xSDK 0.4.0 Release

Motivation

Combinations of multiple software packages developed by different groups are essential for large-scale computational science, where the capabilities needed for modeling, simulation, and analysis are broader than any single team has resources to address. The often tedious trial-and-error process of obtaining, configuring, and installing any single tool may arguably be manageable. However, from the perspective of an end-user application scientist, handling each tool’s installation idiosyncrasies can easily become overwhelming when dealing with several packages in combination. Worse, such problems are compounded by the need for consistency among packages to be used within the same application in terms of compiler, compiler versions and options, and common third-party packages such as BLAS and HDF5.

Spack

xSDK uses Spack for package installation. Green denotes xSDK member packages as of 0.4.0 release.

xsdk-0.4.0-diagram

A goal of xSDK is to simplify the process of working with various xSDK packages in combination. Spack is a package manager for high-performance computing.  We thus provide an xSDK Spack metapackage that includes many xSDK numerical libraries (AMReX*, deal.ii*, DTK*, Hypre, MAGMA, MFEM, Omega_h*, PETSc, PHIST, PLASMA*, PUMI*, SLEPc*, STRUMPACK*, SUNDIALS, SuperLU_dist, Tasmanian*,  and Trilinos ) as well as some commonly needed external packages.

Spack allows the xSDK packages to be deployed with a single command.  The user can optionally choose compilers, MPI implementation, and build options.  We are working toward support of combinatorial test dashboards for all xSDK packages.

*Denotes a package released as part of the xSDK for the first time in version 0.4.0.

 xSDK 0.4.0 release components

Final release date: December 23, 2018

The xSDK spack metapackage (version 0.4.0) includes tested release versions of the following xSDK packages:

  • AMReX
  • deal.ii
  • DTK
  • hypre
  • MAGMA
  • MFEM
  • Omega_h
  • PETSc/TAO
  • PHIST
  • PLASMA
  • PUMI
  • SLEPc
  • STRUMPACK
  • SUNDIALS
  • SuperLU
  • Tasmanian
  • Trilinos
  • Pflotran
  • Alquimia

Users who prefer to work with just one xSDK package rather than several can use Spack to install only that particular package.  Alternatively, they can bypass Spack and instead obtain the package directly from its website and install according to instructions there.

Open source packages installed with xSDK packages

Users can view a tree of dependencies for any Spack package, including xSDK, by running ‘spack spec xsdk’.  This is an example of the dependency tree for the xSDK metapackage as of version 0.4.0:

xsdk@0.4.0%gcc@7.3.0~cuda~debug+omega-h arch=linux-ubuntu18.04-x86_64 
 ^alquimia@xsdk-0.4.0%gcc@7.3.0 build_type=RelWithDebInfo +shared arch=linux-ubuntu18.04-x86_64 
 ^cmake@3.10.2%gcc@7.3.0~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-ubuntu18.04-x86_64 
 ^hdf5@1.10.4%gcc@7.3.0~cxx~debug+fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-ubuntu18.04-x86_64 
 ^mpich@3.3b1%gcc@7.3.0 device=ch3 +hydra netmod=tcp +pmi+romio~verbs arch=linux-ubuntu18.04-x86_64 
 ^numactl@2.0.12%gcc@7.3.0 arch=linux-ubuntu18.04-x86_64 
 ^autoconf@2.69%gcc@7.3.0 arch=linux-ubuntu18.04-x86_64 
 ^automake@1.15.1%gcc@7.3.0 arch=linux-ubuntu18.04-x86_64 
 ^libtool@2.4.6%gcc@7.3.0 arch=linux-ubuntu18.04-x86_64 
 ^m4@1.4.18%gcc@7.3.0 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-ubuntu18.04-x86_64 
 ^zlib@1.2.11%gcc@7.3.0+optimize+pic+shared arch=linux-ubuntu18.04-x86_64 
 ^petsc@3.10.3%gcc@7.3.0~X clanguage=C ~complex~debug+double+hdf5+hypre~int64+metis+mpi~mumps+shared~suite-sparse+superlu-dist+trilinos arch=linux-ubuntu18.04-x86_64 
 ^hypre@2.15.1%gcc@7.3.0~debug~int64~internal-superlu+mpi+shared arch=linux-ubuntu18.04-x86_64 
 ^openblas@0.3.4%gcc@7.3.0 cpu_target= ~ilp64+pic+shared threads=none ~virtual_machine arch=linux-ubuntu18.04-x86_64 
 ^metis@5.1.0%gcc@7.3.0 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1,b1225da886605ea558db7ac08dd8054742ea5afe5ed61ad4d0fe7a495b1270d2 +real64+shared arch=linux-ubuntu18.04-x86_64 
 ^parmetis@4.0.3%gcc@7.3.0 build_type=RelWithDebInfo ~gdb patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d +shared arch=linux-ubuntu18.04-x86_64 
 ^python@2.7.15rc1%gcc@7.3.0+dbm~optimizations patches=123082ab3483ded78e86d7c809e98a804b3465b4683c96bd79a2fd799f572244 +pic+pythoncmd+shared~tk~ucs4 arch=linux-ubuntu18.04-x86_64 
 ^superlu-dist@6.1.0%gcc@7.3.0 build_type=RelWithDebInfo ~int64+shared arch=linux-ubuntu18.04-x86_64 
 ^trilinos@12.14.0-rc1%gcc@7.3.0~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~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=linux-ubuntu18.04-x86_64 
 ^boost@1.69.0%gcc@7.3.0+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 ~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-ubuntu18.04-x86_64 
 ^bzip2@1.0.6%gcc@7.3.0+shared arch=linux-ubuntu18.04-x86_64 
 ^glm@0.9.7.1%gcc@7.3.0 build_type=RelWithDebInfo arch=linux-ubuntu18.04-x86_64 
 ^matio@1.5.13%gcc@7.3.0+hdf5+shared+zlib arch=linux-ubuntu18.04-x86_64 
 ^netcdf@4.6.2%gcc@7.3.0~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+pic+shared arch=linux-ubuntu18.04-x86_64 
 ^pflotran@xsdk-0.4.0%gcc@7.3.0 arch=linux-ubuntu18.04-x86_64 
 ^amrex@18.10.1%gcc@7.3.0~amrdata build_type=Release dimensions=3 ~eb~fortran+linear_solvers+mpi~openmp~particles precision=double ~shared arch=linux-ubuntu18.04-x86_64 
 ^dealii@9.0.1%gcc@7.3.0+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=linux-ubuntu18.04-x86_64 
 ^adol-c@develop%gcc@7.3.0~advanced_branching+atrig_erf~boost+doc+examples~openmp~sparse arch=linux-ubuntu18.04-x86_64 
 ^arpack-ng@3.6.3%gcc@7.3.0+mpi+shared arch=linux-ubuntu18.04-x86_64 
 ^gsl@2.5%gcc@7.3.0 arch=linux-ubuntu18.04-x86_64 
 ^intel-tbb@2019.2%gcc@7.3.0 cxxstd=default patches=ca08c28bdb15582c30777f9303d1986e4c09b3d514776494f3fbf5f19381bfda +shared+tm arch=linux-ubuntu18.04-x86_64 
 ^muparser@2.2.6.1%gcc@7.3.0 arch=linux-ubuntu18.04-x86_64 
 ^nanoflann@1.2.3%gcc@7.3.0 build_type=RelWithDebInfo arch=linux-ubuntu18.04-x86_64 
 ^netlib-scalapack@2.0.2%gcc@7.3.0 build_type=RelWithDebInfo ~pic+shared arch=linux-ubuntu18.04-x86_64 
 ^oce@0.18.3%gcc@7.3.0~X11+tbb arch=linux-ubuntu18.04-x86_64 
 ^p4est@2.0%gcc@7.3.0~openmp patches=8fb829e34e3a1e28afdd6e56e0bdc1d377af569b7ccb9e9d8da0eeb5829ed27e,e9418b1a9347a409be241cd185519b31950e42a7f55b6fb80ce53097657098ee arch=linux-ubuntu18.04-x86_64 
 ^suite-sparse@5.3.0%gcc@7.3.0~cuda~openmp+pic~tbb arch=linux-ubuntu18.04-x86_64 
 ^sundials@3.2.1%gcc@7.3.0+ARKODE+CVODE+CVODES+IDA+IDAS+KINSOL build_type=RelWithDebInfo ~cuda+examples-c~examples-cuda~examples-cxx+examples-f77~examples-f90+examples-install~examples-raja~fcmix+generic-math+hypre~int64~klu~lapack+mpi~openmp~petsc precision=double ~pthread~raja+shared+static~superlu-mt arch=linux-ubuntu18.04-x86_64 
 ^mfem@3.4.0%gcc@7.3.0~conduit~debug+examples~gnutls+gzstream+hypre~lapack~libunwind+metis+miniapps~mpfr+mpi~netcdf~openmp patches=89c03ec2f1802f1c66be0aef9c58b9849ecf0c97246ba0dd77eac898986608b9,cb6f351f1a18a917fe8286921a5f710dde314ef5b7649fa774c6cd2ff631b688 +petsc~pumi~shared+static~suite-sparse+sundials+superlu-dist~threadsafe timer=auto arch=linux-ubuntu18.04-x86_64 
 ^omega-h@9.19.1%gcc@7.3.0 build_type= ~examples+mpi+optimize+shared+symbols~throw~trilinos~warnings+zlib arch=linux-ubuntu18.04-x86_64 
 ^phist@1.7.5%gcc@7.3.0 build_type=RelWithDebInfo ~fortran~host kernel_lib=tpetra +mpi~openmp outlev=2 ~parmetis~scamac+shared~trilinos arch=linux-ubuntu18.04-x86_64 
 ^plasma@18.11.1%gcc@7.3.0 build_type=RelWithDebInfo ~lua+shared arch=linux-ubuntu18.04-x86_64 
 ^pumi@2.2.0%gcc@7.3.0 build_type=RelWithDebInfo ~fortran~shared~zoltan arch=linux-ubuntu18.04-x86_64 
 ^slepc@3.10.1%gcc@7.3.0+arpack~blopex arch=linux-ubuntu18.04-x86_64 
 ^strumpack@3.1.1%gcc@7.3.0~build_dev_tests~build_tests build_type=RelWithDebInfo +c_interface~count_flops+mpi+openmp~parmetis~scotch~task_timers arch=linux-ubuntu18.04-x86_64 
 ^tasmanian@6.0%gcc@7.3.0+blas build_type=Release ~cuda~fortran~magma~mpi~openmp~python+xsdkflags arch=linux-ubuntu18.04-x86_64 

The following open source HPC packages are installed by default with the xSDK.  Note that you may override these and use a preinstalled version if you wish.

                  • Boost C++ headers and libraries
                  • HDF5 low-level parallel IO library
                  • NetCDF high-level parallel IO library
                  • METIS graph partitioner
                  • ParMETIS parallel graph partitioner