Phreeqc Fortran Binary and Overcoming compatibility issues in Alpine

[Knguyen-dev]

Phreeqc Fortran Binary

Let's assume we have our Alpine container and we have some setup that gives us some compatibility with our CO2 fortran binary. In particular something like this:

FROM ghcr.io/astral-sh/uv:python3.9-alpine

RUN apk add curl
RUN apk add libgcc libgfortran gcompat

Alright we have one of our binaries working. Now let's try to integrate our Phreeqc binary within our container.

/app/app/routes/phreeqc # file ./phreeqc
/bin/sh: file: not found

/app/app/routes/phreeqc # ./phreeqc
Error loading shared library libstdc++.so.6: No such file or directory (needed by /app/app/routes/phreeqc/phreeqc)
Error relocating /app/app/routes/phreeqc/phreeqc: _ZNSs6appendEPKcm: symbol not found
Error relocating /app/app/routes/phreeqc/phreeqc: _ZSt7getlineIcSt11char_traitsIcESaIcEERSt13basic_istreamIT_T0_ES7_RSbIS4_S5_T1_ES4_: symbol not found
Error relocating /app/app/routes/phreeqc/phreeqc: _ZNSolsEi: symbol not found
Error relocating /app/app/routes/phreeqc/phreeqc: _ZNSs5clearEv: symbol not found
Error relocating /app/app/routes/phreeqc/phreeqc: _ZSt18_Rb_tree_decrementPKSt18_Rb_tree_node_base: symbol not found
Error relocating /app/app/routes/phreeqc/phreeqc: _ZSt16__throw_bad_castv: symbol not found
... # It went on for another 100 lines or so
/app/app/routes/phreeqc # ldd ./phreeqc
        /lib64/ld-linux-x86-64.so.2 (0x7f456338f000)
Error loading shared library libstdc++.so.6: No such file or directory (needed by ./phreeqc)
        libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7f456338f000)
        libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x7f4563363000)
        libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7f456338f000)
Error relocating ./phreeqc: _ZNSs6appendEPKcm: symbol not found

Let's review. Alpine Linux is a popular minimal base image known for its small size. However, it uses musl libc as its C standard library, which differs from the more widely-used glibc. This discrepancy creates compatibility issues when trying to run precompiled binaries that were compiled with glibc whilst on Alpine. Phreeqc and other Fortran binaries, in particular, are typically compiled with glibc, meaning they rely on glibc-specific functions and libraries that are not available in musl. For instance, the absence of important shared libraries like libstdc++.so.6 (the C++ standard library) causes errors when trying to run these binaries in an Alpine-based container. While gcompat can help bridge some of these gaps by providing partial compatibility with glibc, it does not offer a 100% solution. There will always be some legacy functions or specific glibc features that gcompat cannot replicate, leading to potential runtime issues. So we've reached our limit with gcompat.

To fix this, we'll switch the project to a Debian-based image, a widely used Linux distro that utilizes glibc by default. This will ensure that binaries compiled with glibc, will run smoothly in the container. After running the container in Debian, we can remove stuff like gcompat and even libgcc. However you'll still need libgfortan5 to run the CO2 binary. This is just an example of how certain libraries may still be required to run specific binaries. The switch to Debian isn't only about solving this one problem, but it's also the idea of dealing with issues down the line. Like handling more binaries like supcrtbl or whatever the project needs, being on Debian will make it easier to handle those binaries.