Singularity build problems

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johnwsmac
Posts: 2
Joined: 30. Aug 2022, 18:22

Singularity build problems

Post by johnwsmac »

Hi everyone,

I'm following the GitHub instructions to install OpenOChem on a VM. (Can't post the link at present because my account is too new - will add it when possible.)
I'm at the part where I have to run "sudo singularity build ../env/ochemenv/ochemenv.sif singularity_ochem", but doing so causes the VM (or, sometimes, the host PC) to crash. I've attached the log for one such session.

I'm using:
VirtualBox version 6.1.36 r152435 (Qt5.6.2)
Ubuntu 22.04 (64-bit) guest OS, 8192 MB base memory, 29.30 GB storage, Guest Additions installed
Windows 11 Home 21H2 (64-bit) host OS, 8.00 GB RAM, 237 GB storage (34.6 GB free)

I've also included my current VBoxHardening.log, but it's not for a session where this crash occurred. I can attempt the build once more and send this file for a crashed session, if necessary.

Any ideas on how to fix this and allow the build to complete? I asked on the SingularityCE Slack, but they directed me here.
Attachments
VBox logs.zip
(100.58 KiB) Downloaded 5 times
mpack
Site Moderator
Posts: 39156
Joined: 4. Sep 2008, 17:09
Primary OS: MS Windows 10
VBox Version: PUEL
Guest OSses: Mostly XP

Re: Singularity build problems

Post by mpack »

You have a small problem with arithmetic:
00:00:02.481725 Host RAM: 7540MB (7.3GB) total, 2379MB (2.3GB) available
...
00:00:02.658680 RamSize <integer> = 0x0000000200000000 (8 589 934 592, 8 192 MB, 8.0 GB)
2379MB RAM available minus 8192MB assigned to the VM == (-5813MB) remaining on the host.

A VM needs real RAM. It can't use paged RAM. And obviously you can't assign 8GB RAM to a VM when 8GB is everything your host has. The host OS needs RAM too, in fact it needs most of it to run a 64bit host OS.

Also Ubuntu (64bit) probably would prefer more than 1 CPU core and more than 16MB of graphics RAM.
johnwsmac
Posts: 2
Joined: 30. Aug 2022, 18:22

Re: Singularity build problems

Post by johnwsmac »

I see, thank you for the quick response. I won't have access to a host with more RAM for a few days, unfortunately - and apologies for the rookie mistakes, this is my first time using Linux or VMs, let alone Singularity and OpenOChem.

I'll address these issues when I can use the better host again. (It's actually the original, which is likely how I ended up with this RAM imbalance in the first place.)
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