* [bug#32641] [PATCH] mpi: Factorize openmpi setup build phase.
@ 2018-09-05 13:43 ericbavier
2018-09-07 8:26 ` Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: ericbavier @ 2018-09-05 13:43 UTC (permalink / raw)
To: 32641; +Cc: Eric Bavier
From: Eric Bavier <bavier@cray.com>
* 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)[arguments]: Use it in #:phases.
---
gnu/packages/maths.scm | 92 +++++++++---------------------------------
gnu/packages/mpi.scm | 14 ++++++-
2 files changed, 32 insertions(+), 74 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d2b9df01a..9ec418e82 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -569,14 +569,8 @@ problems in numerical linear algebra.")
(arguments
`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
#:phases (modify-phases %standard-phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because
- ;; 'ssh' could not be found in $PATH. Define this
- ;; variable to placate Open MPI without adding a
- ;; dependency on OpenSSH (the agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(home-page "http://www.netlib.org/scalapack/")
(synopsis "Library for scalable numerical linear algebra")
(description
@@ -1707,14 +1701,8 @@ scientific applications modeled by partial differential equations.")
,@(delete "--with-mpi=0" ,cf)))
((#:phases phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t))))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Library to solve PDEs (with MPI support)")))
(define-public petsc-complex-openmpi
@@ -1845,14 +1833,8 @@ arising after the discretization of partial differential equations.")
(substitute-keyword-arguments (package-arguments slepc)
((#:phases phases '%standard-phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t))))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(inputs
`(("mpi" ,openmpi)
("arpack" ,arpack-ng-openmpi)
@@ -2022,14 +2004,8 @@ sparse system of linear equations A x = b using Guassian elimination.")
(substitute-keyword-arguments (package-arguments mumps)
((#:phases phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
(replace 'check
(lambda _
((assoc-ref ,phases 'check)
@@ -2275,13 +2251,10 @@ CDEFS = -DAdd_"
"/" dir)))
'("lib" "include"))
#t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
(replace 'check
(lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to placate
- ;; Open MPI without adding a dependency on OpenSSH (the agent
- ;; isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
(with-directory-excursion "EXAMPLE"
(invoke "mpirun" "-n" "2"
"./pddrive" "-r" "1" "-c" "2" "g20.rua")
@@ -2374,15 +2347,8 @@ YACC = bison -pscotchyy -y -b y
;; "SCOTCH_PTHREAD_NUMBER=2"
"restrict=__restrict"))))
#t))
- (add-after
- 'build 'build-esmumps
+ (add-after 'build 'build-esmumps
(lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to placate
- ;; Open MPI without adding a dependency on OpenSSH (the agent
- ;; isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-
(invoke "make"
(format #f "-j~a" (parallel-job-count))
"esmumps")))
@@ -2565,14 +2531,8 @@ schemes.")
(assoc-ref %build-inputs "lapack")
" -llapack"))
#:phases (modify-phases %standard-phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because
- ;; 'ssh' could not be found in $PATH. Define this
- ;; variable to placate Open MPI without adding a
- ;; dependency on OpenSSH (the agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(home-page "http://www.p4est.org")
(synopsis "Adaptive mesh refinement on forests of octrees")
(description
@@ -3639,14 +3599,8 @@ problems.")
,@(delete "--without-MPI" ,flags)))
((#:phases phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t))))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Parallel solvers and preconditioners for linear equations")
(description
"HYPRE is a software library of high performance preconditioners and
@@ -3929,6 +3883,8 @@ exclusion algorithms are typical examples of such systems.")
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DGFORTRAN_LIB=gfortran")
#:phases (modify-phases %standard-phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
(add-before 'check 'setup-tests
(lambda _
;; Parallelism is done at the MPI layer.
@@ -4113,16 +4069,6 @@ easily be incorporated into existing simulation codes.")
,flags))
((#:phases phases '%standard-phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- ;; Allow oversubscription in case there are less
- ;; physical cores available in the build environment
- ;; than SUNDIALS wants while testing.
- (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes")
- #t))))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "SUNDIALS with OpenMPI support")))
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index f34b08e4c..7dfec16fc 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
@@ -250,3 +250,15 @@ software vendors, application developers and computer science researchers.")
work correctly with all transports (such as @code{openib}), and the
performance is generally worse than the vanilla @code{openmpi} package, which
only provides @code{MPI_THREAD_FUNNELED}.")))
+
+;;; Build phase to be used for packages that execute MPI code.
+(define-public %openmpi-setup
+ '(lambda _
+ ;; By default, running the test suite would fail because 'ssh' could not
+ ;; be found in $PATH. Define this variable to placate Open MPI without
+ ;; adding a dependency on OpenSSH (the agent isn't used anyway.)
+ (setenv "OMPI_MCA_plm_rsh_agent" (which "false"))
+ ;; Allow oversubscription in case there are less physical cores available
+ ;; in the build environment than the package wants while testing.
+ (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes")
+ #t))
--
2.17.1
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [bug#32641] [PATCH] mpi: Factorize openmpi setup build phase.
2018-09-05 13:43 [bug#32641] [PATCH] mpi: Factorize openmpi setup build phase ericbavier
@ 2018-09-07 8:26 ` Ludovic Courtès
2018-09-13 17:14 ` bug#32641: " Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Ludovic Courtès @ 2018-09-07 8:26 UTC (permalink / raw)
To: ericbavier; +Cc: Eric Bavier, 32641
Hi Eric,
ericbavier@centurylink.net skribis:
> From: Eric Bavier <bavier@cray.com>
>
> * 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)[arguments]: Use it in #:phases.
Good idea, go for it!
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 3+ messages in thread
* bug#32641: [PATCH] mpi: Factorize openmpi setup build phase.
2018-09-07 8:26 ` Ludovic Courtès
@ 2018-09-13 17:14 ` Ludovic Courtès
0 siblings, 0 replies; 3+ messages in thread
From: Ludovic Courtès @ 2018-09-13 17:14 UTC (permalink / raw)
To: ericbavier; +Cc: Eric Bavier, 32641-done
This was pushed as bbe46a4af5972b3b5b434fe5d99ec9a0078b0ab8, closing.
^ permalink raw reply [flat|nested] 3+ messages in thread
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2018-09-05 13:43 [bug#32641] [PATCH] mpi: Factorize openmpi setup build phase ericbavier
2018-09-07 8:26 ` Ludovic Courtès
2018-09-13 17:14 ` bug#32641: " Ludovic Courtès
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