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Add Spack installation instructions to README.md #184

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RMeli
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@RMeli RMeli commented Mar 20, 2023

I finally had someone else reporting a successful GNINA installation with Spack, so it might be worth adding the installation instructions to the README for everyone to try.

My hope is that this will facilitate GNINA adoption even further, and reduce the number of installation issues in the issue tracker.

However, I have no idea if these instructions will actually decrease the number of installation issues. There is always the risk that installation issues will increase with an additional installation method available. Hopefully they will not, and I tried to re-direct installation issues with Spack to the Spack repository.

Before merging this PR, it would be great is other people could try out the installation instructions and provide additional feedback. I'd be happy to help, and to incorporate the feedback in this PR (and the upstream Spack package).

@RMeli
Add Spack installation instructions to README.md
4fa4d2a 
I finally had someone else reporting a successful GNINA installation with Spack, so it might be worth adding the installation instructions to the `README` for everyone to try. 

My hope is that this will facilitate GNINA adoption even further, and reduce the number of installation issues in the issue tracker.

However, I have no idea if these instructions will actually decrease the number of installation issues. There is always the risk that installation issues will increase with an additional installation method available. Hopefully they will not, and I tried to re-direct installation issues with Spack to the Spack repository.

Before merging this PR, it would be great is other people could try out the installation instructions and provide additional feedback. I'd be happy to help, and to incorporate the feedback in this PR (and the upstream Spack package).
@RMeli RMeli requested a review from dkoes March 20, 2023 17:31
@dkoes
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dkoes commented Mar 20, 2023

Hmm.. I tried it and it didn't work.

==> Installing swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg
==> No binary for swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/2a/2af08aced8fcd65cdb5cc62426768914bedc735b1c250325203716f78e39ac9b.tar.gz
==> No patches needed for swig
==> swig: Executing phase: 'autoreconf'
==> swig: Executing phase: 'configure'
==> swig: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' '-j16' 'V=1'

6 errors found in build log:
     132    checking for V8 Javascript library... not found
     133    checking for lua5.4... no
     134    checking for lua5.3... no
     135    checking for lua5.2... no
     136    checking for lua5.1... no
     137    checking for lua... /usr/bin/lua
  >> 138    checking Lua version... /usr/bin/lua: <command line>:1: attempt to 
            call field `match' (a nil value)
     139    stack traceback:
  >> 140    	<command line>:1: in main chunk
     141    	[C]: ?
     142    failed
     143    configure: WARNING: Not Lua 5.x, SWIG does not support this version
             of Lua
     144    checking for mzscheme... no
     145    checking for mzc... no
     146    checking for ocamlc... no

     ...

     330    DEPDIR=.deps depmode=none /bin/bash /tmp/dkoes/spack-stage/spack-st
            age-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Tools/con
            fig/depcomp \
     331    g++ -DHAVE_CONFIG_H   -I../Source/Include -I../Source/CParse -I/tmp
            /dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju
            6kaj6gg/spack-src/Source/Include -I/tmp/dkoes/spack-stage/spack-sta
            ge-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/DOH
             -I/tmp/dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6pnqt7i
            fkevbju6kaj6gg/spack-src/Source/CParse -I/tmp/dkoes/spack-stage/spa
            ck-stage-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Sour
            ce/Doxygen -I/tmp/dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfld
            oyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/Preprocessor -I/tmp/dkoes
            /spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6g
            g/spack-src/Source/Swig -I/tmp/dkoes/spack-stage/spack-stage-swig-4
            .1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/Modules -I/h
            ome/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-
            12.1.0/pcre2-10.42-wn7g4ynok3e2eoaelfr4a2axqe4tyidn/include   -c -o
             Doxygen/doxyentity.o /tmp/dkoes/spack-stage/spack-stage-swig-4.1.1
            -2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/Doxygen/doxyenti
            ty.cxx
     332    source='/tmp/dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6p
            nqt7ifkevbju6kaj6gg/spack-src/Source/Doxygen/doxyparser.cxx' object
            ='Doxygen/doxyparser.o' libtool=no \
     333    DEPDIR=.deps depmode=none /bin/bash /tmp/dkoes/spack-stage/spack-st
            age-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Tools/con
            fig/depcomp \
     334    g++ -DHAVE_CONFIG_H   -I../Source/Include -I../Source/CParse -I/tmp
            /dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju
            6kaj6gg/spack-src/Source/Include -I/tmp/dkoes/spack-stage/spack-sta
            ge-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/DOH
             -I/tmp/dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6pnqt7i
            fkevbju6kaj6gg/spack-src/Source/CParse -I/tmp/dkoes/spack-stage/spa
            ck-stage-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Sour
            ce/Doxygen -I/tmp/dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfld
            oyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/Preprocessor -I/tmp/dkoes
            /spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6g
            g/spack-src/Source/Swig -I/tmp/dkoes/spack-stage/spack-stage-swig-4
            .1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/Modules -I/h
            ome/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-
            12.1.0/pcre2-10.42-wn7g4ynok3e2eoaelfr4a2axqe4tyidn/include   -c -o
             Doxygen/doxyparser.o /tmp/dkoes/spack-stage/spack-stage-swig-4.1.1
            -2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/Source/Doxygen/doxypars
            er.cxx
     335    [spack cc] ERROR: Compiler 'gcc@12.1.0' does not have a C++ compile
            r configured.
  >> 336    make[2]: *** [Makefile:989: Doxygen/doxyentity.o] Error 1
     337    make[2]: *** Waiting for unfinished jobs....
     338    [spack cc] ERROR: Compiler 'gcc@12.1.0' does not have a C++ compile
            r configured.
  >> 339    make[2]: *** [Makefile:989: Doxygen/doxyparser.o] Error 1
     340    /home/dkoes/git/spack/lib/spack/env/gcc/gcc -g -O2 -Wall -W -I.  -o
             ccache-swig ccache.o mdfour.o hash.o execute.o util.o args.o stats
            .o cleanup.o snprintf.o unify.o -lz
     341    make[1]: Leaving directory '/tmp/dkoes/spack-stage/spack-stage-swig
            -4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/spack-build/CCach
            e'
     342    make[2]: Leaving directory '/tmp/dkoes/spack-stage/spack-stage-swig
            -4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/spack-build/Sourc
            e'
  >> 343    make[1]: *** [Makefile:636: all] Error 2
     344    make[1]: Leaving directory '/tmp/dkoes/spack-stage/spack-stage-swig
            -4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-src/spack-build/Sourc
            e'
  >> 345    make: *** [Makefile:36: source] Error 2

See build log for details:
  /tmp/dkoes/spack-stage/spack-stage-swig-4.1.1-2qp3yfldoyk6pnqt7ifkevbju6kaj6gg/spack-build-out.txt

@RMeli
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RMeli commented Mar 20, 2023

Thanks for testing @dkoes!

[spack cc] ERROR: Compiler 'gcc@12.1.0' does not have a C++ compiler configured.

What did you use as installation command and what's the output of spack compiler list and spack compiler info gcc@12.1.0?

The other successful report I had (beside my own test) was with GCC 11.3.0 (and all my tests were with the same compiler too).

@dkoes
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dkoes commented Mar 20, 2023 

==> Available compilers
-- gcc ubuntu22.04-x86_64 ---------------------------------------
gcc@12.1.0  gcc@11.3.0  gcc@9.5.0  gcc@7.5.0

This is in Ubuntu 22.04

@RMeli
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RMeli commented Mar 20, 2023

Can you please try spack install gnina %gcc@11.3.0? The other successful installation (excluding the ones by my) was also on Ubuntu 22, with GCC 11.3.0.

@dkoes
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dkoes commented Mar 20, 2023

I tried that, I tried running spack clean gnina and then installing, and I tried creating a new environment and running spack install --add gnina %gcc@11.3.0 but in all cases it seems dead set on using the gcc-12 compiler. 🤷‍♂️

@RMeli
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RMeli commented Mar 20, 2023 •
edited

Maybe

spack compiler rm gcc@12.1.0
spack uninstall --all
spack clean --all

spack install gnina %gcc@11.3.0

could do the trick? Make sure to use the full version (i.e. 11.3.0 and not 11.3) when specifying compilers, since this might be currently an issue in Spack.

I might soon have access to an Ubuntu 22 system and I might be able to do further tests.

@RMeli RMeli marked this pull request as draft March 20, 2023 20:04
@dkoes
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dkoes commented Mar 20, 2023

Nope

dkoes@jedi:~/git/spack$ spack compiler rm gcc%12.1.0
==> Error: %gcc cannot have multiple compilers

@RMeli
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RMeli commented Mar 20, 2023

Sorry, that was a typo in the original message that I immediately corrected. The correct command is spack compiler rm gcc@12.1.0.

@dkoes
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dkoes commented Mar 21, 2023

Using the right compiler now, but failing to build rdkit:

==> rdkit: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    '/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/gmake-4.4.1-ip4dja5k746uw6vsgapqlgrfwhl3r4vg/bin/make' '-j16'

5 errors found in build log:
     724    make[2]: Entering directory '/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5
            jpbw'
     725    [ 13%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o
     726    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/ML/InfoTheory &&
             /home/dkoes/git/spack/lib/spack/env/gcc/g++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTH
            EORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGE
            N3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -
            I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External -I/tmp/dkoes/spack-stage
            /spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/RingFamilies/RingDecomposerLib/src/RingDecompos
            erLib -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/python-3.10.10-6rzza5e32luo7ftafi6w356q4sktr
            ps5/include/python3.10 -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/py-numpy-1.24.2-igoenicnxfx
            jd74qu3k3hykmhhg75lty/lib/python3.10/site-packages/numpy/core/include -I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jp
            bwkzdeitq32e7n6djlopcdx4dut/spack-src/Code -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/boost-1
            .81.0-q7v3gvenjdebxorr7coq6tybk2kd45a2/include -isystem /usr/include/eigen3 -mpopcnt -Wno-deprecated -Wno-unused-function -fno-s
            trict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++14 -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoB
            itRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /tmp/dkoe
            s/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code/ML/InfoTheory/InfoBitRanker.cpp
     727    In file included from /usr/include/signal.h:328,
     728                     from /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/cat
            ch/catch/single_include/catch2/catch.hpp:8031,
     729                     from /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code/SimDivP
            ickers/catch_tests.cpp:13:
  >> 730    /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/catch/catch/single_includ
            e/catch2/catch.hpp:10815:58: error: call to non-'constexpr' function 'long int sysconf(int)'
     731    10815 |     static constexpr std::size_t sigStackSize = 32768 >= MINSIGSTKSZ ? 32768 : MINSIGSTKSZ;
     732          |                                                          ^~~~~~~~~~~
     733    In file included from /usr/include/x86_64-linux-gnu/bits/sigstksz.h:24,
     734                     from /usr/include/signal.h:328,
     735                     from /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/cat
            ch/catch/single_include/catch2/catch.hpp:8031,
     736                     from /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code/SimDivP
            ickers/catch_tests.cpp:13:
     737    /usr/include/unistd.h:640:17: note: 'long int sysconf(int)' declared here
     738      640 | extern long int sysconf (int __name) __THROW;
     739          |                 ^~~~~~~
     740    In file included from /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code/SimDivP
            ickers/catch_tests.cpp:13:
  >> 741    /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/catch/catch/single_includ
            e/catch2/catch.hpp:10874:45: error: size of array 'altStackMem' is not an integral constant-expression
     742    10874 |     char FatalConditionHandler::altStackMem[sigStackSize] = {};
     743          |                                             ^~~~~~~~~~~~
     744    [ 13%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so
     745    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/Geometry && /hom
            e/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/cmake-3.25.2-jdjp62zx66q2o7rsc5b4lfi2t4m7k275/bin/cmake 
            -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1
     746    /home/dkoes/git/spack/lib/spack/env/gcc/g++ -fPIC  -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wex
            tra -fPIC -O2 -g -DNDEBUG -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2021.09.5 CMake
            Files/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.
            o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o  -Wl,-rpath,/tmp/dkoes/spack-sta
            ge/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/lib:::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ../../lib/libRDKitDataStructs.so.1.2021.09.
            5 ../../lib/libRDKitRDGeneral.so.1.2021.09.5 -ldl
     747    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/Geometry && /hom
            e/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/cmake-3.25.2-jdjp62zx66q2o7rsc5b4lfi2t4m7k275/bin/cmake 
            -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2021.09.5 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitR
            DGeometryLib.so

     ...

     796    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw && /home/dkoes/git/sp
            ack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/cmake-3.25.2-jdjp62zx66q2o7rsc5b4lfi2t4m7k275/bin/cmake -E cmake_depen
            ds "Unix Makefiles" /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src /tmp/dkoes/spa
            ck-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code/ML/InfoTheory/Wrap /tmp/dkoes/spack-stage/s
            pack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09
            _5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/ML/InfoTheory/Wrap /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09
            _5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --c
            olor=
     797    make[2]: Leaving directory '/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5j
            pbw'
     798    /home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/gmake-4.4.1-ip4dja5k746uw6vsgapqlgrfwhl3r4vg/bin/mak
            e  -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build
     799    make[2]: Entering directory '/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5
            jpbw'
     800    [ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o
     801    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/ML/InfoTheory/Wr
            ap && /home/dkoes/git/spack/lib/spack/env/gcc/g++ -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -
            DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS
            _EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_
            URF -DrdInfoTheory_EXPORTS -I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Exter
            nal -I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/RingFamilies/RingDe
            composerLib/src/RingDecomposerLib -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/python-3.10.10-6
            rzza5e32luo7ftafi6w356q4sktrps5/include/python3.10 -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0
            /py-numpy-1.24.2-igoenicnxfxjd74qu3k3hykmhhg75lty/lib/python3.10/site-packages/numpy/core/include -I/tmp/dkoes/spack-stage/spack
            -stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code -isystem /home/dkoes/git/spack/opt/spack/linux-ubuntu22.0
            4-skylake_avx512/gcc-11.3.0/boost-1.81.0-q7v3gvenjdebxorr7coq6tybk2kd45a2/include -isystem /usr/include/eigen3 -mpopcnt -Wno-dep
            recated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++14 -MD -MT Code/ML/InfoThe
            ory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdI
            nfoTheory.dir/InfoBitRanker.cpp.o -c /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-s
            rc/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp
  >> 802    make[2]: *** [Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make:79: Code/SimDivPickers/CMakeFiles/pickersTestsCatch
            .dir/catch_tests.cpp.o] Error 1
     803    make[2]: Leaving directory '/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5j
            pbw'
  >> 804    make[1]: *** [CMakeFiles/Makefile2:13140: Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/all] Error 2
     805    make[1]: *** Waiting for unfinished jobs....
     806    [ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o
     807    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/ML/InfoTheory/Wr
            ap && /home/dkoes/git/spack/lib/spack/env/gcc/g++ -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -
            DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS
            _EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_
            URF -DrdInfoTheory_EXPORTS -I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Exter
            nal -I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/RingFamilies/RingDe
            composerLib/src/RingDecomposerLib -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/python-3.10.10-6
            rzza5e32luo7ftafi6w356q4sktrps5/include/python3.10 -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0
            /py-numpy-1.24.2-igoenicnxfxjd74qu3k3hykmhhg75lty/lib/python3.10/site-packages/numpy/core/include -I/tmp/dkoes/spack-stage/spack
            -stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code -isystem /home/dkoes/git/spack/opt/spack/linux-ubuntu22.0
            4-skylake_avx512/gcc-11.3.0/boost-1.81.0-q7v3gvenjdebxorr7coq6tybk2kd45a2/include -isystem /usr/include/eigen3 -mpopcnt -Wno-dep
            recated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++14 -MD -MT Code/ML/InfoThe
            ory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CM
            akeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6dj
            lopcdx4dut/spack-src/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp
     808    [ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o
     809    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/ML/InfoTheory/Wr
            ap && /home/dkoes/git/spack/lib/spack/env/gcc/g++ -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -
            DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS
            _EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_
            URF -DrdInfoTheory_EXPORTS -I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Exter
            nal -I/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/External/RingFamilies/RingDe
            composerLib/src/RingDecomposerLib -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/python-3.10.10-6
            rzza5e32luo7ftafi6w356q4sktrps5/include/python3.10 -I/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0
            /py-numpy-1.24.2-igoenicnxfxjd74qu3k3hykmhhg75lty/lib/python3.10/site-packages/numpy/core/include -I/tmp/dkoes/spack-stage/spack
            -stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/Code -isystem /home/dkoes/git/spack/opt/spack/linux-ubuntu22.0
            4-skylake_avx512/gcc-11.3.0/boost-1.81.0-q7v3gvenjdebxorr7coq6tybk2kd45a2/include -isystem /usr/include/eigen3 -mpopcnt -Wno-dep
            recated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++14 -MD -MT Code/ML/InfoThe
            ory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInf
            oTheory.dir/rdInfoTheory.cpp.o -c /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-src/
            Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp
     810    [ 14%] Linking CXX static library libRDKitInfoTheory_static.a

     ...

     837    [ 14%] Linking CXX shared module ../../../rdkit/rdBase.so
     838    cd /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/Code/RDBoost/Wrap && 
            /home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/cmake-3.25.2-jdjp62zx66q2o7rsc5b4lfi2t4m7k275/bin/cm
            ake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1
     839    /home/dkoes/git/spack/lib/spack/env/gcc/g++ -fPIC  -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wex
            tra -fPIC -O2 -g -DNDEBUG -shared -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/bzip2-1.0.8-ayen
            32yqwfh7xux7qb5jhoxl7noytqqf/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/expat-2.5.0-v33n7
            7he2y7owffwvtpsg347raeatr2c/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/gdbm-1.23-vvehejrl
            t3moo2ijznwsqckog7oprg25/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/gettext-0.21.1-kwzqam
            d6t5bh4xa4vk46m2lavurowlwu/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/libffi-3.4.4-hkiag3
            hzedyymfjtuz4rgqkdi5nactqj/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/libxcrypt-4.4.33-5x
            k7rnjdcbmosailbppemlgq2kijgdyi/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/ncurses-6.4-5be
            w5exdbnhypc5fl7ncyzve23edj3fy/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/openssl-1.1.1t-v
            il6hnvidmnzrfp6gglukctdoodmtrlj/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/readline-8.2-b
            wwkshfmjfqgou63v5h27dmgurjz47sx/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/sqlite-3.40.1-
            47rn6c2lkna3qjnh37bdbqyfxdf2yrr6/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/util-linux-uu
            id-2.38.1-ruspa4bydy35xkkbmkrojhxaenptzhjs/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/xz-
            5.4.1-vo2g53lp65e2tzo2w7tyagrampcslqbl/lib -L/home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/zlib-1.
            2.13-faprw67c5uo2lf6hlac624se45d2btjy/lib -shared  -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o  -Wl,-rpath,/t
            mp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5jpbw/lib:/home/dkoes/git/spack/
            opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/python-3.10.10-6rzza5e32luo7ftafi6w356q4sktrps5/lib:/home/dkoes/git/spack/
            opt/spack/linux-ubuntu22.04-skylake_avx512/gcc-11.3.0/boost-1.81.0-q7v3gvenjdebxorr7coq6tybk2kd45a2/lib:::::::::::::::::::::::::
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            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
            :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ../../../lib/libRDKitRDBo
            ost.so.1.2021.09.5 ../../../lib/libRDKitRDGeneral.so.1.2021.09.5 -ldl /home/dkoes/git/spack/opt/spack/linux-ubuntu22.04-skylake_
            avx512/gcc-11.3.0/python-3.10.10-6rzza5e32luo7ftafi6w356q4sktrps5/lib/libpython3.10.so /home/dkoes/git/spack/opt/spack/linux-ubu
            ntu22.04-skylake_avx512/gcc-11.3.0/boost-1.81.0-q7v3gvenjdebxorr7coq6tybk2kd45a2/lib/libboost_python310.so.1.81.0
     840    make[2]: Leaving directory '/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5j
            pbw'
     841    [ 14%] Built target rdBase
     842    make[1]: Leaving directory '/tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-5m5j
            pbw'
  >> 843    make: *** [Makefile:159: all] Error 2

See build log for details:
  /tmp/dkoes/spack-stage/spack-stage-rdkit-2021_09_5-5m5jpbwkzdeitq32e7n6djlopcdx4dut/spack-build-out.txt

@RMeli
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RMeli commented Mar 21, 2023 •
edited

Not quite the smooth experience I was hoping for... =(

However, RDKit is one of the last dependencies being built and it's optional. Therefore, if you haven't lost your patience yet, you could try one of the following:

  • Use spack edit gnina to edit the gnina Spack package locally and remove line 57 (depends_on("rdkit")) and line 68 (f"-DRDKIT_INCLUDE_DIR={self.spec['rdkit'].prefix.include}/rdkit"). You should then (hopefully) be able to finish the build with spack install gnina %gcc@11.3.0
  • Checkout my latest PR on Spack GNINA: add cuDNN variant and make RDKit optional spack/spack#36270 from your local Spack instance, which introduces two variants: one variant to build with cuDNN (on by default), one to build gninavis (off by default, making RDKit an opt-in dependency). You can then (hopefully) finish the build with spack install gnina~cudnn~gninavis %gcc@11.3.0 (where ~ in front of the variant name turns off the variant).

I should get a new system in a few days/weeks, so I'll be able to test this locally with Ubuntu 22. In the meantime, I'll try to reproduce the RDKit issues in a Docker container and try to fix them.

@RMeli RMeli mentioned this pull request Mar 21, 2023
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RMeli commented Mar 25, 2023

I managed to reproduce the RDKit issue locally. I think it's the same as rdkit/rdkit#5089. I added a newer version of RDKit, and everything builds without issues.

@RMeli RMeli mentioned this pull request Mar 25, 2023
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@RMeli RMeli mentioned this pull request Jul 18, 2023
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@RMeli RMeli mentioned this pull request Dec 11, 2023
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RMeli commented Dec 18, 2023 •
edited

Added GNINA 1.1 to Spack: spack/spack#41762. gnina@1.1+cudnn builds fine, gnina@1.1+cudnn+gninavis has issues because RDKit errors out.

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