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Local pixi build attempt of Shepa v2.2.16
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.gitattributes
# GitHub syntax highlighting
pixi.lock linguist-language=YAML linguist-generated=true
Raw
.gitignore
# pixi environments
.pixi
*.egg-info
Raw
README.md

Sherpa symbol lookup error

conda-forge/staged-recipes#28084

pixi run start

✨ Pixi task (test): Sherpa-config --help && Sherpa --help

Sherpa-config: configuration tool for the Monte Carlo
               event generator Sherpa: http://sherpa.hepforge.org
Options:
  Sherpa-config --version : returns Sherpa version
  Sherpa-config --prefix  : returns the installation path
  Sherpa-config --incdir  : returns the path of Sherpa headers
  Sherpa-config --libs    : returns the linker line to link with Sherpa
  Sherpa-config --datadir : returns the path of Sherpa data (like Decaydata, PDFs)
  Sherpa-config --ldflags : returns the LDFLAGS used for Sherpa
  Sherpa-config --cppflags : returns the preprocessor FLAGS needed for Sherpa headers
/tmp/debug/sherpa-build-tool-comparison/.pixi/envs/default/bin/Sherpa: symbol lookup error: /tmp/debug/sherpa-build-tool-comparison/.pixi/envs/default/lib/SHERPA-MC/libPhotonsMEs.so.0: undefined symbol: _ZN7METOOLS11PV_Bubble_1ERKdRKSt7complexIdES5_d

Environments

Does the difference in libstdcxx matter here?

$ pixi list libstdcxx
Package                   Version  Build         Size      Kind   Source
libstdcxx                 14.2.0   hc0a3c3a_1    3.7 MiB   conda  libstdcxx-14.2.0-hc0a3c3a_1.conda
libstdcxx-devel_linux-64  13.3.0   h84ea5a7_101  13.4 MiB  conda  libstdcxx-devel_linux-64-13.3.0-h84ea5a7_101.conda
libstdcxx-ng              13.2.0   hc0a3c3a_7    3.7 MiB   conda  libstdcxx-ng-13.2.0-hc0a3c3a_7.conda
$ pixi list gxx
Package            Version  Build       Size      Kind   Source
gxx                13.3.0   h9576a4e_1  52.1 KiB  conda  gxx-13.3.0-h9576a4e_1.conda
gxx_impl_linux-64  13.3.0   hdbfa832_1  12.7 MiB  conda  gxx_impl_linux-64-13.3.0-hdbfa832_1.conda
gxx_linux-64       13.3.0   h6834431_5  29.6 KiB  conda  gxx_linux-64-13.3.0-h6834431_5.conda
$ docker run --rm -ti python:3.12 bash
# apt update && apt install -y g++ git gfortran libsqlite3-dev libzip-dev texinfo
# dpkg --list | grep 'libstdc\|g++\|gcc'
ii  g++                                4:12.2.0-3                     amd64        GNU C++ compiler
ii  g++-12                             12.2.0-14                      amd64        GNU C++ compiler
ii  gcc                                4:12.2.0-3                     amd64        GNU C compiler
ii  gcc-12                             12.2.0-14                      amd64        GNU C compiler
ii  gcc-12-base:amd64                  12.2.0-14                      amd64        GCC, the GNU Compiler Collection (base package)
ii  libgcc-12-dev:amd64                12.2.0-14                      amd64        GCC support library (development files)
ii  libgcc-s1:amd64                    12.2.0-14                      amd64        GCC support library
ii  libstdc++-12-dev:amd64             12.2.0-14                      amd64        GNU Standard C++ Library v3 (development files)
ii  libstdc++6:amd64                   12.2.0-14                      amd64        GNU Standard C++ Library v3

Seems like no, as the following works

$ docker run --rm -ti fedora:40
dnf install g++ git gfortran sqlite3 libzip-devel texinfo autoconf libtool make automake sqlite-devel which
rm -rf sherpa && git clone --recursive https://gitlab.com/sherpa-team/sherpa.git && cd sherpa && git checkout v2.2.16
autoreconf --install
./configure --prefix=/usr/local --with-sqlite3=install CXX="$(command -v g++)" CXXFLAGS="$CXXFLAGS" PYTHON=""
cd Examples/CI/LO_Z/
Sherpa-config --help
Sherpa --help
Sherpa

where

# dnf list installed | grep 'libstdc\|g++\|gcc'
gcc.x86_64                               14.2.1-3.fc40              @updates
gcc-c++.x86_64                           14.2.1-3.fc40              @updates
gcc-gfortran.x86_64                      14.2.1-3.fc40              @updates
libgcc.x86_64                            14.2.1-3.fc40              @updates
libstdc++.x86_64                         14.2.1-3.fc40              @updates
libstdc++-devel.x86_64                   14.2.1-3.fc40              @updates

Though if you install sqlite3 during the build on fedora:40 (--with-sqlite3=install) the version you get is the very old v3.8.2

[root@e6ba080bfa67 debug]# ./bin/sqlite3 --version
3.8.2 2013-12-06 14:53:30 27392118af4c38c5203a04b8013e1afdb1cebd

though on Debian python:3.12 it is v3.40

root@cddd563a0e4d:/# dpkg --list | grep sql
ii  default-libmysqlclient-dev:amd64   1.1.0                          amd64        MySQL database development files (metapackage)
ii  libsqlite3-0:amd64                 3.40.1-2                       amd64        SQLite 3 shared library
ii  libsqlite3-dev:amd64               3.40.1-2                       amd64        SQLite 3 development files
ii  mysql-common                       5.8+1.1.0                      all          MySQL database common files, e.g. /etc/mysql/my.cnf

and both of these work.

Though restricting libsqlite to be capped at v3.40

pixi clean && pixi add cxx-compiler gfortran gnuconfig autoconf libtool make automake which diffutils texinfo git sqlite lhapdf hepmc2 'libsqlite >=3,<3.41'

doesn't help, nor does restricting all gxx related things to be v13.3.0 with

pixi clean && pixi add cxx-compiler gfortran gnuconfig autoconf libtool make automake which diffutils texinfo git sqlite lhapdf hepmc2 'libstdcxx < 14' 'libsqlite >=3,<3.41'

Solution

Remove --as-needed from LDFLAGS to ensure all libraries have symbols defined. c.f. https://linux.die.net/man/1/ld

Conda env LDFLAGS:

$ echo $LDFLAGS
-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$CONDA_PREFIX/lib -Wl,-rpath-link,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib

On macOS remove -dead_strip_dylibs linker flag.

Raw
pixi.lock
version: 5
environments:
default:
channels:
- url: https://conda.anaconda.org/conda-forge/
packages:
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Raw
pixi.toml
[project]
authors = ["Matthew Feickert <[email protected]>"]
channels = ["conda-forge"]
description = "Add a short description here"
name = "sherpa-build-tool-comparison"
platforms = ["linux-64", "osx-64", "osx-arm64"]
version = "0.1.0"
[tasks]
clone = """
rm -rf sherpa && \
git clone --recursive https://gitlab.com/sherpa-team/sherpa.git && \
cd sherpa && \
git checkout v2.2.16
"""
build = """
cd sherpa && \
git clean --force && \
git reset --hard v2.2.16 && \
export LDFLAGS="$(echo $LDFLAGS | sed 's/ -Wl,--as-needed//g')" && \
export LDFLAGS="$(echo $LDFLAGS | sed 's/ -Wl,-dead_strip_dylibs//g')" && \
autoreconf --install && \
./configure \
--prefix=$CONDA_PREFIX \
--enable-hepmc2=$CONDA_PREFIX \
--enable-lhapdf=$CONDA_PREFIX \
--with-sqlite3=$CONDA_PREFIX \
CXX="$CXX" \
CXXFLAGS="$CXXFLAGS" \
LDFLAGS="$LDFLAGS" \
PYTHON="" && \
make --jobs=12 && \
make check && \
make install
"""
# For Sherpa v2, remove '--as-needed' from LDFLAGS to ensure all libraries
# have symbols defined. For macOS remove '-dead_strip_dylibs'.
# c.f. https://linux.die.net/man/1/ld
build-simple = """
cd sherpa && \
git clean --force && \
git reset --hard v2.2.16 && \
export LDFLAGS="$(echo $LDFLAGS | sed 's/ -Wl,--as-needed//g')" && \
export LDFLAGS="$(echo $LDFLAGS | sed 's/ -Wl,-dead_strip_dylibs//g')" && \
autoreconf --install && \
./configure \
--prefix=$CONDA_PREFIX \
--with-sqlite3=$CONDA_PREFIX \
CXX="$CXX" \
CXXFLAGS="$CXXFLAGS" \
LDFLAGS="$LDFLAGS" \
PYTHON="" && \
make --jobs=12 && \
make check && \
make install
"""
test = """
Sherpa-config --help && \
Sherpa --help
"""
start = { depends-on = ["clone", "build", "test"] }
# dependencies generated from the following in a clean env:
# pixi clean && pixi add cxx-compiler gfortran gnuconfig autoconf libtool make automake which diffutils texinfo git sqlite lhapdf hepmc2
[dependencies]
cxx-compiler = ">=1.8.0,<2"
gfortran = ">=13.2.0,<14"
gnuconfig = ">=2020.11.7,<2021"
autoconf = ">=2.71,<3"
libtool = ">=2.4.7,<3"
make = ">=4.4.1,<5"
automake = ">=1.17,<2"
which = ">=2.21,<3"
diffutils = ">=3.10,<4"
texinfo = ">=7.0,<8"
git = ">=2.47.0,<3"
sqlite = ">=3.47.0,<4"
lhapdf = ">=6.5.4,<7"
hepmc2 = ">=2.6.11,<3"
tar = ">=1.34,<2"
sed = ">=4.7,<5"
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