Windows attempt

[jaimergp]

Checklist

• Used a fork of the feedstock to propose changes
• Bumped the build number (if the version is unchanged)
• Reset the build number to 0 (if the version changed)
• Re-rendered with the latest conda-smithy (Use the phrase @conda-forge-admin, please rerender in a comment in this PR for automated rerendering)
• Ensured the license file is being packaged.

Strategies

Building on Windows will take a bit of effort... Amber team recommends the MinGW compilers, but some dependencies are built with other suites, which is specially complicated in the case of Fortran.

Option A: mys2

This is the current status for our first line of dependencies:

Dependency	Windows	Compiler	Fortran support
cython	Yes	MSVC
numpy	Yes	MSVC
scipy	Yes*	MSVC/ifort	Only through ifort! * Windows support happens via manual builds and requires MKL. After 2020.11.04, gfortran enabled builds are also available.
matplotlib	Yes	MSVC
bzip2	Yes	MSVC
zlib	Yes	MSVC
boost-cpp	Yes	MSVC
libnetcdf	Yes	MSVC
netcdf-fortran	NO!		PR here
pthread-stubs	Yes	MinGW
fftw	Yes	MSVC	NO! Previous attempt I might revisit
arpack	Yes	MinGW	Yes
libblas/lapack/lapacke	Yes	MinGW	Yes
readline	NO!

As you can see, there's three main problems:

1. netcdf-fortran: I submitted a PR to solve this, but we might need to wait for a new version upstream.
2. fftw is on Windows but Fortran support is not enabled. I have raised an issue here.

Current status

Suboption A

Let CMake choose the bundled dependencies and build the troublesome deps. This includes boost, netcdf, netcdf-fortran, readline, fftw, and arpack. xblas static lib is being vendored. We might be able to distribute it like this if everything is made static.

Build

• Dependencies are satisfied
• Implemented script
• CMake completes
• Compilation ends successfully
  • FEW is not available because of some missing Perl libraries.

Test

• Test imports
  • pytraj cannot be built on Windows+MinGW. Requires MSVC and maybe a separate packaging.
• Test binaries
  • resp won't start
• Test suite
  • run_test.bat
  • Provide m2-tcsh (done, recipe here)
  • Some binaries are called without the script extension (obviously, Unix-style), but in Windows these are provided with .bat or .exe. We need to provide temporary forwarders so the tests reach the executables.
  • Some input files cannot be found. This looks like a path-conversion issue.
  • parmed's bundled simtk.unit has a numpy C issue (missing DLL importing numpy.core._multiarray_umath).

Suboption B

In this case we use conda-forge libraries. Blocking:

• netcdf-fortran is not available (yet) and compilation fails because of the same issues as in the PR. Once [WIP] Attempt windows netcdf-fortran-feedstock#52 is merged, we might get further. Interesting how this doesn't happen if netcdf is compiled at the same time.
• arpack (lacks arsecond?)
• fftw (no Fortran bindings)
• boost (no compression support)
• readline (not available).

---

Option B: MSVC + flang

With this approach, we would use MSVC compilers for C/C++ and flang for Fortran. Flang packages do not always work (scipy example), so it might be tricky.

Note: This might change in the future because (A) apparently ifort support is coming to CF, and (B) LLVM will provide full flang support.

Large parts of Amber only expect a MinGW-like compiler, so they won't be able to use another compilers unless the name mangling is done in a MinGW-compatible way.

Given the small margin for success here, I won't even try for now :)

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe:

• License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

[jaimergp]

@conda-forge-admin, please rerender

[jaimergp]

@conda-forge-admin, please rerender

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipe) and found some lint.

Here's what I've got...

For recipe:

• Selectors are suggested to take a <two spaces>#<one space>[<expression>] form. See lines [71, 73, 92, 94]

For recipe:

• License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe:

• License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

[jaimergp]

This last commit works (builds) but the tests do not.

[jaimergp]

Managed to run the test suite locally, more or less! Some tests hang so you have to Ctrl+C to skip to the next (happens a couple of times).

These are the results:

Finished test suite for AmberTools at 21 May 2020 15:26:05.

make[1]: Leaving directory 'C:/Users/Jaime/Miniconda3/conda-bld/ambertools_1589972034265/test_tmp/ambertools/test'
809 file comparisons passed
63 file comparisons failed (0 of which can be ignored)
98 tests experienced errors
Test log file saved as /cygdrive/c/Users/Jaime/Miniconda3/conda-bld/ambertools_1589972034265/_test_env/Library/logs/test_at_serial/2020-05-21_12-35-42.log
Test diffs file saved as /cygdrive/c/Users/Jaime/Miniconda3/conda-bld/ambertools_1589972034265/_test_env/Library/logs/test_at_serial/2020-05-21_12-35-42.diff

Full logs and diffs:
2020-05-21_12-35-42.zip

[jaimergp]

Yay, that made the test suite run! Now we can actually test on the CI, awesome! And on Azure there's not Ctrl+C issues, so the results are more "honest":

Finished test suite for AmberTools at Thu May 21 17:50:02 CUT 2020.
899 file comparisons passed
44 file comparisons failed (0 of which can be ignored)
109 tests experienced errors
Test log file saved as /cygdrive/d/bld/ambertools_1590072710262/_test_env/Library/logs/test_at_serial/2020-05-21_16-17-01.log
Test diffs file saved as /cygdrive/d/bld/ambertools_1590072710262/_test_env/Library/logs/test_at_serial/2020-05-21_16-17-01.diff

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I was trying to look for recipes to lint for you, but it appears we have a merge conflict.
Please try to merge or rebase with the base branch to resolve this conflict.

Please ping the 'conda-forge/core' team (using the @ notation in a comment) if you believe this is a bug.

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipe:

• License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

[jaimergp]

Tests seem to get stuck at different parts:

cd fpph && ./Run.fpph_resp

Running locally to investigate why.

[jaimergp]

Ok, that "works" so at least we can run the full suite reliably now.

Summary for now:

Finished test suite for AmberTools at Tue Jun  9 15:38:55 CUT 2020.

925 file comparisons passed
48 file comparisons failed (0 of which can be ignored)
97 tests experienced errors

Detailed analysis coming soon.