# Java gateway process exited before sending its port number **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [January 27, 2020, 12:42pm UTC](https://discuss.hail.is/t/java-gateway-process-exited-before-sending-its-port-number/1260 "2020-01-27T12:42:38Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![gosborcz](https://avatars.discourse-cdn.com/v4/letter/g/34f0e0/32.png) [@gosborcz](https://discuss.hail.is/u/gosborcz)\ **Post date:** [January 27, 2020, 12:42pm UTC](https://discuss.hail.is/t/java-gateway-process-exited-before-sending-its-port-number/1260/1 "2020-01-27T12:42:38Z")
Hi, So I am trying to start using hail on a cluster, and apparently everything that I need should be already there, but when I try to check if hails is working I get the following error: ```auto Initializing Spark and Hail with default parameters... --------------------------------------------------------------------------- Exception Traceback (most recent call last) in () ----> 1 mt = hl.balding_nichols_model(3,100,100) 2 mt._force_count_rows() in balding_nichols_model(n_populations, n_samples, n_variants, n_partitions, pop_dist, fst, af_dist, reference_genome, mixture) /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 582 @decorator 583 def wrapper(__original_func, *args, **kwargs): --> 584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) 585 return __original_func(*args_, **kwargs_) 586 /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/typecheck/check.py in check_all(f, args, kwargs, checks, is_method) 510 if i < len(args): 511 arg = args[i] --> 512 args_.append(checker.check(arg, name, arg_name)) 513 # passed as keyword 514 else: /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/typecheck/check.py in check(self, x, caller, param) 54 for tc in self.checkers: 55 try: ---> 56 return tc.check(x, caller, param) 57 except TypecheckFailure: 58 pass /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/typecheck/check.py in check(self, x, caller, param) 301 for tc, f in self.fs: 302 try: --> 303 return f(tc.check(x, caller, param)) 304 except TypecheckFailure: 305 pass /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/genetics/reference_genome.py in (x) 8 9 rg_type = lazy() ---> 10 reference_genome_type = oneof(transformed((str, lambda x: hl.get_reference(x))), rg_type) 11 12 /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/context.py in get_reference(name) 384 :class:`.ReferenceGenome` 385 """ --> 386 Env.hc() 387 if name == 'default': 388 return default_reference() /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/utils/java.py in hc() 65 import sys 66 sys.stderr.write("Initializing Spark and Hail with default parameters...\n") ---> 67 init() 68 assert Env._hc is not None 69 return Env._hc in init(sc, app_name, master, local, log, quiet, append, min_block_size, branching_factor, tmp_dir, default_reference, idempotent, global_seed, _optimizer_iterations, _backend) /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 583 def wrapper(__original_func, *args, **kwargs): 584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 585 return __original_func(*args_, **kwargs_) 586 587 return wrapper /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/context.py in init(sc, app_name, master, local, log, quiet, append, min_block_size, branching_factor, tmp_dir, default_reference, idempotent, global_seed, _optimizer_iterations, _backend) 277 min_block_size, branching_factor, tmp_dir, 278 default_reference, idempotent, global_seed, --> 279 _optimizer_iterations,_backend) 280 281 in __init__ (self, sc, app_name, master, local, log, quiet, append, min_block_size, branching_factor, tmp_dir, default_reference, idempotent, global_seed, optimizer_iterations, _backend) /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/typecheck/check.py in wrapper(__original_func, *args, **kwargs) 583 def wrapper(__original_func, *args, **kwargs): 584 args_, kwargs_ = check_all(__original_func, args, kwargs, checkers, is_method=is_method) --> 585 return __original_func(*args_, **kwargs_) 586 587 return wrapper /net/software/local/python/3.6.5/lib/python3.6/site-packages/hail/context.py in __init__ (self, sc, app_name, master, local, log, quiet, append, min_block_size, branching_factor, tmp_dir, default_reference, idempotent, global_seed, optimizer_iterations, _backend) 58 conf.set('spark.executor.extraClassPath', './hail-all-spark.jar') 59 if sc is None: ---> 60 SparkContext._ensure_initialized(conf=conf) 61 else: 62 import warnings /net/software/local/python/3.6.5/lib/python3.6/site-packages/pyspark/context.py in _ensure_initialized(cls, instance, gateway, conf) 314 with SparkContext._lock: 315 if not SparkContext._gateway: --> 316 SparkContext._gateway = gateway or launch_gateway(conf) 317 SparkContext._jvm = SparkContext._gateway.jvm 318 /net/software/local/python/3.6.5/lib/python3.6/site-packages/pyspark/java_gateway.py in launch_gateway(conf) 44 :return: a JVM gateway 45 """ ---> 46 return _launch_gateway(conf) 47 48 /net/software/local/python/3.6.5/lib/python3.6/site-packages/pyspark/java_gateway.py in _launch_gateway(conf, insecure) 106 107 if not os.path.isfile(conn_info_file): --> 108 raise Exception("Java gateway process exited before sending its port number") 109 110 with open(conn_info_file, "rb") as info: Exception: Java gateway process exited before sending its port number ``` Could you point me to the problem here? I have some assistance for the cluster, but I don’t really understand what am I missing here for hail to run. Thank you so much! ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [January 27, 2020, 12:50pm UTC](https://discuss.hail.is/t/java-gateway-process-exited-before-sending-its-port-number/1260/2 "2020-01-27T12:50:39Z")
It looks like Spark isn’t starting correctly. 1. Run `pyspark` from your terminal, and then in the REPL, run `spark.range(100).count()` to try to run something. If this doesn’t work, then Spark is misconfigured somehow. 2. If that **does** work, then we need a little more info about how Hail is installed. Can you describe which installation method was used (pip install or compile from source and how) and post the output of `java -version` here? ---
**Author:** ![gosborcz](https://avatars.discourse-cdn.com/v4/letter/g/34f0e0/32.png) [@gosborcz](https://discuss.hail.is/u/gosborcz)\ **Post date:** [January 28, 2020, 1:12am UTC](https://discuss.hail.is/t/java-gateway-process-exited-before-sending-its-port-number/1260/3 "2020-01-28T01:12:32Z")
I can’t run `pyspark` at all for now, as my permissions on this cluster won’t allow me. So that may be the problem. I will post more info here as soon as I fix that. ---
**Author:** ![gosborcz](https://avatars.discourse-cdn.com/v4/letter/g/34f0e0/32.png) [@gosborcz](https://discuss.hail.is/u/gosborcz)\ **Post date:** [February 3, 2020, 1:02am UTC](https://discuss.hail.is/t/java-gateway-process-exited-before-sending-its-port-number/1260/4 "2020-02-03T01:02:28Z")
Hi, it took quite some time to fix my permissions, but the problem was indeed Spark not starting correctly. Everything is working now. Thanks for help. ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [February 3, 2020, 12:24pm UTC](https://discuss.hail.is/t/java-gateway-process-exited-before-sending-its-port-number/1260/5 "2020-02-03T12:24:19Z")
great!