Spack build failures

[edmundmiller]

Getting a build failure using wave-cli to build the example spack image:

Details

java.lang.IllegalStateException: Unexpected response for 'https://wave.seqera.io/v2/wt/fbdd6fcaab96/wave/build/manifests/star-2.5.4a_bwa-0.7.15--1bbd3f1023331159': [400] {"errors":[{"code":"UNKNOWN","message":"INFO[0000] Resolved base name spack/ubuntu-jammy:v0.20.0 to builder \nINFO[0000] Retrieving image manifest spack/ubuntu-jammy:v0.20.0 \nINFO[0000] Retrieving image spack/ubuntu-jammy:v0.20.0 from registry index.docker.io \nINFO[0001] Retrieving image manifest spack/ubuntu-jammy:v0.20.0 \nINFO[0001] Returning cached image manifest              \nINFO[0001] Retrieving image manifest ubuntu:22.04       \nINFO[0001] Retrieving image ubuntu:22.04 from registry index.docker.io \nINFO[0002] Retrieving image manifest ubuntu:22.04       \nINFO[0002] Returning cached image manifest              \nINFO[0002] Built cross stage deps: map[0:[/opt/spack-env /opt/software /opt/._view]] \nINFO[0002] Retrieving image manifest spack/ubuntu-jammy:v0.20.0 \nINFO[0002] Returning cached image manifest              \nINFO[0002] Retrieving image manifest spack/ubuntu-jammy:v0.20.0 \nINFO[0002] Returning cached image manifest              \nINFO[0002] Executing 0 build triggers                   \nINFO[0002] Building stage 'spack/ubuntu-jammy:v0.20.0' [idx: '0', base-idx: '-1'] \nINFO[0002] Checking for cached layer 195996028523.dkr.ecr.eu-west-1.amazonaws.com/wave/build/cache:3c7f60a8c5305502134b52bf40f93ae4046b83466c7748fee70f1cd0015fb175... \nINFO[0002] Using caching version of cmd: RUN mkdir -p /opt/spack-env &&  sed -i -e 's;compilers:;compilers::;'          -e 's;^ *flags: *{};    flags:\\n      cflags: -O3\\n      cxxflags: -O3\\n      fflags: -O3;'          /root/.spack/linux/compilers.yaml && cd /opt/spack-env && spack config add config:install_tree:/opt/software && spack config add concretizer:unify:true && spack config add concretizer:reuse:true && spack config add packages:all:target:[x86_64] && printf \"  view: /opt/view\\n\" >> /opt/spack-env/spack.yaml \nINFO[0002] Checking for cached layer 195996028523.dkr.ecr.eu-west-1.amazonaws.com/wave/build/cache:56d87e8adae6f90946598d324a4c75098ad89484ce3dbe716f793de57e15f07f... \nINFO[0003] Using caching version of cmd: RUN cd /opt/spack-env && fingerprint=\"$(spack gpg trust /var/seqera/spack/key 2>&1 | tee /dev/stderr | sed -nr \"s/^gpg: key ([0-9A-F]{16}): secret key imported$/\\1/p\")\" && spack mirror add seqera-spack s3://seqera-production-spack-binarycache && spack mirror add binary_mirror  https://binaries.spack.io/releases/v0.20 && spack buildcache keys --install --trust && spack -e . concretize -f && spack --env . install && spack -e . buildcache push --allow-root --key \"$fingerprint\" s3://seqera-production-spack-binarycache && spack gc -y && ( find -L /opt/._view/* -type f -exec readlink -f '{}' \\; |     xargs file -i |     grep 'charset=binary' |     grep 'x-executable\\|x-archive\\|x-sharedlib' |     awk -F: '{print $1}' | xargs strip -s ) || true \nINFO[0003] Checking for cached layer 195996028523.dkr.ecr.eu-west-1.amazonaws.com/wave/build/cache:b4aa60d3c34f8ca831279ec0cf8ebd7dc1bcca4e387cb61757fcebd37021d784... \nINFO[0003] No cached layer found for cmd RUN cd /opt/spack-env &&     spack env activate --sh -d . >> /opt/spack-env/z10_spack_environment.sh &&     original_view=$( cd /opt ; ls -1d ._view/* ) &&     sed -i \"s;/view/;/$original_view/;\" /opt/spack-env/z10_spack_environment.sh &&     echo \"# Needed for Perl applications\" >>/opt/spack-env/z10_spack_environment.sh &&     echo \"export PERL5LIB=$(eval ls -d /opt/._view/*/lib/5.*):$PERL5LIB\" >>/opt/spack-env/z10_spack_environment.sh &&     rm -rf /opt/view \nINFO[0003] Unpacking rootfs as cmd COPY spack.yaml /opt/spack-env/spack.yaml requires it. \nINFO[0023] COPY spack.yaml /opt/spack-env/spack.yaml    \nINFO[0023] Taking snapshot of files...                  \nINFO[0023] ARG AWS_STS_REGIONAL_ENDPOINTS               \nINFO[0023] No files changed in this command, skipping snapshotting. \nINFO[0023] ARG AWS_REGION                               \nINFO[0023] No files changed in this command, skipping snapshotting. \nINFO[0023] ARG AWS_DEFAULT_REGION                       \nINFO[0023] No files changed in this command, skipping snapshotting. \nINFO[0023] ARG AWS_ROLE_ARN                             \nINFO[0023] No files changed in this command, skipping snapshotting. \nINFO[0023] ARG AWS_WEB_IDENTITY_TOKEN_FILE              \nINFO[0023] No files changed in this command, skipping snapshotting. \nINFO[0023] ENV   AWS_STS_REGIONAL_ENDPOINTS=${AWS_STS_REGIONAL_ENDPOINTS}   AWS_REGION=${AWS_REGION}   AWS_DEFAULT_REGION=${AWS_DEFAULT_REGION}   AWS_ROLE_ARN=${AWS_ROLE_ARN}   AWS_WEB_IDENTITY_TOKEN_FILE=${AWS_WEB_IDENTITY_TOKEN_FILE} \nINFO[0023] No files changed in this command, skipping snapshotting. \nINFO[0023] RUN mkdir -p /opt/spack-env &&  sed -i -e 's;compilers:;compilers::;'          -e 's;^ *flags: *{};    flags:\\n      cflags: -O3\\n      cxxflags: -O3\\n      fflags: -O3;'          /root/.spack/linux/compilers.yaml && cd /opt/spack-env && spack config add config:install_tree:/opt/software && spack config add concretizer:unify:true && spack config add concretizer:reuse:true && spack config add packages:all:target:[x86_64] && printf \"  view: /opt/view\\n\" >> /opt/spack-env/spack.yaml \nINFO[0023] Found cached layer, extracting to filesystem \nINFO[0024] RUN cd /opt/spack-env && fingerprint=\"$(spack gpg trust /var/seqera/spack/key 2>&1 | tee /dev/stderr | sed -nr \"s/^gpg: key ([0-9A-F]{16}): secret key imported$/\\1/p\")\" && spack mirror add seqera-spack s3://seqera-production-spack-binarycache && spack mirror add binary_mirror  https://binaries.spack.io/releases/v0.20 && spack buildcache keys --install --trust && spack -e . concretize -f && spack --env . install && spack -e . buildcache push --allow-root --key \"$fingerprint\" s3://seqera-production-spack-binarycache && spack gc -y && ( find -L /opt/._view/* -type f -exec readlink -f '{}' \\; |     xargs file -i |     grep 'charset=binary' |     grep 'x-executable\\|x-archive\\|x-sharedlib' |     awk -F: '{print $1}' | xargs strip -s ) || true \nINFO[0024] Found cached layer, extracting to filesystem \nINFO[0025] RUN cd /opt/spack-env &&     spack env activate --sh -d . >> /opt/spack-env/z10_spack_environment.sh &&     original_view=$( cd /opt ; ls -1d ._view/* ) &&     sed -i \"s;/view/;/$original_view/;\" /opt/spack-env/z10_spack_environment.sh &&     echo \"# Needed for Perl applications\" >>/opt/spack-env/z10_spack_environment.sh &&     echo \"export PERL5LIB=$(eval ls -d /opt/._view/*/lib/5.*):$PERL5LIB\" >>/opt/spack-env/z10_spack_environment.sh &&     rm -rf /opt/view \nINFO[0025] Initializing snapshotter ...                 \nINFO[0025] Taking snapshot of full filesystem...        \nINFO[0040] Cmd: docker-shell                            \nINFO[0040] Args: [cd /opt/spack-env &&     spack env activate --sh -d . >> /opt/spack-env/z10_spack_environment.sh &&     original_view=$( cd /opt ; ls -1d ._view/* ) &&     sed -i \"s;/view/;/$original_view/;\" /opt/spack-env/z10_spack_environment.sh &&     echo \"# Needed for Perl applications\" >>/opt/spack-env/z10_spack_environment.sh &&     echo \"export PERL5LIB=$(eval ls -d /opt/._view/*/lib/5.*):$PERL5LIB\" >>/opt/spack-env/z10_spack_environment.sh &&     rm -rf /opt/view] \nINFO[0040] Running: [docker-shell cd /opt/spack-env &&     spack env activate --sh -d . >> /opt/spack-env/z10_spack_environment.sh &&     original_view=$( cd /opt ; ls -1d ._view/* ) &&     sed -i \"s;/view/;/$original_view/;\" /opt/spack-env/z10_spack_environment.sh &&     echo \"# Needed for Perl applications\" >>/opt/spack-env/z10_spack_environment.sh &&     echo \"export PERL5LIB=$(eval ls -d /opt/._view/*/lib/5.*):$PERL5LIB\" >>/opt/spack-env/z10_spack_environment.sh &&     rm -rf /opt/view] \nls: cannot access '._view/*': No such file or directory\nerror building image: error building stage: failed to execute command: waiting for process to exit: exit status 2\n"}]}
	at io.seqera.wave.cli.Client.awaitImage(Client.java:174)
	at io.seqera.wave.cli.App.run(App.java:411)
	at io.seqera.wave.cli.App.main(App.java:217)

https://github.com/Emiller88/auto-wave/pull/5

logs_66.zip