* [bug#32732] [PATCH] gnu: hdf5-parallel-openmpi: Really enable parallel build.
@ 2018-09-13 20:03 Paul Garlick
2018-09-16 21:00 ` Ludovic Courtès
0 siblings, 1 reply; 6+ messages in thread
From: Paul Garlick @ 2018-09-13 20:03 UTC (permalink / raw)
To: 32732; +Cc: Paul Garlick
This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
in the file H5pubconf.h.
* gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
the "--enable-parallel" flag to the list of configure flags. Remove
the incompatible "--enable-cxx" flag. Add 'mpi-setup' phase. Replace
the 'split' phase, omitting the references to the h5fc script which is
not present.
---
gnu/packages/maths.scm | 38 +++++++++++++++++++++++++++++++++++---
1 file changed, 35 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index af41093..85d3884 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1034,10 +1034,13 @@ Swath).")
`(("mpi" ,openmpi)
,@(package-inputs hdf5)))
(arguments
- (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
- ,@(package-arguments hdf5))
+ (substitute-keyword-arguments (package-arguments hdf5)
+ ((#:configure-flags flags)
+ ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
((#:phases phases)
`(modify-phases ,phases
+ (add-after 'build 'mpi-setup
+ ,%openmpi-setup)
(add-before 'check 'patch-tests
(lambda _
;; OpenMPI's mpirun will exit with non-zero status if it
@@ -1051,7 +1054,36 @@ Swath).")
(string-append front back "\n")))
(substitute* "tools/h5diff/testph5diff.sh"
(("/bin/sh") (which "sh")))
- #t))))))
+ #t))
+ (replace 'split
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Move all fortran-related files
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib"))
+ (inc (string-append out "/include"))
+ (ex (string-append out "/share/hdf5_examples/fortran"))
+ (fort (assoc-ref outputs "fortran"))
+ (flib (string-append fort "/lib"))
+ (finc (string-append fort "/include"))
+ (fex (string-append fort "/share/hdf5_examples/fortran")))
+ (mkdir-p flib)
+ (mkdir-p finc)
+ (mkdir-p fex)
+ (for-each (lambda (file)
+ (rename-file file
+ (string-append flib "/" (basename file))))
+ (find-files lib ".*fortran.*"))
+ (for-each (lambda (file)
+ (rename-file file
+ (string-append finc "/" (basename file))))
+ (find-files inc ".*mod"))
+ (for-each (lambda (file)
+ (rename-file file
+ (string-append fex "/" (basename file))))
+ (find-files ex ".*"))
+ (delete-file-recursively ex))
+ #t))))))
(synopsis "Management suite for data with parallel IO support")))
(define-public h5check
--
1.8.3.1
^ permalink raw reply related [flat|nested] 6+ messages in thread* [bug#32732] [PATCH] gnu: hdf5-parallel-openmpi: Really enable parallel build.
2018-09-13 20:03 [bug#32732] [PATCH] gnu: hdf5-parallel-openmpi: Really enable parallel build Paul Garlick
@ 2018-09-16 21:00 ` Ludovic Courtès
2018-09-20 17:59 ` [bug#32732] [PATCH 1/2] gnu: hdf5: Allow for absence of utility script Paul Garlick
0 siblings, 1 reply; 6+ messages in thread
From: Ludovic Courtès @ 2018-09-16 21:00 UTC (permalink / raw)
To: Paul Garlick; +Cc: 32732
Hi Paul,
Paul Garlick <pgarlick@tourbillion-technology.com> skribis:
> This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
> in the file H5pubconf.h.
>
> * gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
> the "--enable-parallel" flag to the list of configure flags. Remove
> the incompatible "--enable-cxx" flag. Add 'mpi-setup' phase. Replace
> the 'split' phase, omitting the references to the h5fc script which is
> not present.
Good catch!
> + (replace 'split
> + (lambda* (#:key inputs outputs #:allow-other-keys)
> + ;; Move all fortran-related files
Instead of duplicating the whole phase minus the h5fc bit, what about
changing the phase in ‘hdf5’ so that it does:
;; Note: When built with --enable-parallel, the 'h5fc' file
;; doesn't exist, hence this condition.
(when (file-exists? (string-append bin "/h5fc"))
(rename-file (string-append bin "/h5fc")
(string-append fbin "/h5fc")))
That way, no need to touch the ‘split’ phase in
‘hdf5-parallel-openmpi’.
If that’s fine with you, could you send an updated patch?
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 6+ messages in thread* [bug#32732] [PATCH 1/2] gnu: hdf5: Allow for absence of utility script.
2018-09-16 21:00 ` Ludovic Courtès
@ 2018-09-20 17:59 ` Paul Garlick
2018-09-20 17:59 ` [bug#32732] [PATCH 2/2] gnu: hdf5-parallel-openmpi: Really enable parallel build Paul Garlick
0 siblings, 1 reply; 6+ messages in thread
From: Paul Garlick @ 2018-09-20 17:59 UTC (permalink / raw)
To: 32732, ludo; +Cc: Paul Garlick
* gnu/packages/maths.scm (hdf5)[arguments]: Add condition to 'split'
phase to check for existence of h5fc script.
---
gnu/packages/maths.scm | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 736bac1..30f1610 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -814,8 +814,11 @@ incompatible with HDF5.")
(mkdir-p flib)
(mkdir-p finc)
(mkdir-p fex)
- (rename-file (string-append bin "/h5fc")
- (string-append fbin "/h5fc"))
+ ;; Note: When built with --enable-parallel, the 'h5fc' file
+ ;; doesn't exist, hence this condition.
+ (when (file-exists? (string-append bin "/h5fc"))
+ (rename-file (string-append bin "/h5fc")
+ (string-append fbin "/h5fc")))
(for-each (lambda (file)
(rename-file file
(string-append flib "/" (basename file))))
--
1.8.3.1
^ permalink raw reply related [flat|nested] 6+ messages in thread* [bug#32732] [PATCH 2/2] gnu: hdf5-parallel-openmpi: Really enable parallel build.
2018-09-20 17:59 ` [bug#32732] [PATCH 1/2] gnu: hdf5: Allow for absence of utility script Paul Garlick
@ 2018-09-20 17:59 ` Paul Garlick
2018-09-21 1:07 ` Eric Bavier
2018-09-24 12:20 ` bug#32732: " Ludovic Courtès
0 siblings, 2 replies; 6+ messages in thread
From: Paul Garlick @ 2018-09-20 17:59 UTC (permalink / raw)
To: 32732, ludo; +Cc: Paul Garlick
This fix ensures that the H5_HAVE_PARALLEL identifier is correctly set
in the file H5pubconf.h.
* gnu/packages/maths.scm (hdf5-parallel-openmpi)[arguments]: Add
the "--enable-parallel" flag to the list of configure flags. Remove
the incompatible "--enable-cxx" flag. Add 'mpi-setup' phase.
---
gnu/packages/maths.scm | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 30f1610..636b485 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1037,10 +1037,13 @@ Swath).")
`(("mpi" ,openmpi)
,@(package-inputs hdf5)))
(arguments
- (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
- ,@(package-arguments hdf5))
+ (substitute-keyword-arguments (package-arguments hdf5)
+ ((#:configure-flags flags)
+ ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
((#:phases phases)
`(modify-phases ,phases
+ (add-after 'build 'mpi-setup
+ ,%openmpi-setup)
(add-before 'check 'patch-tests
(lambda _
;; OpenMPI's mpirun will exit with non-zero status if it
--
1.8.3.1
^ permalink raw reply related [flat|nested] 6+ messages in thread
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2018-09-13 20:03 [bug#32732] [PATCH] gnu: hdf5-parallel-openmpi: Really enable parallel build Paul Garlick
2018-09-16 21:00 ` Ludovic Courtès
2018-09-20 17:59 ` [bug#32732] [PATCH 1/2] gnu: hdf5: Allow for absence of utility script Paul Garlick
2018-09-20 17:59 ` [bug#32732] [PATCH 2/2] gnu: hdf5-parallel-openmpi: Really enable parallel build Paul Garlick
2018-09-21 1:07 ` Eric Bavier
2018-09-24 12:20 ` bug#32732: " Ludovic Courtès
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