sundials: 5.3.0 -> 5.6.1 #107286

doronbehar · 2020-12-20T21:15:23Z

Update some cmake flags and be more explicit regarding index size.

Motivation for this change

Update.

Things done

Tested octave to build with this update.

pkgs/development/libraries/sundials/default.nix

SuperSandro2000 · 2020-12-20T22:40:47Z

Result of nixpkgs-review pr 107286 run on x86_64-darwin 1

3 packages failed to build:

python37Packages.scikits-odes
python38Packages.scikits-odes
python39Packages.scikits-odes

1 package built:

sundials

    return _bootstrap._gcd_import(name[level:], package, level)
test_on_funcs_ida.py:16: in <module>
    from scikits.odes.sundials.ida import StatusEnumIDA
E   ImportError: dlopen(/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so, 2): Library not loaded: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_ida.5.dylib
E     Referenced from: /nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so
E     Reason: image not found
_______________ ERROR collecting test_user_return_vals_cvode.py ________________
ImportError while importing test module '/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/tests/test_user_return_vals_cvode.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/c56kq0k3f3rdgkj3s1z5hw0j4ack9gdg-python3-3.8.6/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
test_user_return_vals_cvode.py:5: in <module>
    from ..sundials.cvode import StatusEnum
E   ImportError: dlopen(/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/cvode.cpython-38-darwin.so, 2): Library not loaded: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_cvode.5.dylib
E     Referenced from: /nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/cvode.cpython-38-darwin.so
E     Reason: image not found
________________ ERROR collecting test_user_return_vals_ida.py _________________
ImportError while importing test module '/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/tests/test_user_return_vals_ida.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/c56kq0k3f3rdgkj3s1z5hw0j4ack9gdg-python3-3.8.6/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
test_user_return_vals_ida.py:5: in <module>
    from ..sundials.ida import StatusEnumIDA
E   ImportError: dlopen(/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so, 2): Library not loaded: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_ida.5.dylib
E     Referenced from: /nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so
E     Reason: image not found
=========================== short test summary info ============================
ERROR test_dae.py
ERROR test_odeint.py
ERROR test_on_funcs.py
ERROR test_on_funcs_ida.py
ERROR test_user_return_vals_cvode.py
ERROR test_user_return_vals_ida.p

markuskowa · 2020-12-20T22:58:44Z

nixpkgs-review on x86_64-linux runs without errors.

doronbehar · 2020-12-21T08:14:00Z

Result of nixpkgs-review pr 107286 run on x86_64-darwin 1
3 packages failed to build:
1 package built:

    return _bootstrap._gcd_import(name[level:], package, level)
test_on_funcs_ida.py:16: in <module>
    from scikits.odes.sundials.ida import StatusEnumIDA
E   ImportError: dlopen(/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so, 2): Library not loaded: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_ida.5.dylib
E     Referenced from: /nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so
E     Reason: image not found
_______________ ERROR collecting test_user_return_vals_cvode.py ________________
ImportError while importing test module '/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/tests/test_user_return_vals_cvode.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/c56kq0k3f3rdgkj3s1z5hw0j4ack9gdg-python3-3.8.6/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
test_user_return_vals_cvode.py:5: in <module>
    from ..sundials.cvode import StatusEnum
E   ImportError: dlopen(/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/cvode.cpython-38-darwin.so, 2): Library not loaded: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_cvode.5.dylib
E     Referenced from: /nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/cvode.cpython-38-darwin.so
E     Reason: image not found
________________ ERROR collecting test_user_return_vals_ida.py _________________
ImportError while importing test module '/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/tests/test_user_return_vals_ida.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/nix/store/c56kq0k3f3rdgkj3s1z5hw0j4ack9gdg-python3-3.8.6/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
test_user_return_vals_ida.py:5: in <module>
    from ..sundials.ida import StatusEnumIDA
E   ImportError: dlopen(/nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so, 2): Library not loaded: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_ida.5.dylib
E     Referenced from: /nix/store/zckarm9nvz67fgg08w41b00nlf381ih3-python3.8-scikits.odes-2.6.1/lib/python3.8/site-packages/scikits/odes/sundials/ida.cpython-38-darwin.so
E     Reason: image not found
=========================== short test summary info ============================
ERROR test_dae.py
ERROR test_odeint.py
ERROR test_on_funcs.py
ERROR test_on_funcs_ida.py
ERROR test_user_return_vals_cvode.py
ERROR test_user_return_vals_ida.p

cc @flokli per bmcage/odes#107 (comment) / LLNL/sundials#19 ?

flokli · 2020-12-21T14:29:00Z

Ouch, I don't have the hardware to properly test this on darwin. It might be this regressed upstream (not sure if there's any darwin testing on their side).

@rb2k, interested to take a look?

rb2k · 2020-12-21T14:37:01Z

As is, there's some other problems when running nixpkgs-review pr 107286 from my side. I think the last force-push might have been a bit dicey:

$ nix-env -f /Users/mseeger/.cache/nixpkgs-review/pr-107286/nixpkgs -qaP --xml --out-path --show-trace --meta
error: --- UndefinedVarError -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- nix-env
at: (36:9) in file: /Users/mseeger/.cache/nixpkgs-review/pr-107286/nixpkgs/pkgs/development/libraries/sundials/default.nix

    35| 
    36|   src = fetchurl {
      |         ^
    37|     url = "https://computation.llnl.gov/projects/${pname}/download/${pname}-${version}.tar.gz";

undefined variable 'fetchurl'
------------------------------------------------------------------------------------------------- show-trace --------------------------------------------------------------------------------------------------
trace: while evaluating 'makeOverridable'
at: (67:24) in file: /Users/mseeger/.cache/nixpkgs-review/pr-107286/nixpkgs/lib/customisation.nix

    66|   */
    67|   makeOverridable = f: origArgs:
      |                        ^
    68|     let

trace: from call site
at: (121:8) in file: /Users/mseeger/.cache/nixpkgs-review/pr-107286/nixpkgs/lib/customisation.nix

   120|       auto = builtins.intersectAttrs (lib.functionArgs f) autoArgs;
   121|     in makeOverridable f (auto // args);
      |        ^
   122| 

trace: while evaluating 'callPackageWith'
at: (117:35) in file: /Users/mseeger/.cache/nixpkgs-review/pr-107286/nixpkgs/lib/customisation.nix

   116|   */
   117|   callPackageWith = autoArgs: fn: args:
      |                                   ^
   118|     let

trace: from call site
at: (16191:14) in file: /Users/mseeger/.cache/nixpkgs-review/pr-107286/nixpkgs/pkgs/top-level/all-packages.nix

 16190| 
 16191|   sundials = callPackage ../development/libraries/sundials {
      |              ^
 16192|     python = python3;

$ git worktree prune
Traceback (most recent call last):
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/bin/.nixpkgs-review-wrapped", line 9, in <module>
    sys.exit(main())
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/lib/python3.8/site-packages/nixpkgs_review/__init__.py", line 10, in main
    cli.main(command, args)
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/lib/python3.8/site-packages/nixpkgs_review/cli/__init__.py", line 228, in main
    args.func(args)
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/lib/python3.8/site-packages/nixpkgs_review/cli/pr.py", line 60, in pr_command
    contexts.append((pr, review.build_pr(pr)))
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/lib/python3.8/site-packages/nixpkgs_review/review.py", line 201, in build_pr
    return self.build_commit(base_rev, pr_rev)
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/lib/python3.8/site-packages/nixpkgs_review/review.py", line 155, in build_commit
    merged_packages = list_packages(str(self.worktree_dir()), check_meta=True)
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/lib/python3.8/site-packages/nixpkgs_review/review.py", line 303, in list_packages
    return parse_packages_xml(nix_env.stdout)
  File "/nix/store/vn4v02vzwq8bslsy4ifch686napfsa0j-nixpkgs-review-2.5.0/lib/python3.8/site-packages/nixpkgs_review/review.py", line 244, in parse_packages_xml
    for (event, elem) in context:
  File "/nix/store/0mabx9absir73mmijrsv0dsyvyya463r-python3-3.8.6/lib/python3.8/xml/etree/ElementTree.py", line 1233, in iterator
    root = pullparser._close_and_return_root()
  File "/nix/store/0mabx9absir73mmijrsv0dsyvyya463r-python3-3.8.6/lib/python3.8/xml/etree/ElementTree.py", line 1280, in _close_and_return_root
    root = self._parser.close()
xml.etree.ElementTree.ParseError: no element found: line 1, column 0

That being said, once it works I would run "nm -gU" on the binary to see if the library is mentioned there.
The path having two /nix/store/ looks very suspicious "/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_ida.5.dylib"

doronbehar · 2020-12-21T22:24:40Z

I think the last force-push might have been a bit dicey:

Correct. I removed the fetchurl from the arguments by mistake.

I removed the patch from our expression although that PR was closed because upstream wrote that it was included in v5.5.0. I didn't find the cmake variables mentioned in the PR in the main CMakeLists.txt but I did find them here:

https://github.com/LLNL/sundials/blob/5cf0b639797d12acd26ccd8459839ac5784abe04/cmake/SundialsSetupCompilers.cmake#L43-L62

Could it be we should set BUILD_SHARED_LIBS on darwin?

rb2k · 2020-12-22T18:14:10Z

Result of nixpkgs-review pr 107286 run on x86_64-darwin 1

1 package marked as broken and skipped:

octave-jit

4 packages failed to build:

octaveFull
python37Packages.scikits-odes
python38Packages.scikits-odes
python39Packages.scikits-odes

4 packages built:

gama
minc_widgets
octave
sundials

idontgetoutmuch · 2020-12-22T18:36:54Z

I am not sure how to test this. I tried

nix-shell -I nixpkgs=/Users/dom/nixpkgs -p sundials

but got

strip is /nix/store/i1mccwrczhhacpk0jn58wmixqiqh1vkb-cctools-binutils-darwin-949.0.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib 
strip: can't process non-object and non-archive file: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/cmake/sundials/SUNDIALSTargets.cmake
strip: can't process non-object and non-archive file: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/cmake/sundials/SUNDIALSConfigVersion.cmake
strip: can't process non-object and non-archive file: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/cmake/sundials/SUNDIALSConfig.cmake
strip: can't process non-object and non-archive file: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/cmake/sundials/SUNDIALSTargets-release.cmake
patching script interpreter paths in /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1
strip is /nix/store/i1mccwrczhhacpk0jn58wmixqiqh1vkb-cctools-binutils-darwin-949.0.1/bin/strip
patching script interpreter paths in /nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples
bash: direnv: command not found

I tried

cd /nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial/
make

but got

[nix-shell:/nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial]$ make
make
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_analytic.c
error: unable to open output file 'ark_analytic.o': 'Permission denied'
1 error generated.
make: *** [Makefile:90: ark_analytic.o] Error 1

doronbehar · 2020-12-22T18:39:53Z

Result of nixpkgs-review pr 107286 run on x86_64-darwin 1
1 package marked as broken and skipped:
4 packages failed to build:
* octaveFull

* python37Packages.scikits-odes

* python38Packages.scikits-odes

* python39Packages.scikits-odes
4 packages built:
* gama

* minc_widgets

* octave

* sundials

Thanks for the report @rb2k. Interesting octaveFull doesn't build but octave does. Maybe @graham33 could please verify that it's not due to this patch? I suspect something qt related on makes octaveFull fail to build on Darwin.

Also, I'd like to know if adding a cmake flag BUILD_SHARED_LIBS for sundials (on Darwin) helps scikit-odes for instance build with this update.

doronbehar · 2020-12-22T18:43:57Z

bash: direnv: command not found

That's weird and seems unrelated to me - you just spawn a nix-shell so perhaps your Bash rc files have a direnv initialization command in them while you don't use direnv anymore?

I tried

cd /nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial/
make

but got

[nix-shell:/nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial]$ make
make
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_analytic.c
error: unable to open output file 'ark_analytic.o': 'Permission denied'

That makes sense - you can't run commands that create files in directories in /nix/store. Maybe try:

cp -r /nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial sundials-C_serial-example
cd sundials-C_serial-example
make

idontgetoutmuch · 2020-12-23T09:56:58Z

bash: direnv: command not found

That's weird and seems unrelated to me - you just spawn a nix-shell so perhaps your Bash rc files have a direnv initialization command in them while you don't use direnv anymore?

Yes probably something I missed when upgrading to Big Sur

I tried

cd /nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial/
make

but got

[nix-shell:/nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial]$ make
make
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_analytic.c
error: unable to open output file 'ark_analytic.o': 'Permission denied'

That makes sense - you can't run commands that create files in directories in /nix/store. Maybe try:

cp -r /nix/store/yxvhx5hm0jhcjpsmdj706kwywicaiwlf-sundials-5.6.1-examples/share/examples/arkode/C_serial sundials-C_serial-example
cd sundials-C_serial-example
make

Ok the examples build but I get segfaults - I am guessing the linker is picking up some incompatible versions of the libs - I continue to investigate.

idontgetoutmuch · 2021-01-04T12:02:36Z

Ok I removed the brew versions and now I get

dom@MacBook-Pro sundials-C_serial-example % make
make
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_analytic.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_analytic_nonlin.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_brusselator.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_brusselator_fp.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_brusselator1D.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_heat1D.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_heat1D_adapt.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_KrylovDemo_prec.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_robertson.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_robertson_constraints.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_robertson_root.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_brusselator_mri.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_onewaycouple_mri.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_twowaycouple_mri.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_reaction_diffusion_mri.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_brusselator_1D_mri.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -O3 -DNDEBUG -O3 -DNDEBUG -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -c ark_kpr_mri.c
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_analytic ark_analytic.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_analytic_nonlin ark_analytic_nonlin.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_brusselator ark_brusselator.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_brusselator_fp ark_brusselator_fp.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_brusselator1D ark_brusselator1D.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_heat1D ark_heat1D.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_heat1D_adapt ark_heat1D_adapt.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_KrylovDemo_prec ark_KrylovDemo_prec.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_robertson ark_robertson.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_robertson_constraints ark_robertson_constraints.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_robertson_root ark_robertson_root.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_brusselator_mri ark_brusselator_mri.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_onewaycouple_mri ark_onewaycouple_mri.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_twowaycouple_mri ark_twowaycouple_mri.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_reaction_diffusion_mri ark_reaction_diffusion_mri.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_brusselator_1D_mri ark_brusselator_1D_mri.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang -o ark_kpr_mri ark_kpr_mri.o  -O3 -DNDEBUG  -I/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include -I/nix/store/9qgpqsikqlg89w9i1hxsmv96rf7475gq-suitesparse-5.8.1-dev/include -L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib -lsundials_arkode -lsundials_nvecserial -lsundials_nvecmanyvector -lm -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib
ld: warning: directory not found for option '-L/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib'
ld: library not found for -lsundials_arkode
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [examples] Error 1

Makefile contains

prefix       = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1
exec_prefix  = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1
includedir   = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include
libdir       = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib

CPP      = /nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang
CPPFLAGS = -O3 -DNDEBUG
CC       = /nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang
CFLAGS   = -O3 -DNDEBUG
LDFLAGS  = 
LIBS     =  -lm

LINKFLAGS = -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib

I changed this to

prefix       = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1
exec_prefix  = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1
includedir   = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/include
libdir       = /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib

CPP      = /nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang
CPPFLAGS = -O3 -DNDEBUG
CC       = /nix/store/511qa169fbxj18b3k2bjwxffqzxw0fag-clang-wrapper-7.1.0/bin/clang
CFLAGS   = -O3 -DNDEBUG
LDFLAGS  = 
LIBS     =  -lm

LINKFLAGS = -Wl,-rpath,/nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib

and now everything builds but I get runtime errors such as

dom@MacBook-Pro sundials-C_serial-example % ./ark_analytic
./ark_analytic
dyld: Library not loaded: /nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1//nix/store/3gmnpv60l1qnvkgh6hd4fis7pqd644q7-sundials-5.6.1/lib/libsundials_arkode.4.dylib
  Referenced from: /Users/dom/sundials-C_serial-example/./ark_analytic
  Reason: image not found
zsh: abort      ./ark_analytic

flokli · 2021-01-04T13:18:38Z

@idontgetoutmuch please don't build sundials manually via make, or via nix-shell. There can be anything leaking in from your global environment. This says very few about whether the actual attribute does build or not - a nix-build -A sundials in a checkout of this would provide much more insight.

I'm not sure about the state of sandboxing on darwin - you might want to remove any globally installed libraries first.

doronbehar · 2021-01-04T13:36:05Z

I think I found out why upstream has introduced this regression:

This line:

https://github.com/LLNL/sundials/blob/5cf0b639797d12acd26ccd8459839ac5784abe04/cmake/SundialsSetupCompilers.cmake#L50

is different than this:

https://github.com/LLNL/sundials/pull/19/files#diff-1e7de1ae2d059d21e1dd75d5812d5a34b0222cef273b7c3a2af62eb747f9d20aR48

Should I open a PR upstream?

doronbehar · 2021-01-04T13:42:46Z

Never mind, I'll open the PR upstream. Justified by:

https://github.com/jtojnar/cmake-snips#assuming-cmake_install_dir-is-relative-path

doronbehar · 2021-01-04T13:50:27Z

@idontgetoutmuch if you could please retest now, I haven't opened the PR upstream but I updated the PR here to include the patch I'll send to them at:

https://github.com/LLNL/sundials/compare/master...doronbehar:rpath_install_dir?expand=1

idontgetoutmuch · 2021-01-04T14:52:20Z

Tested - works like a charm :)

Update some cmake flags and be more explicit regarding index size.

Per https://github.com/jtojnar/nixpkgs-hammering/blob/master/explanations/attribute-ordering.md

doronbehar · 2021-01-04T21:01:03Z

Great, Updated the PR with an updated comment linking to the PR upstream.

doronbehar · 2021-01-04T21:01:51Z

If someone can run a final nixpkgs-review on darwin it'd be great 🙏.

rb2k · 2021-01-04T21:08:23Z

If someone can run a final nixpkgs-review on darwin it'd be great 🙏.

running it :)

rb2k · 2021-01-04T21:36:23Z

Result of nixpkgs-review pr 107286 run on x86_64-darwin 1

1 package marked as broken and skipped:

octave-jit

1 package failed to build:

octaveFull

7 packages built:

gama
minc_widgets
octave
python37Packages.scikits-odes
python38Packages.scikits-odes
python39Packages.scikits-odes
sundials

doronbehar · 2021-01-05T06:26:01Z

Result of nixpkgs-review pr 107286 run on x86_64-darwin 1
1 package marked as broken and skipped:
1 package failed to build:
7 packages built:

Thanks. The fact that octaveFull fails to build while octave isn't is not a regression of this PR:

https://hydra.nixos.org/job/nixpkgs/nixpkgs-20.09-darwin/octaveFull.x86_64-darwin

So I merge this.

ofborg bot requested a review from idontgetoutmuch December 20, 2020 21:24

ofborg bot added 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Dec 20, 2020

SuperSandro2000 reviewed Dec 20, 2020

View reviewed changes

pkgs/development/libraries/sundials/default.nix Show resolved Hide resolved

doronbehar force-pushed the pkg/octave/sundials branch from 8d4fac5 to 1f52d9e Compare December 21, 2020 08:14

doronbehar force-pushed the pkg/octave/sundials branch from 1f52d9e to fbf3fbd Compare December 21, 2020 22:18

ofborg bot added 10.rebuild-linux: 11-100 and removed 10.rebuild-linux: 1-10 labels Dec 21, 2020

doronbehar force-pushed the pkg/octave/sundials branch from fbf3fbd to cf99e7f Compare January 4, 2021 13:49

doronbehar added 3 commits January 4, 2021 22:58

sundials: 5.3.0 -> 5.6.1

da3f98c

Update some cmake flags and be more explicit regarding index size.

sundials: Split outputs for examples

12c9f36

sundials: reorder attributes

442f1ec

Per https://github.com/jtojnar/nixpkgs-hammering/blob/master/explanations/attribute-ordering.md

doronbehar force-pushed the pkg/octave/sundials branch from 24213a2 to 442f1ec Compare January 4, 2021 21:00

doronbehar merged commit a334367 into NixOS:master Jan 5, 2021

doronbehar deleted the pkg/octave/sundials branch January 5, 2021 06:26

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sundials: 5.3.0 -> 5.6.1 #107286

sundials: 5.3.0 -> 5.6.1 #107286

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sundials: 5.3.0 -> 5.6.1 #107286

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doronbehar commented Dec 20, 2020

Motivation for this change

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edited