Comments (10)
Are you sure that you're launching the pyspark shell from the binary distribution with scala 2.11? Maybe you're launching a pip or conda installed version? I'm pretty sure that your error is caused by a scala version mismatch.
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@henrydavidge I am sure that the version of scala I am using is 2.11.12, which comes with the sprak-bin. There is no problem with using spark-shell to start glow. If it is caused by the scala version, the spark-shell should not work properly. , But only pyspark will report an error, the following is the spark-shell startup interface:
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@lsygxw Yep, the fact that you only get an error when using pyspark makes me think that the pyspark shell corresponds to a different spark installation with the wrong scala version.
Try running these commands in the pyspark shell:
>>> spark._jvm.scala.util.Properties.versionString()
>>> spark._jvm.scala.util.Properties.javaVersion()
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@henrydavidge First of all, thank you for your help. The result is as follows after executing in pyspark according to your method:
Are the results as expected?
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Hm, that does look like the right scala and java version. How exactly are you installing glow?
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@henrydavidge Same as the demo on your document pip3 install glow.py
Is it possible to lack some dependency or configuration? My 'spark-env.sh' configuration is as follows:
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I get the same error with the versions below.
____ __
/ __/__ ___ _____/ /__
_\ \/ _ \/ _ `/ __/ '_/
/__ / .__/_,// //_\ version 2.4.3
//
Using Python version 3.6.9 (default, Apr 18 2020 01:56:04)
SparkSession available as 'spark'.
spark._jvm.scala.util.Properties.versionString()
'version 2.11.12'
spark._jvm.scala.util.Properties.javaVersion()
'1.8.0-adoptopenjdk'
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In my case the problem was that I used the dowloaded glow jar file instead of the --packages option because of a corporate proxy. That did not load the dependencies and caused problems.
this was required to get proxy and certificates working:
pyspark --conf "spark.driver.extraJavaOptions=-Djava.net.useSystemProxies=true -Djavax.net.ssl.trustStore=keystore.jks" --packages io.projectglow:glow_2.11:0.4.0
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Ah, thank you for the response @magelan! That explains why I couldn't reproduce. @lsygxw is that your problem as well?
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I'm tentatively going to close. @lsygxw feel free to reopen if your issue persists.
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Related Issues (20)
- VCF Infinity/NaN values are not handled according to VCF spec
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- Load glow mave package from Python HOT 5
- spark.read.format("vcf").load() fails for vcf.bgz files HOT 3
- Cannot write INFO fields with LongType to VCF HOT 2
- Python tests fail with KeyError: '_glow_regression_values' HOT 1
- Logistic regression ValueError: Null fit failed! HOT 2
- AnalysisException: Column 'num_workers' does not exist. HOT 1
- pipe transformer support for file input/output for command line apps HOT 2
- Interaction Tests with GLOW HOT 1
- Spark version upgrade 3.4, 3.3 HOT 5
- Cannot install+use the python glow package any more HOT 2
- Regular updates to work with cloud providers HOT 1
- Problem importing Glow HOT 3
- glow.normalize_variant fails with NullPointerException in NormalizeVariantExpr.scala:55 HOT 4
- Unexpected behaviour when using the SplitMultiallelics Transformer with unbounded INFO fields HOT 2
- import glow throws error: module 'numpy' has no attribute 'unicode'. Did you mean: 'unicode_'? HOT 2
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- Comparision of performance of regenie WGR and glow WGR HOT 2
- Pandas should be pinned <2.0.0 HOT 1
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