):
sitk.ProcessObject.SetGlobalDefaultNumberOfThreads(4) # limit to four threads
img = sitk.ReadImage(filename)
# Do more stuff and store resulting image
# SimpleITK is already multithreaded
return 'someresult'
# [...]
from distributed import Client
client = Client('tcp://scheduler:8786')
futures = client.map(func, ['somefile', 'someotherfile'])
for result in client.gather(futures):
print(result)
Right now, I have to set the number of threads for each worker to one, in order not to overcommit the CPU on the worker node. But in some cases it makes sense to limit the number of cores used by SimpleITK, because the gain is not so high. Instead, I could run multiple function calls in parallel on the same host.
But in that case I would have to calculate all the core usages by hand.
Ideally, I would like to set an arbitrary number of cores each function can use and dask should decide how many parallel functions invocations are started on each node, given the number of available threads. I.e. is it possible to specify the number of threads a function will use?
No, Dask is not able to either limit the number of threads spawned by some function, and doesn't attempt to measure this either.
The only thing I could think you might want to do is use Dask's abstract rsources, where you control how much of each labelled quantity is available per worker and how much each task needs to run.
futures = client.map(func, ['somefile', 'someotherfile'], resources=...)
I don't see an obvious way to assign resources to workers using Cluster() (i.e., the default LocalCluster), you may need to use the CLI.
I'm using a vanilla Dask-Kubernetes setup with two workers and one scheduler to iterate over the lines of some JSON file (and apply some functions which don't appear here for simplicity). I see only one worker ever working, where I'd expect to see two of them, instead.
Hoping that repartitioning would help I've experimented with different values for bag.repartition(num) which return different numbers of lines, but they don't change anything about the worker imbalance and memory consumption concentrating only on one worker.
I think I don't understand the correlation between partitions and workers, and I could not find anything in the Dask documentation about it. Any help or pointers are highly welcome!
import dask.bag as db
def grep_buildings():
base = "https://usbuildingdata.blob.core.windows.net/usbuildings-v1-1/"
b = db.text.read_text(f"{base}/Alabama.zip")
# b = b.repartition(2)
lines = b.take(3_000_000)
return lines
len(grep_buildings())
In your example, you are opening on file, and it is compressed
db.text.read_text(f"{base}/Alabama.zip")
Dask is able to open and process multiple files in parallel, with at least one partition per file. Dask is also able to split a single file into chunks (the blocksize parameter); but this only works for uncompressed data. The reason is, that for whole-file compression methods, the only way to get to some point in the uncompressed stream is to read from the start, so every partition would read most of the data.
Finally, repartition doesn't help you when you start with a single partition: you need to read that whole file before splitting the data into pieces for downstream tasks.
Our company is currently leveraging prefect.io for data workflows (ELT, report generation, ML, etc). We have just started adding the ability to do parallel task execution, which is powered by Dask. Our flows are executed using ephemeral AWS Fargate containers, which will use Dask LocalCluster with a certain number of workers, threads, processes passed into the LocalCluster object.
Our journey on Dask will look very much like this:
Continue using single machine LocalCluster until we out grow max cpu/memory allowed
When we out grow a single container, spawn additional worker containers on the initial container (a la dask-kubernetes) and join them to the LocalCluster.
We're currently starting with containers that have 256 cpu(.25 vCPU) and 512 memory and pinning the LocalCluster to 1 n_workers and 3 threads_per_worker to get a reasonable amount of parallelism. However, this really is guess work. 1 n_workers since its a machine with less than 1 vcpu and 3 threads because that doesn't sound crazy to me based on my previous experience running other python based applications in Fargate. This seems to work fine in a very simply example that just maps a function against a list of items.
RENEWAL_TABLES = [
'Activity',
'CurrentPolicyTermStaus',
'PolicyRenewalStatus',
'PolicyTerm',
'PolicyTermStatus',
'EndorsementPolicyTerm',
'PolicyLifeState'
]
RENEWAL_TABLES_PAIRS = [
(i, 1433 + idx) for idx, i in enumerate(RENEWAL_TABLES)
]
#task(state_handlers=[HANDLER])
def dummy_step():
LOGGER.info('Dummy Step...')
sleep(15)
#task(state_handlers=[HANDLER])
def test_map(table):
LOGGER.info('table: {}...'.format(table))
sleep(15)
with Flow(Path(__file__).stem, SCHEDULE, state_handlers=[HANDLER]) as flow:
first_step = dummy_step()
test_map.map(RENEWAL_TABLES_PAIRS).set_dependencies(upstream_tasks=[first_step])
I see no more than 3 tasks executed at once.
I would really like to understand how to best configure n_workers(single machinne), threads, processes as we expand the size of the single machine out to adding remote workers. I know it depends on my workload, but you could see a combination of things in a single flow where one task does an extract from a database to a csv and another task run a pandas computation. I have seen things online where it seems like it should be threads = number of cpus requested for the documentation, but it seems like you can still achieve parallelism with less than one cpu in Fargate.
Any feedback would be appreciated and could help others looking to leverage Dask in a more ephemeral nature.
Given that Fargate increments from .25 -> .50 -> 1 -> 2 -> 4 for vCPU, I think it’s safe to go with a 1 worker to 1 vcpu setup. However, would be helpful to understand how to choose a good upper limit for number of threads per worker given how Fargate vcpu allotment works.
I have a dynamic Dask Kubernetes cluster.
I want to load 35 parquet files (about 1.2GB) from Gcloud storage into Dask Dataframe then process it with apply() and after saving the result to parquet file to Gcloud.
During loading files from Gcloud storage, a cluster memory usage is increasing to about 3-4GB. Then workers (each worker has 2GB of RAM) are terminated/restarted and some tasks getting lost,
so cluster starts computing the same things in a circle.
I removed apply() operation and leave only read_parquet() to test
if my custom code causes a trouble, but the problem was the same, even with just single read_parquet() operation. This is a code:
client = Client('<ip>:8786')
client.restart()
def command():
client = get_client()
df = dd.read_parquet('gcs://<bucket>/files/name_*.parquet', storage_options={'token':'cloud'}, engine='fastparquet')
df = df.compute()
x = client.submit(command)
x.result()
Note: I'm submitting a single command function to run all necessary commands to avoid problems with gcsfs authentication inside a cluster
After some investigation, I understood that problem could be in .compute() which returns all data to a process, but this process (my command function) is running on a worker. Because of that, a worker doesn't have enough RAM, crashes and lose all computed task which triggers tasks re-run.
My goal is:
to read from parquet files
perform some computations with apply()
and without even returning data from a cluster write it back to Gcloud storage in parquet format.
So, simply I want to keep data on a cluster and not return it back. Just compute and save data somewhere else.
After reading Dask distributed docs, I have found client.persist()/compute() and .scatter() methods. They look like what I need, but I don't really understand how to use them.
Could you, please, help me with client.persist() and client.compute() methods for my example
or suggest another way to do it? Thank you very much!
Dask version: 0.19.1
Dask distributed version: 1.23.1
Python version: 3.5.1
df = dd.read_parquet('gcs://<bucket>/files/name_*.parquet', storage_options={'token':'cloud'}, engine='fastparquet')
df = df.compute() # this triggers computations, but brings all of the data to one machine and creates a Pandas dataframe
df = df.persist() # this triggers computations, but keeps all of the data in multiple pandas dataframes spread across multiple machines
This is a follow-up to this question.
I'm experiencing problems with persisting a large dataset in distributed memory. I have a scheduler running on one machine and 8 workers each running on their own machines connected by 40 gigabit ethernet and a backing Lustre filesystem.
Problem 1:
ds = DataSlicer(dataset) # ~600 GB dataset
dask_array = dask.array.from_array(ds, chunks=(13507, -1, -1), name=False) # ~22 GB chunks
dask_array = client.persist(dask_array)
When inspecting the Dask status dashboard, I see all 28 tasks being assigned to and processed by one worker while the other workers do nothing. Additionally, when every task has finished processing and the tasks are all in the "In memory" state, only 22 GB of RAM (i.e. the first chunk of the dataset) is actually stored on the cluster. Access to the indices within the first chunk are fast, but any other indices force a new round of reading and loading the data before the result returns. This seems contrary to my belief that .persist() should pin the complete dataset across the memory of the workers once it finishes execution. In addition, when I increase the chunk size, one worker often runs out of memory and restarts due to it being assigned multiple huge chunks of data.
Is there a way to manually assign chunks to workers instead of the scheduler piling all of the tasks on one process? Or is this abnormal scheduler behavior? Is there a way to ensure that the entire dataset is loaded into RAM?
Problem 2
I found a temporary workaround by treating each chunk of the dataset as its own separate dask array and persisting each one individually.
dask_arrays = [da.from_delayed(lazy_slice, shape, dtype, name=False) for \
lazy_slice, shape in zip(lazy_slices, shapes)]
for i in range(len(dask_arrays)):
dask_arrays[i] = client.persist(dask_arrays[i])
I tested the bandwidth from persisted and published dask arrays to several parallel readers by calling .compute() on different chunks of the dataset in parallel. I could never achieve more than 2 GB/s aggregate bandwidth from the dask cluster, far below our network's capabilities.
Is the scheduler the bottleneck in this situation, i.e. is all data being funneled through the scheduler to my readers? If this is the case, is there a way to get in-memory data directly from each worker? If this is not the case, what are some other areas in dask I may be able to investigate?