gfortran linking c libraries with conda

Question

I am trying to compile a C++/Fortran program using conda on an Ubuntu 18.04 server where I do not have superuser rights.

I am able to compile correctly the program with t

Answer 1

This answer is a suggested alternative workflow that aims at avoiding the problem rather than an exact diagnosis of the issue in OP.

In my experience, I have found the Conda Forge compiler packages help simplify the creation and use of custom environments for compilation. As an example, here is the YAML definition for the environment I use to build the kallisto software. For your case, I would expect something like

fortran-compiler.yaml

name: fortran-compiler  # name it what you want
channels:
  - conda-forge
  - defaults
dependencies:
  - fortran-compiler
  - cxx-compiler
  - libpng
  - libgd
  - jpeg
  - libnetcdf
  - openlibm
  - xorg-libx11
# include the other required libraries

Create the environment with

conda env create -f fortran-compiler.yaml

then run your compilation with this environment activated. Activating the environment should automatically manage where the linker will look so that the libraries in the environment will be found (this is, in part, what the Conda Forge *-compiler packages provide). The idea is to have as many libraries as possible come from the environment itself.

I find this approach keeps the amount of manual locating and including of library paths to a minimum. However, it does require having to track down the libraries in Conda Forge (e.g., search for libx11), which unfortunately is not always a one-to-one mapping from library name to package name. The advantage is that a compilation environment defined in this way can facilitate transferring across platforms - e.g., the example YAML I have for kallisto works on both osx-64 and linux-64 without any changes - because it explicitly defines that Conda will provide the shared libraries.

Perhaps there are simpler ways to do this, but this is at least what I've found works after having multiple bad experiences trying to use the gcc or clang Anaconda packages directly.