From 06c9921cee26f2dc471a1b80dc22504c0b4a3319 Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Thu, 9 Apr 2026 23:04:23 +0700
Subject: [PATCH 1/8] feat(spark-slurm): support hail

---
 spark-on-slurm/.gitignore                     |    3 +-
 spark-on-slurm/Makefile                       |    7 +-
 spark-on-slurm/Readme.md                      |    5 +-
 .../examples/__pycache__/hail.cpython-311.pyc |  Bin 0 -> 911 bytes
 spark-on-slurm/examples/pi_counter.py         |  113 +
 .../examples/simulate_gwas_by_hail.py         |   51 +
 .../validate_spark.py}                        |    0
 spark-on-slurm/pixi.lock                      | 2222 ++++++++---------
 spark-on-slurm/pixi.toml                      |   11 +-
 spark-on-slurm/sparkhpc/sparkhpc/sparkjob.py  |   57 +-
 .../templates/sparkjob.slurm.template         |    3 +-
 11 files changed, 1258 insertions(+), 1214 deletions(-)
 create mode 100644 spark-on-slurm/examples/__pycache__/hail.cpython-311.pyc
 create mode 100644 spark-on-slurm/examples/pi_counter.py
 create mode 100644 spark-on-slurm/examples/simulate_gwas_by_hail.py
 rename spark-on-slurm/{sparkhpc/run_example.py => examples/validate_spark.py} (100%)

diff --git a/spark-on-slurm/.gitignore b/spark-on-slurm/.gitignore
index 30f1a83..04dd98e 100644
--- a/spark-on-slurm/.gitignore
+++ b/spark-on-slurm/.gitignore
@@ -2,4 +2,5 @@ sparkcluster*
 .spark*
 .cache
 spark_master.out
-job
\ No newline at end of file
+job
+*.log
\ No newline at end of file
diff --git a/spark-on-slurm/Makefile b/spark-on-slurm/Makefile
index 917c8f1..1e1afcd 100644
--- a/spark-on-slurm/Makefile
+++ b/spark-on-slurm/Makefile
@@ -1,5 +1,5 @@
 SLURM_IMAGE:= nttg8100/river-slurm:1.1.0
-.PHONY: setup example clean
+.PHONY: setup example clean install
 
 ${HOME}/.pixi/bin/pixi:
 	curl -sSL https://pixi.sh/install.sh | sh
@@ -32,11 +32,14 @@ get-slurm:
 		exit 1; \
 	fi
 
+install:
+	${HOME}/.pixi/bin/pixi run install-sparkhpc
+
 # inside user river is the standard user with 1001 mapping id, Github Actions does not have this user
 test: ${HOME}/.pixi/bin/pixi start-slurm get-slurm
 	docker exec \
 		-w /tmp/spark \
-		slurm-dev /root/.pixi/bin/pixi run sparkhpc-example
+		slurm-dev /root/.pixi/bin/pixi run sparkhpc-hail
 
 test-slurm-local:
 	${HOME}/.pixi/bin/pixi run sparkhpc-example
diff --git a/spark-on-slurm/Readme.md b/spark-on-slurm/Readme.md
index c459c4d..82e23f3 100644
--- a/spark-on-slurm/Readme.md
+++ b/spark-on-slurm/Readme.md
@@ -23,7 +23,7 @@ When you run the example workflow:
   User entrypoints (`setup`, `example`, `clean`).
 - `pixi.toml`  
   Environment definition and task `sparkhpc-example`.
-- `sparkhpc/run_example.py`  
+- `example/*.py`  
   End-to-end test runner: submit cluster, wait for master, run Spark actions, cleanup.
 - `sparkhpc/sparkhpc/sparkjob.py`  
   Core Spark-on-Slurm orchestration logic.
@@ -110,6 +110,7 @@ squeue -u $USER
 This README describes **Spark-on-Slurm only**. HDFS/Hadoop integration is intentionally deferred for a separate step.
 
 ## References
+
 This toolkit is adapted from the original [sparkhpc project](https://github.com/rokroskar/sparkhpc), which provides a framework for running Spark on HPC environments. However, the original repository is no longer actively maintained and requires updates to function with modern Spark and SLURM configurations.
 
-Therefore, this implementation integrates and modifies the original toolkit with several adjustments to ensure compatibility and reliable operation in current environments.
\ No newline at end of file
+Therefore, this implementation integrates and modifies the original toolkit with several adjustments to ensure compatibility and reliable operation in current environments.
diff --git a/spark-on-slurm/examples/__pycache__/hail.cpython-311.pyc b/spark-on-slurm/examples/__pycache__/hail.cpython-311.pyc
new file mode 100644
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diff --git a/spark-on-slurm/examples/pi_counter.py b/spark-on-slurm/examples/pi_counter.py
new file mode 100644
index 0000000..136f1c8
--- /dev/null
+++ b/spark-on-slurm/examples/pi_counter.py
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+"""
+Calculate Pi using Monte Carlo method in PySpark
+Connects to existing Spark cluster started via sparkcluster CLI
+
+Usage:
+    1. Start cluster: sparkcluster start 4 --partition main --spark-home $SPARK_HOME
+    2. Run this script: python examples/pi_counter.py
+    3. Stop cluster: kill the sparkcluster process or wait for walltime
+"""
+import sys
+import os
+
+# Add sparkhpc to path
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'sparkhpc'))
+
+from sparkhpc import sparkjob
+from pyspark import SparkConf, SparkContext
+from random import random
+from math import pi as math_pi
+import time
+
+def inside(p):
+    """Check if a random point (x, y) is inside the unit circle"""
+    x, y = random(), random()
+    return x*x + y*y <= 1
+
+def main():
+    print(f"\n{'='*70}")
+    print(f"PySpark Pi Calculation - Monte Carlo Method")
+    print(f"{'='*70}")
+    
+    # Get the running cluster (cluster 0)
+    try:
+        sj = sparkjob.sparkjob(clusterid=0)
+    except Exception as e:
+        print(f" Error: Could not find running cluster!")
+        print(f"  Make sure to start cluster first:")
+        print(f"  $ sparkcluster start 4 --partition main --spark-home $SPARK_HOME")
+        print(f"  Error details: {e}")
+        sys.exit(1)
+    
+    print(f"\nConnecting to Spark cluster...")
+    print(f"  Cluster ID: 0")
+    print(f"  Job ID: {sj.jobid}")
+    
+    # Wait for master to be available
+    print(f"\nWaiting for Spark Master (timeout: 60 seconds)...")
+    deadline = time.time() + 60
+    master_url = None
+    
+    while time.time() < deadline:
+        try:
+            master_url = sj.master_url()
+            if master_url:
+                print(f" Master URL: {master_url}")
+                break
+        except:
+            pass
+        time.sleep(0.5)
+    
+    if not master_url:
+        print(" Could not connect to Spark master!")
+        print(f"  Verify cluster is running:")
+        print(f"  $ squeue")
+        print(f"  Check logs:")
+        print(f"  $ tail spark_master.out")
+        sys.exit(1)
+    
+    ui_url = sj.master_ui()
+    print(f" Master UI: {ui_url}")
+    
+    # Create SparkContext and connect to the master
+    print(f"\nCreating SparkContext...")
+    conf = SparkConf().setMaster(master_url).setAppName("PiCalculator")
+    sc = SparkContext(conf=conf)
+    
+    try:
+        # Calculate pi
+        num_samples = 100000000  # 100 million samples
+        num_partitions = 4
+        
+        print(f"\nCalculating Pi with {num_samples:,} samples across {num_partitions} partitions...")
+        print(f"This will take 15-20 seconds...\n")
+        
+        # Create RDD and calculate pi
+        start_time = time.time()
+        count = sc.parallelize(range(0, num_samples), num_partitions).filter(lambda _: inside(_)).count()
+        elapsed_time = time.time() - start_time
+        
+        # Calculate result
+        pi_estimate = 4.0 * count / num_samples
+        error = abs(pi_estimate - math_pi)
+        accuracy = (1 - error/math_pi) * 100
+        
+        print(f"{'='*70}")
+        print(f"RESULTS:")
+        print(f"{'='*70}")
+        print(f"Pi estimated value: {pi_estimate:.10f}")
+        print(f"Actual Pi value:    {math_pi:.10f}")
+        print(f"Error:              {error:.10f}")
+        print(f"Accuracy:           {accuracy:.6f}%")
+        print(f"Execution time:     {elapsed_time:.2f} seconds")
+        print(f"Points inside:      {count:,} / {num_samples:,}")
+        print(f"{'='*70}\n")
+        
+    finally:
+        print(f"Stopping SparkContext...")
+        sc.stop()
+        print(f" Job completed successfully!")
+
+if __name__ == "__main__":
+    main()
diff --git a/spark-on-slurm/examples/simulate_gwas_by_hail.py b/spark-on-slurm/examples/simulate_gwas_by_hail.py
new file mode 100644
index 0000000..9382142
--- /dev/null
+++ b/spark-on-slurm/examples/simulate_gwas_by_hail.py
@@ -0,0 +1,51 @@
+from pyspark.sql import SparkSession
+import hail as hl
+from sparkhpc import sparkjob
+import sys
+import os
+
+# Connect to existing Spark cluster
+sj_list = sparkjob.sparkjob().current_clusters()
+if not sj_list:
+    print("ERROR: No running Spark cluster found!")
+    print("Please start a cluster first with: sparkcluster start <ncores>")
+    sys.exit(1)
+
+cluster = sj_list[0]
+master_url = cluster.master_url()
+print(f"Connecting to Spark cluster at {master_url}")
+
+# Get Hail JAR path
+hail_dir = os.path.dirname(hl.__file__)
+hail_jar = os.path.join(hail_dir, 'backend', 'hail-all-spark.jar')
+print(f"Using Hail JAR: {hail_jar}")
+
+# Connect to the existing cluster with Hail JAR and serialization configuration
+spark = (SparkSession.builder
+    .master(master_url)
+    .appName("GWAS-Hail")
+    .config("spark.jars", hail_jar)
+    .config("spark.driver.extraClassPath", hail_jar)
+    .config("spark.executor.extraClassPath", f"./hail-all-spark.jar:{hail_jar}")
+    .config("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
+    .config("spark.kryo.registrator", "is.hail.kryo.HailKryoRegistrator")
+    .getOrCreate())
+
+print(f"Spark version: {spark.version}")
+print(f"Spark master: {spark.sparkContext.master}")
+print(f"Spark serializer: {spark.sparkContext.getConf().get('spark.serializer')}")
+
+print("\nInitializing Hail...")
+hl.init(sc=spark.sparkContext)
+print("✓ Hail initialized successfully!")
+
+# Submit jobs to simulate the data
+mt = hl.balding_nichols_model(n_populations=3,
+                              n_samples=500,
+                              n_variants=500_000,
+                              n_partitions=32)
+mt = mt.annotate_cols(drinks_coffee = hl.rand_bool(0.33))
+gwas = hl.linear_regression_rows(y=mt.drinks_coffee,
+                                 x=mt.GT.n_alt_alleles(),
+                                 covariates=[1.0])
+gwas.order_by(gwas.p_value).show(25)
\ No newline at end of file
diff --git a/spark-on-slurm/sparkhpc/run_example.py b/spark-on-slurm/examples/validate_spark.py
similarity index 100%
rename from spark-on-slurm/sparkhpc/run_example.py
rename to spark-on-slurm/examples/validate_spark.py
diff --git a/spark-on-slurm/pixi.lock b/spark-on-slurm/pixi.lock
index 8ff17cc..77bd0d3 100644
--- a/spark-on-slurm/pixi.lock
+++ b/spark-on-slurm/pixi.lock
@@ -4,32 +4,15 @@ environments:
     channels:
     - url: https://conda.anaconda.org/conda-forge/
     - url: https://conda.anaconda.org/bioconda/
+    indexes:
+    - https://pypi.org/simple
     options:
       pypi-prerelease-mode: if-necessary-or-explicit
     packages:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-auth-0.10.1-h2d2dd48_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-cal-0.9.13-h2c9d079_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-common-0.12.6-hb03c661_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-compression-0.3.2-h8b1a151_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-event-stream-0.6.0-h9b893ba_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-http-0.10.12-h4bacb7b_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-io-0.26.3-hc87160b_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-mqtt-0.15.2-he9ea9c5_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-s3-0.11.5-h6d69fc9_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-c-sdkutils-0.2.4-h8b1a151_4.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-checksums-0.2.10-h8b1a151_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-crt-cpp-0.37.4-h4c8aef7_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/aws-sdk-cpp-1.11.747-hc3785e1_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-core-cpp-1.16.2-h206d751_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-identity-cpp-1.13.3-hed0cdb0_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-blobs-cpp-12.16.0-hdd73cc9_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-common-cpp-12.12.0-ha7a2c86_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/azure-storage-files-datalake-cpp-12.14.0-h52c5a47_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.6-hb03c661_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-he90730b_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
@@ -39,99 +22,47 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.17.1-h27c8c51_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-h5888daf_1005.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/glog-0.7.1-hbabe93e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-13.2.1-h6083320_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-14.1.0-h6083320_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-78.3-h33c6efd_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.22.2-ha1258a1_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.18-h0c24ade_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.1.0-hdb68285_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libabseil-20260107.1-cxx17_h7b12aa8_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libarrow-23.0.1-ha7f89c6_9_cpu.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libarrow-acero-23.0.1-h635bf11_9_cpu.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libarrow-compute-23.0.1-h53684a4_9_cpu.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libarrow-dataset-23.0.1-h635bf11_9_cpu.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libarrow-substrait-23.0.1-hb4dd7c2_9_cpu.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.11.0-6_h4a7cf45_openblas.conda
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-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.11.0-6_h0358290_openblas.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcrc32c-1.1.2-h9c3ff4c_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h7a8fb5f_6.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.19.0-hcf29cc6_0.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.12-hf998b51_1.conda
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       - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_18.conda
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+- pypi: https://files.pythonhosted.org/packages/e0/f9/0595336914c5619e5f28a1fb793285925a8cd4b432c9da0a987836c7f822/shellingham-1.5.4-py2.py3-none-any.whl
+  name: shellingham
+  version: 1.5.4
+  sha256: 7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686
+  requires_python: '>=3.7'
+- pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
+  name: six
+  version: 1.17.0
+  sha256: 4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274
+  requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*'
+- pypi: https://files.pythonhosted.org/packages/32/46/9cb0e58b2deb7f82b84065f37f3bffeb12413f947f9388e4cac22c4621ce/sortedcontainers-2.4.0-py2.py3-none-any.whl
+  name: sortedcontainers
+  version: 2.4.0
+  sha256: a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0
+- pypi: https://files.pythonhosted.org/packages/99/55/db07de81b5c630da5cbf5c7df646580ca26dfaefa593667fc6f2fe016d2e/tabulate-0.10.0-py3-none-any.whl
+  name: tabulate
+  version: 0.10.0
+  sha256: f0b0622e567335c8fabaaa659f1b33bcb6ddfe2e496071b743aa113f8774f2d3
+  requires_dist:
+  - wcwidth ; extra == 'widechars'
+  requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/d7/c1/eb8f9debc45d3b7918a32ab756658a0904732f75e555402972246b0b8e71/tenacity-9.1.4-py3-none-any.whl
+  name: tenacity
+  version: 9.1.4
+  sha256: 6095a360c919085f28c6527de529e76a06ad89b23659fa881ae0649b867a9d55
+  requires_dist:
+  - reno ; extra == 'doc'
+  - sphinx ; extra == 'doc'
+  - pytest ; extra == 'test'
+  - tornado>=4.5 ; extra == 'test'
+  - typeguard ; extra == 'test'
+  requires_python: '>=3.10'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
   sha256: cafeec44494f842ffeca27e9c8b0c27ed714f93ac77ddadc6aaf726b5554ebac
   md5: cffd3bdd58090148f4cfcd831f4b26ab
@@ -1945,6 +1710,31 @@ packages:
   purls: []
   size: 3301196
   timestamp: 1769460227866
+- pypi: https://files.pythonhosted.org/packages/b2/04/7b5705d5b3c0fab088f434f9c83edac1573830ca49ccf29fb83bf7178eec/tornado-6.5.5-cp39-abi3-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+  name: tornado
+  version: 6.5.5
+  sha256: e74c92e8e65086b338fd56333fb9a68b9f6f2fe7ad532645a290a464bcf46be5
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/4a/91/48db081e7a63bb37284f9fbcefda7c44c277b18b0e13fbc36ea2335b71e6/typer-0.24.1-py3-none-any.whl
+  name: typer
+  version: 0.24.1
+  sha256: 112c1f0ce578bfb4cab9ffdabc68f031416ebcc216536611ba21f04e9aa84c9e
+  requires_dist:
+  - click>=8.2.1
+  - shellingham>=1.3.0
+  - rich>=12.3.0
+  - annotated-doc>=0.0.2
+  requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl
+  name: typing-extensions
+  version: 4.15.0
+  sha256: f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/b0/70/d460bd685a170790ec89317e9bd33047988e4bce507b831f5db771e142de/tzdata-2026.1-py2.py3-none-any.whl
+  name: tzdata
+  version: '2026.1'
+  sha256: 4b1d2be7ac37ceafd7327b961aa3a54e467efbdb563a23655fbfe0d39cfc42a9
+  requires_python: '>=2'
 - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
   sha256: 1d30098909076af33a35017eed6f2953af1c769e273a0626a04722ac4acaba3c
   md5: ad659d0a2b3e47e38d829aa8cad2d610
@@ -1952,6 +1742,39 @@ packages:
   purls: []
   size: 119135
   timestamp: 1767016325805
+- pypi: https://files.pythonhosted.org/packages/39/08/aaaad47bc4e9dc8c725e68f9d04865dbcb2052843ff09c97b08904852d84/urllib3-2.6.3-py3-none-any.whl
+  name: urllib3
+  version: 2.6.3
+  sha256: bf272323e553dfb2e87d9bfd225ca7b0f467b919d7bbd355436d3fd37cb0acd4
+  requires_dist:
+  - brotli>=1.2.0 ; platform_python_implementation == 'CPython' and extra == 'brotli'
+  - brotlicffi>=1.2.0.0 ; platform_python_implementation != 'CPython' and extra == 'brotli'
+  - h2>=4,<5 ; extra == 'h2'
+  - pysocks>=1.5.6,!=1.5.7,<2.0 ; extra == 'socks'
+  - backports-zstd>=1.0.0 ; python_full_version < '3.14' and extra == 'zstd'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/8a/ca/0864176a649838b838f36d44bf31c451597ab363b60dc9e09c9630619d41/uvloop-0.21.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+  name: uvloop
+  version: 0.21.0
+  sha256: 8a375441696e2eda1c43c44ccb66e04d61ceeffcd76e4929e527b7fa401b90fb
+  requires_dist:
+  - setuptools>=60 ; extra == 'dev'
+  - cython~=3.0 ; extra == 'dev'
+  - sphinx~=4.1.2 ; extra == 'docs'
+  - sphinxcontrib-asyncio~=0.3.0 ; extra == 'docs'
+  - sphinx-rtd-theme~=0.5.2 ; extra == 'docs'
+  - aiohttp>=3.10.5 ; extra == 'test'
+  - flake8~=5.0 ; extra == 'test'
+  - psutil ; extra == 'test'
+  - pycodestyle~=2.9.0 ; extra == 'test'
+  - pyopenssl~=23.0.0 ; extra == 'test'
+  - mypy>=0.800 ; extra == 'test'
+  requires_python: '>=3.8.0'
+- pypi: https://files.pythonhosted.org/packages/5d/8f/a32a99fc03e4b37e31b57cb9cefc65050ea08147a8ce12f288616b05ef54/wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+  name: wrapt
+  version: 1.17.3
+  sha256: b32888aad8b6e68f83a8fdccbf3165f5469702a7544472bdf41f582970ed3311
+  requires_python: '>=3.8'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda
   sha256: c12396aabb21244c212e488bbdc4abcdef0b7404b15761d9329f5a4a39113c4b
   md5: fb901ff28063514abb6046c9ec2c4a45
@@ -2102,17 +1925,20 @@ packages:
   purls: []
   size: 32808
   timestamp: 1727964811275
-- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.2-h25fd6f3_2.conda
-  sha256: 245c9ee8d688e23661b95e3c6dd7272ca936fabc03d423cdb3cdee1bbcf9f2f2
-  md5: c2a01a08fc991620a74b32420e97868a
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libzlib 1.3.2 h25fd6f3_2
-  license: Zlib
-  license_family: Other
-  purls: []
-  size: 95931
-  timestamp: 1774072620848
+- pypi: https://files.pythonhosted.org/packages/a8/a9/d23012099dc88ec69a29c6407b41d89681cb674c2043cd5b467c7e299c08/xyzservices-2026.3.0-py3-none-any.whl
+  name: xyzservices
+  version: 2026.3.0
+  sha256: 503183d4b322bfebc3c50cdd21192aa3e81e36c5efbf9133d54ae82143e0576b
+  requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/9a/64/c53487d9f4968045b8afa51aed7ca44f58b2589e772f32745f3744476c82/yarl-1.23.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
+  name: yarl
+  version: 1.23.0
+  sha256: 99c8a9ed30f4164bc4c14b37a90208836cbf50d4ce2a57c71d0f52c7fb4f7598
+  requires_dist:
+  - idna>=2.0
+  - multidict>=4.0
+  - propcache>=0.2.1
+  requires_python: '>=3.10'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
   sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
   md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
diff --git a/spark-on-slurm/pixi.toml b/spark-on-slurm/pixi.toml
index d313f55..8806973 100644
--- a/spark-on-slurm/pixi.toml
+++ b/spark-on-slurm/pixi.toml
@@ -6,9 +6,16 @@ platforms = ["linux-64"]
 version = "0.1.0"
 
 [tasks]
-sparkhpc-example = "python sparkhpc/run_example.py"
+install-sparkhpc= "pip install -e sparkhpc"
+sparkhpc-validate = "python examples/validate_spark.py"
+sparkhpc-pi = "sparkcluster start 2 && python examples/pi_counter.py"
+sparkhpc-hail = "sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py"
 
 [dependencies]
 python = "3.11.*"
 openjdk = "==17.0.18"
-pyspark = ">=4.1.1,<5"
+
+[pypi-dependencies]
+pip = ">=26.0.1, <27"
+hail = "==0.2.137"
+pyspark = ">=3.5.8, <4"
diff --git a/spark-on-slurm/sparkhpc/sparkhpc/sparkjob.py b/spark-on-slurm/sparkhpc/sparkhpc/sparkjob.py
index 246376b..ce44f72 100644
--- a/spark-on-slurm/sparkhpc/sparkhpc/sparkjob.py
+++ b/spark-on-slurm/sparkhpc/sparkhpc/sparkjob.py
@@ -81,10 +81,33 @@ def _resolve_spark_home(explicit_spark_home=None):
 
     try:
         import pyspark
-        pyspark_home = os.path.dirname(pyspark.__file__)
-        if os.path.exists(pyspark_home):
-            return pyspark_home
-    except Exception:
+        pyspark_module = os.path.dirname(pyspark.__file__)
+        
+        # Check if pyspark has jars directory (typical for pip/conda/pixi installations)
+        if os.path.exists(os.path.join(pyspark_module, 'jars')):
+            return pyspark_module
+        
+        # For traditional Spark distributions, try to find the root
+        # pyspark is at /path/to/spark/python/pyspark or /path/to/spark/lib/python/pyspark
+        # Try going up to find a directory with bin/spark-submit and jars/
+        site_packages = os.path.dirname(pyspark_module)
+        python_lib = os.path.dirname(site_packages)
+        lib_dir = os.path.dirname(python_lib)
+        conda_env_root = os.path.dirname(lib_dir)
+        
+        # Check if environment root has spark binaries
+        if os.path.exists(os.path.join(conda_env_root, 'bin', 'spark-submit')):
+            if os.path.exists(os.path.join(conda_env_root, 'jars')):
+                return conda_env_root
+            if os.path.exists(os.path.join(conda_env_root, 'bin', 'spark-class')):
+                return conda_env_root
+        
+        # Fallback: check parent directory (for non-standard layouts)
+        parent = os.path.dirname(conda_env_root)
+        if os.path.exists(os.path.join(parent, 'bin', 'spark-submit')):
+            return parent
+            
+    except Exception as e:
         pass
 
     return os.path.join(os.path.expanduser('~'), 'spark')
@@ -148,7 +171,8 @@ def __init__(self,
                 spark_home=None,
                 master_log_dir=None,
                 master_log_filename='spark_master.out',
-                scheduler=None):
+                scheduler=None,
+                partition=None):
         """
         Creates a SparkJob
         
@@ -187,6 +211,8 @@ def __init__(self,
         scheduler: string
             specify manually which scheduler you want to use; 
             usually the automatic determination will work fine so this should not be used
+        partition: string
+            SLURM partition to submit the job to (e.g., 'gpu', 'cpu', 'long', etc.)
 
         Example usage:
         
@@ -243,7 +269,8 @@ def __init__(self,
                               'master_log_filename': master_log_filename,
                               'scheduler': scheduler,
                               'workdir': os.getcwd(),
-                              'extra_scheduler_options': extra_scheduler_options
+                              'extra_scheduler_options': extra_scheduler_options,
+                              'partition': partition
                               }
 
         signal.signal(signal.SIGINT, self._sigint_handler)
@@ -357,11 +384,24 @@ def submit(self):
 
         if self.template is None: 
             template_file = templates[self.__class__]
-            template_str = resources.files('sparkhpc').joinpath('templates', template_file).read_text()
+            # Try to get template from package resources first (for installed packages)
+            try:
+                template_str = resources.files('sparkhpc').joinpath('templates').joinpath(template_file).read_text()
+            except (FileNotFoundError, TypeError, AttributeError):
+                # Fallback for development versions: use file path relative to this module
+                template_dir = os.path.join(os.path.dirname(__file__), 'templates')
+                template_path = os.path.join(template_dir, template_file)
+                with open(template_path) as f:
+                    template_str = f.read()
         else : 
             with open(self.template) as template_file: 
                 template_str = template_file.read()
 
+        # Construct partition directive
+        partition_directive = ""
+        if self.partition:
+            partition_directive = "#SBATCH -p {partition}".format(partition=self.partition)
+
         job = template_str.format(walltime=self.walltime, 
                                   ncores=self.ncores, 
                                   cores_per_executor=self.cores_per_executor,
@@ -372,7 +412,8 @@ def submit(self):
                                   spark_home=self.spark_home,
                                   master_log_dir=self.master_log_dir,
                                   master_log_filename=self.master_log_filename,
-                                  extra_scheduler_options=self.extra_scheduler_options)
+                                  extra_scheduler_options=self.extra_scheduler_options,
+                                  partition=partition_directive)
 
         with open('job', 'w') as jobfile: 
             jobfile.write(job)
diff --git a/spark-on-slurm/sparkhpc/sparkhpc/templates/sparkjob.slurm.template b/spark-on-slurm/sparkhpc/sparkhpc/templates/sparkjob.slurm.template
index ebe34e9..7a640b2 100755
--- a/spark-on-slurm/sparkhpc/sparkhpc/templates/sparkjob.slurm.template
+++ b/spark-on-slurm/sparkhpc/sparkhpc/templates/sparkjob.slurm.template
@@ -5,8 +5,9 @@
 #SBATCH -n {number_of_executors:d} # requesting n tasks
 #SBATCH -c {cores_per_executor:d}
 #SBATCH --mem-per-cpu={memory_per_core:d} 
-#SBATCH -N {number_of_executors:d}
+#SBATCH -N 1 # number of nodes
 #SBATCH --ntasks-per-core=1
+{partition}
 
 # setup the spark paths
 import os

From 49c6f9d4ee961f6cc6d841af3f3d5d866de3f5ed Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Thu, 9 Apr 2026 23:06:09 +0700
Subject: [PATCH 2/8] chore: add spark slurm to readme

---
 Readme.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Readme.md b/Readme.md
index 6e235c3..1ce4921 100644
--- a/Readme.md
+++ b/Readme.md
@@ -3,3 +3,4 @@
 Genomics Kit integrates the utilities for bioinformatics analysis
 
 1. [igv-report](./igv-report): Generate the IGV report html format
+2. [spark-on-slurm](./spark-on-slurm/): Spark on SLURM cluster configuration

From f5e26518a947c7c7714e00eaba70c48800ac59cf Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Thu, 9 Apr 2026 23:21:37 +0700
Subject: [PATCH 3/8] fix: install sparkhpc

---
 spark-on-slurm/Makefile  | 2 +-
 spark-on-slurm/pixi.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/spark-on-slurm/Makefile b/spark-on-slurm/Makefile
index 1e1afcd..2051f83 100644
--- a/spark-on-slurm/Makefile
+++ b/spark-on-slurm/Makefile
@@ -39,7 +39,7 @@ install:
 test: ${HOME}/.pixi/bin/pixi start-slurm get-slurm
 	docker exec \
 		-w /tmp/spark \
-		slurm-dev /root/.pixi/bin/pixi run sparkhpc-hail
+		slurm-dev bash -c "/root/.pixi/bin/pixi run install && /root/.pixi/bin/pixi run sparkhpc-hail"
 
 test-slurm-local:
 	${HOME}/.pixi/bin/pixi run sparkhpc-example
diff --git a/spark-on-slurm/pixi.toml b/spark-on-slurm/pixi.toml
index 8806973..46986bc 100644
--- a/spark-on-slurm/pixi.toml
+++ b/spark-on-slurm/pixi.toml
@@ -6,7 +6,7 @@ platforms = ["linux-64"]
 version = "0.1.0"
 
 [tasks]
-install-sparkhpc= "pip install -e sparkhpc"
+install = "pip install -e sparkhpc"
 sparkhpc-validate = "python examples/validate_spark.py"
 sparkhpc-pi = "sparkcluster start 2 && python examples/pi_counter.py"
 sparkhpc-hail = "sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py"

From 2df7ddbbea4bf94dfac7e7257a6744735901a5f7 Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Thu, 9 Apr 2026 23:35:11 +0700
Subject: [PATCH 4/8] chore: add bash history to gitignore

---
 spark-on-slurm/.bash_history | 6 ------
 spark-on-slurm/.gitignore    | 3 ++-
 2 files changed, 2 insertions(+), 7 deletions(-)
 delete mode 100644 spark-on-slurm/.bash_history

diff --git a/spark-on-slurm/.bash_history b/spark-on-slurm/.bash_history
deleted file mode 100644
index 5bc9a2a..0000000
--- a/spark-on-slurm/.bash_history
+++ /dev/null
@@ -1,6 +0,0 @@
-squeue
-sinfo
-ls
-cd 
-ls
-make example
diff --git a/spark-on-slurm/.gitignore b/spark-on-slurm/.gitignore
index 04dd98e..bb5a52a 100644
--- a/spark-on-slurm/.gitignore
+++ b/spark-on-slurm/.gitignore
@@ -3,4 +3,5 @@ sparkcluster*
 .cache
 spark_master.out
 job
-*.log
\ No newline at end of file
+*.log
+.bash_history
\ No newline at end of file

From b5c619b5827a1dc61f2258248573061a8ae1bea6 Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Thu, 9 Apr 2026 23:38:48 +0700
Subject: [PATCH 5/8] fix: install editable sparkhpc

---
 spark-on-slurm/pixi.lock | 64 ++++++++++++++++++++++++++++++++--------
 spark-on-slurm/pixi.toml |  5 ++--
 2 files changed, 55 insertions(+), 14 deletions(-)

diff --git a/spark-on-slurm/pixi.lock b/spark-on-slurm/pixi.lock
index 77bd0d3..565541d 100644
--- a/spark-on-slurm/pixi.lock
+++ b/spark-on-slurm/pixi.lock
@@ -58,13 +58,17 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openjdk-17.0.18-ha668962_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.47-haa7fec5_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh8b19718_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.15-hd63d673_0_cpython.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-82.0.1-pyh332efcf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.13-he1eb515_0.conda
@@ -124,11 +128,9 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/cf/c5/9fcb7e0e69cef59cf10c746b84f7d58b08bc66a6b7d459783c5a4f6101a6/numpy-2.4.4-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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-      - pypi: https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/bf/c9/63f8d545568d9ab91476b1818b4741f521646cbdd151c6efebf40d6de6f7/pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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       - pypi: https://files.pythonhosted.org/packages/e9/bd/e51a61b1054f09437acfbc2ff9106c30d1eb76bc1453d428399946781253/pillow-12.2.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
-      - pypi: https://files.pythonhosted.org/packages/de/f0/c81e05b613866b76d2d1066490adf1a3dbc4ee9d9c839961c3fc8a6997af/pip-26.0.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e5/ae/580600f441f6fc05218bd6c9d5794f4aef072a7d9093b291f1c50a9db8bc/plotly-5.24.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/52/6a/57f43e054fb3d3a56ac9fc532bc684fc6169a26c75c353e65425b3e56eef/propcache-0.4.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/bd/db/ea0203e495be491c85af87b66e37acfd3bf756fd985f87e46fc5e3bf022c/py4j-0.10.9.9-py2.py3-none-any.whl
@@ -1247,11 +1249,18 @@ packages:
   version: 3.11.8
   sha256: 5f8952d6d2505c003e8f0224ff7858d341fa4e33fef82b91c4ff0ef070f2393c
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl
-  name: packaging
-  version: '26.0'
-  sha256: b36f1fef9334a5588b4166f8bcd26a14e521f2b55e6b9de3aaa80d3ff7a37529
-  requires_python: '>=3.8'
+- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda
+  sha256: c1fc0f953048f743385d31c468b4a678b3ad20caffdeaa94bed85ba63049fd58
+  md5: b76541e68fea4d511b1ac46a28dcd2c6
+  depends:
+  - python >=3.8
+  - python
+  license: Apache-2.0
+  license_family: APACHE
+  purls:
+  - pkg:pypi/packaging?source=compressed-mapping
+  size: 72010
+  timestamp: 1769093650580
 - pypi: https://files.pythonhosted.org/packages/bf/c9/63f8d545568d9ab91476b1818b4741f521646cbdd151c6efebf40d6de6f7/pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
   name: pandas
   version: 2.3.3
@@ -1395,11 +1404,19 @@ packages:
   - trove-classifiers>=2024.10.12 ; extra == 'tests'
   - defusedxml ; extra == 'xmp'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/de/f0/c81e05b613866b76d2d1066490adf1a3dbc4ee9d9c839961c3fc8a6997af/pip-26.0.1-py3-none-any.whl
-  name: pip
-  version: 26.0.1
-  sha256: bdb1b08f4274833d62c1aa29e20907365a2ceb950410df15fc9521bad440122b
-  requires_python: '>=3.9'
+- conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh8b19718_0.conda
+  sha256: 8e1497814a9997654ed7990a79c054ea5a42545679407acbc6f7e809c73c9120
+  md5: 67bdec43082fd8a9cffb9484420b39a2
+  depends:
+  - python >=3.10,<3.13.0a0
+  - setuptools
+  - wheel
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/pip?source=compressed-mapping
+  size: 1181790
+  timestamp: 1770270305795
 - conda: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda
   sha256: 43d37bc9ca3b257c5dd7bf76a8426addbdec381f6786ff441dc90b1a49143b6a
   md5: c01af13bdc553d1a8fbfff6e8db075f0
@@ -1664,6 +1681,17 @@ packages:
   - ruff>=0.12.0 ; extra == 'dev'
   - cython-lint>=0.12.2 ; extra == 'dev'
   requires_python: '>=3.11'
+- conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-82.0.1-pyh332efcf_0.conda
+  sha256: 82088a6e4daa33329a30bc26dc19a98c7c1d3f05c0f73ce9845d4eab4924e9e1
+  md5: 8e194e7b992f99a5015edbd4ebd38efd
+  depends:
+  - python >=3.10
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/setuptools?source=compressed-mapping
+  size: 639697
+  timestamp: 1773074868565
 - pypi: https://files.pythonhosted.org/packages/e0/f9/0595336914c5619e5f28a1fb793285925a8cd4b432c9da0a987836c7f822/shellingham-1.5.4-py2.py3-none-any.whl
   name: shellingham
   version: 1.5.4
@@ -1770,6 +1798,18 @@ packages:
   - pyopenssl~=23.0.0 ; extra == 'test'
   - mypy>=0.800 ; extra == 'test'
   requires_python: '>=3.8.0'
+- conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda
+  sha256: d6cf2f0ebd5e09120c28ecba450556ce553752652d91795442f0e70f837126ae
+  md5: bdbd7385b4a67025ac2dba4ef8cb6a8f
+  depends:
+  - packaging >=24.0
+  - python >=3.10
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/wheel?source=hash-mapping
+  size: 31858
+  timestamp: 1769139207397
 - pypi: https://files.pythonhosted.org/packages/5d/8f/a32a99fc03e4b37e31b57cb9cefc65050ea08147a8ce12f288616b05ef54/wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
   name: wrapt
   version: 1.17.3
diff --git a/spark-on-slurm/pixi.toml b/spark-on-slurm/pixi.toml
index 46986bc..1fafd93 100644
--- a/spark-on-slurm/pixi.toml
+++ b/spark-on-slurm/pixi.toml
@@ -6,7 +6,8 @@ platforms = ["linux-64"]
 version = "0.1.0"
 
 [tasks]
-install = "pip install -e sparkhpc"
+install = "python -m pip install -e sparkhpc"
+install-sparkhpc = "python -m pip install -e sparkhpc"
 sparkhpc-validate = "python examples/validate_spark.py"
 sparkhpc-pi = "sparkcluster start 2 && python examples/pi_counter.py"
 sparkhpc-hail = "sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py"
@@ -14,8 +15,8 @@ sparkhpc-hail = "sparkcluster start 2 && sleep 10 && python examples/simulate_gw
 [dependencies]
 python = "3.11.*"
 openjdk = "==17.0.18"
+pip = ">=26.0.1"
 
 [pypi-dependencies]
-pip = ">=26.0.1, <27"
 hail = "==0.2.137"
 pyspark = ">=3.5.8, <4"

From d08a95012d03c03255419240c7f055ec77ceaed2 Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Thu, 9 Apr 2026 23:52:02 +0700
Subject: [PATCH 6/8] fix: install editable sparkhpc

---
 spark-on-slurm/Makefile  | 2 +-
 spark-on-slurm/pixi.toml | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/spark-on-slurm/Makefile b/spark-on-slurm/Makefile
index 2051f83..1e1afcd 100644
--- a/spark-on-slurm/Makefile
+++ b/spark-on-slurm/Makefile
@@ -39,7 +39,7 @@ install:
 test: ${HOME}/.pixi/bin/pixi start-slurm get-slurm
 	docker exec \
 		-w /tmp/spark \
-		slurm-dev bash -c "/root/.pixi/bin/pixi run install && /root/.pixi/bin/pixi run sparkhpc-hail"
+		slurm-dev /root/.pixi/bin/pixi run sparkhpc-hail
 
 test-slurm-local:
 	${HOME}/.pixi/bin/pixi run sparkhpc-example
diff --git a/spark-on-slurm/pixi.toml b/spark-on-slurm/pixi.toml
index 1fafd93..ebb9233 100644
--- a/spark-on-slurm/pixi.toml
+++ b/spark-on-slurm/pixi.toml
@@ -7,10 +7,9 @@ version = "0.1.0"
 
 [tasks]
 install = "python -m pip install -e sparkhpc"
-install-sparkhpc = "python -m pip install -e sparkhpc"
 sparkhpc-validate = "python examples/validate_spark.py"
-sparkhpc-pi = "sparkcluster start 2 && python examples/pi_counter.py"
-sparkhpc-hail = "sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py"
+sparkhpc-pi = "python sparkhpc/scripts/sparkcluster start 2 && python examples/pi_counter.py"
+sparkhpc-hail = "python sparkhpc/scripts/sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py"
 
 [dependencies]
 python = "3.11.*"

From 0eb0ef3ecfacaf61007fe203de0be5448455c7d1 Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Thu, 9 Apr 2026 23:58:24 +0700
Subject: [PATCH 7/8] fix: add local sparkhpc to pixi

---
 spark-on-slurm/pixi.lock | 71 +++++++++++-----------------------------
 spark-on-slurm/pixi.toml |  7 ++--
 2 files changed, 22 insertions(+), 56 deletions(-)

diff --git a/spark-on-slurm/pixi.lock b/spark-on-slurm/pixi.lock
index 565541d..420dad1 100644
--- a/spark-on-slurm/pixi.lock
+++ b/spark-on-slurm/pixi.lock
@@ -58,17 +58,13 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openjdk-17.0.18-ha668962_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.47-haa7fec5_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh8b19718_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.11.15-hd63d673_0_cpython.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-82.0.1-pyh332efcf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.13-he1eb515_0.conda
@@ -108,6 +104,7 @@ environments:
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+      - pypi: https://files.pythonhosted.org/packages/a4/cb/7d2bb508f4ca00a043fd53e8156c11767799d3f534bf451a0942211d5def/findspark-2.0.1-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/11/b1/71a477adc7c36e5fb628245dfbdea2166feae310757dea848d02bd0689fd/frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/e9/eb/c6c2478d8a8d633460be40e2a8a6f8f429171997a35a96f81d3b680dec83/google_auth-2.49.1-py3-none-any.whl
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@@ -128,6 +125,7 @@ environments:
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+      - pypi: https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl
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       - pypi: https://files.pythonhosted.org/packages/f1/a9/a10a10f12e50993b5a3568a1a90fd70b85f83edc451875d312bf60cd39b8/parsimonious-0.11.0-py3-none-any.whl
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@@ -165,6 +163,7 @@ environments:
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       - pypi: https://files.pythonhosted.org/packages/a8/a9/d23012099dc88ec69a29c6407b41d89681cb674c2043cd5b467c7e299c08/xyzservices-2026.3.0-py3-none-any.whl
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+      - pypi: ./sparkhpc
 packages:
 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
   build_number: 20
@@ -497,6 +496,10 @@ packages:
   - objgraph>=1.7.2 ; extra == 'graph'
   - gprof2dot>=2022.7.29 ; extra == 'profile'
   requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/a4/cb/7d2bb508f4ca00a043fd53e8156c11767799d3f534bf451a0942211d5def/findspark-2.0.1-py2.py3-none-any.whl
+  name: findspark
+  version: 2.0.1
+  sha256: e5d5415ff8ced6b173b801e12fc90c1eefca1fb6bf9c19c4fc1f235d4222e753
 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
   sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b
   md5: 0c96522c6bdaed4b1566d11387caaf45
@@ -1249,18 +1252,11 @@ packages:
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   sha256: 5f8952d6d2505c003e8f0224ff7858d341fa4e33fef82b91c4ff0ef070f2393c
   requires_python: '>=3.10'
-- conda: https://conda.anaconda.org/conda-forge/noarch/packaging-26.0-pyhcf101f3_0.conda
-  sha256: c1fc0f953048f743385d31c468b4a678b3ad20caffdeaa94bed85ba63049fd58
-  md5: b76541e68fea4d511b1ac46a28dcd2c6
-  depends:
-  - python >=3.8
-  - python
-  license: Apache-2.0
-  license_family: APACHE
-  purls:
-  - pkg:pypi/packaging?source=compressed-mapping
-  size: 72010
-  timestamp: 1769093650580
+- pypi: https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl
+  name: packaging
+  version: '26.0'
+  sha256: b36f1fef9334a5588b4166f8bcd26a14e521f2b55e6b9de3aaa80d3ff7a37529
+  requires_python: '>=3.8'
 - pypi: https://files.pythonhosted.org/packages/bf/c9/63f8d545568d9ab91476b1818b4741f521646cbdd151c6efebf40d6de6f7/pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
   name: pandas
   version: 2.3.3
@@ -1404,19 +1400,6 @@ packages:
   - trove-classifiers>=2024.10.12 ; extra == 'tests'
   - defusedxml ; extra == 'xmp'
   requires_python: '>=3.10'
-- conda: https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh8b19718_0.conda
-  sha256: 8e1497814a9997654ed7990a79c054ea5a42545679407acbc6f7e809c73c9120
-  md5: 67bdec43082fd8a9cffb9484420b39a2
-  depends:
-  - python >=3.10,<3.13.0a0
-  - setuptools
-  - wheel
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/pip?source=compressed-mapping
-  size: 1181790
-  timestamp: 1770270305795
 - conda: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda
   sha256: 43d37bc9ca3b257c5dd7bf76a8426addbdec381f6786ff441dc90b1a49143b6a
   md5: c01af13bdc553d1a8fbfff6e8db075f0
@@ -1681,17 +1664,6 @@ packages:
   - ruff>=0.12.0 ; extra == 'dev'
   - cython-lint>=0.12.2 ; extra == 'dev'
   requires_python: '>=3.11'
-- conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-82.0.1-pyh332efcf_0.conda
-  sha256: 82088a6e4daa33329a30bc26dc19a98c7c1d3f05c0f73ce9845d4eab4924e9e1
-  md5: 8e194e7b992f99a5015edbd4ebd38efd
-  depends:
-  - python >=3.10
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/setuptools?source=compressed-mapping
-  size: 639697
-  timestamp: 1773074868565
 - pypi: https://files.pythonhosted.org/packages/e0/f9/0595336914c5619e5f28a1fb793285925a8cd4b432c9da0a987836c7f822/shellingham-1.5.4-py2.py3-none-any.whl
   name: shellingham
   version: 1.5.4
@@ -1706,6 +1678,13 @@ packages:
   name: sortedcontainers
   version: 2.4.0
   sha256: a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0
+- pypi: ./sparkhpc
+  name: sparkhpc
+  version: 0.3.post4
+  sha256: e04b7a91a93671f75bd1ce0cb032d4e8d5911a8a97acaea1ec8f77bbbf55d49b
+  requires_dist:
+  - click
+  - findspark
 - pypi: https://files.pythonhosted.org/packages/99/55/db07de81b5c630da5cbf5c7df646580ca26dfaefa593667fc6f2fe016d2e/tabulate-0.10.0-py3-none-any.whl
   name: tabulate
   version: 0.10.0
@@ -1798,18 +1777,6 @@ packages:
   - pyopenssl~=23.0.0 ; extra == 'test'
   - mypy>=0.800 ; extra == 'test'
   requires_python: '>=3.8.0'
-- conda: https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda
-  sha256: d6cf2f0ebd5e09120c28ecba450556ce553752652d91795442f0e70f837126ae
-  md5: bdbd7385b4a67025ac2dba4ef8cb6a8f
-  depends:
-  - packaging >=24.0
-  - python >=3.10
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/wheel?source=hash-mapping
-  size: 31858
-  timestamp: 1769139207397
 - pypi: https://files.pythonhosted.org/packages/5d/8f/a32a99fc03e4b37e31b57cb9cefc65050ea08147a8ce12f288616b05ef54/wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
   name: wrapt
   version: 1.17.3
diff --git a/spark-on-slurm/pixi.toml b/spark-on-slurm/pixi.toml
index ebb9233..be438ea 100644
--- a/spark-on-slurm/pixi.toml
+++ b/spark-on-slurm/pixi.toml
@@ -6,16 +6,15 @@ platforms = ["linux-64"]
 version = "0.1.0"
 
 [tasks]
-install = "python -m pip install -e sparkhpc"
 sparkhpc-validate = "python examples/validate_spark.py"
-sparkhpc-pi = "python sparkhpc/scripts/sparkcluster start 2 && python examples/pi_counter.py"
-sparkhpc-hail = "python sparkhpc/scripts/sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py"
+sparkhpc-pi = "sparkcluster start 2 && python examples/pi_counter.py"
+sparkhpc-hail = "sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py"
 
 [dependencies]
 python = "3.11.*"
 openjdk = "==17.0.18"
-pip = ">=26.0.1"
 
 [pypi-dependencies]
 hail = "==0.2.137"
 pyspark = ">=3.5.8, <4"
+sparkhpc = { path = "./sparkhpc", editable = true }
\ No newline at end of file

From 4416e7b19df47e74b8161653576e32d1726ceb77 Mon Sep 17 00:00:00 2001
From: nttg8100 <nttg8100@gmail>
Date: Fri, 10 Apr 2026 00:04:03 +0700
Subject: [PATCH 8/8] fix: spark cluster

---
 spark-on-slurm/.gitignore                    |   2 +-
 spark-on-slurm/sparkhpc/scripts/sparkcluster | 104 +++++++++++++++++++
 2 files changed, 105 insertions(+), 1 deletion(-)
 create mode 100755 spark-on-slurm/sparkhpc/scripts/sparkcluster

diff --git a/spark-on-slurm/.gitignore b/spark-on-slurm/.gitignore
index bb5a52a..6246335 100644
--- a/spark-on-slurm/.gitignore
+++ b/spark-on-slurm/.gitignore
@@ -1,4 +1,4 @@
-sparkcluster*
+sparkcluster-.*log
 .spark*
 .cache
 spark_master.out
diff --git a/spark-on-slurm/sparkhpc/scripts/sparkcluster b/spark-on-slurm/sparkhpc/scripts/sparkcluster
new file mode 100755
index 0000000..9a3e676
--- /dev/null
+++ b/spark-on-slurm/sparkhpc/scripts/sparkcluster
@@ -0,0 +1,104 @@
+#!/bin/env python
+#
+#
+# CLI for starting and running Spark standalone clusters on HPC resources
+#
+#
+
+from __future__ import print_function
+import click
+import sparkhpc
+from sparkhpc import sparkjob
+import subprocess
+import os
+import logging
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger('sparkhpc')
+
+home = os.path.expanduser('~')
+
+SCHEDULER = sparkjob.get_scheduler()
+
+@click.group()
+def cli():
+    pass
+
+@cli.command()
+@click.argument('ncores', type=int)
+@click.option('--walltime', default="00:30", help="Walltime in HH:MM format")
+@click.option('--jobname', default='sparkcluster', help='Name to use for the job')
+@click.option('--template', default=None, help='Job template path')
+@click.option('--memory-per-executor', default=2000, envvar='SPARK_EXECUTOR_MEMORY',
+              help='Memory to reserve for each executor (i.e. the JVM) in MB')
+@click.option('--memory-per-core', default=2000,
+              help='Memory per core to request from scheduler in MB')
+@click.option('--cores-per-executor', default=1,
+              help='Cores per executor')
+@click.option('--spark-home', default=None, envvar='SPARK_HOME', 
+              help='Location of the Spark distribution')
+@click.option('--partition', default=None,
+              help='SLURM partition to submit job to')
+@click.option('--wait', default=False, is_flag=True, help='Wait until the job starts')
+def start(ncores, 
+          walltime, 
+          jobname, 
+          template, 
+          memory_per_executor, 
+          memory_per_core, 
+          cores_per_executor,
+          spark_home, 
+          partition,
+          wait):
+    """Start the spark cluster as a batch job"""
+    
+    sj = sparkjob.sparkjob(ncores=ncores, 
+                           walltime=walltime, 
+                           jobname=jobname, 
+                           template=template, 
+                           memory_per_core=memory_per_core,
+                           memory_per_executor=memory_per_executor, 
+                           cores_per_executor=cores_per_executor,
+                           spark_home=spark_home,
+                           partition=partition)
+    
+    if wait: 
+        logger.info(' Waiting for job to start - ctrl-c to stop')
+        sj.wait_to_start()
+    else:
+        sj.submit()
+    
+
+@cli.command()
+def info():
+    """Get info about currently running clusters"""
+    sparkhpc.show_clusters()
+
+
+@cli.command()
+@click.argument('clusterid')
+def stop(clusterid):
+    """Kill a currently running cluster ('all' to kill all clusters)"""
+    sjs = sparkjob.sparkjob().current_clusters()
+
+    if clusterid == 'all': 
+        if len(sjs) == 0: 
+            logger.info(' No clusters running')
+        for sj in sjs: 
+            sj.stop()
+    elif int(clusterid) < len(sjs): 
+        sjs[int(clusterid)].stop()
+    else: 
+        raise RuntimeError('Cluster %s does not exist'%clusterid)
+
+
+@cli.command()
+@click.option('--memory', default='2000M', help='Memory for each executor using a Java memory string')
+@click.option('--timeout', default=30, help='Timeout for starting spark master')
+@click.option('--cores-per-executor', default=1, help='Number of cores per executor')
+def launch(memory, timeout, cores_per_executor):
+    """Launch the Spark master and workers within a current job context"""
+    sparkjob.start_cluster(memory, timeout=timeout, cores_per_executor=cores_per_executor)
+
+if __name__ == "__main__":
+    cli()