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@vsoch
vsoch / bumblings.md
Last active Jun 3, 2019
AskCI Brain Bumblings: Ideas for what I'd like to see more of, or inspiration for posts and tag themes
View bumblings.md

Brain Bumblings

Ideas for what I'd like to see more of, or inspiration for posts and tag themes

@vsoch
vsoch / Dockerfile
Last active May 15, 2019
An example multistage Dockerfile to install gvim and then throw the extra stuff away!
View Dockerfile
FROM ubuntu:18.04 as base
# docker build -t vanessa/vim .
RUN apt-get update && apt-get install -y git \
gcc \
libncurses5-dev \
libncursesw5-dev \
build-essential
@vsoch
vsoch / result.json
Last active May 11, 2019
An example of using the watchme psutils decorator to monitor resource usage of a function
View result.json
[
{
"num_ctx_switches": {
"voluntary": 1,
"involuntary": 0
},
"ionice": {
"ioclass": "IOPRIO_CLASS_NONE",
"value": 4
},
@vsoch
vsoch / Singularity
Last active May 8, 2019
An example of setting a custom environment variable already defined in the container
View Singularity
Bootstrap: docker
From: centos:7
# sudo singularity build lamps.simg Singularity
%environment
now=`date '+%Y_%m_%d'`
hostname=`hostname`
APPNAME="lammps"
@vsoch
vsoch / output_file.md
Created May 4, 2019
Saving output to a file and printing to terminal
View output_file.md

This is executing a command to the container to list at the root (/) and then redirect stdout and stderr to "out.txt"

$ singularity exec salad_latest.sif ls / 2>&1 | tee out.txt
bin
code
dev
environment
etc
home
@vsoch
vsoch / analyze_ubuntu.md
Created May 3, 2019
Container Diff Examples
View analyze_ubuntu.md
$ container-diff analyze --type=apt ubuntu:16.04

-----Apt-----

Packages found in ubuntu:16.04:
NAME                        VERSION                              SIZE
-adduser                    3.113 nmu3ubuntu4                    648K
-apt                        1.2.31                               3.4M
-base-files                 9.4ubuntu4.8                         312K
@vsoch
vsoch / markdown-details.md
Last active May 1, 2019
An example of how to put a really long error log (or similar) in markdown! It's all about details. :)
View markdown-details.md

Lots of discussion, blardee boo, and here is my Dockerfile that is important to you!

FROM debian:stretch-backports

LABEL authors="@bnmnetp,@vsoch,@yarikoptic"

# docker build -t runstone/server .
@vsoch
vsoch / singularity-pull-examples.md
Last active Apr 25, 2019
All the ways you can pull a Singularity container from shub.
View singularity-pull-examples.md

Ways to Pull

How do you pull, my friend? Let me count the ways!

1. Pull by Tag

$ singularity pull shub://vsoch/singularity-images:latest
 35.30 MiB / 35.30 MiB [=========================================================================================================================================] 100.00% 4.07 MiB/s 8s
111
@vsoch
vsoch / package-investigation.md
Last active Apr 24, 2019
Singularity package investigation (again) reveals that self.stage.source_path is not reliable
View package-investigation.md

This is a debugging session for spack. The issue is that the self.stage.source_path changes (unexpectedly) in the middle of do_stage, and it's not clear why this happens. I'm at the HEAD of the repo, just pulled the fix to remove the empty line:

commit b92fe5f248892069674de2f090e4da879b5c83d4 (HEAD -> update/package-singularity, origin/update/package-singularity)
Author: Vanessa Sochat <vsochat@stanford.edu>
Date:   Wed Apr 24 09:58:08 2019 -0400

    removing blank link
    
    Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
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