alterlab-zarr

Zarr Python

Overview

Zarr is a Python library for storing large N-dimensional arrays with chunking and compression. Apply this skill for efficient parallel I/O, cloud-native workflows, and seamless integration with NumPy, Dask, and Xarray.

Quick Start

Installation

uv pip install zarr

Requires Python 3.11+. For cloud storage support, install additional packages:

uv pip install s3fs  # For S3
uv pip install gcsfs  # For Google Cloud Storage

Basic Array Creation

import zarr
import numpy as np

# Create a 2D array with chunking and compression
z = zarr.create_array(
    store="data/my_array.zarr",
    shape=(10000, 10000),
    chunks=(1000, 1000),
    dtype="f4"
)

# Write data using NumPy-style indexing
z[:, :] = np.random.random((10000, 10000))

# Read data
data = z[0:100, 0:100]  # Returns NumPy array

Core Operations

Creating Arrays

Zarr provides multiple convenience functions for array creation:

# Create empty array
z = zarr.zeros(shape=(10000, 10000), chunks=(1000, 1000), dtype='f4',
               store='data.zarr')

# Create filled arrays
z = zarr.ones((5000, 5000), chunks=(500, 500))
z = zarr.full((1000, 1000), fill_value=42, chunks=(100, 100))

# Create from existing data
data = np.arange(10000).reshape(100, 100)
z = zarr.array(data, chunks=(10, 10), store='data.zarr')

# Create like another array
z2 = zarr.zeros_like(z)  # Matches shape, chunks, dtype of z

Opening Existing Arrays

# Open array (read/write mode by default)
z = zarr.open_array('data.zarr', mode='r+')

# Read-only mode
z = zarr.open_array('data.zarr', mode='r')

# The open() function auto-detects arrays vs groups
z = zarr.open('data.zarr')  # Returns Array or Group

Reading and Writing Data

Zarr arrays support NumPy-like indexing:

# Write entire array
z[:] = 42

# Write slices
z[0, :] = np.arange(100)
z[10:20, 50:60] = np.random.random((10, 10))

# Read data (returns NumPy array)
data = z[0:100, 0:100]
row = z[5, :]

# Advanced indexing
z.vindex[[0, 5, 10], [2, 8, 15]]  # Coordinate indexing
z.oindex[0:10, [5, 10, 15]]       # Orthogonal indexing
z.blocks[0, 0]                     # Block/chunk indexing

Resizing and Appending

# Resize array
z.resize(15000, 15000)  # Expands or shrinks dimensions

# Append data along an axis
z.append(np.random.random((1000, 10000)), axis=0)  # Adds rows

Chunking Strategies

Chunking is critical for performance. Choose chunk sizes and shapes based on access patterns.

Chunk Size Guidelines

• Minimum chunk size: 1 MB recommended for optimal performance
• Balance: Larger chunks = fewer metadata operations; smaller chunks = better parallel access
• Memory consideration: Entire chunks must fit in memory during compression

# Configure chunk size (aim for ~1MB per chunk)
# For float32 data: 1MB = 262,144 elements = 512×512 array
z = zarr.zeros(
    shape=(10000, 10000),
    chunks=(512, 512),  # ~1MB chunks
    dtype='f4'
)

Aligning Chunks with Access Patterns

Critical: Chunk shape dramatically affects performance based on how data is accessed.

# If accessing rows frequently (first dimension)
z = zarr.zeros((10000, 10000), chunks=(10, 10000))  # Chunk spans columns

# If accessing columns frequently (second dimension)
z = zarr.zeros((10000, 10000), chunks=(10000, 10))  # Chunk spans rows

# For mixed access patterns (balanced approach)
z = zarr.zeros((10000, 10000), chunks=(1000, 1000))  # Square chunks

Performance example: For a (200, 200, 200) array, reading along the first dimension:

• Using chunks (1, 200, 200): ~107ms
• Using chunks (200, 200, 1): ~1.65ms (65× faster!)

Sharding for Large-Scale Storage

When arrays have millions of small chunks, use sharding to group chunks into larger storage objects:

from zarr.codecs import ShardingCodec, BytesCodec
from zarr.codecs.blosc import BloscCodec

# Create array with sharding
z = zarr.create_array(
    store='data.zarr',
    shape=(100000, 100000),
    chunks=(100, 100),  # Small chunks for access
    shards=(1000, 1000),  # Groups 100 chunks per shard
    dtype='f4'
)

Benefits:

• Reduces file system overhead from millions of small files
• Improves cloud storage performance (fewer object requests)
• Prevents filesystem block size waste

Important: Entire shards must fit in memory before writing.

Compression

Zarr applies compression per chunk to reduce storage while maintaining fast access.

Configuring Compression

from zarr.codecs.blosc import BloscCodec
from zarr.codecs import GzipCodec, ZstdCodec

# Default: Blosc with Zstandard
z = zarr.zeros((1000, 1000), chunks=(100, 100))  # Uses default compression

# Configure Blosc codec
z = zarr.create_array(
    store='data.zarr',
    shape=(1000, 1000),
    chunks=(100, 100),
    dtype='f4',
    codecs=[BloscCodec(cname='zstd', clevel=5, shuffle='shuffle')]
)

# Available Blosc compressors: 'blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib', 'zstd'

# Use Gzip compression
z = zarr.create_array(
    store='data.zarr',
    shape=(1000, 1000),
    chunks=(100, 100),
    dtype='f4',
    codecs=[GzipCodec(level=6)]
)

# Disable compression
z = zarr.create_array(
    store='data.zarr',
    shape=(1000, 1000),
    chunks=(100, 100),
    dtype='f4',
    codecs=[BytesCodec()]  # No compression
)

Compression Performance Tips

• Blosc (default): Fast compression/decompression, good for interactive workloads
• Zstandard: Better compression ratios, slightly slower than LZ4
• Gzip: Maximum compression, slower performance
• LZ4: Fastest compression, lower ratios
• Shuffle: Enable shuffle filter for better compression on numeric data

# Optimal for numeric scientific data
codecs=[BloscCodec(cname='zstd', clevel=5, shuffle='shuffle')]

# Optimal for speed
codecs=[BloscCodec(cname='lz4', clevel=1)]

# Optimal for compression ratio
codecs=[GzipCodec(level=9)]

Storage Backends

Zarr supports multiple storage backends through a flexible storage interface.

Local Filesystem (Default)

from zarr.storage import LocalStore

# Explicit store creation
store = LocalStore('data/my_array.zarr')
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))

# Or use string path (creates LocalStore automatically)
z = zarr.open_array('data/my_array.zarr', mode='w', shape=(1000, 1000),
                    chunks=(100, 100))

In-Memory Storage

from zarr.storage import MemoryStore

# Create in-memory store
store = MemoryStore()
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))

# Data exists only in memory, not persisted

ZIP File Storage

from zarr.storage import ZipStore

# Write to ZIP file
store = ZipStore('data.zip', mode='w')
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))
z[:] = np.random.random((1000, 1000))
store.close()  # IMPORTANT: Must close ZipStore

# Read from ZIP file
store = ZipStore('data.zip', mode='r')
z = zarr.open_array(store=store)
data = z[:]
store.close()

Cloud Storage (S3, GCS)

import s3fs
import zarr

# S3 storage
s3 = s3fs.S3FileSystem(anon=False)  # Use credentials
store = s3fs.S3Map(root='my-bucket/path/to/array.zarr', s3=s3)
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))
z[:] = data

# Google Cloud Storage
import gcsfs
gcs = gcsfs.GCSFileSystem(project='my-project')
store = gcsfs.GCSMap(root='my-bucket/path/to/array.zarr', gcs=gcs)
z = zarr.open_array(store=store, mode='w', shape=(1000, 1000), chunks=(100, 100))

Cloud Storage Best Practices:

• Use consolidated metadata to reduce latency: zarr.consolidate_metadata(store)
• Align chunk sizes with cloud object sizing (typically 5-100 MB optimal)
• Enable parallel writes using Dask for large-scale data
• Consider sharding to reduce number of objects

Groups and Hierarchies

Groups organize multiple arrays hierarchically, similar to directories or HDF5 groups.

Creating and Using Groups

# Create root group
root = zarr.group(store='data/hierarchy.zarr')

# Create sub-groups
temperature = root.create_group('temperature')
precipitation = root.create_group('precipitation')

# Create arrays within groups
temp_array = temperature.create_array(
    name='t2m',
    shape=(365, 720, 1440),
    chunks=(1, 720, 1440),
    dtype='f4'
)

precip_array = precipitation.create_array(
    name='prcp',
    shape=(365, 720, 1440),
    chunks=(1, 720, 1440),
    dtype='f4'
)

# Access using paths
array = root['temperature/t2m']

# Visualize hierarchy
print(root.tree())
# Output:
# /
#  ├── temperature
#  │   └── t2m (365, 720, 1440) f4
#  └── precipitation
#      └── prcp (365, 720, 1440) f4

H5py-Compatible API

Zarr provides an h5py-compatible interface for familiar HDF5 users:

# Create group with h5py-style methods
root = zarr.group('data.zarr')
dataset = root.create_dataset('my_data', shape=(1000, 1000), chunks=(100, 100),
                              dtype='f4')

# Access like h5py
grp = root.require_group('subgroup')
arr = grp.require_dataset('array', shape=(500, 500), chunks=(50, 50), dtype='i4')

Attributes and Metadata

Attach custom metadata to arrays and groups using attributes:

# Add attributes to array
z = zarr.zeros((1000, 1000), chunks=(100, 100))
z.attrs['description'] = 'Temperature data in Kelvin'
z.attrs['units'] = 'K'
z.attrs['created'] = '2024-01-15'
z.attrs['processing_version'] = 2.1

# Attributes are stored as JSON
print(z.attrs['units'])  # Output: K

# Add attributes to groups
root = zarr.group('data.zarr')
root.attrs['project'] = 'Climate Analysis'
root.attrs['institution'] = 'Research Institute'

# Attributes persist with the array/group
z2 = zarr.open('data.zarr')
print(z2.attrs['description'])

Important: Attributes must be JSON-serializable (strings, numbers, lists, dicts, booleans, null).

Integration with NumPy, Dask, and Xarray

NumPy Integration

Zarr arrays implement the NumPy array interface:

import numpy as np
import zarr

z = zarr.zeros((1000, 1000), chunks=(100, 100))

# Use NumPy functions directly
result = np.sum(z, axis=0)  # NumPy operates on Zarr array
mean = np.mean(z[:100, :100])

# Convert to NumPy array
numpy_array = z[:]  # Loads entire array into memory

Dask Integration

Dask provides lazy, parallel computation on Zarr arrays:

import dask.array as da
import zarr

# Create large Zarr array
z = zarr.open('data.zarr', mode='w', shape=(100000, 100000),
              chunks=(1000, 1000), dtype='f4')

# Load as Dask array (lazy, no data loaded)
dask_array = da.from_zarr('data.zarr')

# Perform computations (parallel, out-of-core)
result = dask_array.mean(axis=0).compute()  # Parallel computation

# Write Dask array to Zarr
large_array = da.random.random((100000, 100000), chunks=(1000, 1000))
da.to_zarr(large_array, 'output.zarr')

Benefits:

• Process datasets larger than memory
• Automatic parallel computation across chunks
• Efficient I/O with chunked storage

Xarray Integration

Xarray provides labeled, multidimensional arrays with Zarr backend:

import xarray as xr
import zarr

# Open Zarr store as Xarray Dataset (lazy loading)
ds = xr.open_zarr('data.zarr')

# Dataset includes coordinates and metadata
print(ds)

# Access variables
temperature = ds['temperature']

# Perform labeled operations
subset = ds.sel(time='2024-01', lat=slice(30, 60))

# Write Xarray Dataset to Zarr
ds.to_zarr('output.zarr')

# Create from scratch with coordinates
ds = xr.Dataset(
    {
        'temperature': (['time', 'lat', 'lon'], data),
        'precipitation': (['time', 'lat', 'lon'], data2)
    },
    coords={
        'time': pd.date_range('2024-01-01', periods=365),
        'lat': np.arange(-90, 91, 1),
        'lon': np.arange(-180, 180, 1)
    }
)
ds.to_zarr('climate_data.zarr')

Benefits:

• Named dimensions and coordinates
• Label-based indexing and selection
• Integration with pandas for time series
• NetCDF-like interface familiar to climate/geospatial scientists

Parallel Computing and Synchronization

Thread-Safe Operations

from zarr import ThreadSynchronizer
import zarr

# For multi-threaded writes
synchronizer = ThreadSynchronizer()
z = zarr.open_array('data.zarr', mode='r+', shape=(10000, 10000),
                    chunks=(1000, 1000), synchronizer=synchronizer)

# Safe for concurrent writes from multiple threads
# (when writes don't span chunk boundaries)

Process-Safe Operations

from zarr import ProcessSynchronizer
import zarr

# For multi-process writes
synchronizer = ProcessSynchronizer('sync_data.sync')
z = zarr.open_array('data.zarr', mode='r+', shape=(10000, 10000),
                    chunks=(1000, 1000), synchronizer=synchronizer)

# Safe for concurrent writes from multiple processes

Note:

• Concurrent reads require no synchronization
• Synchronization only needed for writes that may span chunk boundaries
• Each process/thread writing to separate chunks needs no synchronization

Consolidated Metadata

For hierarchical stores with many arrays, consolidate metadata into a single file to reduce I/O operations:

import zarr

# After creating arrays/groups
root = zarr.group('data.zarr')
# ... create multiple arrays/groups ...

# Consolidate metadata
zarr.consolidate_metadata('data.zarr')

# Open with consolidated metadata (faster, especially on cloud storage)
root = zarr.open_consolidated('data.zarr')

Benefits:

• Reduces metadata read operations from N (one per array) to 1
• Critical for cloud storage (reduces latency)
• Speeds up tree() operations and group traversal

Cautions:

• Metadata can become stale if arrays update without re-consolidation
• Not suitable for frequently-updated datasets
• Multi-writer scenarios may have inconsistent reads

Performance Optimization

Checklist for Optimal Performance

1. Chunk Size: Aim for 1-10 MB per chunk

   # For float32: 1MB = 262,144 elements
   chunks = (512, 512)  # 512×512×4 bytes = ~1MB
   

2. Chunk Shape: Align with access patterns

   # Row-wise access → chunk spans columns: (small, large)
   # Column-wise access → chunk spans rows: (large, small)
   # Random access → balanced: (medium, medium)
   

3. Compression: Choose based on workload

   # Interactive/fast: BloscCodec(cname='lz4')
   # Balanced: BloscCodec(cname='zstd', clevel=5)
   # Maximum compression: GzipCodec(level=9)
   

4. Storage Backend: Match to environment

   # Local: LocalStore (default)
   # Cloud: S3Map/GCSMap with consolidated metadata
   # Temporary: MemoryStore
   

5. Sharding: Use for large-scale datasets

   # When you have millions of small chunks
   shards=(10*chunk_size, 10*chunk_size)
   

6. Parallel I/O: Use Dask for large operations

   import dask.array as da
   dask_array = da.from_zarr('data.zarr')
   result = dask_array.compute(scheduler='threads', num_workers=8)
   

Profiling and Debugging

# Print detailed array information
print(z.info)

# Output includes:
# - Type, shape, chunks, dtype
# - Compression codec and level
# - Storage size (compressed vs uncompressed)
# - Storage location

# Check storage size
print(f"Compressed size: {z.nbytes_stored / 1e6:.2f} MB")
print(f"Uncompressed size: {z.nbytes / 1e6:.2f} MB")
print(f"Compression ratio: {z.nbytes / z.nbytes_stored:.2f}x")

Common Patterns and Best Practices

Pattern: Time Series Data

# Store time series with time as first dimension
# This allows efficient appending of new time steps
z = zarr.open('timeseries.zarr', mode='a',
              shape=(0, 720, 1440),  # Start with 0 time steps
              chunks=(1, 720, 1440),  # One time step per chunk
              dtype='f4')

# Append new time steps
new_data = np.random.random((1, 720, 1440))
z.append(new_data, axis=0)

Pattern: Large Matrix Operations

import dask.array as da

# Create large matrix in Zarr
z = zarr.open('matrix.zarr', mode='w',
              shape=(100000, 100000),
              chunks=(1000, 1000),
              dtype='f8')

# Use Dask for parallel computation
dask_z = da.from_zarr('matrix.zarr')
result = (dask_z @ dask_z.T).compute()  # Parallel matrix multiply

Pattern: Cloud-Native Workflow

import s3fs
import zarr

# Write to S3
s3 = s3fs.S3FileSystem()
store = s3fs.S3Map(root='s3://my-bucket/data.zarr', s3=s3)

# Create array with appropriate chunking for cloud
z = zarr.open_array(store=store, mode='w',
                    shape=(10000, 10000),
                    chunks=(500, 500),  # ~1MB chunks
                    dtype='f4')
z[:] = data

# Consolidate metadata for faster reads
zarr.consolidate_metadata(store)

# Read from S3 (anywhere, anytime)
store_read = s3fs.S3Map(root='s3://my-bucket/data.zarr', s3=s3)
z_read = zarr.open_consolidated(store_read)
subset = z_read[0:100, 0:100]

Pattern: Format Conversion

# HDF5 to Zarr
import h5py
import zarr

with h5py.File('data.h5', 'r') as h5:
    dataset = h5['dataset_name']
    z = zarr.array(dataset[:],
                   chunks=(1000, 1000),
                   store='data.zarr')

# NumPy to Zarr
import numpy as np
data = np.load('data.npy')
z = zarr.array(data, chunks='auto', store='data.zarr')

# Zarr to NetCDF (via Xarray)
import xarray as xr
ds = xr.open_zarr('data.zarr')
ds.to_netcdf('data.nc')

Common Issues and Solutions

Issue: Slow Performance

Diagnosis: Check chunk size and alignment

print(z.chunks)  # Are chunks appropriate size?
print(z.info)    # Check compression ratio

Solutions:

• Increase chunk size to 1-10 MB
• Align chunks with access pattern
• Try different compression codecs
• Use Dask for parallel operations

Issue: High Memory Usage

Cause: Loading entire array or large chunks into memory

Solutions:

# Don't load entire array
# Bad: data = z[:]
# Good: Process in chunks
for i in range(0, z.shape[0], 1000):
    chunk = z[i:i+1000, :]
    process(chunk)

# Or use Dask for automatic chunking
import dask.array as da
dask_z = da.from_zarr('data.zarr')
result = dask_z.mean().compute()  # Processes in chunks

Issue: Cloud Storage Latency

Solutions:

# 1. Consolidate metadata
zarr.consolidate_metadata(store)
z = zarr.open_consolidated(store)

# 2. Use appropriate chunk sizes (5-100 MB for cloud)
chunks = (2000, 2000)  # Larger chunks for cloud

# 3. Enable sharding
shards = (10000, 10000)  # Groups many chunks

Issue: Concurrent Write Conflicts

Solution: Use synchronizers or ensure non-overlapping writes

from zarr import ProcessSynchronizer

sync = ProcessSynchronizer('sync.sync')
z = zarr.open_array('data.zarr', mode='r+', synchronizer=sync)

# Or design workflow so each process writes to separate chunks

Additional Resources

For detailed API documentation, advanced usage, and the latest updates:

• Official Documentation: https://zarr.readthedocs.io/
• Zarr Specifications: https://zarr-specs.readthedocs.io/
• GitHub Repository: https://github.com/zarr-developers/zarr-python
• Community Chat: https://gitter.im/zarr-developers/community

Related Libraries:

• Xarray: https://docs.xarray.dev/ (labeled arrays)
• Dask: https://docs.dask.org/ (parallel computing)
• NumCodecs: https://numcodecs.readthedocs.io/ (compression codecs)