Nexus support for Kagayaki cluster at JAIST

[ichibha]

Proposed changes

This PR implements the Nexus settings for Kagayaki cluster at JAIST.

What type(s) of changes does this code introduce?

• New feature

Does this introduce a breaking change?

• No

What systems has this change been tested on?

Kagayaki cluster at JAIST.

Checklist

• Yes. This PR is up to date with current the current state of 'develop'
• N/A, only Python scripts are revised. Code added or changed in the PR has been clang-formatted.
• No. This PR adds tests to cover any new code, or to catch a bug that is being fixed
• No. Documentation has been added (if appropriate)

[jtkrogel]

@ichibha all tests pass with nxs-test?

[prckent]

The Nexus tests are failing in CI. Maybe we need some more examples on how to add a machine and have the tests pass?

[ichibha]

At least, I have to add Kagayaki in test_machines.py. I try to solve the errors myself first to pass this PR.

[jtkrogel]

See also #4068 (comment)

[jtkrogel]

@ichibha any luck?

[ichibha]

@jtkrogel Currently, this specific test is the only one that fails. Is it related to the updates I made?

Before submitting the pull request, I have two tasks to complete:

• Confirm that job_write_ref['kagayaki'] functions correctly in the current environment.
• Enable the specification of number of OMP threads.

 61/69 qdens_radial............................   Failed  12.76 sec
Test name     : qdens_radial
Test sublabel : test_radial_density
Test exception: "AssertionError: "
Test backtrace:
  File "/Users/maezono/qmcpack/nexus//bin/nxs-test", line 478, in run
    self.operation()
  File "/Users/maezono/qmcpack/nexus//bin/nxs-test", line 1631, in qdens_radial
    nunit_all()
  File "/Users/maezono/qmcpack/nexus//bin/nxs-test", line 362, in nunit_all
    run_external_unit_test(test_name,unit_test)
  File "/Users/maezono/qmcpack/nexus//bin/nxs-test", line 388, in run_external_unit_test
    unit_test()
  File "/Users/maezono/qmcpack/nexus/tests/unit/test_qdens_radial.py", line 155, in test_radial_density
    assert(text_eq(out,out_ref))

[ichibha]

@jtkrogel I wanted to inform you that the current version of our feature branch successfully passes all tests in the nxs-test suite with the exception of test 61/qdens_radial. I've been able to confirm that the generated PBS files are functioning as expected.

Given the above, I believe the branch is in a suitable state for merging. Please could you review and consider approving the merge request?

[ichibha]

I performed nxs-test of the latest develop branch, and 61/qdens_radial failed.
Thus, the failure at 61/qdens_radial would not be because of my updates.

[mdewing]

Test this please

[mdewing]

@jtkrogel Is PR this okay with you? The nexus tests pass for me locally.

[jtkrogel]

Yes it is. The qdens radial issue may be environment dependent and should be handled separately.

[prckent]

Based on discussion above