mpi: Factorize openmpi setup build phase.
* gnu/packages/mpi.scm (%openmpi-setup): New variable. * gnu/packages/maths.scm (scalapack, slepc-openmpi, mumps-openmpi) (superlu-dist, p4est, petsc-openmpi, hypre-openmpi, elemental) (sundials-openmpi, arpack-ng-openmpi)[arguments]: Use it in #:phases.
This commit is contained in:
Eric Bavier
Eric Bavier
parent
5882078e8c
commit
bbe46a4af5
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@ -511,14 +511,8 @@ large scale eigenvalue problems.")
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''("--enable-mpi"))
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((#:phases phases '%standard-phases)
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`(modify-phases ,phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to
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;; placate Open MPI without adding a dependency on OpenSSH (the
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;; agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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#t))))))
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(add-before 'check 'mpi-setup
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,%openmpi-setup)))))
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(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
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(define-public lapack
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@ -579,14 +573,8 @@ problems in numerical linear algebra.")
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(arguments
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`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
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#:phases (modify-phases %standard-phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because
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;; 'ssh' could not be found in $PATH. Define this
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;; variable to placate Open MPI without adding a
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;; dependency on OpenSSH (the agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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#t)))))
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(add-before 'check 'mpi-setup
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,%openmpi-setup))))
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(home-page "http://www.netlib.org/scalapack/")
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(synopsis "Library for scalable numerical linear algebra")
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(description
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@ -1717,14 +1705,8 @@ scientific applications modeled by partial differential equations.")
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,@(delete "--with-mpi=0" ,cf)))
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((#:phases phases)
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`(modify-phases ,phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to
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;; placate Open MPI without adding a dependency on OpenSSH (the
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;; agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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#t))))))
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(add-before 'check 'mpi-setup
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,%openmpi-setup)))))
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(synopsis "Library to solve PDEs (with MPI support)")))
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(define-public petsc-complex-openmpi
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@ -1855,14 +1837,8 @@ arising after the discretization of partial differential equations.")
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(substitute-keyword-arguments (package-arguments slepc)
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((#:phases phases '%standard-phases)
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`(modify-phases ,phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to
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;; placate Open MPI without adding a dependency on OpenSSH (the
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;; agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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#t))))))
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(add-before 'check 'mpi-setup
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,%openmpi-setup)))))
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(inputs
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`(("mpi" ,openmpi)
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("arpack" ,arpack-ng-openmpi)
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@ -2032,14 +2008,8 @@ sparse system of linear equations A x = b using Guassian elimination.")
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(substitute-keyword-arguments (package-arguments mumps)
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((#:phases phases)
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`(modify-phases ,phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to
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;; placate Open MPI without adding a dependency on OpenSSH (the
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;; agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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#t))
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(add-before 'check 'mpi-setup
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,%openmpi-setup)
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(replace 'check
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(lambda _
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((assoc-ref ,phases 'check)
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@ -2285,13 +2255,10 @@ CDEFS = -DAdd_"
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"/" dir)))
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'("lib" "include"))
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#t))
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(add-before 'check 'mpi-setup
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,%openmpi-setup)
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(replace 'check
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to placate
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;; Open MPI without adding a dependency on OpenSSH (the agent
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;; isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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(with-directory-excursion "EXAMPLE"
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(invoke "mpirun" "-n" "2"
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"./pddrive" "-r" "1" "-c" "2" "g20.rua")
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@ -2384,15 +2351,8 @@ YACC = bison -pscotchyy -y -b y
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;; "SCOTCH_PTHREAD_NUMBER=2"
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"restrict=__restrict"))))
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#t))
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(add-after
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'build 'build-esmumps
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(add-after 'build 'build-esmumps
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to placate
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;; Open MPI without adding a dependency on OpenSSH (the agent
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;; isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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(invoke "make"
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(format #f "-j~a" (parallel-job-count))
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"esmumps")))
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@ -2575,14 +2535,8 @@ schemes.")
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(assoc-ref %build-inputs "lapack")
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" -llapack"))
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#:phases (modify-phases %standard-phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because
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;; 'ssh' could not be found in $PATH. Define this
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;; variable to placate Open MPI without adding a
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;; dependency on OpenSSH (the agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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#t)))))
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(add-before 'check 'mpi-setup
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,%openmpi-setup))))
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(home-page "http://www.p4est.org")
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(synopsis "Adaptive mesh refinement on forests of octrees")
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(description
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@ -3649,14 +3603,8 @@ problems.")
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,@(delete "--without-MPI" ,flags)))
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((#:phases phases)
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`(modify-phases ,phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to
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;; placate Open MPI without adding a dependency on OpenSSH (the
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;; agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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#t))))))
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(add-before 'check 'mpi-setup
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,%openmpi-setup)))))
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(synopsis "Parallel solvers and preconditioners for linear equations")
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(description
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"HYPRE is a software library of high performance preconditioners and
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@ -3939,6 +3887,8 @@ exclusion algorithms are typical examples of such systems.")
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"-DCMAKE_INSTALL_LIBDIR=lib"
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"-DGFORTRAN_LIB=gfortran")
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#:phases (modify-phases %standard-phases
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(add-before 'check 'mpi-setup
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,%openmpi-setup)
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(add-before 'check 'setup-tests
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(lambda _
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;; Parallelism is done at the MPI layer.
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@ -4123,16 +4073,6 @@ easily be incorporated into existing simulation codes.")
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,flags))
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((#:phases phases '%standard-phases)
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`(modify-phases ,phases
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(add-before 'check 'set-test-environment
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(lambda _
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;; By default, running the test suite would fail because 'ssh'
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;; could not be found in $PATH. Define this variable to
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;; placate Open MPI without adding a dependency on OpenSSH (the
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;; agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
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;; Allow oversubscription in case there are less
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;; physical cores available in the build environment
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;; than SUNDIALS wants while testing.
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(setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes")
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#t))))))
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(add-before 'check 'mpi-setup
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,%openmpi-setup)))))
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(synopsis "SUNDIALS with OpenMPI support")))
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@ -1,5 +1,5 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
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;;; Copyright © 2014, 2015, 2018 Eric Bavier <bavier@member.fsf.org>
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;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
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;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
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@ -250,3 +250,15 @@ software vendors, application developers and computer science researchers.")
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work correctly with all transports (such as @code{openib}), and the
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performance is generally worse than the vanilla @code{openmpi} package, which
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only provides @code{MPI_THREAD_FUNNELED}.")))
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;;; Build phase to be used for packages that execute MPI code.
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(define-public %openmpi-setup
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'(lambda _
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;; By default, running the test suite would fail because 'ssh' could not
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;; be found in $PATH. Define this variable to placate Open MPI without
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;; adding a dependency on OpenSSH (the agent isn't used anyway.)
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(setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
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;; Allow oversubscription in case there are less physical cores available
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;; in the build environment than the package wants while testing.
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(setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes")
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#t))
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