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RAxML: init at 8.2.11 (SSE3 & MPI) #34531

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merged 1 commit into from Feb 10, 2018
Merged

RAxML: init at 8.2.11 (SSE3 & MPI) #34531

merged 1 commit into from Feb 10, 2018

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unode
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@unode unode commented Feb 2, 2018

This can potentially be extended to cover all the other compilation targets.
SSE3-PTHREADS and MPI being the most commonly used.

Motivation for this change

RAxML is a widely used software for phylogenetic tree inference

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Fits CONTRIBUTING.md.

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unode commented Feb 2, 2018

@GrahamcOfBorg build raxml
@GrahamcOfBorg build raxml-mpi

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Failure on aarch64-linux (full log)

Partial log (click to expand)

updateAutotoolsGnuConfigScriptsPhase
configuring
no configure script, doing nothing
building
rm -f *.o raxmlHPC-PTHREADS-SSE3
gcc  -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -O2 -fomit-frame-pointer -funroll-loops     -c -o axml.o axml.c
gcc: error: unrecognized command line option '-msse3'
make: *** [<builtin>: axml.o] Error 1
builder for '/nix/store/17hyyfnz6ywcffplxcddd28xfs0m9adl-RAxML-8.2.11.drv' failed with exit code 2
error: build of '/nix/store/17hyyfnz6ywcffplxcddd28xfs0m9adl-RAxML-8.2.11.drv' failed

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Success on x86_64-linux (full log)

Partial log (click to expand)

gcc  -o raxmlHPC-PTHREADS-SSE3 axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o  fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o   -lm -pthread   
installing
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/p91p9dd2hg0ipfgv4s9br5mq0mns0ay6-RAxML-8.2.11
shrinking /nix/store/p91p9dd2hg0ipfgv4s9br5mq0mns0ay6-RAxML-8.2.11/bin/raxmlHPC-PTHREADS-SSE3
strip is /nix/store/mdyy001q67hiks0g24ra53z7ckm4jfr4-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/p91p9dd2hg0ipfgv4s9br5mq0mns0ay6-RAxML-8.2.11/bin 
patching script interpreter paths in /nix/store/p91p9dd2hg0ipfgv4s9br5mq0mns0ay6-RAxML-8.2.11
checking for references to /tmp/nix-build-RAxML-8.2.11.drv-0 in /nix/store/p91p9dd2hg0ipfgv4s9br5mq0mns0ay6-RAxML-8.2.11...
/nix/store/p91p9dd2hg0ipfgv4s9br5mq0mns0ay6-RAxML-8.2.11

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Success on x86_64-linux (full log)

Partial log (click to expand)

mpicc  -o raxmlHPC-MPI axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o  -lm  
installing
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/s8sz4zg2vkj65j94gpv2py7yim4nslr3-RAxML-8.2.11
shrinking /nix/store/s8sz4zg2vkj65j94gpv2py7yim4nslr3-RAxML-8.2.11/bin/raxmlHPC-MPI
strip is /nix/store/mdyy001q67hiks0g24ra53z7ckm4jfr4-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/s8sz4zg2vkj65j94gpv2py7yim4nslr3-RAxML-8.2.11/bin 
patching script interpreter paths in /nix/store/s8sz4zg2vkj65j94gpv2py7yim4nslr3-RAxML-8.2.11
checking for references to /tmp/nix-build-RAxML-8.2.11.drv-0 in /nix/store/s8sz4zg2vkj65j94gpv2py7yim4nslr3-RAxML-8.2.11...
/nix/store/s8sz4zg2vkj65j94gpv2py7yim4nslr3-RAxML-8.2.11

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Failure on aarch64-linux (full log)

Partial log (click to expand)

updateAutotoolsGnuConfigScriptsPhase
configuring
no configure script, doing nothing
building
rm -f *.o raxmlHPC-MPI
mpicc  -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -msse   -c -o axml.o axml.c
gcc: error: unrecognized command line option '-msse'; did you mean '-fdse'?
make: *** [<builtin>: axml.o] Error 1
builder for '/nix/store/8ycsz9hkp5aw4prl19pxrw3ddy1gvkjc-RAxML-8.2.11.drv' failed with exit code 2
error: build of '/nix/store/8ycsz9hkp5aw4prl19pxrw3ddy1gvkjc-RAxML-8.2.11.drv' failed

@unode
RAxML: init at 8.2.11 (SSE3 & MPI)
05889c5 
This can potentially be extended to cover all the other compilation
targets. SSE3-PTHREADS and MPI being the most commonly used.
@Mic92 Mic92 merged commit 80b096b into NixOS:master Feb 10, 2018
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