slurm: 17.11.9-2 -> 18.08.0-1 #45925

markuskowa · 2018-09-02T00:47:36Z

Motivation for this change

Update slurm and adapt nixos module.

Things done

Update slurm
Update pySlurm to 20180811
Add option clusterName to module.
slurm 18.08 requires ClusterName to be set.

Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)
- NixOS
- macOS
- other Linux distributions
Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
Tested execution of all binary files (usually in ./result/bin/)
Determined the impact on package closure size (by running nix path-info -S before and after)
Fits CONTRIBUTING.md.

markuskowa · 2018-09-02T00:58:53Z

@GrahamcOfBorg test slurm

GrahamcOfBorg · 2018-09-02T01:01:54Z

Success on x86_64-linux (full log)

Attempted: slurm

Partial log (click to expand)

gzipping man pages under /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1/share/man/
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1/lib  /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1/bin  /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1/sbin
patching script interpreter paths in /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1
checking for references to /build in /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1...
moving /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1/sbin/* to /nix/store/sm0kzp4zmd2b0nsn9azq333rifc3nl5j-slurm-18.08.0-1/bin
shrinking RPATHs of ELF executables and libraries in /nix/store/5d49qj34yjrm8lfycig0swg3yvjja29m-slurm-18.08.0-1-dev
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/5d49qj34yjrm8lfycig0swg3yvjja29m-slurm-18.08.0-1-dev
checking for references to /build in /nix/store/5d49qj34yjrm8lfycig0swg3yvjja29m-slurm-18.08.0-1-dev...

GrahamcOfBorg · 2018-09-02T01:03:42Z

Success on x86_64-linux (full log)

Attempted: tests.slurm

Partial log (click to expand)

3 out of 3 tests succeeded
test script finished in 14.35s
cleaning up
killing node2 (pid 600)
killing node1 (pid 612)
killing submit (pid 624)
killing node3 (pid 636)
killing control (pid 648)
vde_switch: EOF on stdin, cleaning up and exiting
vde_switch: Could not remove ctl dir '/build/vde1.ctl': Directory not empty

GrahamcOfBorg · 2018-09-02T01:28:25Z

Success on aarch64-linux (full log)

Attempted: slurm

Partial log (click to expand)

strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1/lib  /nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1/bin  /nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1/sbin
patching script interpreter paths in /nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1
checking for references to /build in /nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1...
moving /nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1/sbin/* to /nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1/bin
shrinking RPATHs of ELF executables and libraries in /nix/store/lvyqbbzjsikpzz9i71dscg04wf4ffh09-slurm-18.08.0-1-dev
strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
patching script interpreter paths in /nix/store/lvyqbbzjsikpzz9i71dscg04wf4ffh09-slurm-18.08.0-1-dev
checking for references to /build in /nix/store/lvyqbbzjsikpzz9i71dscg04wf4ffh09-slurm-18.08.0-1-dev...
/nix/store/v3xik0rhnpdx8qhnm836d0lfvvnz7c7j-slurm-18.08.0-1

GrahamcOfBorg · 2018-09-02T01:29:41Z

Success on aarch64-linux (full log)

Attempted: tests.slurm

Partial log (click to expand)

test script finished in 29.67s
cleaning up
killing node2 (pid 631)
killing node1 (pid 643)
killing submit (pid 656)
killing control (pid 670)
killing node3 (pid 683)
vde_switch: EOF on stdin, cleaning up and exiting
vde_switch: Could not remove ctl dir '/build/vde1.ctl': Directory not empty
/nix/store/5jrm5cm52yvdll37n7iii5iwwpfhmd8d-vm-test-run-slurm

xeji · 2018-09-02T04:49:12Z

@GrahamcOfBorg build python27Packages.pyslurm python36Packages.pyslurm

GrahamcOfBorg · 2018-09-02T04:49:39Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: python27Packages.pyslurm, python36Packages.pyslurm

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

GrahamcOfBorg · 2018-09-02T04:53:00Z

Failure on x86_64-linux (full log)

Attempted: python27Packages.pyslurm, python36Packages.pyslurm

Partial log (click to expand)

INFO:
INFO: Cython version 0.28.3 installed
INFO:
INFO: Clean - checking for objects to clean
INFO: Clean - completed
INFO: Build - Found Slurm header in /nix/store/5d49qj34yjrm8lfycig0swg3yvjja29m-slurm-18.08.0-1-dev/include
INFO: Build - Detected Slurm version - 0x120800 (18.08.00)
ERROR: Build - Incorrect slurm version detected, require Slurm-17.11.00 to slurm-17.11.07
builder for '/nix/store/f8mxrjr04g89z2gqvdhznmdxmx6jd329-python3.6-pyslurm-20180604.drv' failed with exit code 1
error: build of '/nix/store/4g55liskbgins3kwz3c15jipqkbha0p6-python2.7-pyslurm-20180604.drv', '/nix/store/f8mxrjr04g89z2gqvdhznmdxmx6jd329-python3.6-pyslurm-20180604.drv' failed

xeji · 2018-09-02T04:56:51Z

Looks like pyslurm needs to be updated as well.

GrahamcOfBorg · 2018-09-02T04:56:58Z

Failure on aarch64-linux (full log)

Attempted: python27Packages.pyslurm, python36Packages.pyslurm

Partial log (click to expand)

INFO:
INFO: Cython version 0.28.3 installed
INFO:
INFO: Clean - checking for objects to clean
INFO: Clean - completed
INFO: Build - Found Slurm header in /nix/store/lvyqbbzjsikpzz9i71dscg04wf4ffh09-slurm-18.08.0-1-dev/include
INFO: Build - Detected Slurm version - 0x120800 (18.08.00)
ERROR: Build - Incorrect slurm version detected, require Slurm-17.11.00 to slurm-17.11.07
builder for '/nix/store/6w3rd43pjg1m3g9w76r1zkcrn2wr035l-python3.6-pyslurm-20180604.drv' failed with exit code 1
error: build of '/nix/store/1s64vk49fl70x8z40k3mylzydprv8n0a-python2.7-pyslurm-20180604.drv', '/nix/store/6w3rd43pjg1m3g9w76r1zkcrn2wr035l-python3.6-pyslurm-20180604.drv' failed

markuskowa · 2018-09-02T09:58:30Z

pySlurm seems to be very particular about the slurm version. Looks like this update has to wait then until pySlurm is updated.

xeji · 2018-09-02T10:01:57Z

Yes, unfortunately pyslurm upstream only supports slurm 17.11.9

veprbl · 2018-09-03T23:06:04Z

I think that pyslurm pretending to not support new slurm versions is often for no reason. Looking at commits [1] I see no real ABI changes, but bumps of max version every time with no real change to the code. I wonder if we could just drop this check.

[1] https://github.com/PySlurm/pyslurm/commits/master

markuskowa · 2018-09-04T12:46:58Z

@veprbl I agree. The choice in pyslurm is not clear to me. However, when I remove the version check, I get an error. It seems not to be compatible. Bumping the pyslurm version to the latest git revision, does also not work.

warning: pyslurm/pyslurm.pyx:59:4: 'id_t' redeclared
warning: pyslurm/pyslurm.pyx:62:10: 'PRIO_PROCESS' redeclared
warning: pyslurm/pyslurm.pyx:67:4: 'const_char_ptr' redeclared
warning: pyslurm/pyslurm.pyx:68:4: 'const_char_pptr' redeclared
warning: pyslurm/pyslurm.pyx:71:13: 'ALPS_CRAY_SYSTEM' redeclared
warning: pyslurm/slurm.pxd:15:4: 'size_t' redeclared
warning: pyslurm/slurm.pxd:241:8: 'WAIT_POWER_NOT_AVAIL' redeclared
warning: pyslurm/slurm.pxd:242:8: 'WAIT_POWER_RESERVED' redeclared
warning: pyslurm/slurm.pxd:1752:4: 'dynamic_plugin_data_t' redeclared
warning: pyslurm/slurm.pxd:1754:4: 'bitstr_t' redeclared
warning: pyslurm/slurm.pxd:2416:4: 'slurmdb_assoc_rec_t' redeclared
warning: pyslurm/slurm.pxd:2433:4: 'slurmdb_cluster_rec_t' redeclared
error: command 'gcc' failed with exit status 1

xeji · 2018-09-04T12:51:28Z

I suggest opening an upstream issue to support latest slurm.

markuskowa · 2018-09-04T12:59:28Z

PySlurm/pyslurm#126

giovtorres · 2018-09-05T02:01:43Z

Hi, I help to maintain PySlurm. The versioning could certainly be improved. The version checks are sanity checks to make sure that PySlurm is compiled against the right version of Slurm. This was necessary a few years back when there would be changes to slurm.h in the middle of branch, say the .5 micro version, and newer versions of PySlurm would then break for micro versions .1 thru .4. Over the last 2 major/minor versions, however, I've noticed the API has stabilized quite a bit and this has become unnecessary, but that's not to say it can't happen again.

Switching between major or minor versions almost always requires updates to PySlurm that match the changes to the slurm headers and any code in the API that is wrapped or referenced by PySlurm.

I updated the test container to 18.08.0 over the weekend and I've started to update PySlurm for 18.08.0-1.

markuskowa · 2018-09-07T08:06:34Z

@giovtorres Thanks!

slurm 18.08 requires ClusterName to be set (set to default).

xeji · 2018-09-08T21:15:54Z

There's still a merge conflict

markuskowa · 2018-09-08T21:22:04Z

The conflict is resolved. I did a rebase. Just added a new version of pySlurm. It should build now properly.

markuskowa · 2018-09-08T21:34:17Z

@GrahamcOfBorg build python37Packages.pyslurm

xeji · 2018-09-08T21:40:08Z

don't have python37 yet 😄
@GrahamcOfBorg build python36Packages.pyslurm

GrahamcOfBorg · 2018-09-08T21:40:38Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: python36Packages.pyslurm

Partial log (click to expand)


a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

markuskowa · 2018-09-08T21:43:12Z

We actually do: /nix/store/q38ddqq7nz82lv6z0arl5wdk9s3w3j96-python3-3.7.0
though it's not the default yet

GrahamcOfBorg · 2018-09-08T21:44:08Z

Success on x86_64-linux (full log)

Attempted: python36Packages.pyslurm

Partial log (click to expand)

Successfully installed pyslurm-18.8.0.1
/build/source
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/l0ifdjd7xrn0h5vqy5njpyhdy79i0awh-python3.6-pyslurm-20180908
shrinking /nix/store/l0ifdjd7xrn0h5vqy5njpyhdy79i0awh-python3.6-pyslurm-20180908/lib/python3.6/site-packages/pyslurm/pyslurm.cpython-36m-x86_64-linux-gnu.so
strip is /nix/store/h0lbngpv6ln56hjj59i6l77vxq25flbz-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/l0ifdjd7xrn0h5vqy5njpyhdy79i0awh-python3.6-pyslurm-20180908/lib
patching script interpreter paths in /nix/store/l0ifdjd7xrn0h5vqy5njpyhdy79i0awh-python3.6-pyslurm-20180908
checking for references to /build in /nix/store/l0ifdjd7xrn0h5vqy5njpyhdy79i0awh-python3.6-pyslurm-20180908...
/nix/store/l0ifdjd7xrn0h5vqy5njpyhdy79i0awh-python3.6-pyslurm-20180908

GrahamcOfBorg · 2018-09-08T21:53:45Z

Success on aarch64-linux (full log)

Attempted: python36Packages.pyslurm

Partial log (click to expand)

Successfully installed pyslurm-18.8.0.1
/build/source
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/n05g43f2bha5iqga5vx5vaksralvyr1i-python3.6-pyslurm-20180908
shrinking /nix/store/n05g43f2bha5iqga5vx5vaksralvyr1i-python3.6-pyslurm-20180908/lib/python3.6/site-packages/pyslurm/pyslurm.cpython-36m-aarch64-linux-gnu.so
strip is /nix/store/y4ymnvgxygpq05h03kyzbj572zmh6zla-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/n05g43f2bha5iqga5vx5vaksralvyr1i-python3.6-pyslurm-20180908/lib
patching script interpreter paths in /nix/store/n05g43f2bha5iqga5vx5vaksralvyr1i-python3.6-pyslurm-20180908
checking for references to /build in /nix/store/n05g43f2bha5iqga5vx5vaksralvyr1i-python3.6-pyslurm-20180908...
/nix/store/n05g43f2bha5iqga5vx5vaksralvyr1i-python3.6-pyslurm-20180908

GrahamcOfBorg · 2018-09-08T22:04:57Z

Failure on x86_64-linux (full log)

Attempted: python37Packages.pyslurm

Partial log (click to expand)

ALL DONE (1/4)
ALL DONE (2/4)
FAILED (3/4)
ALL DONE (3/4)
ALL DONE (0/4)
Errors for shards 3
ALL DONE
builder for '/nix/store/qp9kcqj18id2yv7s5b5f8d8y4pgp77i5-python3.7-Cython-0.28.3.drv' failed with exit code 1
cannot build derivation '/nix/store/qxg5pri882q5g2r6qd8q15zhs4916w7h-python3.7-pyslurm-20180908.drv': 1 dependencies couldn't be built
error: build of '/nix/store/qxg5pri882q5g2r6qd8q15zhs4916w7h-python3.7-pyslurm-20180908.drv' failed

GrahamcOfBorg · 2018-09-08T23:15:03Z

Timed out, unknown build status on aarch64-linux (full log)

Attempted: python37Packages.pyslurm

Partial log (click to expand)

    1/0
ZeroDivisionError: integer division or modulo by zero
Exception ignored in: <yield_from_pep380.test_broken_getattr_handling.<locals>.Broken object at 0xffff7457af98>
Traceback (most recent call last):
  File "tests/run/yield_from_pep380.pyx", line 574, in yield_from_pep380.test_broken_getattr_handling.Broken.__getattr__
    1/0
ZeroDivisionError: integer division or modulo by zero
building of '/nix/store/m0hj1w7m861l8zh0p92ac4kcll7vz7n4-python3.7-Cython-0.28.3.drv' timed out after 3600 seconds
cannot build derivation '/nix/store/2p138wgpfhlzd6k2nkkyx5yirllnxkm6-python3.7-pyslurm-20180908.drv': 1 dependencies couldn't be built
error: build of '/nix/store/2p138wgpfhlzd6k2nkkyx5yirllnxkm6-python3.7-pyslurm-20180908.drv' failed

xeji · 2018-09-09T09:26:51Z

Is this ready to merge? (If you like to work on python37 support, that should probably be a separate PR)

markuskowa · 2018-09-09T11:52:35Z

Yes, I would say it is ready. Python 3.7 seems to be very experimental as of now. I couldn't even find hydra builds.

…

On Sun, 9 Sep 2018, 11:26 xeji, ***@***.***> wrote: Is this ready to merge? (If you like to work on python37 support, that should probably be a separate PR) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#45925 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AZPmldkpcLlUAB17FPC5bpNTibhncSpFks5uZN7egaJpZM4WWa5m> .

GrahamcOfBorg added 6.topic: nixos 8.has: module (update) 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Sep 2, 2018

markuskowa changed the title ~~slurm: 17.11.9-2 -> 18.08.0-1~~ [WIP] slurm: 17.11.9-2 -> 18.08.0-1 Sep 2, 2018

xeji added the 2.status: wait-for-upstream Waiting for upstream fix (or their other action). label Sep 2, 2018

xeji mentioned this pull request Sep 7, 2018

pythonPackages.pyslurm: 20180604 -> 20180811 #46187

Merged

9 tasks

markuskowa requested a review from FRidh as a code owner September 8, 2018 21:14

markuskowa added 2 commits September 8, 2018 23:14

slurm: 17.11.9-2 -> 18.08.0-1

7a5b421

nixos/slurm: add option clusterName

0051772

slurm 18.08 requires ClusterName to be set (set to default).

pyslurm: 20180811 -> 20180908

7dd2f4e

markuskowa force-pushed the ompi-up branch from eeeca7c to 7dd2f4e Compare September 8, 2018 21:17

GrahamcOfBorg added the 6.topic: python label Sep 8, 2018

xeji removed the 2.status: wait-for-upstream Waiting for upstream fix (or their other action). label Sep 8, 2018

xeji changed the title ~~[WIP] slurm: 17.11.9-2 -> 18.08.0-1~~ slurm: 17.11.9-2 -> 18.08.0-1 Sep 9, 2018

xeji merged commit 17c51ef into NixOS:master Sep 9, 2018

markuskowa deleted the ompi-up branch September 11, 2018 22:12

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slurm: 17.11.9-2 -> 18.08.0-1 #45925

slurm: 17.11.9-2 -> 18.08.0-1 #45925

markuskowa commented Sep 2, 2018 •

edited

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edited

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slurm: 17.11.9-2 -> 18.08.0-1 #45925

slurm: 17.11.9-2 -> 18.08.0-1 #45925

Conversation

markuskowa commented Sep 2, 2018 • edited

Motivation for this change

Things done

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