{chem}[foss/2021b] LAMMPS v29Sep2021 update3 by sassy-crick · Pull Request #15869 · easybuilders/easybuild-easyconfigs

sassy-crick · 2022-07-14T16:51:22Z

(created using eb --new-pr)

Requires:

requires EasyBlock PR 2213

Yet anther version of LAMMPS. Based on PR #14653 but with YAFF, some changes to the way the user-modules are handled but that seems to be still not working well in the LAMMPS EasyBlock PR #2213.

We might want to bring the various LAMMPS PRs together and decide the best way forward I would like to suggest.

… [2213](easybuilders/easybuild-easyblocks#2213)

boegelbot · 2022-07-14T17:50:22Z

@sassy-crick: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/2671844018
Output from first failing test suite run:

ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 325, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: netCDF/4.8.1-foss-2021b-HDF5-1.10.8, Voro++/0.4.6-foss-2021b, kim-api/2.3.0-foss-2021b, yaff/1.6.0-foss-2021b (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 312, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: netCDF/4.8.1-foss-2021b-HDF5-1.10.8, Voro++/0.4.6-foss-2021b, kim-api/2.3.0-foss-2021b, yaff/1.6.0-foss-2021b (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 811, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: netCDF/4.8.1-foss-2021b-HDF5-1.10.8, Voro++/0.4.6-foss-2021b, kim-api/2.3.0-foss-2021b, yaff/1.6.0-foss-2021b (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 15044 tests in 888.300s

FAILED (errors=3)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

ocaisa · 2022-07-14T20:00:36Z

+]
+
+user_packages = [
+    'CGDNA',


These won't be picked up here (any more), they need to be moved to general_packages

This is where I put them originally, both with and without the USER- prefix.
Moving them to the general_packages list still does not build them:

CMake Warning: Manually-specified variables were not used by the project: BOOST_ROOT BUILD_EXE BUILD_LIB Boost_NO_SYSTEM_PATHS DOWNLOAD_EIGEN3 EIGEN3_INCLUDE_DIR Eigen3_DIR PKG_CGDNA PKG_CGSDK PKG_DPD PKG_LB PKG_MEAMC PKG_MESO PKG_REAXC PKG_SDPD PKG_SMD PKG_SNAP PKG_USER-INTEL PKG_USER-OMP

So something is still not working as I would expect it.

ocaisa · 2022-07-20T07:39:03Z

I suggest we close this in favour of #15877, which is the latest stable release of LAMMPS.

Also, I discovered there is actually no need for a YAFF dependency in LAMMPS at all, the necessary code is included (from my reading of the docs).

sassy-crick · 2022-08-01T11:23:06Z

I suggest we close this in favour of #15877, which is the latest stable release of LAMMPS.

I would agree if the user did not specify that particular version. How about I am upgrading this version with the good work you done for PR #15877 so we got that on in EasyBuild as well, for the reason I just mentioned? Happy to take no as an answer and stuff it into our own, closed repository.

Also, I discovered there is actually no need for a YAFF dependency in LAMMPS at all, the necessary code is included (from my reading of the docs).

Yes, you are right. I noticed that as well when we discussed it but did not have a chance to look into that as I was on AL. I will remove it.

sassy-crick · 2022-08-01T17:08:30Z

To add value to this: This is the update-3 version of v29Sep2021, which has the YAFF sanity check from PR ##14653 and all the modules from PR #15877 in the hope somebody might find that useful.
Unfortunately, YAFF does not build with HDF5-1.12.x and thus the different version for NetCDF. I am aware that this is not ideal!
Let me know what you think of it.

boegelbot · 2022-08-02T09:52:48Z

@sassy-crick: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/2776518916
Output from first failing test suite run:

ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 325, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: netCDF/4.8.1-foss-2021b-HDF5-1.10.8, yaff/1.6.0-foss-2021b (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 312, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: netCDF/4.8.1-foss-2021b-HDF5-1.10.8, yaff/1.6.0-foss-2021b (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 811, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: netCDF/4.8.1-foss-2021b-HDF5-1.10.8, yaff/1.6.0-foss-2021b (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 15122 tests in 750.167s

FAILED (errors=3)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice you me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

ocaisa · 2022-08-03T06:36:14Z

I suggest we close this in favour of #15877, which is the latest stable release of LAMMPS.

I would agree if the user did not specify that particular version. How about I am upgrading this version with the good work you done for PR #15877 so we got that on in EasyBuild as well, for the reason I just mentioned? Happy to take no as an answer and stuff it into our own, closed repository.

The user probably specified that version because that was the last stable release of LAMMPS, however the version in #15877 is the most recent stable release. Unless there is a material need for that particular version (and I haven't seen a reason that there would be), I think it would be best to stick with the latest stable release.

Unfortunately, YAFF does not build with HDF5-1.12.x and thus the different version for NetCDF. I am aware that this is not ideal! Let me know what you think of it.

If I understand things correctly, the reason you are including yaff as a dependency is solely to run that sanity check, that doesn't seem like a great reason to me particularly when it comes with having to swap the netCDF version.

sassy-crick · 2022-08-03T13:20:30Z

If I understand things correctly, the reason you are including yaff as a dependency is solely to run that sanity check, that doesn't seem like a great reason to me particularly when it comes with having to swap the netCDF version.

No, that does not come from me, that comes from the original PR #14653 which goes back some time. I think it does make sense to test more, the question is what is the best way forward. As suggested in PR #15854 it might be good to have a quick chat in the next EB user meeting. Maybe.

sassy-crick · 2023-10-23T11:16:52Z

I will close this in favour of #15877, which is the newer stable release of LAMMPS

YAFF added, user-modules moved to correct list, requires EasyBlock PR…

fc799e1

… [2213](easybuilders/easybuild-easyblocks#2213)

sassy-crick changed the title ~~YAFF added, user-modules moved to correct list, requires EasyBlock PR [2213](https://github.com/easybuilders/easybuild-easyblocks/pull/2213)~~ {chem}[foss/2020b] LAMMPS v29Sep2021 Jul 14, 2022

ocaisa reviewed Jul 14, 2022

View reviewed changes

jfgrimm changed the title ~~{chem}[foss/2020b] LAMMPS v29Sep2021~~ {chem}[foss/2021b] LAMMPS v29Sep2021 Jul 15, 2022

Update-3 EC file for this version

9693764

sassy-crick changed the title ~~{chem}[foss/2021b] LAMMPS v29Sep2021~~ {chem}[foss/2021b] LAMMPS v29Sep2021 update3 Aug 1, 2022

sassy-crick mentioned this pull request Aug 3, 2022

{chem}[foss/2021b] yaff v1.6.0 w/ Python 3.9.6 #15854

Closed

1 task

sassy-crick mentioned this pull request Aug 3, 2022

HDF5 version > 1.10 not working molmod/yaff#76

Open

sassy-crick closed this Oct 23, 2023

sassy-crick deleted the 20220714175117_new_pr_LAMMPS29Sep2021 branch October 23, 2023 11:18

boegel mentioned this pull request Jan 14, 2024

{data}[gompi/2021b] netCDF v4.8.1 w/ HDF5 1.10.8 #15868

Closed

boegel added the update label Jan 14, 2024

boegel added this to the 4.x milestone Jan 14, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

{chem}[foss/2021b] LAMMPS v29Sep2021 update3#15869

{chem}[foss/2021b] LAMMPS v29Sep2021 update3#15869
sassy-crick wants to merge 2 commits intoeasybuilders:developfrom
sassy-crick:20220714175117_new_pr_LAMMPS29Sep2021

sassy-crick commented Jul 14, 2022 •

edited

Loading

Uh oh!

boegelbot commented Jul 14, 2022

Uh oh!

ocaisa Jul 14, 2022

Uh oh!

sassy-crick Jul 15, 2022

Uh oh!

ocaisa commented Jul 20, 2022

Uh oh!

sassy-crick commented Aug 1, 2022

Uh oh!

sassy-crick commented Aug 1, 2022

Uh oh!

boegelbot commented Aug 2, 2022

Uh oh!

ocaisa commented Aug 3, 2022 •

edited

Loading

Uh oh!

sassy-crick commented Aug 3, 2022

Uh oh!

sassy-crick commented Oct 23, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

sassy-crick commented Jul 14, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

boegelbot commented Jul 14, 2022

Uh oh!

ocaisa Jul 14, 2022

Choose a reason for hiding this comment

Uh oh!

sassy-crick Jul 15, 2022

Choose a reason for hiding this comment

Uh oh!

ocaisa commented Jul 20, 2022

Uh oh!

sassy-crick commented Aug 1, 2022

Uh oh!

sassy-crick commented Aug 1, 2022

Uh oh!

boegelbot commented Aug 2, 2022

Uh oh!

ocaisa commented Aug 3, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

sassy-crick commented Aug 3, 2022

Uh oh!

sassy-crick commented Oct 23, 2023

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

sassy-crick commented Jul 14, 2022 •

edited

Loading

ocaisa commented Aug 3, 2022 •

edited

Loading