Illegal instruction

[Tintest]

Hello, I'm trying to use graphmap2 in a singularity image (which is the only container technology available on the HPC infrastructure I'm working with).

I manage to made a working docker container on my local PC, but when I'm building the singularity image from the docker container, I cannot execute the graphmap2 executable.

Dockerfile :

################## BASE IMAGE ######################
FROM ubuntu:18.04 as base

################## METADATA ######################

LABEL description="Docker image for executing Graphmap2"
LABEL tags="Genomics"

################## INSTALL ######################
RUN apt-get update \
    && apt-get install -y apt-utils build-essential zlib1g-dev libbz2-dev pkg-config cmake libncurses5-dev autoconf git gcc g++ \
    && git clone https://github.com/lbcb-sci/graphmap2 \
    && cd graphmap2 \
    && make modules \
    && make -j 4 testing

Making the docker container :

docker build -f Dockerfile_graphmap2_v1.0 -t tintest/graphmap2:v1.0.0 .
docker push tintest/graphmap2:v1.0.0

The working docker container :

docker run e6323ba65ab2 graphmap2/bin/./graphmap2
Usage:
  graphmap2/bin/./graphmap2 tool

Options
    tool       STR   Specifies the tool to run:
                       align - the entire GraphMap pipeline.
                       owler - Overlapping With Long Erroneous Reads.


GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
GraphMap is licensed under The MIT License.

Version: v0.6.1
Build date: Aug  5 2019 at 14:05:47

Making the singularity image :

singularity build graphmap2.simg docker://tintest/graphmap2:v1.0.0 .
singularity exec graphmap2.simg graphmap2/bin/./graphmap2

The not working singularity images :

singularity exec graphmap2.simg graphmap2/bin/./graphmap2
Illegal instruction

Do you have any experience with singularity or any idea to help me solve this ?

Or if you could add a bioconda recipe for graphmap2, maybe it could help me to execute graphmap2 on a HPC infrastructure without the need of a container technology.

Regards.

[dschwoerer]

Most likely you are compiling on a different architecture then the HPC system. Without further information it is not possible to say what is going on.

Either the HPC system doesnt support some of the extensions that are used, which could be avoided by not using march=native (but will result in slower code) or the HPC system is a completely different architecture, in which case you either need to cross compile, or compile directly on the HPC system.