based on environment tutorial, my understanding was that all root packages are conretized simultaneously so that we don't build multiple dependencies. This does not seem to be the case for the following example:
Steps to reproduce the issue
$ spack env create temp
$ spack env activate temp
$ spack add dealii
$ spack add valgrind
$ spack concretize -f
==> Concretizing dealii
[+] s5ctayk dealii@develop%clang@10.0.0-apple~adol-c+arpack~assimp build_type=DebugRelease ~cuda cuda_arch= ~doc~gmsh+gsl+hdf5~int64+metis+mpi+muparser~nanoflann+netcdf~oce+optflags+p4est~petsc~python+scalapack~slepc~sundials+trilinos arch=darwin-mojave-x86_64
[+] rmphnvs ^arpack-ng@3.6.3%clang@10.0.0-apple+mpi+shared arch=darwin-mojave-x86_64
[+] uuwucyz ^cmake@3.12.3%clang@10.0.0-apple~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=darwin-mojave-x86_64
[+] zvaa4lh ^ncurses@6.1%clang@10.0.0-apple~symlinks~termlib arch=darwin-mojave-x86_64
[+] b5gm23c ^pkgconf@1.4.2%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] t4zg4vb ^openssl@1.0.2o%clang@10.0.0-apple+systemcerts arch=darwin-mojave-x86_64
[+] igk7of6 ^perl@5.26.2%clang@10.0.0-apple+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=darwin-mojave-x86_64
[+] 4ldnoio ^gdbm@1.14.1%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] 722dzmg ^readline@7.0%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] uw6agny ^zlib@1.2.11%clang@10.0.0-apple+optimize+pic+shared arch=darwin-mojave-x86_64
[+] v2t5rno ^openblas@0.3.3%clang@10.0.0-apple cpu_target= ~ilp64 patches=47cfa7a952ac7b2e4632c73ae199d69fb54490627b66a62c681e21019c4ddc9d,714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33 +pic+shared threads=none ~virtual_machine arch=darwin-mojave-x86_64
[+] 6owrpmt ^openmpi@3.1.3%clang@10.0.0-apple~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=darwin-mojave-x86_64
[+] irsuwjw ^hwloc@1.11.9%clang@10.0.0-apple~cairo~cuda+libxml2~pci+shared arch=darwin-mojave-x86_64
[+] 5ansovh ^libxml2@2.9.8%clang@10.0.0-apple~python arch=darwin-mojave-x86_64
[+] i47twa3 ^xz@5.2.4%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] 2solnba ^boost@1.68.0%clang@10.0.0-apple+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=b37164268f34f7133cbc9a4066ae98fda08adf51e1172223f6a969909216870f +program_options+python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=darwin-mojave-x86_64
[+] syohzw5 ^bzip2@1.0.6%clang@10.0.0-apple+shared arch=darwin-mojave-x86_64
[+] te2wy74 ^diffutils@3.6%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] nunzf4z ^python@2.7.15%clang@10.0.0-apple+dbm~optimizations patches=123082ab3483ded78e86d7c809e98a804b3465b4683c96bd79a2fd799f572244 +pic+pythoncmd~shared~tk~ucs4 arch=darwin-mojave-x86_64
[+] ndtg2ny ^sqlite@3.23.1%clang@10.0.0-apple~functions arch=darwin-mojave-x86_64
[+] 3xp3xgx ^gsl@2.5%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] lzwprfv ^hdf5@1.10.4%clang@10.0.0-apple~cxx~debug~fortran+hl+mpi+pic+shared~szip~threadsafe arch=darwin-mojave-x86_64
[+] wmzjbao ^intel-tbb@2019%clang@10.0.0-apple cxxstd=default patches=ca08c28bdb15582c30777f9303d1986e4c09b3d514776494f3fbf5f19381bfda +shared+tm arch=darwin-mojave-x86_64
[+] tokytep ^metis@5.1.0%clang@10.0.0-apple build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 +real64+shared arch=darwin-mojave-x86_64
[+] 5ammk4l ^muparser@2.2.6.1%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] uh4jqye ^netcdf@4.6.1%clang@10.0.0-apple~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+shared arch=darwin-mojave-x86_64
[+] azyaray ^m4@1.4.18%clang@10.0.0-apple patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=darwin-mojave-x86_64
[+] yzxmqil ^libsigsegv@2.11%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] wjxt2y6 ^netcdf-cxx@4.2%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] udk3fgd ^netlib-scalapack@2.0.2%clang@10.0.0-apple build_type=RelWithDebInfo ~pic+shared arch=darwin-mojave-x86_64
[+] pjavlko ^p4est@2.0%clang@10.0.0-apple~openmp patches=8fb829e34e3a1e28afdd6e56e0bdc1d377af569b7ccb9e9d8da0eeb5829ed27e,e9418b1a9347a409be241cd185519b31950e42a7f55b6fb80ce53097657098ee arch=darwin-mojave-x86_64
[+] wuz6miy ^autoconf@2.69%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] 5mmp44g ^automake@1.16.1%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] 6uxuqma ^libtool@2.4.6%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] xkgsfwe ^suite-sparse@5.3.0%clang@10.0.0-apple~cuda~openmp+pic~tbb arch=darwin-mojave-x86_64
[+] twdxche ^trilinos@12.12.1%clang@10.0.0-apple~alloptpkgs+amesos+amesos2+anasazi+aztec+belos+boost build_type=RelWithDebInfo ~cgns~complex~dtk+epetra+epetraext+exodus+explicit_template_instantiation~float+fortran~fortrilinos+gtest+hdf5+hypre+ifpack+ifpack2~intrepid~intrepid2~isorropia+kokkos+metis~minitensor+ml+muelu+mumps~nox~openmp patches=7ba0dea6c8407322c21970e549f2988fdfeeda8e3a5e0bb178207471142c1047,95420650aee640da31d5adc4ad8dcd3f67ae3e7d4736e167f7b3991e8ff47e0e ~phalanx~piro~pnetcdf~python+rol~rythmos+sacado~shards+shared~stk+suite-sparse~superlu+superlu-dist~teko~tempus+teuchos+tpetra~x11~xsdkflags~zlib+zoltan+zoltan2 arch=darwin-mojave-x86_64
[+] wkxhidy ^glm@0.9.7.1%clang@10.0.0-apple build_type=RelWithDebInfo arch=darwin-mojave-x86_64
[+] hmnkxye ^hypre@2.15.1%clang@10.0.0-apple~debug~int64~internal-superlu+mpi~shared arch=darwin-mojave-x86_64
[+] qgfey32 ^matio@1.5.9%clang@10.0.0-apple+hdf5+shared+zlib arch=darwin-mojave-x86_64
[+] y2ckdum ^mumps@5.1.1%clang@10.0.0-apple+complex+double+float~int64~metis+mpi~parmetis~ptscotch~scotch+shared arch=darwin-mojave-x86_64
[+] pigioig ^parmetis@4.0.3%clang@10.0.0-apple build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=darwin-mojave-x86_64
[+] uwlpi7b ^superlu-dist@5.3.0%clang@10.0.0-apple build_type=RelWithDebInfo ~int64+shared arch=darwin-mojave-x86_64
==> Concretizing valgrind
- 3cbq25o valgrind@3.14.0%clang@10.0.0-apple+boost+mpi+only64bit~ubsan arch=darwin-mojave-x86_64
- r573dgz ^boost@1.68.0%clang@10.0.0-apple+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy+program_options+python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=darwin-mojave-x86_64
[+] syohzw5 ^bzip2@1.0.6%clang@10.0.0-apple+shared arch=darwin-mojave-x86_64
[+] te2wy74 ^diffutils@3.6%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] nunzf4z ^python@2.7.15%clang@10.0.0-apple+dbm~optimizations patches=123082ab3483ded78e86d7c809e98a804b3465b4683c96bd79a2fd799f572244 +pic+pythoncmd~shared~tk~ucs4 arch=darwin-mojave-x86_64
[+] 4ldnoio ^gdbm@1.14.1%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] 722dzmg ^readline@7.0%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] zvaa4lh ^ncurses@6.1%clang@10.0.0-apple~symlinks~termlib arch=darwin-mojave-x86_64
[+] b5gm23c ^pkgconf@1.4.2%clang@10.0.0-apple arch=darwin-mojave-x86_64
[+] t4zg4vb ^openssl@1.0.2o%clang@10.0.0-apple+systemcerts arch=darwin-mojave-x86_64
[+] igk7of6 ^perl@5.26.2%clang@10.0.0-apple+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=darwin-mojave-x86_64
[+] uw6agny ^zlib@1.2.11%clang@10.0.0-apple+optimize+pic+shared arch=darwin-mojave-x86_64
[+] ndtg2ny ^sqlite@3.23.1%clang@10.0.0-apple~functions arch=darwin-mojave-x86_64
[+] 6owrpmt ^openmpi@3.1.3%clang@10.0.0-apple~cuda+cxx_exceptions fabrics= ~java~legacylaunchers~memchecker~pmi schedulers= ~sqlite3~thread_multiple+vt arch=darwin-mojave-x86_64
[+] irsuwjw ^hwloc@1.11.9%clang@10.0.0-apple~cairo~cuda+libxml2~pci+shared arch=darwin-mojave-x86_64
[+] 5ansovh ^libxml2@2.9.8%clang@10.0.0-apple~python arch=darwin-mojave-x86_64
[+] i47twa3 ^xz@5.2.4%clang@10.0.0-apple arch=darwin-mojave-x86_64```
Error Message
So it looks like boost will be re-installed for valgrind.
My best guess is that this is related to patching of boost from deal.II.
Information on your system
- macOS 10.14.1
packages.yaml
valgrind:
variants: ~ubsan
boost:
variants: +thread+system+serialization+iostreams+python
dealii:
version: [develop]
variants: ~doc+optflags~python~adol-c~assimp~gmsh~nanoflann~oce~petsc~slepc~sundials
based on environment tutorial, my understanding was that all
rootpackages are conretized simultaneously so that we don't build multiple dependencies. This does not seem to be the case for the following example:Steps to reproduce the issue
Error Message
So it looks like
boostwill be re-installed forvalgrind.My best guess is that this is related to patching of
boostfromdeal.II.Information on your system
packages.yaml