GNU bug report logs -
#32732
[PATCH] gnu: hdf5-parallel-openmpi: Really enable parallel build.
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Report forwarded
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guix-patches <at> gnu.org
:
bug#32732
; Package
guix-patches
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(Thu, 13 Sep 2018 20:08:02 GMT)
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Paul Garlick <pgarlick <at> tourbillion-technology.com>
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New bug report received and forwarded. Copy sent to
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(Thu, 13 Sep 2018 20:08:05 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
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
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guix-patches <at> gnu.org
:
bug#32732
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(Sun, 16 Sep 2018 21:01:01 GMT)
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Message #8 received at 32732 <at> debbugs.gnu.org (full text, mbox):
Hi Paul,
Paul Garlick <pgarlick <at> 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’.
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bug#32732
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(Thu, 20 Sep 2018 18:02:01 GMT)
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Message #11 received at 32732 <at> debbugs.gnu.org (full text, mbox):
* 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
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guix-patches <at> gnu.org
:
bug#32732
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guix-patches
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(Thu, 20 Sep 2018 18:03:02 GMT)
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Message #14 received at 32732 <at> debbugs.gnu.org (full text, mbox):
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
Information forwarded
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guix-patches <at> gnu.org
:
bug#32732
; Package
guix-patches
.
(Fri, 21 Sep 2018 01:08:02 GMT)
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Message #17 received at 32732 <at> debbugs.gnu.org (full text, mbox):
[Message part 1 (text/plain, inline)]
On Thu, 20 Sep 2018 18:59:57 +0100
Paul Garlick <pgarlick <at> tourbillion-technology.com> wrote:
> 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.
> ---
LGTM! Thanks!
BTW, I'm working on creating a package for hdf5 version 1.10.3. There
are a couple packages, and maybe users, that still need 1.8, so I'm
adding it separately.
`~Eric
[Message part 2 (application/pgp-signature, inline)]
Reply sent
to
ludo <at> gnu.org (Ludovic Courtès)
:
You have taken responsibility.
(Mon, 24 Sep 2018 12:21:02 GMT)
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Notification sent
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Paul Garlick <pgarlick <at> tourbillion-technology.com>
:
bug acknowledged by developer.
(Mon, 24 Sep 2018 12:21:02 GMT)
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Message #22 received at 32732-done <at> debbugs.gnu.org (full text, mbox):
Paul Garlick <pgarlick <at> 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.
Pushed a few days ago as 45201bf245856954cb8368c328e54773a0a81156.
Thanks!
Ludo’.
bug archived.
Request was from
Debbugs Internal Request <help-debbugs <at> gnu.org>
to
internal_control <at> debbugs.gnu.org
.
(Tue, 23 Oct 2018 11:24:04 GMT)
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This bug report was last modified 5 years and 158 days ago.
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