AFNI recipe does not work correctly in Singularity build #585
Comments
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it seems that in Singularity, the environment variables made in 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 $NEWVARand during the build, I get the following output, which shows that the updated for help in debugging, here are the Dockerfile and Singularity file for the command Dockerfile# Generated by Neurodocker and Reproenv.
FROM fedora:36
ENV PATH="/opt/afni-latest:$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# 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. |
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indeed, singularity does not make related:
i think the solution would be to add @stebo85 - what do you think? if apptainer / singularity developers are reading, then i would like to say that i find this behavior highly unexpected. |
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Dear @kaczmarj - great find - that explains the problems. I tried adding I know it's not elegant, but would anything else speak against re-exporting the environment variables in the post section? at least it works :? @vsoch - could you maybe have quick look at what we are getting wrong here? Kind regards |
fine with me if there's no better solution. |
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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):
This results in:
@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
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