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ReproNim / neurodocker

Generate custom Docker and Singularity images, and minimize existing containers
https://www.repronim.org/neurodocker/
Apache License 2.0
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AFNI recipe does not work correctly in Singularity build #585

Open stebo85 opened 11 months ago

stebo85 commented 11 months ago

This is a left-over from issue #584, but I opened a new issue to keep it focussed on the actual problem.

Building afni with singularity currently doesn't work (but works with docker):

singularity run docker://repronim/neurodocker:latest generate singularity \
    --pkg-manager yum \
    --base-image fedora:36 \
    --afni method=binaries version=latest install_r_pkgs=true > /cubric/collab/359_curiosity/tamas/misc/afni-binaries-r.Singularityfile

singularity build --remote /cubric/collab/359_curiosity/tamas/images/afni-binaries-r.sif /cubric/collab/359_curiosity/tamas/misc/afni-binaries-r.Singularityfile

This results in:

/.post.script: line 47: rPkgsInstall: command not found

@kaczmarj, Is there a difference in how Singularity files are written in Neurodocker as compared to how docker files are written that would explain why a tool is not on the path in Singularity, but is on Path when building in Docker?

Thank you Steffen

kaczmarj commented 11 months ago

it seems that in Singularity, the environment variables made in %environment are not available in %post. am i correct?

i tested this using a small Singularity file

# Test whether updated environment variables like PATH are available in %post.

Bootstrap: docker
From: fedora:36

%environment
export PATH="/opt/afni-latest:$PATH"
export NEWVAR="ThisIsATest"

%post
echo $PATH
echo $NEWVAR

and during the build, I get the following output, which shows that the updated PATH variable is not available in %post.

INFO:    Starting build...
Getting image source signatures
Copying blob c7bef7d09442 skipped: already exists  
Copying config 4d934e266f done  
Writing manifest to image destination
Storing signatures
2023/10/25 10:38:22  info unpack layer: sha256:c7bef7d09442a4c4deef8e8120027e7fa3f163c7b5a0afedc3f2c4c2e7652e1c
INFO:    Running post scriptlet
+ echo /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ echo

INFO:    Adding environment to container
INFO:    Creating SIF file...
INFO:    Build complete: foobar

for help in debugging, here are the Dockerfile and Singularity file for the command 

singularity run docker://repronim/neurodocker:latest generate singularity \
    --pkg-manager yum \
    --base-image fedora:36 \
    --afni method=binaries version=latest install_r_pkgs=true
Dockerfile ```dockerfile # Generated by Neurodocker and Reproenv. FROM fedora:36 ENV PATH="/opt/afni-latest:$PATH" \ AFNI_PLUGINPATH="/opt/afni-latest" RUN yum install -y -q \ R \ cmake \ curl \ ed \ gsl \ libGLU \ libXp \ libXpm \ libcurl-devel \ libgomp \ libjpeg-turbo-devel \ libpng12 \ mesa-dri-drivers \ mesa-dri-drivers \ mesa-libGLw \ ncurses-compat-libs \ netpbm-progs \ openmotif \ openssl-devel \ python-is-python3 \ python3-pip \ tcsh \ udunits2-devel \ unzip \ wget \ which \ which \ xorg-x11-fonts-misc \ xorg-x11-server-Xvfb \ && yum clean all \ && rm -rf /var/cache/yum/* \ && gsl_path="$(find / -name 'libgsl.so.??' || printf '')" \ && if [ -n "$gsl_path" ]; then \ ln -sfv "$gsl_path" "$(dirname $gsl_path)/libgsl.so.0"; \ fi \ && ldconfig \ && mkdir -p /opt/afni-latest \ && echo "Downloading AFNI ..." \ && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \ | tar -xz -C /opt/afni-latest --strip-components 1 \ && yum install -y -q \ R-devel \ && yum clean all \ && rm -rf /var/cache/yum/* \ && rPkgsInstall -pkgs ALL # Save specification to JSON. RUN printf '{ \ "pkg_manager": "yum", \ "existing_users": [ \ "root" \ ], \ "instructions": [ \ { \ "name": "from_", \ "kwds": { \ "base_image": "fedora:36" \ } \ }, \ { \ "name": "env", \ "kwds": { \ "PATH": "/opt/afni-latest:$PATH", \ "AFNI_PLUGINPATH": "/opt/afni-latest" \ } \ }, \ { \ "name": "run", \ "kwds": { \ "command": "yum install -y -q \\\\\\n R \\\\\\n cmake \\\\\\n curl \\\\\\n ed \\\\\\n gsl \\\\\\n libGLU \\\\\\n libXp \\\\\\n libXpm \\\\\\n libcurl-devel \\\\\\n libgomp \\\\\\n libjpeg-turbo-devel \\\\\\n libpng12 \\\\\\n mesa-dri-drivers \\\\\\n mesa-dri-drivers \\\\\\n mesa-libGLw \\\\\\n ncurses-compat-libs \\\\\\n netpbm-progs \\\\\\n openmotif \\\\\\n openssl-devel \\\\\\n python-is-python3 \\\\\\n python3-pip \\\\\\n tcsh \\\\\\n udunits2-devel \\\\\\n unzip \\\\\\n wget \\\\\\n which \\\\\\n which \\\\\\n xorg-x11-fonts-misc \\\\\\n xorg-x11-server-Xvfb\\nyum clean all\\nrm -rf /var/cache/yum/*\\n\\ngsl_path=\\"$\(find / -name '"'"'libgsl.so.??'"'"' || printf '"'"''"'"'\)\\"\\nif [ -n \\"$gsl_path\\" ]; then \\\\\\n ln -sfv \\"$gsl_path\\" \\"$\(dirname $gsl_path\)/libgsl.so.0\\"; \\\\\\nfi\\nldconfig\\nmkdir -p /opt/afni-latest\\necho \\"Downloading AFNI ...\\"\\ncurl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \\\\\\n| tar -xz -C /opt/afni-latest --strip-components 1\\n yum install -y -q \\\\\\n R-devel\\nyum clean all\\nrm -rf /var/cache/yum/*\\n rPkgsInstall -pkgs ALL" \ } \ } \ ] \ }' > /.reproenv.json # End saving to specification to JSON. ```
Singularity ```singularity # Generated by Neurodocker and Reproenv. Bootstrap: docker From: fedora:36 %environment export PATH="/opt/afni-latest:$PATH" export AFNI_PLUGINPATH="/opt/afni-latest" %post yum install -y -q \ R \ cmake \ curl \ ed \ gsl \ libGLU \ libXp \ libXpm \ libcurl-devel \ libgomp \ libjpeg-turbo-devel \ libpng12 \ mesa-dri-drivers \ mesa-dri-drivers \ mesa-libGLw \ ncurses-compat-libs \ netpbm-progs \ openmotif \ openssl-devel \ python-is-python3 \ python3-pip \ tcsh \ udunits2-devel \ unzip \ wget \ which \ which \ xorg-x11-fonts-misc \ xorg-x11-server-Xvfb yum clean all rm -rf /var/cache/yum/* gsl_path="$(find / -name 'libgsl.so.??' || printf '')" if [ -n "$gsl_path" ]; then \ ln -sfv "$gsl_path" "$(dirname $gsl_path)/libgsl.so.0"; \ fi ldconfig mkdir -p /opt/afni-latest echo "Downloading AFNI ..." curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \ | tar -xz -C /opt/afni-latest --strip-components 1 yum install -y -q \ R-devel yum clean all rm -rf /var/cache/yum/* rPkgsInstall -pkgs ALL # Save specification to JSON. printf '{ \ "pkg_manager": "yum", \ "existing_users": [ \ "root" \ ], \ "instructions": [ \ { \ "name": "from_", \ "kwds": { \ "base_image": "fedora:36" \ } \ }, \ { \ "name": "env", \ "kwds": { \ "PATH": "/opt/afni-latest:$PATH", \ "AFNI_PLUGINPATH": "/opt/afni-latest" \ } \ }, \ { \ "name": "run", \ "kwds": { \ "command": "yum install -y -q \\\\\\n R \\\\\\n cmake \\\\\\n curl \\\\\\n ed \\\\\\n gsl \\\\\\n libGLU \\\\\\n libXp \\\\\\n libXpm \\\\\\n libcurl-devel \\\\\\n libgomp \\\\\\n libjpeg-turbo-devel \\\\\\n libpng12 \\\\\\n mesa-dri-drivers \\\\\\n mesa-dri-drivers \\\\\\n mesa-libGLw \\\\\\n ncurses-compat-libs \\\\\\n netpbm-progs \\\\\\n openmotif \\\\\\n openssl-devel \\\\\\n python-is-python3 \\\\\\n python3-pip \\\\\\n tcsh \\\\\\n udunits2-devel \\\\\\n unzip \\\\\\n wget \\\\\\n which \\\\\\n which \\\\\\n xorg-x11-fonts-misc \\\\\\n xorg-x11-server-Xvfb\\nyum clean all\\nrm -rf /var/cache/yum/*\\n\\ngsl_path=\\"$\(find / -name '"'"'libgsl.so.??'"'"' || printf '"'"''"'"'\)\\"\\nif [ -n \\"$gsl_path\\" ]; then \\\\\\n ln -sfv \\"$gsl_path\\" \\"$\(dirname $gsl_path\)/libgsl.so.0\\"; \\\\\\nfi\\nldconfig\\nmkdir -p /opt/afni-latest\\necho \\"Downloading AFNI ...\\"\\ncurl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \\\\\\n| tar -xz -C /opt/afni-latest --strip-components 1\\n yum install -y -q \\\\\\n R-devel\\nyum clean all\\nrm -rf /var/cache/yum/*\\n rPkgsInstall -pkgs ALL" \ } \ } \ ] \ }' > /.reproenv.json # End saving to specification to JSON. ```
kaczmarj commented 11 months ago

indeed, singularity does not make %environment variables available in %post by default...

related:

i think the solution would be to add . $SINGULARITY_ENVIRONMENT to the beginning of %post.

@stebo85 - what do you think?

if apptainer / singularity developers are reading, then i would like to say that i find this behavior highly unexpected.

stebo85 commented 11 months ago

Dear @kaczmarj - great find - that explains the problems.

I tried adding . $SINGULARITY_ENVIRONMENT to the %post section, but this results in:

INFO:    Running post scriptlet
+ . /.singularity.d/env/91-environment.sh
/.post.script: line 1: /.singularity.d/env/91-environment.sh: No such file or directory
FATAL:   While performing build: while running engine: exit status 1

I know it's not elegant, but would anything else speak against re-exporting the environment variables in the post section?

Bootstrap: docker
From: fedora:36

%environment
export PATH="/opt/afni-latest:$PATH"
export NEWVAR="ThisIsATest"

%post
export PATH="/opt/afni-latest:$PATH"
export NEWVAR="ThisIsATest"

echo $PATH
echo $NEWVAR

at least it works :?

INFO:    Running post scriptlet
+ export PATH=/opt/afni-latest:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/opt/afni-latest:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export NEWVAR=ThisIsATest
+ NEWVAR=ThisIsATest
+ echo /opt/afni-latest:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
/opt/afni-latest:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ echo ThisIsATest
ThisIsATest

@vsoch - could you maybe have quick look at what we are getting wrong here?

Kind regards Steffen

kaczmarj commented 11 months ago

I know it's not elegant, but would anything else speak against re-exporting the environment variables in the post section?

fine with me if there's no better solution.