* [bug#34647] [PATCH] gnu: python-petsc4py: Update to 10.3.1.
@ 2019-02-25 13:26 Paul Garlick
2019-02-26 1:55 ` Leo Famulari
0 siblings, 1 reply; 4+ messages in thread
From: Paul Garlick @ 2019-02-25 13:26 UTC (permalink / raw)
To: 34647; +Cc: Paul Garlick
* gnu/packages/maths.scm (python-petsc4py): Update to 10.3.1.
---
gnu/packages/maths.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 74554e2..a39323e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1797,14 +1797,14 @@ scientific applications modeled by partial differential equations.")
(define-public python-petsc4py
(package
(name "python-petsc4py")
- (version "3.10.0")
+ (version "3.10.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "petsc4py" version))
(sha256
(base32
- "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
+ "094hcnran0r2z1wlvmjswsz3ski1m9kqrl5l0ax8jjhnk55x0flh"))))
(build-system python-build-system)
(arguments
`(#:phases
--
1.8.3.1
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#34647] [PATCH] gnu: python-petsc4py: Update to 10.3.1.
2019-02-25 13:26 [bug#34647] [PATCH] gnu: python-petsc4py: Update to 10.3.1 Paul Garlick
@ 2019-02-26 1:55 ` Leo Famulari
2019-02-26 15:06 ` Paul Garlick
0 siblings, 1 reply; 4+ messages in thread
From: Leo Famulari @ 2019-02-26 1:55 UTC (permalink / raw)
To: Paul Garlick; +Cc: 34647
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On Mon, Feb 25, 2019 at 01:26:09PM +0000, Paul Garlick wrote:
> * gnu/packages/maths.scm (python-petsc4py): Update to 10.3.1.
I tested this update by building fenics on top of it. On my x86-63
machine, it failed as below. Is this expected or a reason to block the
python-petsc4py update?
------
[ 95%] Building CXX object dolfin/CMakeFiles/dolfin.dir/nls/TAOLinearBoundSolver.cpp.o
cd /tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/build/dolfin && /gnu/store/n2p1zs14y89lwkg9da68y12pc10c6sw9-gcc-5.5.0/bin/c++ -DDOLFIN_VERSION=\"2018.1.0\" -DHAS_CHOLMOD -DHAS_HDF5 -DHAS_MPI -DHAS_PETSC -DHAS_SCOTCH -DHAS_SLEPC -DHAS_SUNDIALS -DHAS_UMFPACK -DHAS_ZLIB -DNDEBUG -Ddolfin_EXPORTS -I/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/fenics-project-dolfin-948dc42cc4e0 -I/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/build -I/gnu/store/9ghap4fk37lqzpcxplrswvg0yfmwm64x-sundials-openmpi-3.1.1/include -isystem /gnu/store/4vciqisw09sfpb3dc5nshynwgrv7sh1d-python-fenics-ffc-2018.1.0/lib/python3.7/site-packages/ffc/backends/ufc -isystem /gnu/store/kd4byfi7fyck8i0qy298ghrr0ig8cxay-eigen-3.3.5/include/eigen3 -isystem /gnu/store/gw08kjck9zpib5v2vc3jdrws5a838gpd-hdf5-parallel-openmpi-1.8.21/include -isystem /gnu/store/2y704qn8mjljnmswf87dky0nzzlbld1d-suitesparse-4.5.5/include -isystem /gnu/store/xbbiqkjdl8xs018qk217p7fqqgnzdk67-pt-scotch32-6.0.6/include -isystem /gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/include -isystem /gnu/store/lpd53a5zszm9mzzn68i7a1cwcf0nymvy-openmpi-4.0.0/include -isystem /gnu/store/pz22lgiw476i9fla6ds5f1shchndk7ny-boost-1.69.0/include -O2 -g -DNDEBUG -fPIC -std=c++11 -o CMakeFiles/dolfin.dir/nls/TAOLinearBoundSolver.cpp.o -c /tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/fenics-project-dolfin-948dc42cc4e0/dolfin/nls/TAOLinearBoundSolver.cpp
/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/fenics-project-dolfin-948dc42cc4e0/dolfin/nls/PETScSNESSolver.cpp:51:64: error: ‘SNESTEST’ was not declared in this scope
{"test", {"Tool to verify Jacobian approximation", SNESTEST}},
^
/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/fenics-project-dolfin-948dc42cc4e0/dolfin/nls/PETScSNESSolver.cpp:68:56: error: could not convert ‘{{"default", {"default SNES method", ""}}, {"newtonls", {"Line search method", "newtonls"}}, {"newtontr", {"Trust region method", "newtontr"}}, {"test", {"Tool to verify Jacobian approximation", <expression error>}}, {"ngmres", {"Nonlinear generalised minimum residual method", "ngmres"}}, {"nrichardson", {"Richardson nonlinear method (Picard iteration)", "nrichardson"}}, {"vinewtonrsls", {"Reduced space active set solver method (for bounds)", "vinewtonrsls"}}, {"vinewtonssls", {"Reduced space active set solver method (for bounds)", "vinewtonssls"}}, {"qn", {"Limited memory quasi-Newton", "qn"}}, {"ncg", {"Nonlinear conjugate gradient method", "ncg"}}, {"fas", {"Full Approximation Scheme nonlinear multigrid method", "fas"}}, {"nasm", {"Nonlinear Additive Schwartz", "nasm"}}, {"anderson", {"Anderson mixing method", "anderson"}}, {"aspin", {"Additive-Schwarz Preconditioned Inexact Newton", "aspin"}}, {"ms", {"Multistage smoothers", "ms"}}}’ from ‘<brace-enclosed initializer list>’ to ‘const std::map<std::__cxx11::basic_string<char>, std::pair<std::__cxx11::basic_string<char>, const char* const> >’
{"ms", {"Multistage smoothers", SNESMS}} };
^
[ 95%] Building CXX object dolfin/CMakeFiles/dolfin.dir/parameter/GlobalParameters.cpp.o
cd /tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/build/dolfin && /gnu/store/n2p1zs14y89lwkg9da68y12pc10c6sw9-gcc-5.5.0/bin/c++ -DDOLFIN_VERSION=\"2018.1.0\" -DHAS_CHOLMOD -DHAS_HDF5 -DHAS_MPI -DHAS_PETSC -DHAS_SCOTCH -DHAS_SLEPC -DHAS_SUNDIALS -DHAS_UMFPACK -DHAS_ZLIB -DNDEBUG -Ddolfin_EXPORTS -I/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/fenics-project-dolfin-948dc42cc4e0 -I/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/build -I/gnu/store/9ghap4fk37lqzpcxplrswvg0yfmwm64x-sundials-openmpi-3.1.1/include -isystem /gnu/store/4vciqisw09sfpb3dc5nshynwgrv7sh1d-python-fenics-ffc-2018.1.0/lib/python3.7/site-packages/ffc/backends/ufc -isystem /gnu/store/kd4byfi7fyck8i0qy298ghrr0ig8cxay-eigen-3.3.5/include/eigen3 -isystem /gnu/store/gw08kjck9zpib5v2vc3jdrws5a838gpd-hdf5-parallel-openmpi-1.8.21/include -isystem /gnu/store/2y704qn8mjljnmswf87dky0nzzlbld1d-suitesparse-4.5.5/include -isystem /gnu/store/xbbiqkjdl8xs018qk217p7fqqgnzdk67-pt-scotch32-6.0.6/include -isystem /gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/include -isystem /gnu/store/lpd53a5zszm9mzzn68i7a1cwcf0nymvy-openmpi-4.0.0/include -isystem /gnu/store/pz22lgiw476i9fla6ds5f1shchndk7ny-boost-1.69.0/include -O2 -g -DNDEBUG -fPIC -std=c++11 -o CMakeFiles/dolfin.dir/parameter/GlobalParameters.cpp.o -c /tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/fenics-project-dolfin-948dc42cc4e0/dolfin/parameter/GlobalParameters.cpp
make[2]: *** [dolfin/CMakeFiles/dolfin.dir/build.make:2770: dolfin/CMakeFiles/dolfin.dir/nls/PETScSNESSolver.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/build'
make[1]: *** [CMakeFiles/Makefile2:276: dolfin/CMakeFiles/dolfin.dir/all] Error 2
make[1]: Leaving directory '/tmp/guix-build-fenics-dolfin-2018.1.0.post1.drv-0/build'
make: *** [Makefile:144: all] Error 2
Backtrace:
4 (primitive-load "/gnu/store/fvv87kxqx1lnw75y2qyqq5srwm7…")
In ice-9/eval.scm:
191:35 3 (_ _)
In srfi/srfi-1.scm:
863:16 2 (every1 #<procedure 763720 at /gnu/store/6bwkbm3a80v0x…> …)
In /gnu/store/6bwkbm3a80v0xab5qsicij7bjvmn5yna-module-import/guix/build/gnu-build-system.scm:
799:28 1 (_ _)
In /gnu/store/6bwkbm3a80v0xab5qsicij7bjvmn5yna-module-import/guix/build/utils.scm:
616:6 0 (invoke _ . _)
/gnu/store/6bwkbm3a80v0xab5qsicij7bjvmn5yna-module-import/guix/build/utils.scm:616:6: In procedure invoke:
Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "make" arguments: ("-j" "4") exit-status: 2 term-signal: #f stop-signal: #f] 56df80>)'.
builder for `/gnu/store/znvp5a2xnqvzgg9sdbz4wc67wgk3ilrv-fenics-dolfin-2018.1.0.post1.drv' failed with exit code 1
build of /gnu/store/znvp5a2xnqvzgg9sdbz4wc67wgk3ilrv-fenics-dolfin-2018.1.0.post1.drv failed
View build log at '/var/log/guix/drvs/zn/vp5a2xnqvzgg9sdbz4wc67wgk3ilrv-fenics-dolfin-2018.1.0.post1.drv.bz2'.
cannot build derivation `/gnu/store/v152180dwfgwjk6bpxxf0bni8dcd013n-fenics-2018.1.0.post1.drv': 1 dependencies couldn't be built
guix build: error: build of `/gnu/store/v152180dwfgwjk6bpxxf0bni8dcd013n-fenics-2018.1.0.post1.drv' failed
------
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^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#34647] [PATCH] gnu: python-petsc4py: Update to 10.3.1.
2019-02-26 1:55 ` Leo Famulari
@ 2019-02-26 15:06 ` Paul Garlick
2019-02-26 22:26 ` bug#34647: " Leo Famulari
0 siblings, 1 reply; 4+ messages in thread
From: Paul Garlick @ 2019-02-26 15:06 UTC (permalink / raw)
To: Leo Famulari; +Cc: 34647
Hi Leo,
> I tested this update by building fenics on top of it. On my x86-63
> machine, it failed as below. Is this expected or a reason to block
> the python-petsc4py update?
Thank you for doing the fenics test too.
I have fixed the build problem for fenics-dolfin in patch #34668.
These patches for python-petsc4py and fenics-dolfin have been made
necessary by the recent update of the PETSc dependency. Essentially,
a symbol that used to be referenced in these packages is no longer
made available by PETSc.
Best regards,
Paul.
^ permalink raw reply [flat|nested] 4+ messages in thread
* bug#34647: [PATCH] gnu: python-petsc4py: Update to 10.3.1.
2019-02-26 15:06 ` Paul Garlick
@ 2019-02-26 22:26 ` Leo Famulari
0 siblings, 0 replies; 4+ messages in thread
From: Leo Famulari @ 2019-02-26 22:26 UTC (permalink / raw)
To: Paul Garlick; +Cc: 34647-done
[-- Attachment #1: Type: text/plain, Size: 871 bytes --]
On Tue, Feb 26, 2019 at 03:06:03PM +0000, Paul Garlick wrote:
> Hi Leo,
>
> > I tested this update by building fenics on top of it. On my x86-63
^
Oops, silly typo ----------------------------------------------------|
> > machine, it failed as below. Is this expected or a reason to block
> > the python-petsc4py update?
>
> Thank you for doing the fenics test too.
>
> I have fixed the build problem for fenics-dolfin in patch #34668.
Great!
> These patches for python-petsc4py and fenics-dolfin have been made
> necessary by the recent update of the PETSc dependency. Essentially,
> a symbol that used to be referenced in these packages is no longer
> made available by PETSc.
Okay, I've pushed the python-petsc4py update as
758439cf4b20851d25c1d72d289cc6d4556ccda2
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^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2019-02-26 22:27 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2019-02-25 13:26 [bug#34647] [PATCH] gnu: python-petsc4py: Update to 10.3.1 Paul Garlick
2019-02-26 1:55 ` Leo Famulari
2019-02-26 15:06 ` Paul Garlick
2019-02-26 22:26 ` bug#34647: " Leo Famulari
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