Arch Linux User Repository

I've updated to 9.5.2 and patched SUNDIALS.

9.6 should be out in the next month or two!

@bartus thanks - I pushed a fix!

Small bug in prepare() function.

Using $(pwd) resoults in build failure when non-default SRCDEST is used.

Please use ${srcdir} env var in pleace of a $(pwd)

-  patch --strip=1 --input=$(pwd)/../sundials-7.patch --directory=dealii-$pkgver
+  patch --strip=1 --input=${srcdir}/sundials-7.patch --directory=dealii-$pkgver

https://wiki.archlinux.org/title/Makepkg#Package_output

I've updated to 9.5.2 and patched SUNDIALS.

9.6 should be out in the next month or two!

Thanks for the reports.

Backporting fixes will take some time - I'll try to get this done this week.

Also test #22 fails:

24/24 Test #22: quick_tests/p4est.mpirun=10.debug .........................***Failed    0.14 sec

96% tests passed, 1 tests failed out of 24

Total Test time (real) =  46.97 sec

The following tests FAILED:
         22 - quick_tests/p4est.mpirun=10.debug (Failed)
Errors while running CTest
Output from these tests are in: /mnt/storage/archie/aur/deal-ii/src/build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

detailed output:

Directory: /mnt/storage/archie/aur/deal-ii/src/build/tests/quick_tests/p4est.debug/mpirun=10
"quick_tests/p4est.mpirun=10.debug" start time: Jun 14 18:21 CEST
Output:
----------------------------------------------------------
make[7]: *** [CMakeFiles/quick_tests.p4est.mpirun10.debug.test.dir/build.make:78: p4est.debug/mpirun=10/output] Error 1
make[6]: *** [CMakeFiles/Makefile2:1295: CMakeFiles/quick_tests.p4est.mpirun10.debug.test.dir/all] Error 2
make[5]: *** [CMakeFiles/Makefile2:1302: CMakeFiles/quick_tests.p4est.mpirun10.debug.test.dir/rule] Error 2
make[4]: *** [Makefile:680: quick_tests.p4est.mpirun10.debug.test] Error 2
Test quick_tests/p4est.mpirun=10.debug: RUN
===============================   OUTPUT BEGIN  ===============================
[ 66%] Built target quick_tests.p4est.debug
[100%] Generating p4est.debug/mpirun=10/output
quick_tests/p4est.mpirun=10.debug: BUILD successful.
quick_tests/p4est.mpirun=10.debug: RUN failed. ------ Return code 1
quick_tests/p4est.mpirun=10.debug: RUN failed. ------ Result: /mnt/storage/archie/aur/deal-ii/src/build/tests/quick_tests/p4est.debug/mpirun=10/failing_output
quick_tests/p4est.mpirun=10.debug: RUN failed. ------ Partial output:
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 10
slots that were requested by the application:

  /mnt/storage/archie/aur/deal-ii/src/build/tests/quick_tests/p4est.debug/p4est.debug

Either request fewer procs for your application, or make more slots
available for use.

A "slot" is the PRRTE term for an allocatable unit where we can
launch a process.  The number of slots available are defined by the
environment in which PRRTE processes are run:

  1. Hostfile, via "slots=N" clauses (N defaults to number of
     processor cores if not provided)
  2. The --host command line parameter, via a ":N" suffix on the
     hostname (N defaults to 1 if not provided)
  3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
  4. If none of a hostfile, the --host command line parameter, or an
     RM is present, PRRTE defaults to the number of processor cores

In all the above cases, if you want PRRTE to default to the number
of hardware threads instead of the number of processor cores, use the
--use-hwthread-cpus option.

Alternatively, you can use the --map-by :OVERSUBSCRIBE option to ignore the
number of available slots when deciding the number of processes to
launch.
--------------------------------------------------------------------------


quick_tests/p4est.mpirun=10.debug: ******    RUN failed    *******

===============================    OUTPUT END   ===============================
Expected stage PASSED - aborting
CMake Error at /mnt/storage/archie/aur/deal-ii/src/build/share/deal-ii/scripts/run_test.cmake:116 (message):
  *** abort


<end of output>
Test time =   0.14 sec
----------------------------------------------------------
Test Failed.
"quick_tests/p4est.mpirun=10.debug" end time: Jun 14 18:21 CEST
"quick_tests/p4est.mpirun=10.debug" time elapsed: 00:00:00
----------------------------------------------------------

Sundials support no longer seems functional:

/mnt/storage/archie/aur/deal-ii/src/dealii-9.5.2/source/sundials/ida.cc:428:7: note: candidate is: ‘constexpr dealii::SUNDIALS::IDA<dealii::Vector<double> >::reset(double, double, dealii::Vector<double>&, dealii::Vector<double>&)::<lambda(int, int, N_Vector, N_Vector, N_Vector, SUNMatrix, void*, N_Vector, N_Vector, N_Vector)>::operator int (*)(int, int, N_Vector, N_Vector, N_Vector, SUNMatrix, void*, N_Vector, N_Vector, N_Vector)() const’ (near match)
  428 |       [](realtype tt,
      |       ^
/mnt/storage/archie/aur/deal-ii/src/dealii-9.5.2/source/sundials/ida.cc:428:7: note:   no known conversion from ‘int (*)(int, int, N_Vector, N_Vector, N_Vector, SUNMatrix, void*, N_Vector, N_Vector, N_Vector)’ {aka ‘int (*)(int, int, _generic_N_Vector*, _generic_N_Vector*, _generic_N_Vector*, _generic_SUNMatrix*, void*, _generic_N_Vector*, _generic_N_Vector*, _generic_N_Vector*)’} to ‘IDALsJacFn’ {aka ‘int (*)(double, double, _generic_N_Vector*, _generic_N_Vector*, _generic_N_Vector*, _generic_SUNMatrix*, void*, _generic_N_Vector*, _generic_N_Vector*, _generic_N_Vector*)’}
/usr/include/idas/idas_ls.h:90:59: note:   initializing argument 2 of ‘int IDASetJacFn(void*, IDALsJacFn)’
   90 | SUNDIALS_EXPORT int IDASetJacFn(void* ida_mem, IDALsJacFn jac);
      |                                                ~~~~~~~~~~~^~~
/mnt/storage/archie/aur/deal-ii/src/dealii-9.5.2/source/sundials/ida.cc: In instantiation of ‘void dealii::SUNDIALS::IDA<VectorType>::reset(double, double, VectorType&, VectorType&) [with VectorType = dealii::BlockVector<double>]’:
/mnt/storage/archie/aur/deal-ii/src/dealii-9.5.2/source/sundials/ida.cc:522:18:   required from here
  522 |   template class IDA<BlockVector<double>>;
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~
/mnt/storage/archie/aur/deal-ii/src/dealii-9.5.2/source/sundials/ida.cc:230:7: error: invalid user-defined conversion from ‘dealii::SUNDIALS::IDA<dealii::BlockVector<double> >::reset(double, double, dealii::BlockVector<double>&, dealii::BlockVector<double>&)::<lambda(int, N_Vector, N_Vector, N_Vector, void*)>’ to ‘IDAResFn’ {aka ‘int (*)(double, _generic_N_Vector*, _generic_N_Vector*, _generic_N_Vector*, void*)’} [-fpermissive]
  230 |       [](realtype tt, N_Vector yy, N_Vector yp, N_Vector rr, void *user_data)
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  231 |         -> int {
      |         ~~~~~~~~
  232 |         IDA<VectorType> &solver = *static_cast<IDA<VectorType> *>(user_data);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  233 | 
      |        
  234 |         auto *src_yy   = internal::unwrap_nvector_const<VectorType>(yy);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  235 |         auto *src_yp   = internal::unwrap_nvector_const<VectorType>(yp);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  236 |         auto *residual = internal::unwrap_nvector<VectorType>(rr);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  237 | 
      |        
  238 |         return Utilities::call_and_possibly_capture_exception(
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  239 |           solver.residual,
      |           ~~~~~~~~~~~~~~~~
  240 |           solver.pending_exception,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~
  241 |           tt,
      |           ~~~
  242 |           *src_yy,
      |           ~~~~~~~~
  243 |           *src_yp,
      |           ~~~~~~~~
  244 |           *residual);
      |           ~~~~~~~~~~~
  245 |       },

Thanks - we're actually putting out a new patch release soon (we need 9.5.2) so I'll change those once we finalize that.

Hi, I suggest make this two changes, first one related with this, otherwise namcap will show this error:

deal-ii E: LGPL is not a valid SPDX license identifier. See https://spdx.org/licenses/ for valid identifiers, or prefix the identifier with 'LicenseRef-', if it is custom.

The last one is about extra signature checking.

---
 .SRCINFO | 13 ++++++++-----
 PKGBUILD | 12 ++++++------
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/.SRCINFO b/.SRCINFO
index 10d0848..0057036 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,12 +1,12 @@
 pkgbase = deal-ii
    pkgdesc = An Open Source Finite Element Differential Equations Analysis Library
-   pkgver = 9.5.1
+   pkgver = 9.5.2
    pkgrel = 1
-   url = http://www.dealii.org/
+   url = https://www.dealii.org
    install = deal-ii.install
    arch = i686
    arch = x86_64
-   license = LGPL
+   license = LGPL-2.1-or-later
    makedepends = cmake
    depends = boost
    depends = trilinos
@@ -33,7 +33,10 @@ pkgbase = deal-ii
    optdepends = tbb: High level abstract threading library
    optdepends = suitesparse: A collection of sparse matrix libraries
    optdepends = zlib: Compression library implementing the deflate compression method found in gzip and PKZIP
-   source = https://github.com/dealii/dealii/releases/download/v9.5.1/dealii-9.5.1.tar.gz
-   sha1sums = a94989a9e4c3b8599aceacf71d7156621c1d7426
+   source = https://github.com/dealii/dealii/releases/download/v9.5.2/dealii-9.5.2.tar.gz
+   source = https://github.com/dealii/dealii/releases/download/v9.5.2/dealii-9.5.2.tar.gz.asc
+   validpgpkeys = 1EE97BF66221FC3069B5CF90B5A4E06FBD3A97A3
+   sha1sums = 126183aaaf75eaa1b4c3812f6e44aa32a60f4da1
+   sha1sums = SKIP

 pkgname = deal-ii
diff --git a/PKGBUILD b/PKGBUILD
index 13e475c..0bd9d31 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,15 +1,14 @@
 # Maintainer: David Wells <drwells.aur at fastmail dot com>
-
 # Contributor: Florian Dang <florian dot coin at gmail dot com>

 pkgname=deal-ii
 _realname=dealii
-pkgver=9.5.1
+pkgver=9.5.2
 pkgrel=1
 pkgdesc="An Open Source Finite Element Differential Equations Analysis Library"
 arch=("i686" "x86_64")
-url="http://www.dealii.org/"
-license=('LGPL')
+url="https://www.dealii.org"
+license=('LGPL-2.1-or-later')
 # deal.II depends on Kokkos which is implicitly provided by Trilinos. Trilinos
 # does not yet support configuration with an external copy of Kokkos so do not
 # yet depend on that package.
@@ -44,8 +43,9 @@ optdepends=(
       )
 makedepends=('cmake')
 install=deal-ii.install
-source=(https://github.com/dealii/dealii/releases/download/v$pkgver/${_realname}-$pkgver.tar.gz)
-sha1sums=('a94989a9e4c3b8599aceacf71d7156621c1d7426')
+source=(https://github.com/dealii/dealii/releases/download/v$pkgver/${_realname}-$pkgver.tar.gz{,.asc})
+sha1sums=('126183aaaf75eaa1b4c3812f6e44aa32a60f4da1' 'SKIP')
+validpgpkeys=('1EE97BF66221FC3069B5CF90B5A4E06FBD3A97A3') # Matthias Maier <tamiko@43-1.org>
 # where to install deal.II: change to something else (e.g., /opt/deal.II/)
 # if desired.
 _installation_prefix=/usr
-- 
2.43.0

I updated to 9.5.1 and made Trilinos a required dependency to avoid the conflict. Once the Trilinos package is updated to include provides=('kokkos') then we can switch this back and make kokkos the (correct) dependency.

I wanted to get this done by now but I'm heading on vacation so it will have to wait until Saturday. We need to put out a 9.5.1 release due to some obscure Trilinos problems so this will need to be updated at that point anyway.

Thanks for investigating - I didn't realize the AUR had its own Kokkos package. To the best of my knowledge, Trilinos cannot be configured with an external Kokkos (they're working on it) so that's going to conflict with deal.II (though deal.II - Trilinos + external Kokkos should be OK).