Missing header auxv.h

[peastman]

Conda-forge documentation

• I could not solve my problem using the conda-forge documentation.

Installed packages

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
binutils                  2.36.1               hdd6e379_2    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                 hf3e587d_7    conda-forge
c-compiler                1.4.1                h166bdaf_0    conda-forge
ca-certificates           2022.2.1             h06a4308_0  
certifi                   2021.10.8        py39hf3d152e_1    conda-forge
compilers                 1.4.1                ha770c72_0    conda-forge
cxx-compiler              1.4.1                h924138e_0    conda-forge
fortran-compiler          1.4.1                h2a4ca65_0    conda-forge
gcc                       10.3.0               he2824d0_7    conda-forge
gcc_impl_linux-64         10.3.0              hf2f2afa_14    conda-forge
gcc_linux-64              10.3.0               hc39de41_7    conda-forge
gfortran                  10.3.0               h18518b4_7    conda-forge
gfortran_impl_linux-64    10.3.0              h73f4979_14    conda-forge
gfortran_linux-64         10.3.0               hb09a455_7    conda-forge
gxx                       10.3.0               he2824d0_7    conda-forge
gxx_impl_linux-64         10.3.0              hf2f2afa_14    conda-forge
gxx_linux-64              10.3.0               h2593f52_7    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     10.3.0              he6cfe16_14    conda-forge
libgcc-ng                 11.2.0              h1d223b6_14    conda-forge
libgfortran5              11.2.0              h5c6108e_14    conda-forge
libgomp                   11.2.0              h1d223b6_14    conda-forge
libsanitizer              10.3.0              h26c7422_14    conda-forge
libstdcxx-devel_linux-64  10.3.0              he6cfe16_14    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_14    conda-forge
ncurses                   6.3                  h7f8727e_2  
openssl                   3.0.0                h7f98852_2    conda-forge
pip                       21.2.4           py39h06a4308_0  
python                    3.9.7           hf930737_3_cpython    conda-forge
python_abi                3.9                      2_cp39    conda-forge
readline                  8.1.2                h7f8727e_1  
setuptools                58.0.4           py39h06a4308_0  
sqlite                    3.38.0               hc218d9a_0  
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tk                        8.6.11               h1ccaba5_0  
tzdata                    2021e                hda174b7_0  
wheel                     0.37.1             pyhd3eb1b0_0  
xz                        5.2.5                h7b6447c_0  
zlib                      1.2.11               h7f8727e_4

Environment info

active environment : test
    active env location : /home/peastman/miniconda3/envs/test
            shell level : 2
       user config file : /home/peastman/.condarc
 populated config files : 
          conda version : 4.10.1
    conda-build version : 3.18.10
         python version : 3.7.9.final.0
       virtual packages : __cuda=11.6=0
                          __linux=5.3.0=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/peastman/miniconda3  (writable)
      conda av data dir : /home/peastman/miniconda3/etc/conda
  conda av metadata url : https://repo.anaconda.com/pkgs/main
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/peastman/miniconda3/pkgs
                          /home/peastman/.conda/pkgs
       envs directories : /home/peastman/miniconda3/envs
                          /home/peastman/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.1 requests/2.24.0 CPython/3.7.9 Linux/5.3.0-7648-generic ubuntu/18.04.6 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Issue

My code compiles without problem when using system compilers, but if I use the CondaForge compilers package, it fails on x86 Linux with the error

/home/runner/work/openmm/openmm/libraries/asmjit/asmjit/core/cpuinfo.cpp:18:12: fatal error: sys/auxv.h: No such file or directory
   18 |   #include <sys/auxv.h>
      |            ^~~~~~~~~~~~
compilation terminated.

sys/auxv.h is part of glibc. It's standard on all Linux distributions. But it's missing from the version of glibc for x86 Linux distributed by CondaForge.

[isuruf]

See our docs on using a newer glibc

[isuruf]

https://conda-forge.org/docs/maintainer/knowledge_base.html#using-centos-7

[peastman]

Thanks!

[awf]

See our docs on using a newer glibc

To expand on this for future visitors, (from conda-forge/ctng-compiler-activation-feedstock#88 (comment))

You need to install sysroot_linux-64>=2.16 to get sys/auxv.h.

[zhanwenchen]

I solved a problem with installing conda gcc on a SLURM-based HPC by using only main channel (-c main) libs:

conda install gxx_linux-64 gcc_linux-64 libstdcxx libstdcxx-ng libcxx libcxxabi libstdcxx-devel_linux-64

[mfansler]

I solved a problem with installing conda gcc on a SLURM-based HPC by using only main channel (-c main) libs:

conda install gxx_linux-64 gcc_linux-64 libstdcxx libstdcxx-ng libcxx libcxxabi libstdcxx-devel_linux-64

I would not recommend this. IME, the packages shown here are not things that end-users should need to manually specify in an environment. Have you tried installing c-compiler and cxx-compiler instead of specifying gcc and gxx?