gnina
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gnina
Add Spack installation instructions to README.md
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).
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 '[email protected]' 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 '[email protected]' 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
Thanks for testing @dkoes!
[spack cc] ERROR: Compiler '[email protected]' 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 [email protected]?
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).
==> Available compilers
-- gcc ubuntu22.04-x86_64 ---------------------------------------
[email protected] [email protected] [email protected] [email protected]
This is in Ubuntu 22.04
Can you please try spack install gnina %[email protected]? The other successful installation (excluding the ones by my) was also on Ubuntu 22, with GCC 11.3.0.
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 %[email protected] but in all cases it seems dead set on using the gcc-12 compiler. :man_shrugging:
Maybe
spack compiler rm [email protected]
spack uninstall --all
spack clean --all
spack install gnina %[email protected]
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.
Nope
dkoes@jedi:~/git/spack$ spack compiler rm gcc%12.1.0
==> Error: %gcc cannot have multiple compilers
Sorry, that was a typo in the original message that I immediately corrected. The correct command is spack compiler rm [email protected].
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:::::::::::::::::::::::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
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:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ../../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
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 gninato edit thegninaSpack 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 withspack install gnina %[email protected] - Checkout my latest PR on Spack https://github.com/spack/spack/pull/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 withspack install gnina~cudnn~gninavis %[email protected](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.
I managed to reproduce the RDKit issue locally. I think it's the same as https://github.com/rdkit/rdkit/issues/5089. I added a newer version of RDKit, and everything builds without issues.
Added GNINA 1.1 to Spack: https://github.com/spack/spack/pull/41762. [email protected]+cudnn builds fine, [email protected]+cudnn+gninavis has issues because RDKit errors out.