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id1 : jvm   34

Lessons learned about monitoring the JVM in the era of containers
Java Virtual Machine (JVM) has been around for a long time (1994) so it’s hardly a surprise there are hundreds of tools to monitor its health and performance. We could use profiler tools (like…
jvm  docker 
23 days ago by id1
java native interface - JNI in Dataflow - Stack Overflow
How to account for external dependencies with Google Dataflow via Java/JVM languages...
apache-beam  google-dataflow  google  cloud-computing  stackoverflow  jvm 
october 2019 by id1
A comparison of three programming languages for a full-fledged next-generation sequencing tool | BMC Bioinformatics | Full Text
elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other SAM/BAM tools, management of heap memory is a complex task in elPrep, and it became a serious productivity bottleneck in its original implementation language during recent further development of elPrep. We therefore investigated three alternative programming languages: Go and Java using a concurrent, parallel garbage collector on the one hand, and C++17 using reference counting on the other hand for handling large amounts of heap objects. We reimplemented elPrep in all three languages and benchmarked their runtime performance and memory use. The Go implementation performs best, yielding the best balance between runtime performance and memory use. While the Java benchmarks report a somewhat faster runtime than the Go benchmarks, the memory use of the Java runs is significantly higher. The C++17 benchmarks run significantly slower than both Go and Java, while using somewhat more memory than the Go runs. Our analysis shows that concurrent, parallel garbage collection is better at managing a large heap of objects than reference counting in our case. Based on our benchmark results, we selected Go as our new implementation language for elPrep, and recommend considering Go as a good candidate for developing other bioinformatics tools for processing SAM/BAM data as well.
bioinformatics  genetics  scientific-computing  golang  jvm  c-library 
september 2019 by id1
Upgrading from Java 8 to Java 12
The current pace of change in Java might be intimidating, and it can certainly seem like upgrading from Java 8, which the majority of applications are still running on, to Java 12 could be difficult.
java  jvm 
may 2019 by id1
Covariance and Contravariance – Venkatesh-Prasad Ranganath – Medium
In the below Kotlin code snippet, Producer class is covariant in type parameter T and Consumer class is contravariant in type parameter T. In other words, T is a covariant type parameter of Producer…
programming  scala  jvm 
may 2019 by id1
yEd - Graph Editor
High-quality software components for graph analysis, automatic graph layout, and visualization.
visualization  jvm 
may 2019 by id1
Using Clojure + GraalVM for shell scripting – Denis Isidoro – Medium
How to keep your sanity when Bash isn’t the right tool for the job, without sacrificing startup time
clojure  jvm  graalvm 
april 2019 by id1

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