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Linking issue with 9.3.0 build 11 for libgfortran against libquadmath #36

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brianv0 opened this issue Jul 31, 2020 · 12 comments
Open

Linking issue with 9.3.0 build 11 for libgfortran against libquadmath #36

brianv0 opened this issue Jul 31, 2020 · 12 comments

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@brianv0
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brianv0 commented Jul 31, 2020 •
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Issue:
When using the compilers package to compile code, I get linking errors against libquadmath.so.0 on linux seemingly with 9.3.0 build 11 which I did not get a week ago with a slightly different environment.

Below is a snippet from our logs:

[2020-07-31T08:01:07.989183Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/x86_64-conda_cos6-linux-gnu-c++ -o tests/decoratedImage -Wl,-rpath-link -Wl,/j/ws/stack-os-matrix/d318ecacbb/lsstsw/build/afw/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/astshim/20.0.0+1/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/geom/20.0.0-2-gec03fae+6/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/sphgeom/20.0.0-3-gd2e950e/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_config/20.0.0+4/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_persistence/20.0.0+5/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_policy/20.0.0+4/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/log/20.0.0-1-gd1c87d7+2/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_base/20.0.0-1-g8a53f90+2/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/utils/20.0.0+3/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_exceptions/20.0.0+3/lib:/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/base/20.0.0-4-g4a2362f/lib -fno-lto -Wl,-rpath=/j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib tests/decoratedImage.o -Llib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/astshim/20.0.0+1/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/geom/20.0.0-2-gec03fae+6/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/sphgeom/20.0.0-3-gd2e950e/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_persistence/20.0.0+5/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_policy/20.0.0+4/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/log/20.0.0-1-gd1c87d7+2/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/daf_base/20.0.0-1-g8a53f90+2/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/utils/20.0.0+3/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/pex_exceptions/20.0.0+3/lib -L/j/ws/stack-os-matrix/d318ecacbb/lsstsw/stack/4d6ba77/Linux64/base/20.0.0-4-g4a2362f/lib -L/j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib -L/j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/python3.7/config-3.7m-x86_64-linux-gnu -lafw -lastshim -last -last_pal -last_grf_2.0 -last_grf_3.2 -last_grf_5.6 -last_grf3d -last_pass2 -last_err -lm -lboost_serialization -lcfitsio -lgsl -lgslcblas -lMinuit2 -lgeom -lsphgeom -lfftw3f -lfftw3 -lboost_math_c99 -ldaf_persistence -lpex_policy -lboost_filesystem -lboost_system -llog -llog4cxx -ldaf_base -lboost_regex -lutils -lpex_exceptions -lbase -lpthread -lboost_unit_test_framework
[2020-07-31T08:01:08.613851Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libquadmath.so.0, needed by /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/./libgfortran.so.4, not found (try using -rpath or -rpath-link)
[2020-07-31T08:01:08.614308Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/./libgfortran.so.4: undefined reference to `fmodq@QUADMATH_1.0'
[2020-07-31T08:01:08.614804Z] /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /j/ws/stack-os-matrix/d318ecacbb/home/.conda/envs/lsst-scipipe-4d6ba77/lib/./libgfortran.so.4: undefined reference to `quadmath_snprintf@QUADMATH_1.0'
[additional symbol errors here]

Here is a diff of my environment export between versions which work and don't work:

diff --git a/etc/conda3_packages-linux-64.yml b/etc/conda3_packages-linux-64.yml
index 06870cb..35c8ab5 100644
--- a/etc/conda3_packages-linux-64.yml
+++ b/etc/conda3_packages-linux-64.yml
@@ -38,7 +38,7 @@ dependencies:
   - bzip2=1.0.8=h516909a_2
   - c-ares=1.16.1=h516909a_0
   - c-compiler=1.1.1=h516909a_0
-  - ca-certificates=2020.6.20=hecda079_0
+  - ca-certificates=2020.6.24=0
   - certifi=2020.6.20=py37hc8dfbb8_0
   - cffi=1.14.1=py37h2b28604_0
   - cfitsio=3.470=hce51eda_6
@@ -137,10 +137,10 @@ dependencies:
   - libev=4.33=h516909a_0
   - libevent=2.1.10=hcdb4288_1
   - libffi=3.2.1=he1b5a44_1007
-  - libgcc-ng=9.3.0=h24d8f2e_11
+  - libgcc-ng=9.2.0=h24d8f2e_2
   - libgfortran=3.0.0=1
-  - libgfortran-ng=7.5.0=hdf63c60_11
-  - libgomp=9.3.0=h24d8f2e_11
+  - libgfortran-ng=7.5.0=hdf63c60_6
+  - libgomp=9.2.0=h24d8f2e_2
   - libiconv=1.15=h516909a_1006
   - liblapack=3.8.0=17_openblas
   - libnghttp2=1.41.0=hab1572f_1
@@ -149,7 +149,7 @@ dependencies:
   - libpq=12.3=h5513abc_0
   - libprotobuf=3.11.0=h8b12597_0
   - libssh2=1.9.0=hab1572f_5
-  - libstdcxx-ng=9.3.0=hdf63c60_11
+  - libstdcxx-ng=9.2.0=hdf63c60_2
   - libtiff=4.1.0=hc7e4089_6
   - libuuid=2.32.1=h14c3975_1000
   - libuv=1.38.0=h516909a_0

Environment (conda list): 
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/git-lfs-2.11.0-0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2020.6.20-hecda079_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.34-h53a641e_7.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-7.5.0-hdf63c60_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-9.3.0-hdf63c60_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-mpich.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.34-h53a641e_7.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgomp-9.3.0-h24d8f2e_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-0_gnu.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/binutils-2.34-h2122c62_9.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.34-hc952b39_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-9.3.0-h24d8f2e_11.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/blosc-1.20.0-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/brotli-1.0.7-he1b5a44_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.16.1-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/eigen-3.3.7-hc9558a2_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/expat-2.2.9-he1b5a44_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.8-nompi_h7f3a6c3_1111.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-7.5.0-hd420e75_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gflags-2.2.2-he1b5a44_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/icu-58.2-hf484d3e_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/jpeg-9d-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lapack-3.6.1-ha44fe06_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libapr-1.6.5-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libapriconv-1.2.2-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.2.1-he1b5a44_1007.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.15-h516909a_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.10-pthreads_hb3c22a3_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h14c3975_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libuv-1.38.0-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.1.0-h516909a_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lz4-c-1.8.3-he1b5a44_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lzo-2.10-h14c3975_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/make-4.3-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/minuit2_standalone-6.18.00-he1b5a44_101.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/mpich-3.2.1-hc99cbb1_1014.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.2-he1b5a44_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/openssl-1.1.1g-h516909a_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pcre-8.44-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/perl-5.26.2-h516909a_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h14c3975_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/re2-2020.04.01-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/rhash-1.3.6-h14c3975_1001.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.8-he1b5a44_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/starlink-ast-9.1.0-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h14c3975_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.9-h14c3975_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h14c3975_1007.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xpa-2.1.20-he1b5a44_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.5-h516909a_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.11-h516909a_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.70.0-ha2d47e9_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/doxygen-1.8.18-hd1b7508_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gcc_linux-64-7.5.0-h09487f9_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.8.1-hc5be6a0_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-7.5.0-hdf63c60_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/glog-0.4.0-h49b9bf7_3.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-7.5.0-hdf63c60_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.10.6-nompi_h3c11f04_100.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libaprutil-1.6.1-ha1d75be_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libblas-3.8.0-17_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-h46ee950_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-hcdb4288_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.41.0-hab1572f_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.37-hed695b0_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libprotobuf-3.11.0-h8b12597_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.9.0-hab1572f_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.13-h14c3975_1002.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.9.9-h13577e0_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/minuit2-6.18.00-minuit2_standalone.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ndarray-1.5.3-h75f6862_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/readline-8.0-he28a2e2_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.10-hed695b0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.4.4-h3b9ef0a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/apr-1.6.5-h516909a_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/c-compiler-1.1.1-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/freetype-2.10.2-he06d7ca_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gfortran_linux-64-7.5.0-h09487f9_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/grpc-cpp-1.25.0-h213be95_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gxx_linux-64-7.5.0-h09487f9_20.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.17.1-hfafb76e_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.8.0-17_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.8.0-17_openblas.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.1.0-hc7e4089_6.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.32.3-hcee41ef_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/thrift-cpp-0.12.0-hf3afdfd_1004.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.6.9-h516909a_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cxx-compiler-1.1.1-hc9558a2_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.13.1-he4413a7_1000.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/fortran-compiler-1.1.1-he991be0_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/gsl-2.6-h294904e_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.11-hbd6801e_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.71.1-hcdd3856_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libpq-12.3-h5513abc_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/log4cxx-0.10.0-h66fa5af_2.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/pgplot-5.2.2-hac706ba_1006.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/python-3.7.8-h6f2ec95_0_cpython.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/apipkg-1.5-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.3-py_1.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/asn1crypto-1.4.0-pyh9f0ad1d_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/attrs-19.3.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backoff-1.8.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backports-1.0-py_2.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/backports.csv-1.0.7-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/boto-2.49.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cfitsio-3.470-hce51eda_6.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/click-7.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/cloudpickle-1.5.0-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/cmake-3.18.0-h5c55442_0.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.3-py_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/compilers-1.1.1-0.tar.bz2
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Details about conda and system ( conda info ): 
$ conda info
@brianv0 brianv0 changed the title Linking issue with 9.3.0 build 11 Linking issue with 9.3.0 build 11 for libgfortran against libquadmath Jul 31, 2020
@beckermr
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beckermr commented Aug 1, 2020

cc @isuruf this looks somewhat serious and I'm stumped.

Should we pull the 9.3.0 builds for now?

@isuruf
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isuruf commented Aug 1, 2020

#37

@beckermr
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beckermr commented Aug 1, 2020

Thank you!

@isuruf
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isuruf commented Aug 1, 2020

@brianv0, can you confirm that this issue is fixed?

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brianv0 commented Aug 1, 2020

awesome, running our CI right now, I'll get back to you today

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brianv0 commented Aug 3, 2020

I still had the issue, but I'm a bit confused why. I did see libquadmath.so.0

[2020-08-01T20:58:48.010862Z] /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin/x86_64-conda_cos6-linux-gnu-c++ -o tests/background -Wl,-rpath-link -Wl,/lsstsw/build/afw/lib:/lsstsw/stack/73733da/Linux64/astshim/20.0.0+f45b7d88f4/lib:/lsstsw/stack/73733da/Linux64/geom/20.0.0-2-gec03fae+4d82fa78bb/lib:/lsstsw/stack/73733da/Linux64/sphgeom/20.0.0-3-gd2e950e+f45b7d88f4/lib:/lsstsw/stack/73733da/Linux64/pex_config/20.0.0+9457a788fe/lib:/lsstsw/stack/73733da/Linux64/daf_persistence/20.0.0+ef667cdf05/lib:/lsstsw/stack/73733da/Linux64/pex_policy/20.0.0+eb0b68971d/lib:/lsstsw/stack/73733da/Linux64/log/20.0.0-1-gd1c87d7+54d12611dd/lib:/lsstsw/stack/73733da/Linux64/daf_base/20.0.0-1-g8a53f90+e0c9560612/lib:/lsstsw/stack/73733da/Linux64/utils/20.0.0+95dc160249/lib:/lsstsw/stack/73733da/Linux64/pex_exceptions/20.0.0+117106b506/lib:/lsstsw/stack/73733da/Linux64/base/20.0.0-4-g4a2362f+f45b7d88f4/lib -fno-lto -Wl,-rpath=/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib tests/background.o -Llib -L/lsstsw/stack/73733da/Linux64/astshim/20.0.0+f45b7d88f4/lib -L/lsstsw/stack/73733da/Linux64/geom/20.0.0-2-gec03fae+4d82fa78bb/lib -L/lsstsw/stack/73733da/Linux64/sphgeom/20.0.0-3-gd2e950e+f45b7d88f4/lib -L/lsstsw/stack/73733da/Linux64/daf_persistence/20.0.0+ef667cdf05/lib -L/lsstsw/stack/73733da/Linux64/pex_policy/20.0.0+eb0b68971d/lib -L/lsstsw/stack/73733da/Linux64/log/20.0.0-1-gd1c87d7+54d12611dd/lib -L/lsstsw/stack/73733da/Linux64/daf_base/20.0.0-1-g8a53f90+e0c9560612/lib -L/lsstsw/stack/73733da/Linux64/utils/20.0.0+95dc160249/lib -L/lsstsw/stack/73733da/Linux64/pex_exceptions/20.0.0+117106b506/lib -L/lsstsw/stack/73733da/Linux64/base/20.0.0-4-g4a2362f+f45b7d88f4/lib -L/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib -L/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/python3.7/config-3.7m-x86_64-linux-gnu -lafw -lastshim -last -last_pal -last_grf_2.0 -last_grf_3.2 -last_grf_5.6 -last_grf3d -last_pass2 -last_err -lm -lboost_serialization -lcfitsio -lgsl -lgslcblas -lMinuit2 -lgeom -lsphgeom -lfftw3f -lfftw3 -lboost_math_c99 -ldaf_persistence -lpex_policy -lboost_filesystem -lboost_system -llog -llog4cxx -ldaf_base -lboost_regex -lutils -lpex_exceptions -lbase -lpthread -lboost_unit_test_framework
[2020-08-01T20:58:48.630943Z] /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libquadmath.so.0, needed by /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/./libgfortran.so.4, not found (try using -rpath or -rpath-link)
[2020-08-01T20:58:48.631211Z] /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/./libgfortran.so.4: undefined reference to `fmodq@QUADMATH_1.0'

Cleaned up version:

[2020-08-01T20:58:48.010862Z] /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin/x86_64-conda_cos6-linux-gnu-c++ \
    -o tests/background \
    -Wl,-rpath-link \
    -Wl,/lsstsw/build/afw/lib:/lsstsw/stack/73733da/Linux64/astshim/20.0.0+f45b7d88f4/lib:/lsstsw/stack/73733da/Linux64/geom/20.0.0-2-gec03fae+4d82fa78bb/lib:/lsstsw/stack/73733da/Linux64/sphgeom/20.0.0-3-gd2e950e+f45b7d88f4/lib:/lsstsw/stack/73733da/Linux64/pex_config/20.0.0+9457a788fe/lib:/lsstsw/stack/73733da/Linux64/daf_persistence/20.0.0+ef667cdf05/lib:/lsstsw/stack/73733da/Linux64/pex_policy/20.0.0+eb0b68971d/lib:/lsstsw/stack/73733da/Linux64/log/20.0.0-1-gd1c87d7+54d12611dd/lib:/lsstsw/stack/73733da/Linux64/daf_base/20.0.0-1-g8a53f90+e0c9560612/lib:/lsstsw/stack/73733da/Linux64/utils/20.0.0+95dc160249/lib:/lsstsw/stack/73733da/Linux64/pex_exceptions/20.0.0+117106b506/lib:/lsstsw/stack/73733da/Linux64/base/20.0.0-4-g4a2362f+f45b7d88f4/lib \
    -fno-lto \
##### This is the conda-env directory
    -Wl,-rpath=/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib \ 
    tests/background.o \
    -Llib -L/lsstsw/stack/73733da/Linux64/astshim/20.0.0+f45b7d88f4/lib -L/lsstsw/stack/73733da/Linux64/geom/20.0.0-2-gec03fae+4d82fa78bb/lib \
    -L/lsstsw/stack/73733da/Linux64/sphgeom/20.0.0-3-gd2e950e+f45b7d88f4/lib -L/lsstsw/stack/73733da/Linux64/daf_persistence/20.0.0+ef667cdf05/lib \
    -L/lsstsw/stack/73733da/Linux64/pex_policy/20.0.0+eb0b68971d/lib -L/lsstsw/stack/73733da/Linux64/log/20.0.0-1-gd1c87d7+54d12611dd/lib \
    -L/lsstsw/stack/73733da/Linux64/daf_base/20.0.0-1-g8a53f90+e0c9560612/lib -L/lsstsw/stack/73733da/Linux64/utils/20.0.0+95dc160249/lib \
    -L/lsstsw/stack/73733da/Linux64/pex_exceptions/20.0.0+117106b506/lib -L/lsstsw/stack/73733da/Linux64/base/20.0.0-4-g4a2362f+f45b7d88f4/lib \
    -L/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib -L/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/python3.7/config-3.7m-x86_64-linux-gnu\
    -lafw -lastshim -last -last_pal -last_grf_2.0 -last_grf_3.2 -last_grf_5.6 -last_grf3d -last_pass2 -last_err -lm -lboost_serialization -lcfitsio \
    -lgsl -lgslcblas -lMinuit2 -lgeom -lsphgeom -lfftw3f -lfftw3 -lboost_math_c99 -ldaf_persistence -lpex_policy -lboost_filesystem -lboost_system -llog \
    -llog4cxx -ldaf_base -lboost_regex -lutils -lpex_exceptions -lbase -lpthread -lboost_unit_test_framework
[2020-08-01T20:58:48.630943Z] /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: warning: libquadmath.so.0, needed by /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/./libgfortran.so.4, not found (try using -rpath or -rpath-link)
[2020-08-01T20:58:48.631211Z] /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.5.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/./libgfortran.so.4: undefined reference to `fmodq@QUADMATH_1.0'

You'll see the line above with the env's lib directory:

-Wl,-rpath=/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib

And we verify that libquadmath.so.0 is in that directory:

(lsst-scipipe-tickets-DM-26148.73733da) root@9014056e77a5:/lsstsw/build/afw# ls /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libquad*
/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libquadmath.so  /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libquadmath.so.0  /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libquadmath.so.0.0.0

Do I need to adjust my flags?

@isuruf
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isuruf commented Aug 3, 2020

Can you try looking at which files are different in the two environments?

@beckermr
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beckermr commented Aug 4, 2020

@brianv0 can you ls -lah the quadmath SO's in lib? I'd be good to make sure the links and files are setup correctly.

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beckermr commented Aug 4, 2020

Also which compilers are you using? I see conda_cos6 in the HOST. You should not be seeing this if you are using the latest compilers.

@brianv0
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brianv0 commented Aug 4, 2020 

# which $CC
/lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin/x86_64-conda_cos6-linux-gnu-cc
# ls -al /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/bin | grep gcc
lrwxrwxrwx  1 root root       31 Aug  1 19:59 cc -> x86_64-conda_cos6-linux-gnu-gcc
lrwxrwxrwx  1 root root       31 Aug  1 19:59 gcc -> x86_64-conda_cos6-linux-gnu-gcc
lrwxrwxrwx  1 root root       34 Aug  1 19:59 gcc-ar -> x86_64-conda_cos6-linux-gnu-gcc-ar
lrwxrwxrwx  1 root root       34 Aug  1 19:59 gcc-nm -> x86_64-conda_cos6-linux-gnu-gcc-nm
lrwxrwxrwx  1 root root       38 Aug  1 19:59 gcc-ranlib -> x86_64-conda_cos6-linux-gnu-gcc-ranlib
lrwxrwxrwx  1 root root       31 Aug  1 19:59 x86_64-conda_cos6-linux-gnu-cc -> x86_64-conda_cos6-linux-gnu-gcc
-rwxrwxr-x  2 root root   904032 May 14 14:41 x86_64-conda_cos6-linux-gnu-gcc
-rwxrwxr-x  2 root root    25520 May 14 14:41 x86_64-conda_cos6-linux-gnu-gcc-ar
-rwxrwxr-x  2 root root    25488 May 14 14:41 x86_64-conda_cos6-linux-gnu-gcc-nm
-rwxrwxr-x  2 root root    25488 May 14 14:41 x86_64-conda_cos6-linux-gnu-gcc-ranlib
# 
# ls -lah /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libqua*
lrwxrwxrwx 1 root root   20 Aug  1 19:59 /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libquadmath.so -> libquadmath.so.0.0.0
lrwxrwxrwx 1 root root   20 Aug  1 19:59 /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libquadmath.so.0 -> libquadmath.so.0.0.0
-rwxrwxr-x 2 root root 945K Aug  1 08:37 /lsstsw/miniconda/envs/lsst-scipipe-tickets-DM-26148.73733da/lib/libquadmath.so.0.0.0
# 
# conda list | grep "gfortr\|gcc"
_libgcc_mutex             0.1                 conda_forge    conda-forge
gcc_impl_linux-64         7.5.0                hd420e75_6    conda-forge
gcc_linux-64              7.5.0               h09487f9_20    conda-forge
gfortran_impl_linux-64    7.5.0                hdf63c60_6    conda-forge
gfortran_linux-64         7.5.0               h09487f9_20    conda-forge
libgcc-ng                 9.3.0               h24d8f2e_13    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.5.0               hdf63c60_13    conda-forge
# conda list | grep "compiler"
c-compiler                1.1.1                h516909a_0    conda-forge
compilers                 1.1.1                         0    conda-forge
cxx-compiler              1.1.1                hc9558a2_0    conda-forge
fortran-compiler          1.1.1                he991be0_0    conda-forge

@beckermr
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beckermr commented Aug 4, 2020 •
edited
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Those builds are very old. They should work, but maybe they are broken. Can you try builds of *_impl_linux-64 with build number 13 or 14?

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beckermr commented Aug 4, 2020 •
edited
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also, what is pulling in this?

libgfortran               3.0.0                         1    conda-forge

IDK where that other libgfortran comes from...

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