CO2 Fortran Binary not found and How To Handle Old Binaries

[Knguyen-dev]

Introduction

Our Python web app is running Alpine Linux (via a Docker container), which is needed for our UV package manager. This app needs to execute a Fortran binary called main, which performs CO2 solubility calculations. Even though main is present in the file system, and marked as executable (we gave file perms in Dockerfile), we had issues running it. First we saw that when our web app tried to run the file, we got a "Permission denied" error. Then, after doing docker exec inside the container, we saw that the main binary didn't have execution permissions. That's straightforward, we just need to give the container execution permissions.

# Give the owner (root) read, write, and run permissions for anything inside the app. This 
# is fine, the container is isolated, it's not messing with our host machine stuff, etc.
RUN --chmod=755 /app

But now, when trying to run the binary, we're getting "File not found", which is different and a little misleading. We went into our container and ran some commands

# Runs and shows the file exists; we can see it exists and can be executed 
# Output -rwxr-xr-x 1 root root 22352 Apr 19 04:43 main
ls -l main

# Tries to execute binary but we get output: /bin/sh: ./main: not found
./main

# Tries to see what type of file it is; we know it's a Fortran binary from outside knowledge 
# output: /bin/sh: file: not found
file ./main

# What's going on here?

Even though the file exists and has execution permissions, it's doesn't show up? It's not running? This can happen when a binary depends on other files (shared libraries), and those dependencies aren't available in the container. So those "file not found" messages were a bit misleading. Here's how we found the dependencies weren't there:

# Check the dependencies the binary needs to run
ldd ./main

# Here's the output. We're missing stuff. It means the binary is dynamically linked and needs certain runtime libraries to work.
# IBM Article: https://www.ibm.com/docs/en/openxl-c-and-cpp-aix/17.1.3?topic=cc-dynamic-static-linking
        /lib64/ld-linux-x86-64.so.2 (0x7f113f6ce000)
Error loading shared library libgfortran.so.5: No such file or directory (needed by ./main)
        libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7f113f6ce000)
Error loading shared library libgcc_s.so.1: No such file or directory (needed by ./main)
        libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7f113f6ce000)
Error relocating ./main: _gfortran_transfer_real_write: symbol not found
Error relocating ./main: _gfortran_st_read_done: symbol not found
Error relocating ./main: _gfortran_transfer_real: symbol not found
Error relocating ./main: _gfortran_transfer_character_write: symbol not found
Error relocating ./main: _gfortran_st_read: symbol not found
Error relocating ./main: __powidf2: symbol not found
Error relocating ./main: _gfortran_st_write_done: symbol not found
Error relocating ./main: _gfortran_set_options: symbol not found
Error relocating ./main: _gfortran_set_args: symbol not found
Error relocating ./main: _gfortran_st_write: symbol not found

We're running our app in an Alpine Linux container, which is minimal and uses a library called musl instead of the usual glibc used by most Linux distros. To give background, these are different implementation's of the C standard library. So C has a set of specifications for the functions to be provided in its "standard" library. glibc is a popular implementation of that standard library. Musl is mainly used in light-weight settings, but in general most binaries you'll see are compiled on systems that use glibc. Our Fortran library was compiled in glibc so it expects glibc and specific glibc functions to exist. However, since Alpine doesn't have that, it's not going to work. To solve this, we'll install gcompat, which is a compatibility layer for glib on musl systems.

# Add this line
RUN apk add --no--cache libgcc libgfortran gcompat

Now exec into the container and try running the program:

# Run program; and 
./main

# Your output will look like this, which is good:
 ---------CO2 solubility in aqueous NaCl solution---------
 ref: Duan Z, Sun R, Zhu C, Chou I (Marine Chemistry, 2006, v98, 131-139)
   T-P-X range of this model: 273-533 K, 0-2000 bar, 0-4.5 mNaCl
   Unit---T: K, P(total): bar, mNaCl and mCO2: mol/kgH2O
 -------------------------------------------------------
 Please enter temperature(K), pressure(bar) and mNaCl(m)

Let me explain what each of those do again:

• gfortran: This is a GNU Fortran compiler, so you'll need this if you're compiling Fortran code inside the Docker container. However, if you are just running a precompiled binary, you don't need this. So this is not needed since we're only running pre-compiled binaries, but I'll still mention it in case someone in the future wants to add the fortran source code here and compile them here.
• libgfortran: A runtime library used by Fortran programs compiled with gfortran. It's required if your binary was compiled with gfortran and uses its features, which most do. And finally we also know it's necessary since it was present in the ldd error logs.
• libgcc: GCC runtime support, needed for exception handling and other routines. Honestly you don't really need to know this in-depth, all you know is it's a dependency that was listed on the ldd command for things that were missing so we add i.
• gcompat: Alpine uses musl libc instead of glibc; most binaries (like ours) expect glibc. This software is a compatibility layer that lets glibc compiled binaries run on musl and therefore Alpine.

So in summary, Alpine uses musl to compile binaries, but many programs (like our Fortran binary) are compiled with glibc. We can install gcompat to let these glibc-compiled binaries run properly on Alpine by mimicking the behavior and structure that glibc-based programs expect. So, for future developers, here's some advice:

If you're using Alpine Linux and a precompiled binary gives a weird "file not found" error, even though the file is there:

• Run ldd to check dependencies
• Make sure the required libraries are installed
• On Alpine, install gcompat to run glibc-compiled programs
• Or if your options are getting exhausted, switch to a linux distro that uses glibc instead of musl.