Files copied inside singularity not found (intel_psxe building block) about hpc-container-maker

[samcmill]

What is your Singularity build command line?

[VI-gha]

sudo singularity build aocc.sif aocc.def  INFO:    Starting build...Getting image source signaturesCopying blob d519e2592276 skipped: already exists  Copying blob d22d2dfcfa9c skipped: already exists  Copying blob b3afe92c540b [--------------------------------------] 0.0b / 0.0bCopying config d0de749f24 done  Writing manifest to image destinationStoring signatures2021/02/21 22:28:50  info unpack layer: sha256:d519e2592276828ca171d85e0532899cd4f98c70f5c697b45fa2e126e9f9fe492021/02/21 22:28:51  info unpack layer: sha256:d22d2dfcfa9cd230ed3c47defec2670d45081598c721dd85cafc34ea459f970e2021/02/21 22:28:51  info unpack layer: sha256:b3afe92c540b778c64ca316d1e679d55d2d2e812e450f516a808ee591f0c3f77INFO:    Copying aocc-compiler-2.3.0.tar to /tmp/build-temp-807170343/rootfs/var/tmp/aocc-compiler-2.3.0.tar(...)+ tar -xvf /var/tmp/aocc-compiler-2.3.0.tar -C /usr/localtar: /var/tmp/aocc-compiler-2.3.0.tar: Cannot open: No such file or directorytar: Error is not recoverable: exiting nowFATAL:   While performing build: while running engine: exit status 2 Files copies inside singularity end up in a temporary folder (here it is /tmp/build-temp-807170343/rootfs/var/tmp instead of /var/tmp) and cannot be used during the build On Sunday, 21 February 2021, 21:07:34 CET, Scott McMillan <[email protected]> wrote: What is your Singularity build command line? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[VI-gha]

I have tried something similar with the AOCC compiler (which is much smaller) and get the same type of error
This reproduces it (I just kept the bare minimum)

BootStrap: docker
From: ubuntu:18.04

%files
aocc-compiler-2.3.0.tar /var/tmp

%post
tar -xvf /var/tmp/aocc-compiler-2.3.0.tar -C /usr/local
cd /usr/local/aocc-compiler-2.3.0
bash install.sh

What is fundamentally wrong with that?

[samcmill]

What version of Singularity and OS are you using? I can't reproduce the issue with 3.5.3 on Linux (CentOS 7).

It might be apptainer/singularity#5514? That only impacts 3.6 and later on WSL. The workaround in that case is to use a directory that is not bind mounted from the host into the container, so please try hpccm --working-directory /other/path ...

[VI-gha]

I am using  singularity version 3.6.4  and for the os NAME="Ubuntu"VERSION="20.04.2 LTS (Focal Fossa)" On Monday, 22 February 2021, 15:53:09 CET, Scott McMillan <[email protected]> wrote: What version of Singularity and OS are you using? I can't reproduce the issue with 3.5.3 on Linux (CentOS 7). It might be apptainer/singularity#5514? That only impacts 3.6 and later on WSL. The workaround in that case is to use a directory that is not bind mounted from the host into the container, so please try hpccm --working-directory /other/path ... — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[VI-gha]

I am not sure I understand what you mean by "hpccm --working-directory /other/path ..." I tried this hpccm recipe: # Working directoryStage0 += workdir(directory='/opt/src') # AOCCStage0 += copy(src='aocc-compiler-2.3.0.tar', dest='/opt/src/aocc-compiler-2.3.0.tar')Stage0 += shell(commands=['tar -xvf /opt/src/aocc-compiler-2.3.0.tar -C /opt/src', 'cd /opt/src/aocc-compiler-2.3.0', 'bash install.sh']) which translated into: BootStrap: dockerFrom: ubuntu:18.04%post    . /.singularity.d/env/10-docker*.sh %post    cd /    mkdir -p /opt/src    cd /opt/src %files    aocc-compiler-2.3.0.tar /opt/src/aocc-compiler-2.3.0.tar %post    cd /    tar -xvf /opt/src/aocc-compiler-2.3.0.tar -C /opt/src    cd /opt/src/aocc-compiler-2.3.0    bash install.sh and still gives the same error as before INFO:    Starting build...Getting image source signaturesCopying blob d519e2592276 skipped: already exists  Copying blob d22d2dfcfa9c skipped: already exists  Copying blob b3afe92c540b [--------------------------------------] 0.0b / 0.0bCopying config d0de749f24 done  Writing manifest to image destinationStoring signatures2021/02/22 17:20:34  info unpack layer: sha256:d519e2592276828ca171d85e0532899cd4f98c70f5c697b45fa2e126e9f9fe492021/02/22 17:20:35  info unpack layer: sha256:d22d2dfcfa9cd230ed3c47defec2670d45081598c721dd85cafc34ea459f970e2021/02/22 17:20:35  info unpack layer: sha256:b3afe92c540b778c64ca316d1e679d55d2d2e812e450f516a808ee591f0c3f77INFO:    Copying aocc-compiler-2.3.0.tar to /tmp/build-temp-966361227/rootfs/opt/src/aocc-compiler-2.3.0.tarINFO:    Running post scriptlet+ . /.singularity.d/env/10-docker2singularity.sh+ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin+ cd /+ mkdir -p /opt/src+ cd /opt/src+ cd /+ tar -xvf /opt/src/aocc-compiler-2.3.0.tar -C /opt/srctar (child): xz: Cannot exec: No such file or directorytar (child): Error is not recoverable: exiting nowtar: Child returned status 2tar: Error is not recoverable: exiting nowFATAL:   While performing build: while running engine: exit status 2 This is exactly what happens with intel_psxe On Monday, 22 February 2021, 16:55:42 CET, [email protected] <[email protected]> wrote: I am using  singularity version 3.6.4  and for the os NAME="Ubuntu"VERSION="20.04.2 LTS (Focal Fossa)" On Monday, 22 February 2021, 15:53:09 CET, Scott McMillan <[email protected]> wrote: What version of Singularity and OS are you using? I can't reproduce the issue with 3.5.3 on Linux (CentOS 7). It might be apptainer/singularity#5514? That only impacts 3.6 and later on WSL. The workaround in that case is to use a directory that is not bind mounted from the host into the container, so please try hpccm --working-directory /other/path ... — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[samcmill]

The --working-directory option changes the location inside the container to use as the working (staging) directory.

For example, if the recipe is:

Stage0 += baseimage(image='ubuntu:18.04')

Stage0 += intel_psxe(eula=True, license='license.lic', tarball='parallel_studio_xe_2020_update4_cluster_edition.tgz')

Then hpccm --recipe 341.py --format singularity --working-directory /opt outputs:

BootStrap: docker
From: ubuntu:18.04
%post
    . /.singularity.d/env/10-docker*.sh

# Intel Parallel Studio XE
%post
    apt-get update -y
    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
        build-essential \
        cpio
    rm -rf /var/lib/apt/lists/*
%files
    parallel_studio_xe_2020_update4_cluster_edition.tgz /opt/parallel_studio_xe_2020_update4_cluster_edition.tgz
%files
    license.lic /opt/license.lic
%post
    cd /
    mkdir -p /opt && tar -x -f /opt/parallel_studio_xe_2020_update4_cluster_edition.tgz -C /opt -z
    sed -i -e 's/^#\?\(COMPONENTS\)=.*/\1=DEFAULTS/g' \
        -e 's|^#\?\(PSET_INSTALL_DIR\)=.*|\1=/opt/intel|g' \
        -e 's/^#\?\(ACCEPT_EULA\)=.*/\1=accept/g' \
        -e 's/^#\?\(ACTIVATION_TYPE\)=.*/\1=license_file/g' \
        -e 's|^#\?\(ACTIVATION_LICENSE_FILE\)=.*|\1=/opt/license.lic|g' /opt/parallel_studio_xe_2020_update4_cluster_edition/silent.cfg
    cd /opt/parallel_studio_xe_2020_update4_cluster_edition && ./install.sh --silent=silent.cfg
    rm -rf /opt/parallel_studio_xe_2020_update4_cluster_edition.tgz /opt/parallel_studio_xe_2020_update4_cluster_edition
%post
    cd /
    echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> /etc/bash.bashrc

Note that the tarball is copied to /opt rather than /var/tmp.

This looks like a Singularity issue, not a HPCCM issue? Have you filed an issue at https://github.com/hpcng/singularity/issues?

[VI-gha]

Thanks, I did not know this option with --working-directory /opt I am going to give it a try On Tuesday, 23 February 2021, 16:20:56 CET, Scott McMillan <[email protected]> wrote: The --working-directory option changes the location inside the container to use as the working (staging) directory. For example, if the recipe is: Stage0 += baseimage(image='ubuntu:18.04') Stage0 += intel_psxe(eula=True, license='license.lic', tarball='parallel_studio_xe_2020_update4_cluster_edition.tgz') Then hpccm --recipe 341.py --format singularity --working-directory /opt outputs: BootStrap: docker From: ubuntu:18.04 %post . /.singularity.d/env/10-docker*.sh # Intel Parallel Studio XE %post apt-get update -y DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \ build-essential \ cpio rm -rf /var/lib/apt/lists/* %files parallel_studio_xe_2020_update4_cluster_edition.tgz /opt/parallel_studio_xe_2020_update4_cluster_edition.tgz %files license.lic /opt/license.lic %post cd / mkdir -p /opt && tar -x -f /opt/parallel_studio_xe_2020_update4_cluster_edition.tgz -C /opt -z sed -i -e 's/^#\?\(COMPONENTS\)=.*/\1=DEFAULTS/g' \ -e 's|^#\?\(PSET_INSTALL_DIR\)=.*|\1=/opt/intel|g' \ -e 's/^#\?\(ACCEPT_EULA\)=.*/\1=accept/g' \ -e 's/^#\?\(ACTIVATION_TYPE\)=.*/\1=license_file/g' \ -e 's|^#\?\(ACTIVATION_LICENSE_FILE\)=.*|\1=/opt/license.lic|g' /opt/parallel_studio_xe_2020_update4_cluster_edition/silent.cfg cd /opt/parallel_studio_xe_2020_update4_cluster_edition && ./install.sh --silent=silent.cfg rm -rf /opt/parallel_studio_xe_2020_update4_cluster_edition.tgz /opt/parallel_studio_xe_2020_update4_cluster_edition %post cd / echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> /etc/bash.bashrc Note that the tarball is copied to /opt rather than /var/tmp. This looks like a Singularity issue, not a HPCCM issue? Have you filed an issue at https://github.com/hpcng/singularity/issues? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[VI-gha]

@samcmill

Thanks again Scott, it worked when using --working-directory /opt
I guess that others will have the same problem: would it not be better if that was documented or if the intel_psxe building block was modified to use %setup+cp instead of %files?

%setup
    cp parallel_studio_xe_2020_update4_cluster_edition.tgz /var/tmp/parallel_studio_xe_2020_update4_cluster_edition.tgz
    cp license.lic /var/tmp/license.lic

[samcmill]

Thanks @VI-gha. I need to investigate the apparent Singularity changed %files behavior. The solution may be to use %setup, I'm not sure.

I'm going to close this issue and open a new one focused on the Singularity behavior change.