| Issue |
133158
|
| Summary |
OMP: Error #13: Assertion failure at kmp_affinity.cpp(981).
|
| Labels |
|
| Assignees |
|
| Reporter |
kjobson-neuro
|
I am compiling a Docker container to run neuroimaging software. When I execute one of my commands to use [FSL](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/), the above error occurs. I will include my Dockerfile below that I use to compile the container. Happy to provide more information, I am not a programmer and do not really understand what is happening here or what info would be most helpful. I do not have this issue on Linux OS.
MacOS: 15.3.2 (24D81)
Docker v4.39.0
Command causing the error: fslmerge -t ${workdir}/all_data.nii.gz $m0_file $asl_file
`ARG TARGETARCH
FROM --platform=linux/amd64 ubuntu:jammy
#
## Download stages
#
# Utilities for downloading packages
RUN apt-get update && \
apt-get install -y --no-install-recommends \
binutils \
bzip2 \
ca-certificates \
curl \
unzip && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# FreeSurfer 7.3.2
COPY freesurfer7.3-exclude.txt /usr/local/etc/freesurfer7.3-exclude.txt
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \
| tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3-exclude.txt
# ANTs 2.5.3
# Old ANTs code, save in case new doesn't work
RUN mkdir /opt/ants && \
curl -fsSL https://github.com/ANTsX/ANTs/releases/download/v2.4.3/ants-2.4.3-centos7-X64-gcc.zip -o ants.zip && \
unzip ants.zip -d /opt && \
rm ants.zip
ENV FSLDIR="/opt/fsl-6.0.7.1" \
PATH="/opt/fsl-6.0.7.1/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-6.0.7.1/bin/fsltclsh" \
FSLWISH="/opt/fsl-6.0.7.1/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
ca-certificates \
curl \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libice6 \
libopenblas-base \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
nano \
python3 \
sudo \
wget \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Installing FSL ..." \
&& curl -fsSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | python3 - -d /opt/fsl-6.0.7.1 -V 6.0.7.1
#
# Main stage
#
# Create the FW environment
ENV FLYWHEEL=/flywheel/v0
RUN mkdir -p ${FLYWHEEL}
WORKDIR ${FLYWHEEL}
# Configure APT
ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"
RUN apt-get update && \
apt-get install -y --no-install-recommends \
ca-certificates \
curl \
gnupg && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Configure PPAs for libpng12 and libxp6
RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \
&& GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \
&& echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \
&& echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list
# Simulate SetUpFreeSurfer.sh
ENV OS="Linux" \
FS_OVERRIDE=0 \
FIX_VERTEX_AREA="" \
FSF_OUTPUT_FORMAT="nii.gz" \
FREESURFER_HOME="/opt/freesurfer" \
FSLDIR="/opt/fsl-6.0.7.1/"
ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
MNI_DIR="$FREESURFER_HOME/mni" \
LOCAL_DIR="$FREESURFER_HOME/local" \
MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
MNI_DATAPATH="$FREESURFER_HOME/mni/data"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
# ANTs config
ENV ANTSPATH="/opt/ants-2.4.3/bin" \
PATH="$ANTSPATH:$PATH"
# FSL environment
ENV LANG="C.UTF-8" \
LC_ALL="C.UTF-8" \
LC_NUMERIC="en_US.UTF-8" \
PYTHONNOUSERSITE=1 \
FSLDIR="/opt/fsl-6.0.7.1" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q" \
PATH="/opt/fsl-6.0.7.1/bin:$PATH" \
LD_LIBRARY_PATH=""
# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1
#################
RUN apt-get update && \
apt-get install -y --no-install-recommends \
binutils \
bzip2 \
ca-certificates \
curl \
python3 \
python3-pip \
zip \
jq \
gnupg \
lsb-release \
netbase \
pipx \
dcm2niix \
libc6-amd64-cross \
bsdmainutils \
unzip && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Installing and setting up python packages
RUN pipx ensurepath
RUN pipx install numpy \
&& pipx install scipy --include-deps \
&& pipx install nibabel \
&& pipx install matplotlib --include-deps \
&& pipx install transforms3d --include-deps \
&& pipx install flywheel-sdk --include-deps \
&& pip3 install aspose-words
# Copy stuff over & change permissions
COPY ./input/ ${FLYWHEEL}/input/
COPY ./workflows/ ${FLYWHEEL}/workflows/
COPY ./pipeline_singlePLD.sh ${FLYWHEEL}/
RUN chmod -R 777 ${FLYWHEEL}
# Configure entrypoints-
ENTRYPOINT ["/bin/bash", "/flywheel/v0/pipeline_singlePLD.sh"]`
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