scikits-odes: init at 2.4.0 #64195

flokli · 2019-07-02T21:48:35Z

Motivation for this change

This adds scikits.odes, a scikit offering extra ode/dae solvers, as an extension to what is available in scipy.

It's not yet compatible with sundials 4.x, so we add sundials_3, too.

Things done

cc @idontgetoutmuch

flokli · 2019-07-02T21:50:15Z

@GrahamcOfBorg build python3.pkgs.scikits-odes

idontgetoutmuch

This works for me on macOS 10.13.6 (17G65).

flokli · 2019-07-03T10:14:11Z

One test breaks on aarch64:

running install tests
============================= test session starts ==============================
platform linux -- Python 3.7.3, pytest-4.6.3, py-1.7.0, pluggy-0.12.0
rootdir: /nix/store/4vkp4sslmcw3a7zia81yd8y6kdpbjkl2-python3.7-scikits.odes-2.4.0/lib/python3.7/site-packages/scikits/odes/tests
collected 81 items

test_dae.py ...F                                                         [  4%]
test_dop.py .                                                            [  6%]
test_get_info.py .....                                                   [ 12%]
test_odeint.py .....                                                     [ 18%]
test_on_funcs.py ............                                            [ 33%]
test_on_funcs_ida.py ............                                        [ 48%]
test_user_return_vals_cvode.py ........................                  [ 77%]
test_user_return_vals_ida.py ..................                          [100%]

=================================== FAILURES ===================================
______________________________ TestDae.test_lsodi ______________________________

self = <odes.tests.test_dae.TestDae testMethod=test_lsodi>

    def test_lsodi(self):
        """Check the lsodi solver"""
        for problem_cls in PROBLEMS_LSODI:
            problem = problem_cls()
>           self._do_problem(problem, 'lsodi', **problem.lsodi_pars)

test_dae.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test_dae.py:34: in _do_problem
    soln = ig.step(time, z[i], zprime[i])
../dae.py:439: in step
    return self._integrator.step(t, y_retn, yp_retn)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <scikits.odes.lsodiint.lsodi object at 0xffff7af8d3c8>, t = 400.0
y_retn = array([4.70187465e-01, 3.48124556e-06, 5.29809054e-01])
yp_retn = array([4.50537891e-01, 3.22315111e-06, 5.49458886e-01])

    def step(self, t, y_retn, yp_retn = None):
        """ See dae.DaeBase
        """
        if not self.initialized:
            raise ValueError('Method ''init_step'' has to be called prior to the'
                    'first call of ''step'' method, or after changing options')
        if t > 0.0:
            if self.tstop is None:
                itask = 1
                self.call_args[3] = 1
            else:
                itask = self.call_args[3]
                self.call_args[3] = 4
            self.y, self.yp, self.t = self.__run(self.y, self.yp, self.t, t)
            self.call_args[3] = itask
        else:
            itask = self.call_args[3]
            if self.tstop is None:
                self.call_args[3] = 2
            else:
                self.call_args[3] = 5
            self.y, self.yp, self.t  = self.__run(self.y, self.yp, self.t, -t)
            self.call_args[3] = itask
        y_retn[:] = self.y[:]
        if yp_retn is not None:
>           yp_retn[:] = self.yp[:]
E           TypeError: 'NoneType' object is not subscriptable

../lsodiint.py:376: TypeError
----------------------------- Captured stdout call -----------------------------
lsodi: excess work done on this call (check all inputs).
lsodi: present residual is [-1.17961196e-15  5.42101086e-20 -6.17733149e-12]
=============================== warnings summary ===============================
test_dae.py::TestDae::test_ida_old_api
test_dae.py::TestDae::test_ida_old_api
test_dae.py::TestDae::test_ida_old_api
  /nix/store/4vkp4sslmcw3a7zia81yd8y6kdpbjkl2-python3.7-scikits.odes-2.4.0/lib/python3.7/site-packages/scikits/odes/dae.py:389: DeprecationWarning: Old api is deprecated, move to new api
    return self._integrator.init_step(t0, y0, yp0, y_ic0_retn, yp_ic0_retn)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=============== 1 failed, 80 passed, 3 warnings in 1.89 seconds ================
builder for '/nix/store/gagbwvvk5hwfmn4cj667azympm6x5lz5-python3.7-scikits.odes-2.4.0.drv' failed with exit code 1
error: build of '/nix/store/gagbwvvk5hwfmn4cj667azympm6x5lz5-python3.7-scikits.odes-2.4.0.drv' failed

Any idea what could be the reason for that?

idontgetoutmuch · 2019-07-03T12:26:09Z

I have never used the differential algebraic part of SUNDIALS. I think the only thing one can do is report it to the maintainers of scikits-odes. One of the problems I've had in the past is that if a matrix is selected at random and is close to being singular then tests will fail. Maybe it's something like that?

flokli · 2019-07-03T12:47:34Z

I could reproduce it multiple times, and only on aarch64, so it might be an arch-specific issue.

FRidh · 2019-07-17T08:38:49Z

Please move the numpy patch out. It causes this to be a mass-rebuild.

flokli · 2019-07-18T00:33:16Z

Please move the numpy patch out. It causes this to be a mass-rebuild.

I'd still like to eventually see this change land in master. What about dropping it from here, and file that change against staging?

FRidh · 2019-07-19T07:16:17Z

yes, open a separate PR for it

flokli · 2019-07-20T12:03:37Z

took the numpy patch out and rebased on latest master.

flokli · 2019-07-20T12:14:20Z

@GrahamcOfBorg build python3.pkgs.scikits-odes

steinitznavican · 2019-07-30T12:14:56Z

This works

cmake -DLAPACK_ENABLE=ON \
-DLAPACK_LIBRARIES="/usr/local/opt/openblas/lib/libblas.dylib;/usr/local/opt/openblas/lib/liblapack.dylib" \
-DSUNDIALS_INDEX_TYPE=int32_t \
-DCMAKE_INSTALL_PREFIX=/Users/dominic.steinitz/MySundials/instdir \
-DEXAMPLES_INSTALL_PATH=/Users/dominic.steinitz/MySundials/instdir/examples \
-DEXAMPLES_INSTALL=ON \
-DEXAMPLES_ENABLE_C=ON \
/Users/dominic.steinitz/sundials-3.1.1

-- The Fortran compiler identification is GNU 9.1.0
-- Searching for a Fortran compiler... /usr/local/bin/gfortran
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Trying to compile and link a simple Fortran program... OK
-- Determining Fortran name-mangling scheme... OK
-- Looking for LAPACK libraries... OK
-- Checking if LAPACK works... OK
-- Added NVECTOR_SERIAL module
-- Added SUNMATRIX_DENSE module
-- Added SUNMATRIX_BAND module
-- Added SUNMATRIX_SPARSE module
-- Added SUNLINSOL_BAND module
-- Added SUNLINSOL_DENSE module
-- Added SUNLINSOL_LAPACKBAND module
-- Added SUNLINSOL_LAPACKDENSE module
-- Added SUNLINSOL_SPGMR module
-- Added SUNLINSOL_SPFGMR module
-- Added SUNLINSOL_SPBCGS module
-- Added SUNLINSOL_SPTFQMR module
-- Added SUNLINSOL_PCG module
-- Added ARKODE module
-- Added CVODE module
-- Added CVODES module
-- Added IDA module
-- Added IDAS module
-- Added KINSOL module
-- Configuring done
CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   sundials_arkode_shared
   sundials_cvode_shared
   sundials_cvodes_shared
   sundials_ida_shared
   sundials_idas_shared
   sundials_kinsol_shared
   sundials_nvecserial_shared
   sundials_sunlinsolband_shared
   sundials_sunlinsoldense_shared
   sundials_sunlinsollapackband_shared
   sundials_sunlinsollapackdense_shared
   sundials_sunlinsolpcg_shared
   sundials_sunlinsolspbcgs_shared
   sundials_sunlinsolspfgmr_shared
   sundials_sunlinsolspgmr_shared
   sundials_sunlinsolsptfqmr_shared
   sundials_sunmatrixband_shared
   sundials_sunmatrixdense_shared
   sundials_sunmatrixsparse_shared

This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /Users/dominic.steinitz/mySundials-3.1.1

bash-3.2$ make test
make test
Running tests...
Test project /Users/dominic.steinitz/mySundials-3.1.1
      Start  1: ark_analytic
 1/49 Test  #1: ark_analytic ......................................   Passed    0.11 sec
      Start  2: ark_robertson
 2/49 Test  #2: ark_robertson .....................................   Passed    0.07 sec
      Start  3: cvRoberts_dns
 3/49 Test  #3: cvRoberts_dns .....................................   Passed    0.06 sec
      Start  4: cvsRoberts_dns
 4/49 Test  #4: cvsRoberts_dns ....................................   Passed    0.06 sec
      Start  5: idaRoberts_dns
 5/49 Test  #5: idaRoberts_dns ....................................   Passed    0.06 sec
      Start  6: idasRoberts_dns
 6/49 Test  #6: idasRoberts_dns ...................................   Passed    0.06 sec
      Start  7: kinRoberts_fp
 7/49 Test  #7: kinRoberts_fp .....................................   Passed    0.07 sec
      Start  8: test_nvector_serial_1000_0
 8/49 Test  #8: test_nvector_serial_1000_0 ........................   Passed    0.06 sec
      Start  9: test_nvector_serial_10000_0
 9/49 Test  #9: test_nvector_serial_10000_0 .......................   Passed    0.07 sec
      Start 10: test_sunmatrix_dense_100_100_0
10/49 Test #10: test_sunmatrix_dense_100_100_0 ....................   Passed    0.06 sec
      Start 11: test_sunmatrix_dense_200_1000_0
11/49 Test #11: test_sunmatrix_dense_200_1000_0 ...................   Passed    0.07 sec
      Start 12: test_sunmatrix_dense_2000_100_0
12/49 Test #12: test_sunmatrix_dense_2000_100_0 ...................   Passed    0.07 sec
      Start 13: test_sunmatrix_band_10_2_3_0
13/49 Test #13: test_sunmatrix_band_10_2_3_0 ......................   Passed    0.06 sec
      Start 14: test_sunmatrix_band_300_7_4_0
14/49 Test #14: test_sunmatrix_band_300_7_4_0 .....................   Passed    0.06 sec
      Start 15: test_sunmatrix_band_1000_8_8_0
15/49 Test #15: test_sunmatrix_band_1000_8_8_0 ....................   Passed    0.06 sec
      Start 16: test_sunmatrix_band_5000_3_20_0
16/49 Test #16: test_sunmatrix_band_5000_3_20_0 ...................   Passed    0.08 sec
      Start 17: test_sunmatrix_sparse_400_400_0_0
17/49 Test #17: test_sunmatrix_sparse_400_400_0_0 .................   Passed    0.06 sec
      Start 18: test_sunmatrix_sparse_450_450_1_0
18/49 Test #18: test_sunmatrix_sparse_450_450_1_0 .................   Passed    0.07 sec
      Start 19: test_sunmatrix_sparse_200_1000_0_0
19/49 Test #19: test_sunmatrix_sparse_200_1000_0_0 ................   Passed    0.06 sec
      Start 20: test_sunmatrix_sparse_6000_350_0_0
20/49 Test #20: test_sunmatrix_sparse_6000_350_0_0 ................   Passed    0.10 sec
      Start 21: test_sunmatrix_sparse_500_5000_1_0
21/49 Test #21: test_sunmatrix_sparse_500_5000_1_0 ................   Passed    0.13 sec
      Start 22: test_sunmatrix_sparse_4000_800_1_0
22/49 Test #22: test_sunmatrix_sparse_4000_800_1_0 ................   Passed    0.14 sec
      Start 23: test_sunlinsol_band_10_2_3_0
23/49 Test #23: test_sunlinsol_band_10_2_3_0 ......................   Passed    0.06 sec
      Start 24: test_sunlinsol_band_300_7_4_0
24/49 Test #24: test_sunlinsol_band_300_7_4_0 .....................   Passed    0.06 sec
      Start 25: test_sunlinsol_band_1000_8_8_0
25/49 Test #25: test_sunlinsol_band_1000_8_8_0 ....................   Passed    0.06 sec
      Start 26: test_sunlinsol_band_5000_3_100_0
26/49 Test #26: test_sunlinsol_band_5000_3_100_0 ..................   Passed    0.09 sec
      Start 27: test_sunlinsol_dense_10_0
27/49 Test #27: test_sunlinsol_dense_10_0 .........................   Passed    0.06 sec
      Start 28: test_sunlinsol_dense_100_0
28/49 Test #28: test_sunlinsol_dense_100_0 ........................   Passed    0.06 sec
      Start 29: test_sunlinsol_dense_500_0
29/49 Test #29: test_sunlinsol_dense_500_0 ........................   Passed    0.15 sec
      Start 30: test_sunlinsol_dense_1000_0
30/49 Test #30: test_sunlinsol_dense_1000_0 .......................   Passed    0.69 sec
      Start 31: test_sunlinsol_lapackband_10_2_3_0
31/49 Test #31: test_sunlinsol_lapackband_10_2_3_0 ................   Passed    0.07 sec
      Start 32: test_sunlinsol_lapackband_300_7_4_0
32/49 Test #32: test_sunlinsol_lapackband_300_7_4_0 ...............   Passed    0.06 sec
      Start 33: test_sunlinsol_lapackband_1000_8_8_0
33/49 Test #33: test_sunlinsol_lapackband_1000_8_8_0 ..............   Passed    0.06 sec
      Start 34: test_sunlinsol_lapackband_5000_3_100_0
34/49 Test #34: test_sunlinsol_lapackband_5000_3_100_0 ............   Passed    0.08 sec
      Start 35: test_sunlinsol_lapackdense_10_0
35/49 Test #35: test_sunlinsol_lapackdense_10_0 ...................   Passed    0.06 sec
      Start 36: test_sunlinsol_lapackdense_100_0
36/49 Test #36: test_sunlinsol_lapackdense_100_0 ..................   Passed    0.06 sec
      Start 37: test_sunlinsol_lapackdense_500_0
37/49 Test #37: test_sunlinsol_lapackdense_500_0 ..................   Passed    0.08 sec
      Start 38: test_sunlinsol_lapackdense_1000_0
38/49 Test #38: test_sunlinsol_lapackdense_1000_0 .................   Passed    0.13 sec
      Start 39: test_sunlinsol_spgmr_serial_100_1_1_100_1e-13_0
39/49 Test #39: test_sunlinsol_spgmr_serial_100_1_1_100_1e-13_0 ...   Passed    0.06 sec
      Start 40: test_sunlinsol_spgmr_serial_100_2_1_100_1e-13_0
40/49 Test #40: test_sunlinsol_spgmr_serial_100_2_1_100_1e-13_0 ...   Passed    0.06 sec
      Start 41: test_sunlinsol_spgmr_serial_100_1_2_100_1e-13_0
41/49 Test #41: test_sunlinsol_spgmr_serial_100_1_2_100_1e-13_0 ...   Passed    0.06 sec
      Start 42: test_sunlinsol_spgmr_serial_100_2_2_100_1e-13_0
42/49 Test #42: test_sunlinsol_spgmr_serial_100_2_2_100_1e-13_0 ...   Passed    0.06 sec
      Start 43: test_sunlinsol_spfgmr_serial_100_1_100_1e-13_0
43/49 Test #43: test_sunlinsol_spfgmr_serial_100_1_100_1e-13_0 ....   Passed    0.06 sec
      Start 44: test_sunlinsol_spfgmr_serial_100_2_100_1e-13_0
44/49 Test #44: test_sunlinsol_spfgmr_serial_100_2_100_1e-13_0 ....   Passed    0.06 sec
      Start 45: test_sunlinsol_spbcgs_serial_100_1_100_1e-13_0
45/49 Test #45: test_sunlinsol_spbcgs_serial_100_1_100_1e-13_0 ....   Passed    0.06 sec
      Start 46: test_sunlinsol_spbcgs_serial_100_2_100_1e-13_0
46/49 Test #46: test_sunlinsol_spbcgs_serial_100_2_100_1e-13_0 ....   Passed    0.06 sec
      Start 47: test_sunlinsol_sptfqmr_serial_100_1_100_1e-13_0
47/49 Test #47: test_sunlinsol_sptfqmr_serial_100_1_100_1e-13_0 ...   Passed    0.06 sec
      Start 48: test_sunlinsol_sptfqmr_serial_100_2_100_1e-13_0
48/49 Test #48: test_sunlinsol_sptfqmr_serial_100_2_100_1e-13_0 ...   Passed    0.06 sec
      Start 49: test_sunlinsol_pcg_serial_100_200_1e-13_0
49/49 Test #49: test_sunlinsol_pcg_serial_100_200_1e-13_0 .........   Passed    0.06 sec

100% tests passed, 0 tests failed out of 49

Total Test time (real) =   4.20 sec

steinitznavican · 2019-07-30T13:05:22Z

The nix derivation uses cmake to generate

-DCMAKE_FIND_PACKAGE_NO_SYSTEM_PACKAGE_REGISTRY=ON \
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON \
-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_SKIP_BUILD_RPATH=ON \
-DCMAKE_INSTALL_INCLUDEDIR=/nix/store/hq8bh2mwhm10vwr9w38n2hy3zrw1q2zz-sundials-3.2.1/include \
-DCMAKE_INSTALL_LIBDIR=/nix/store/hq8bh2mwhm10vwr9w38n2hy3zrw1q2zz-sundials-3.2.1/lib \
-DCMAKE_INSTALL_NAME_DIR=/nix/store/hq8bh2mwhm10vwr9w38n2hy3zrw1q2zz-sundials-3.2.1/lib \
-DCMAKE_POLICY_DEFAULT_CMP0025=NEW \
-DCMAKE_OSX_DEPLOYMENT_TARGET= \
-DCMAKE_OSX_SYSROOT= \
-DCMAKE_FIND_FRAMEWORK=last \
-DCMAKE_STRIP=/nix/store/p20s2ajhyhq6lbjsdyywsnvz3xf41jz8-cctools-binutils-darwin/bin/strip \
-DCMAKE_RANLIB=/nix/store/p20s2ajhyhq6lbjsdyywsnvz3xf41jz8-cctools-binutils-darwin/bin/ranlib \
-DCMAKE_AR=/nix/store/p20s2ajhyhq6lbjsdyywsnvz3xf41jz8-cctools-binutils-darwin/bin/ar \
-DCMAKE_C_COMPILER=clang \
-DCMAKE_CXX_COMPILER=clang++ \
-DCMAKE_INSTALL_PREFIX=/nix/store/hq8bh2mwhm10vwr9w38n2hy3zrw1q2zz-sundials-3.2.1 \
-DEXAMPLES_INSTALL_PATH=/nix/store/hq8bh2mwhm10vwr9w38n2hy3zrw1q2zz-sundials-3.2.1/share/examples \
-DEXAMPLES_INSTALL=ON \
-DEXAMPLES_ENABLE_C=ON \
-DSUNDIALS_INDEX_TYPE=int32_t \
-DLAPACK_ENABLE=ON \
-DLAPACK_LIBRARIES=/nix/store/qcjzcrxwynyd7xyay58r3kl6qxq6qpxw-openblas-0.3.6/lib/libblas.dylib;/nix/store/qcjzcrxwynyd7xyay58r3kl6qxq6qpxw-openblas-0.3.6/lib/liblapack.dylib

@flokli if I run cmake outside of nix, I get a populated directory. How do I retain the equivalent directory in nix?

steinitznavican · 2019-07-30T15:05:00Z

I have this

  postInstall = ''
                  mkdir $out/easytofind
                  echo $(ls) > $out/easytofind/foo.txt
                  cp -r LapackTest $out/easytofind/LapackTest
                  cd $out/easytofind/LapackTest
                  make
                  ./ltest > $out/easytofind/ltest.out
                '';

but sadly don't get what I wanted

/nix/store/sy5iwww8nc4a7mdb3ls44q96i0kxy2dx-cmake-3.14.5/bin/cmake -S/private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest -B/private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest --check-build-system CMakeFiles/Makefile.cmake 0
-- The C compiler identification is Clang 7.1.0
-- Check for working C compiler: /nix/store/b8i7jqbkq80h6v03pnnkpihiq72iplwq-clang-wrapper-7.1.0/bin/clang
-- Check for working C compiler: /nix/store/b8i7jqbkq80h6v03pnnkpihiq72iplwq-clang-wrapper-7.1.0/bin/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest
/nix/store/sy5iwww8nc4a7mdb3ls44q96i0kxy2dx-cmake-3.14.5/bin/cmake -E cmake_progress_start /private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest/CMakeFiles /private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/nix/store/s41pkl0pjqxfq2hxfcmfc03205njp4sc-sundials-3.2.1/easytofind/LapackTest'
make[1]: CMakeFiles/Makefile2: No such file or directory
make[1]: *** No rule to make target 'CMakeFiles/Makefile2'.  Stop.
make[1]: Leaving directory '/nix/store/s41pkl0pjqxfq2hxfcmfc03205njp4sc-sundials-3.2.1/easytofind/LapackTest'
make: *** [Makefile:87: all] Error 2

steinitznavican · 2019-07-30T15:13:07Z

This is a bit better but still fails.

  postInstall = ''
                  mkdir $out/easytofind
                  echo $(ls) > $out/easytofind/foo.txt
                  cp -r . $out/easytofind
                  cd $out/easytofind/LapackTest
                  make
                  ./ltest > $out/easytofind/ltest.out
                '';

/nix/store/sy5iwww8nc4a7mdb3ls44q96i0kxy2dx-cmake-3.14.5/bin/cmake -S/private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest -B/private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest --check-build-system CMakeFiles/Makefile.cmake 0
-- The C compiler identification is Clang 7.1.0
-- Check for working C compiler: /nix/store/b8i7jqbkq80h6v03pnnkpihiq72iplwq-clang-wrapper-7.1.0/bin/clang
-- Check for working C compiler: /nix/store/b8i7jqbkq80h6v03pnnkpihiq72iplwq-clang-wrapper-7.1.0/bin/clang -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest
/nix/store/sy5iwww8nc4a7mdb3ls44q96i0kxy2dx-cmake-3.14.5/bin/cmake -E cmake_progress_start /private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest/CMakeFiles /private/var/folders/1g/xdjj8dy15k932b80r197qcnr0000gp/T/nix-build-sundials-3.2.1.drv-0/sundials-3.2.1/build/LapackTest/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/nix/store/84h3i703qzjkf876pxvc7ny9vqcqj28i-sundials-3.2.1/easytofind/LapackTest'
make[1]: CMakeFiles/Makefile2: No such file or directory
make[1]: *** No rule to make target 'CMakeFiles/Makefile2'.  Stop.
make[1]: Leaving directory '/nix/store/84h3i703qzjkf876pxvc7ny9vqcqj28i-sundials-3.2.1/easytofind/LapackTest'
make: *** [Makefile:87: all] Error 2

flokli · 2019-08-01T12:35:42Z

CMake can be convinced to use a working RUNPATH during testPhase, by following https://gitlab.kitware.com/cmake/community/wikis/doc/cmake/RPATH-handling#always-full-rpath. I opened LLNL/sundials#19 upstream.

flokli · 2019-08-01T12:37:20Z

liblapack needed to be built with shared library support (BUILD_SHARED_LIBS=ON), after that, sundials was able to use everything just fine from only liblapack, without openblas involved. I guess the previous segfaults were mostly due to us using incompatible libraries there.

flokli · 2019-08-01T12:38:14Z

@GrahamcOfBorg build python3.pkgs.scikits-odes

flokli · 2019-08-02T12:50:27Z

@GrahamcOfBorg build python2.pkgs.scikits-odes python3.pkgs.scikits-odes

idontgetoutmuch · 2019-08-07T16:07:45Z

Any reason this can't be merged?

flokli · 2019-08-08T15:10:00Z

Hm. It would have been nice if we heard back from LLNL/sundials about the patches we sent upstream, but their repo seems to be only code dumps of release snapshots so far, so I don't really see if and how patches are merged in 😢

I did not yet include the patch from LLNL/sundials#21 to remove test flakiness into this PR. It doesn't apply cleanly on sundials_3 (which we need for scikits-odes until bmcage/odes#98 is solved).

I really hope LLNL/sundials is moving development to github soon as indicated on LLNL/sundials#8 (comment) - a sundials 3 branch containing a rebased patch would be really cool - nixpkgs policy is to not include patches into nixpkgs directly, but fetch them if possible…

That's needed for scikits.odes. Upstream bug to migrate to sundials 4: bmcage/odes#98

This test fails on MacOS otherwise, due to slightly different math. Only add for sundials 4, it's not in sundials_3 yet.

The provided patch doesn't apply cleanly on sundials_3 (no SundialsTesting.cmake, SundialsAddTest.cmake containing trailing whitespaces inside context), so for now we just disable tests for sundials_3 - scikits-odes plans to move to sundials 4 anyways - see bmcage/odes#106.

flokli · 2019-09-08T23:06:42Z

I included the non-flakyness patches for sundials 4, and disabled tests for sundials_3, as the patches don't apply cleanly there.

I also bumped scikits-odes to 2.4.0-9-g93075ae, containing the aarch64 and macos patches from bmcage/odes#104 and bmcage/odes#105.

flokli · 2019-09-08T23:07:11Z

@GrahamcOfBorg build python.pkgs.scikits-odes python3.pkgs.scikits-odes sundials

flokli requested a review from FRidh July 2, 2019 21:48

ofborg bot added 6.topic: python 8.has: package (new) 10.rebuild-darwin: 501+ 10.rebuild-darwin: 501-1000 10.rebuild-linux: 501+ 10.rebuild-linux: 1001-2500 labels Jul 2, 2019

flokli force-pushed the scikits-odes branch 2 times, most recently from b9602e3 to d4b0479 Compare July 2, 2019 22:26

idontgetoutmuch approved these changes Jul 3, 2019

View reviewed changes

idontgetoutmuch mentioned this pull request Jul 8, 2019

Make Install Process Easier bmcage/odes#96

Closed

flokli force-pushed the scikits-odes branch 2 times, most recently from 87b3c53 to 2a37885 Compare July 20, 2019 12:03

ofborg bot added 2.status: merge conflict and removed 2.status: merge conflict labels Jul 20, 2019

flokli mentioned this pull request Jul 20, 2019

python.pkgs.numpy: don't exclude f2py test anymore #65157

Merged

10 tasks

ofborg bot added 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 and removed 10.rebuild-darwin: 501+ 10.rebuild-darwin: 501-1000 10.rebuild-linux: 501+ labels Jul 20, 2019

flokli force-pushed the scikits-odes branch from 457ed06 to 1ca1c55 Compare August 1, 2019 12:37

flokli force-pushed the scikits-odes branch 3 times, most recently from 0e679d8 to 65f600c Compare August 2, 2019 12:49

flokli mentioned this pull request Aug 2, 2019

Sundials test patch not yet upstreamed. flokli/nixpkgs#2

Closed

8 tasks

ofborg bot added the 11.by: package-maintainer label Aug 2, 2019

flokli and others added 7 commits September 8, 2019 15:15

sundials: use cmakeFlags

d9ce716

sundials: enable tests

ad3023e

sundials: add lapack support

5f48e89

sundials_3: init at 3.2.1

7e9e22f

That's needed for scikits.odes. Upstream bug to migrate to sundials 4: bmcage/odes#98

sundials: relax tolerance for test_sunmatrix_sparse

ac12bdf

This test fails on MacOS otherwise, due to slightly different math. Only add for sundials 4, it's not in sundials_3 yet.

python.pkgs.scikits-odes: init at 2.4.0-9-g93075ae

652448f

flokli force-pushed the scikits-odes branch from 65f600c to 652448f Compare September 8, 2019 23:05

ofborg bot requested a review from idontgetoutmuch September 8, 2019 23:19

flokli merged commit a77fba2 into NixOS:master Sep 8, 2019

flokli deleted the scikits-odes branch September 8, 2019 23:32

idontgetoutmuch mentioned this pull request Sep 9, 2019

Installation via nix instructions. bmcage/odes#102

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

scikits-odes: init at 2.4.0 #64195

scikits-odes: init at 2.4.0 #64195

flokli commented Jul 2, 2019 •

edited

flokli commented Jul 2, 2019 •

edited

idontgetoutmuch left a comment

flokli commented Jul 3, 2019

idontgetoutmuch commented Jul 3, 2019

flokli commented Jul 3, 2019 via email

FRidh commented Jul 17, 2019

flokli commented Jul 18, 2019

FRidh commented Jul 19, 2019

flokli commented Jul 20, 2019

flokli commented Jul 20, 2019

steinitznavican commented Jul 30, 2019 •

edited

steinitznavican commented Jul 30, 2019 •

edited

steinitznavican commented Jul 30, 2019

steinitznavican commented Jul 30, 2019

flokli commented Aug 1, 2019

flokli commented Aug 1, 2019

flokli commented Aug 1, 2019

flokli commented Aug 2, 2019

idontgetoutmuch commented Aug 7, 2019

flokli commented Aug 8, 2019

flokli commented Sep 8, 2019

flokli commented Sep 8, 2019

scikits-odes: init at 2.4.0 #64195

scikits-odes: init at 2.4.0 #64195

Conversation

flokli commented Jul 2, 2019 • edited

Motivation for this change

Things done

flokli commented Jul 2, 2019 • edited

idontgetoutmuch left a comment

Choose a reason for hiding this comment

flokli commented Jul 3, 2019

idontgetoutmuch commented Jul 3, 2019

flokli commented Jul 3, 2019 via email

FRidh commented Jul 17, 2019

flokli commented Jul 18, 2019

FRidh commented Jul 19, 2019

flokli commented Jul 20, 2019

flokli commented Jul 20, 2019

steinitznavican commented Jul 30, 2019 • edited

steinitznavican commented Jul 30, 2019 • edited

steinitznavican commented Jul 30, 2019

steinitznavican commented Jul 30, 2019

flokli commented Aug 1, 2019

flokli commented Aug 1, 2019

flokli commented Aug 1, 2019

flokli commented Aug 2, 2019

idontgetoutmuch commented Aug 7, 2019

flokli commented Aug 8, 2019

flokli commented Sep 8, 2019

flokli commented Sep 8, 2019

flokli commented Jul 2, 2019 •

edited

flokli commented Jul 2, 2019 •

edited

steinitznavican commented Jul 30, 2019 •

edited

steinitznavican commented Jul 30, 2019 •

edited