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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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Hisat2 processes won't fully die - Linux server #158

Open megan-kc opened 6 years ago

megan-kc commented 6 years ago

I was running hisat2 on a Linux HPC system and wanted to kill an alignment process that had been running for almost 24 hours, as I suspected something was probably wrong with the command or the file for it to run that long. This has happened twice now on 2 separate paired-read files. The first time I killed the process using Ctrl-C, the second time i used the kill PID command. Both times caused the process to not actually die, but they did stop consuming memory. The directory containing the files became inaccessible until the server was reset (thus actually fully killing the processes).

I don't know if this is even relevant to the hisat2 program itself, but I thought it wouldn't hurt to ask to see if you had any ideas on why this is occurring or how I can safely end hisat2 if I run into the same thing again.

shwina commented 6 years ago

We are seeing a similar issue with hisat2 hanging and leaving behind zombie processes. We suspect that the problem may be running hisat2 on a shared filesystem, as running on local file system did not result in the problem.