Windows Subsystem for Linux (WSL): Segmentation Fault (PLINK 1.9)

[mjbeyeler]

Hello!

I'd like to use PLINK 1.9 (Linux 64-bit) on my Windows 10 PC, using the fairly new WSL Ubuntu (https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux).

Unfortunately, when I try using it, I get a segmentation fault. Are any of you able to run PLINK 1.9 on Windows, or is there a general incompatibility btwn. WSL and PLINK 1.9 at the moment?

Best
Michael

[chrchang]

It worked on my Windows 10 laptop the last time I tried it; I don't know whether that's because I was using a newer version of WSL, or there's some other reason.

Is there a reason you can't use the regular Windows 32- or 64-bit builds?

[mjbeyeler]

The strange thing is, the Windows 64-bit version of PLINK 1.9 runs in WSL, whereas the Linux 64-bit version doesn't (gives the segmentation fault).

The reason why I'd like to use the Linux version, is to program a script that works on both Windows and Ubuntu. I could program a workaround, but it would be awesome to get the Linux version to run on WSL.

[chrchang]

Well, I actually got the Windows 10 laptop for the explicit purpose of investigating a WSL crash report a while ago, but "unfortunately" the Linux build ran fine... If you're familiar with C, you could try inserting debug print statements and/or using a debugger to try to isolate where the segfault is occurring.

[mjbeyeler]

@chrchang Are you sure that Plink 1.9 is working fine on WSL?

I have a new laptop now, I installed WSL, downloaded the latest Plink 1.9 stable beta, and then ran the toy example command

./plink --file toy --freq --out toy_analysis

which gives me the error

PLINK v1.90p 64-bit (10 Apr 2018)              www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to toy_analysis.log.
Options in effect:
  --file toy
  --freq
  --out toy_analysis

Segmentation fault (core dumped)

The same command ran perfectly fine when using CMD Plink on the same laptop.

Edit: For the record: plink2 seems to work so far on WSL.

[chrchang]

As I stated above, plink 1.9 appears to work on some WSL setups and not others, and unfortunately, the Windows 10 laptop I bought for the express purpose of trying to replicate WSL bug reports was not able to reproduce this.

Unless you can provide me a remote login which lets me e.g. inspect the core dump, and/or insert debug-prints and recompile until I've isolated the cause, you'll have to do that yourself and tell me what you find; it is not reasonable for me to spend thousands of dollars buying Windows machines with different configurations until I run into one that's similar enough to yours.

[mjbeyeler]

That's perfectly understandable. Unfortunately I'm not proficient enough to do debug prints, but I'm lucky and PLINK2 alpha seems to work and also have all features that I currently need, so I guess I'll stick with PLINK2 for now.

Anyway, thanks for your responses!

[aheinzel]

Just wanted to add my recent experience with plink on WSL (Ubuntu 16.04.4 LTS).

I had an issue with the precompiled Linux 64bit version (PLINK v1.90p 64-bit (7 Aug 2018)) on WSL - Core dump upon execution with a bed file (e.g. plink --bfile cohort --make-bed --out test2). However, with the same version compiled from source the operation could be completed successfully.

[chrchang]

Closing this since WSL2 exists, which should have improved compatibility across the board.