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gromacs: don't force build with gcc #129648

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gromacs: build with clang
junghans Apr 28, 2023
8c47fc4
gromacs: run different test
junghans May 1, 2023
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21 changes: 10 additions & 11 deletions Formula/gromacs.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,10 @@ class Gromacs < Formula
depends_on "gcc" # for OpenMP
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@eirrgang eirrgang May 17, 2023

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Do we need depends_on "gcc" # for OpenMP or is it even the appropriate way to ensure an omp facility if we always depend on openblas? I mean, is the omp dependence of openblas sufficiently transitive?

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@fxcoudert fxcoudert May 17, 2023

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We prefer dependencies to be explicit than transitive, when there is a direct dependency.

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@eirrgang eirrgang May 17, 2023 •
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We prefer dependencies to be explicit than transitive, when there is a direct dependency.

Sounds good. In order to be both explicit and correct, how would gromacs.rb reference the (brew) package dependency to get appropriate CMake hints? (I think the only available CMake input variable is OpenMP_CXX_INCLUDE_DIR, since the details are normally so compiler-specific.)

It seems like we might need the choice of libomp vs. libgomp to be coupled to the choice of clang vs. gcc?

Or is there a way to inspect the openblas dependency and just use whatever it used?

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@fxcoudert fxcoudert May 18, 2023

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There is no choice to be had: formulas don't really have options, and binaries shipped are built on our CI machines.

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@eirrgang eirrgang May 18, 2023

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I think you are saying

  • the gromacs formula declares a dependency on openblas, so it can and should encode decisions needed to build compatibly, per the openblas formula
  • gromacs should therefore declare a dependency on libgomp
  • the formula encodes its toolchain, which in this case must be gcc based

Are all three of those points correct?

I'm particularly unclear on that last one, since it would seem to invalidate the whole premise of this pull request (which has not yet been outright rejected). It seems like any one of those points, though, would invalidate much of this change.

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@fxcoudert fxcoudert May 18, 2023

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Yes (except there is no libgomp, it is a part of gcc). I have not outright closed the PR because I wanted to see if any other maintainer felt differently about it, but it seems not, so I'll close it now.

depends_on "openblas"
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@carlocab carlocab Apr 28, 2023

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Note that OpenBLAS uses libgomp, so you'll be mixing OpenMP implementations here.

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@junghans junghans Apr 29, 2023

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Hmm, not sure what do about this....

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@eirrgang eirrgang May 15, 2023

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Note that OpenBLAS uses libgomp, so you'll be mixing OpenMP implementations here.

So is it appropriate to just replace libomp with libgomp below?

Or is it reasonable to entirely leave out the depends_on "libomp" entirely to just get transitive installation dependency or does it provide necessary build-time details?

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@fxcoudert fxcoudert May 17, 2023

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I simply don't think we can build that with libomp

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@fxcoudert fxcoudert May 17, 2023

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To be clearer: I think the issue is in the (proposed) votca formula and should be fixed there. We don't want to introduce this mixed-OpenMP linkage.

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@junghans junghans May 18, 2023

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I simply don't think we can build that with libomp

What is the actual problem with that? I have seen openblas being built with clang using spack.io before.

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@junghans junghans May 18, 2023

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To be clearer: I think the issue is in the (proposed) votca formula and should be fixed there. We don't want to introduce this mixed-OpenMP linkage.

Again I am not sure about this either, we build VOTCA on large variety different compiler and library combination without problems. And I of course tried to restrict votca to gcc as well, which led to this error: #129512 (comment)
because boost was build with clang.

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@junghans junghans May 18, 2023

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I simply don't think we can build that with libomp

What is the actual problem with that? I have seen openblas being built with clang using spack.io before.

If I believe:
https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/openblas/package.py#L205-L209
clang+openmp should works for openblas>0.2.19.


fails_with :clang
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@eirrgang eirrgang May 17, 2023

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I would be happy to test again, compiling with clang. It seems like it would be nice to remove this broad clang-avoidance. But what is the mechanism for choosing compiler toolchain for either brew install -s gromacs or for the built-package repositories?

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@eirrgang eirrgang May 17, 2023

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update:

  • I tried brew install --cc llvm_clang -s gromacs, but I don't seem to be set up for that.
  • I tried brew install --cc clang -s gromacs but brew still invoked CMake with cmake -S . -B build -DGROMACS_CXX_COMPILER=/usr/local/opt/gcc/bin/g++-13 -DGMX_VERSION_STRING_OF_FORK=Homebrew -DGMX_INSTALL_LEGACY_API=ON

on_macos do
depends_on "libomp"
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@eirrgang eirrgang May 17, 2023

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This change may have succeeded in establishing a package dependency, but without additional CMake arguments, the build system configuration is still free to find libgomp if it is available and finds it preferable. I assume that is what happened in my test.

end

fails_with gcc: "5"
fails_with gcc: "6"

Expand All @@ -35,24 +38,20 @@ def install
"CMAKE_INSTALL_DATADIR"

# Avoid superenv shim reference
gcc = Formula["gcc"]
cc = gcc.opt_bin/"gcc-#{gcc.any_installed_version.major}"
cxx = gcc.opt_bin/"g++-#{gcc.any_installed_version.major}"
inreplace "src/gromacs/gromacs-hints.in.cmake" do |s|
s.gsub! "@CMAKE_LINKER@", "/usr/bin/ld"
s.gsub! "@CMAKE_C_COMPILER@", cc
s.gsub! "@CMAKE_CXX_COMPILER@", cxx
s.gsub! "@CMAKE_C_COMPILER@", ENV.cc
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@eirrgang eirrgang May 17, 2023

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Where does ENV come from?

s.gsub! "@CMAKE_CXX_COMPILER@", ENV.cxx
end

inreplace "src/buildinfo.h.cmakein" do |s|
s.gsub! "@BUILD_C_COMPILER@", cc
s.gsub! "@BUILD_CXX_COMPILER@", cxx
s.gsub! "@BUILD_C_COMPILER@", ENV.cc
s.gsub! "@BUILD_CXX_COMPILER@", ENV.cxx
end

inreplace "src/gromacs/gromacs-config.cmake.cmakein", "@GROMACS_CXX_COMPILER@", cxx
inreplace "src/gromacs/gromacs-config.cmake.cmakein", "@GROMACS_CXX_COMPILER@", ENV.cxx

args = %W[
-DGROMACS_CXX_COMPILER=#{cxx}
-DGMX_VERSION_STRING_OF_FORK=#{tap.user}
-DGMX_INSTALL_LEGACY_API=ON
]
Expand All @@ -76,6 +75,6 @@ def caveats
end

test do
system "#{bin}/gmx", "help"
system "#{bin}/gmx", "-version"
end
end