Lib issues with 1.3.0 on Ubuntu

[celine-mercier]

Hello,

We are trying to upgrade to the new helios version but ran into some lib linking issues. We can probably find ways around it, but we were wondering what glibc version you have been compiling with? We suspect the issues come from us maybe running an older version, maybe because we are still on Ubuntu 20.04.

Best Celine

[han16nah]

Hi @celine-mercier,

thanks for reporting the issue! Can you give a few more details and send the error message(s)?

We left out some libraries in the distribution which we thought were not needed, specifically:

• libc.so.6
• libgcc_s.so.1
• libm.so.6
• libpthread.so.0
• libresolv.so.2
• libstdc++.so.6

However, if you're having issues because one of these is missing or there are conflicts, we will consider including them!

The helios executable is actually compiled with Ubuntu 20.04. We use the GitHub artifacts, so compilation is exactly like in the workflow file.

I have tested v1.3.0 on Ubunutu 22.04 where we have this libc.so.6:

~/Downloads/helios-plusplus-lin$ /lib/x86_64-linux-gnu/libc.so.6

GNU C Library (Ubuntu GLIBC 2.35-0ubuntu3.4) stable release version 2.35.
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
Compiled by GNU CC version 11.4.0.
libc ABIs: UNIQUE IFUNC ABSOLUTE
For bug reporting instructions, please see:
<https://bugs.launchpad.net/ubuntu/+source/glibc/+bugs>.

~/Downloads/helios-plusplus-lin$ file /lib/x86_64-linux-gnu/libc.so.6

/lib/x86_64-linux-gnu/libc.so.6: ELF 64-bit LSB shared object, x86-64, version 1 (GNU/Linux), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, BuildID[sha1]=a43bfc8428df6623cd498c9c0caeb91aec9be4f9, for GNU/Linux 3.2.0, stripped

Again, thanks for the important feedback.

[tik0]

Hi @celine-mercier and @han16nah

I've made my first experiences with helios and I had also a linking problem on my fresh vanilla Ubuntu 20.04 and helios 1.3.0. Maybe those insights can help you with that (btw. python links to python3.8):

First of all, I've checked that the LD_LIBRARY_PATH is empty and I also checked the linkage of python. Everything looks fine:

~/Downloads/helios-plusplus-lin/run$ printenv LD_LIBRARY_PATH
~/Downloads/helios-plusplus-lin/run$ ldd $(which python)
        linux-vdso.so.1 (0x00007ffe277b0000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7980417000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f79803f4000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f79803ee000)
        libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f79803e9000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f798029a000)
        libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f798026c000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f798024e000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f7980651000)

Then I sourced the heliosShell file, such that the run folder is appended to the LD_LIBRARY_PATH. This causes the issue, that the linking does no longer work for the python executable:

~/Downloads/helios-plusplus-lin/run$ ..
~/Downloads/helios-plusplus-lin$ source ../heliosShell.sh
~/Downloads/helios-plusplus-lin$ cd -
~/Downloads/helios-plusplus-lin/run$ python
~/Downloads/helios-plusplus-lin/run$ ldd $(which python)
/bin/bash: symbol lookup error: /bin/bash: undefined symbol: dlopen, version GLIBC_2.2.5

Adding the native OS library path fixed the linking issue and I can now import pyhelios as expected:

~/Downloads/helios-plusplus-lin/run$ export LD_LIBRARY_PATH="/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH}"
~/Downloads/helios-plusplus-lin/run$ ldd $(which python)
        linux-vdso.so.1 (0x00007ffe277b0000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7980417000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f79803f4000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f79803ee000)
        libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f79803e9000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f798029a000)
        libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f798026c000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f798024e000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f7980651000)
~/Downloads/helios-plusplus-lin$ python
Python 3.8.10 (default, May 26 2023, 14:05:08)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyhelios
>>>