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{2023.06}[foss/2021a] ESPResSo v4.2.1 #332

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maxim-masterov
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Add ESPResSo for 2021a without CUDA support

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eessi-bot bot commented Sep 12, 2023

Instance eessi-bot-citc-aws is configured to build:

  • arch x86_64/generic for repo eessi-2021.12
  • arch x86_64/generic for repo eessi.org-2023.06-compat
  • arch x86_64/generic for repo eessi.io-2023.06-compat
  • arch x86_64/generic for repo eessi-2023.06-software
  • arch x86_64/intel/haswell for repo eessi-2021.12
  • arch x86_64/intel/haswell for repo eessi.org-2023.06-compat
  • arch x86_64/intel/haswell for repo eessi.io-2023.06-compat
  • arch x86_64/intel/haswell for repo eessi-2023.06-software
  • arch x86_64/intel/skylake_avx512 for repo eessi-2021.12
  • arch x86_64/intel/skylake_avx512 for repo eessi.org-2023.06-compat
  • arch x86_64/intel/skylake_avx512 for repo eessi.io-2023.06-compat
  • arch x86_64/intel/skylake_avx512 for repo eessi-2023.06-software
  • arch x86_64/amd/zen2 for repo eessi-2021.12
  • arch x86_64/amd/zen2 for repo eessi.org-2023.06-compat
  • arch x86_64/amd/zen2 for repo eessi.io-2023.06-compat
  • arch x86_64/amd/zen2 for repo eessi-2023.06-software
  • arch x86_64/amd/zen3 for repo eessi-2021.12
  • arch x86_64/amd/zen3 for repo eessi.org-2023.06-compat
  • arch x86_64/amd/zen3 for repo eessi.io-2023.06-compat
  • arch x86_64/amd/zen3 for repo eessi-2023.06-software
  • arch aarch64/generic for repo eessi-2021.12
  • arch aarch64/generic for repo eessi.org-2023.06-compat
  • arch aarch64/generic for repo eessi.io-2023.06-compat
  • arch aarch64/generic for repo eessi-2023.06-software
  • arch aarch64/neoverse_n1 for repo eessi-2021.12
  • arch aarch64/neoverse_n1 for repo eessi.org-2023.06-compat
  • arch aarch64/neoverse_n1 for repo eessi.io-2023.06-compat
  • arch aarch64/neoverse_n1 for repo eessi-2023.06-software
  • arch aarch64/neoverse_v1 for repo eessi-2021.12
  • arch aarch64/neoverse_v1 for repo eessi.org-2023.06-compat
  • arch aarch64/neoverse_v1 for repo eessi.io-2023.06-compat
  • arch aarch64/neoverse_v1 for repo eessi-2023.06-software

eessi-2023.06-eb-4.8.0-2021a.yml Outdated Show resolved Hide resolved
@maxim-masterov
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maxim-masterov commented Oct 2, 2023

ERROR: Failed to get data for PR #18746 from easybuilders/easybuild-easyconfigs (HTTP Error 403: rate limit exceeded)
Please check PR #, account and repo.

Where did the 18746 come from?

@boegel
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boegel commented Oct 4, 2023

@maxim-masterov That comes from eessi-2023.06-eb-4.8.0-2021b.yml, and the fact that all easystack files are being processed in CI, regardless of which easystack was changed in the PR.
That's not easy to change, but we could look into using a GitHub token to make it less likely to run into rate limits.

For now, ignore the CI failures (they'll fail anyway until this module is installed), and let's trigger a test build?

It would be helpful if you first sync your PR branch here with current 2023.06, to pick up #351

@maxim-masterov
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bot: build repo:eessi-2023.06-software arch:x86_64/generic
bot: build repo:eessi-2023.06-software arch:aarch64/neoverse_v1

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Updates by the bot instance eessi-bot-citc-aws (click for details)
  • received bot command build repo:eessi-2023.06-software arch:x86_64/generic from maxim-masterov

    • expanded format: build repository:eessi-2023.06-software architecture:x86_64/generic
  • received bot command build repo:eessi-2023.06-software arch:aarch64/neoverse_v1 from maxim-masterov

    • expanded format: build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1
  • handling command build repository:eessi-2023.06-software architecture:x86_64/generic resulted in:

  • handling command build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1 resulted in:

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New job on instance eessi-bot-citc-aws for architecture x86_64-generic for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.10/pr_332/7704

date job status comment
Oct 04 08:59:19 UTC 2023 submitted job id 7704 awaits release by job manager
Oct 04 08:59:53 UTC 2023 released job awaits launch by Slurm scheduler
Oct 04 09:04:01 UTC 2023 running job 7704 is running
Oct 04 09:07:10 UTC 2023 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-7704.out
❌ found message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-x86_64-generic-1696410381.tar.gzsize: 0 MiB (211151 bytes)
entries: 3
modules under 2023.06/software/linux/x86_64/generic/modules/all
no module files in tarball
software under 2023.06/software/linux/x86_64/generic/software
no software packages in tarball
other under 2023.06/software/linux/x86_64/generic
.lmod/cache/spiderT.lua
.lmod/cache/spiderT.luac_5.1
.lmod/cache/timestamp

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New job on instance eessi-bot-citc-aws for architecture aarch64-neoverse_v1 for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.10/pr_332/7705

date job status comment
Oct 04 08:59:27 UTC 2023 submitted job id 7705 awaits release by job manager
Oct 04 08:59:50 UTC 2023 released job awaits launch by Slurm scheduler
Oct 04 09:02:57 UTC 2023 running job 7705 is running
Oct 04 09:07:08 UTC 2023 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-7705.out
❌ found message matching ERROR:
✅ no message matching FAILED:
✅ no message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-aarch64-neoverse_v1-1696410392.tar.gzsize: 0 MiB (210743 bytes)
entries: 3
modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all
no module files in tarball
software under 2023.06/software/linux/aarch64/neoverse_v1/software
no software packages in tarball
other under 2023.06/software/linux/aarch64/neoverse_v1
.lmod/cache/spiderT.lua
.lmod/cache/spiderT.luac_5.1
.lmod/cache/timestamp

@maxim-masterov
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Incorporated changes in PR 18963

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bot: build repo:eessi-2023.06-software arch:x86_64/generic
bot: build repo:eessi-2023.06-software arch:aarch64/neoverse_v1

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Updates by the bot instance eessi-bot-mc-aws (click for details)
  • received bot command build repo:eessi-2023.06-software arch:x86_64/generic from maxim-masterov

    • expanded format: build repository:eessi-2023.06-software architecture:x86_64/generic
  • received bot command build repo:eessi-2023.06-software arch:aarch64/neoverse_v1 from maxim-masterov

    • expanded format: build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1
  • handling command build repository:eessi-2023.06-software architecture:x86_64/generic resulted in:

    • no jobs were submitted
  • handling command build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1 resulted in:

    • no jobs were submitted

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Updates by the bot instance eessi-bot-citc-aws (click for details)
  • received bot command build repo:eessi-2023.06-software arch:x86_64/generic from maxim-masterov

    • expanded format: build repository:eessi-2023.06-software architecture:x86_64/generic
  • received bot command build repo:eessi-2023.06-software arch:aarch64/neoverse_v1 from maxim-masterov

    • expanded format: build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1
  • handling command build repository:eessi-2023.06-software architecture:x86_64/generic resulted in:

  • handling command build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1 resulted in:

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New job on instance eessi-bot-citc-aws for architecture x86_64-generic for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.10/pr_332/8226

date job status comment
Oct 11 09:38:14 UTC 2023 submitted job id 8226 awaits release by job manager
Oct 11 09:38:53 UTC 2023 released job awaits launch by Slurm scheduler
Oct 11 09:53:03 UTC 2023 running job 8226 is running
Oct 11 10:19:07 UTC 2023 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-8226.out
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-x86_64-generic-1697019461.tar.gzsize: 34 MiB (36166601 bytes)
entries: 17154
modules under 2023.06/software/linux/x86_64/generic/modules/all
Boost.MPI/1.76.0-gompi-2021a.lua
libsodium/1.0.18-GCCcore-10.3.0.lua
OpenPGM/5.2.122-GCCcore-10.3.0.lua
Pint/0.20.1-GCCcore-10.3.0.lua
ZeroMQ/4.3.4-GCCcore-10.3.0.lua
software under 2023.06/software/linux/x86_64/generic/software
Boost.MPI/1.76.0-gompi-2021a
libsodium/1.0.18-GCCcore-10.3.0
OpenPGM/5.2.122-GCCcore-10.3.0
Pint/0.20.1-GCCcore-10.3.0
ZeroMQ/4.3.4-GCCcore-10.3.0
other under 2023.06/software/linux/x86_64/generic
.lmod/cache/spiderT.lua
.lmod/cache/spiderT.luac_5.1
.lmod/cache/timestamp

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New job on instance eessi-bot-citc-aws for architecture aarch64-neoverse_v1 for repository eessi-2023.06-software in job dir /mnt/shared/home/bot/eessi-bot-software-layer/jobs/2023.10/pr_332/8227

date job status comment
Oct 11 09:38:22 UTC 2023 submitted job id 8227 awaits release by job manager
Oct 11 09:38:49 UTC 2023 released job awaits launch by Slurm scheduler
Oct 11 09:43:16 UTC 2023 running job 8227 is running
Oct 11 10:19:05 UTC 2023 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-8227.out
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-aarch64-neoverse_v1-1697019503.tar.gzsize: 35 MiB (36888057 bytes)
entries: 17154
modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all
Boost.MPI/1.76.0-gompi-2021a.lua
libsodium/1.0.18-GCCcore-10.3.0.lua
OpenPGM/5.2.122-GCCcore-10.3.0.lua
Pint/0.20.1-GCCcore-10.3.0.lua
ZeroMQ/4.3.4-GCCcore-10.3.0.lua
software under 2023.06/software/linux/aarch64/neoverse_v1/software
Boost.MPI/1.76.0-gompi-2021a
libsodium/1.0.18-GCCcore-10.3.0
OpenPGM/5.2.122-GCCcore-10.3.0
Pint/0.20.1-GCCcore-10.3.0
ZeroMQ/4.3.4-GCCcore-10.3.0
other under 2023.06/software/linux/aarch64/neoverse_v1
.lmod/cache/spiderT.lua
.lmod/cache/spiderT.luac_5.1
.lmod/cache/timestamp

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bot: build repo:eessi-2023.06-software arch:aarch64/neoverse_v1

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Updates by the bot instance eessi-bot-mc-aws (click for details)
  • received bot command build repo:eessi-2023.06-software arch:aarch64/neoverse_v1 from casparvl

    • expanded format: build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1
  • handling command build repository:eessi-2023.06-software architecture:aarch64/neoverse_v1 resulted in:

    • no jobs were submitted

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bot: show_config

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Updates by the bot instance eessi-bot-mc-aws (click for details)

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eessi-bot bot commented Oct 23, 2023

Instance eessi-bot-mc-aws is configured to build:

  • arch x86_64/generic for repo eessi-hpc.org-2023.06-compat
  • arch x86_64/generic for repo eessi-hpc.org-2023.06-software
  • arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-compat
  • arch x86_64/intel/haswell for repo eessi-hpc.org-2023.06-software
  • arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-compat
  • arch x86_64/intel/skylake_avx512 for repo eessi-hpc.org-2023.06-software
  • arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-compat
  • arch x86_64/amd/zen2 for repo eessi-hpc.org-2023.06-software
  • arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-compat
  • arch x86_64/amd/zen3 for repo eessi-hpc.org-2023.06-software
  • arch aarch64/generic for repo eessi-hpc.org-2023.06-compat
  • arch aarch64/generic for repo eessi-hpc.org-2023.06-software
  • arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-compat
  • arch aarch64/neoverse_n1 for repo eessi-hpc.org-2023.06-software
  • arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-compat
  • arch aarch64/neoverse_v1 for repo eessi-hpc.org-2023.06-software

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bot: build repo:eessi-hpc.org-2023.06-software arch:aarch64/neoverse_v1

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Updates by the bot instance eessi-bot-mc-aws (click for details)
  • received bot command build repo:eessi-hpc.org-2023.06-software arch:aarch64/neoverse_v1 from casparvl

    • expanded format: build repository:eessi-hpc.org-2023.06-software architecture:aarch64/neoverse_v1
  • handling command build repository:eessi-hpc.org-2023.06-software architecture:aarch64/neoverse_v1 resulted in:

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New job on instance eessi-bot-mc-aws for architecture aarch64-neoverse_v1 for repository eessi-hpc.org-2023.06-software in job dir /project/def-users/SHARED/jobs/2023.10/pr_332/341

date job status comment
Oct 23 13:10:51 UTC 2023 submitted job id 341 awaits release by job manager
Oct 23 13:11:18 UTC 2023 released job awaits launch by Slurm scheduler
Oct 23 13:15:20 UTC 2023 running job 341 is running
Oct 23 13:34:42 UTC 2023 finished
😢 FAILURE (click triangle for details)
Details
✅ job output file slurm-341.out
❌ found message matching ERROR:
❌ found message matching FAILED:
❌ found message matching required modules missing:
❌ no message matching No missing installations
✅ found message matching .tar.gz created!
Artefacts
eessi-2023.06-software-linux-aarch64-neoverse_v1-1698068037.tar.gzsize: 35 MiB (36901920 bytes)
entries: 17154
modules under 2023.06/software/linux/aarch64/neoverse_v1/modules/all
Boost.MPI/1.76.0-gompi-2021a.lua
libsodium/1.0.18-GCCcore-10.3.0.lua
OpenPGM/5.2.122-GCCcore-10.3.0.lua
Pint/0.20.1-GCCcore-10.3.0.lua
ZeroMQ/4.3.4-GCCcore-10.3.0.lua
software under 2023.06/software/linux/aarch64/neoverse_v1/software
Boost.MPI/1.76.0-gompi-2021a
libsodium/1.0.18-GCCcore-10.3.0
OpenPGM/5.2.122-GCCcore-10.3.0
Pint/0.20.1-GCCcore-10.3.0
ZeroMQ/4.3.4-GCCcore-10.3.0
other under 2023.06/software/linux/aarch64/neoverse_v1
.lmod/cache/spiderT.lua
.lmod/cache/spiderT.luac_5.1
.lmod/cache/timestamp

@casparvl
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The build that is failing is IPython:

======================================================================
FAIL: test_aimport_module_completer (IPython.core.tests.test_completer.TestCompleter)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cvmfs/pilot.eessi-hpc.org/versions/2023.06/software/linux/aarch64/neoverse_v1/software/IPython/7.25.0-GCCcore-10.3.0/lib/python3.9/site-packages/IPython/core/tests/test_completer.py"
, line 1057, in test_aimport_module_completer
    nt.assert_in("io", matches)
AssertionError: 'io' not found in []
-------------------- >> begin captured stdout << ---------------------

Caching the list of root modules, please wait!
(This will only be done once - type '%rehashx' to reset cache!)

This is taking too long, we give up.


--------------------- >> end captured stdout << ----------------------
    """Fail immediately, with the given message."""
>>  raise self.failureException("'io' not found in []")

-------------------- >> begin captured logging << --------------------
parso.python.diff: DEBUG: diff parser start
parso.python.diff: DEBUG: line_lengths old: 1; new: 1
parso.python.diff: DEBUG: -> code[replace] old[1:1] new[1:1]
parso.python.diff: DEBUG: parse_part from 1 to 1 (to 0 in part parser)
parso.python.diff: DEBUG: diff parser end
--------------------- >> end captured logging << ---------------------

======================================================================
FAIL: test_import_module_completer (IPython.core.tests.test_completer.TestCompleter)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/cvmfs/pilot.eessi-hpc.org/versions/2023.06/software/linux/aarch64/neoverse_v1/software/IPython/7.25.0-GCCcore-10.3.0/lib/python3.9/site-packages/IPython/core/tests/test_completer.py", line 1070, in test_import_module_completer
    nt.assert_in("io", matches)
AssertionError: 'io' not found in ['id', 'if', 'import', 'in', 'input', 'int', 'ip', 'is', 'isinstance', 'issubclass', 'iter']
-------------------- >> begin captured stdout << ---------------------

Caching the list of root modules, please wait!
(This will only be done once - type '%rehashx' to reset cache!)

This is taking too long, we give up.


--------------------- >> end captured stdout << ----------------------
    """Fail immediately, with the given message."""
>>  raise self.failureException("'io' not found in ['id', 'if', 'import', 'in', 'input', 'int', 'ip', 'is', 'isinstance', 'issubclass', 'iter']")


----------------------------------------------------------------------
Ran 640 tests in 89.278s

FAILED (SKIP=12, failures=2)
______________________________________________________________________
Test suite completed for system with the following information:
IPython version: 7.25.0
IPython commit : 63a5c09ed (installation)
IPython package: /cvmfs/pilot.eessi-hpc.org/versions/2023.06/software/linux/aarch64/neoverse_v1/software/IPython/7.25.0-GCCcore-10.3.0/lib/python3.9/site-packages/IPython
Python version : 3.9.5 (default, Jun 20 2023, 22:13:36) [GCC 10.3.0]
sys.executable : /cvmfs/pilot.eessi-hpc.org/versions/2023.06/software/linux/aarch64/neoverse_v1/software/Python/3.9.5-GCCcore-10.3.0/bin/python
Platform       : Linux-4.18.0-477.27.1.el8_8.aarch64-aarch64-with-glibc2.37

Tools and libraries available at test time:
   pygments sqlite3

Tools and libraries NOT available at test time:
   matplotlib

Status: ERROR - 1 out of 7 test groups failed (core). Took 110.717s.

You may wish to rerun these, with:
  iptest core

) (at easybuild/framework/easyblock.py:3639 in _sanity_check_step)

So, it's actually IPython that is failing to build, because of a failure in the test group core, specifically the tests test_aimport_module_completer and test_import_module_completer.

I've tried the build interactively on the neoverse_v1 architecture, but there, the IPython build completes without issue...

@casparvl
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Interactively, I do error out on the ESPResSo build btw...

93% tests passed, 15 tests failed out of 201

Label Time Summary:
gpu             = 2615.38 sec*proc (56 tests)
long            = 5463.20 sec*proc (13 tests)
parallel        = 1377.92 sec*proc (45 tests)
parallel_odd    =   3.92 sec*proc (1 test)

Total Test time (real) = 4275.02 sec

The following tests FAILED:
          3 - save_checkpoint__therm_lb__p3m_cpu__lj__lb_cpu_ascii (Timeout)
          4 - test_checkpoint__therm_lb__p3m_cpu__lj__lb_cpu_ascii (Failed)
         54 - interactions_non-bonded (Timeout)
         64 - rigid_bond (Timeout)
         66 - rotational_inertia (Timeout)
         76 - constant_pH_stats (Timeout)
         79 - lb_stokes_sphere (Timeout)
         93 - virtual_sites_relative (Failed)
        101 - integrator_npt_stats (Timeout)
        111 - lb_stats (Timeout)
        116 - dpd_stats (Timeout)
        145 - random_pairs (Timeout)
        151 - thermostats_anisotropic (Timeout)
        183 - galilei (Timeout)
        190 - elc_vs_analytic (Timeout)
Errors while running CTest

But we can worry about that later (if it occurs also when the bot does it).

@casparvl
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So, I've done a bit of reading. It fails in the Autocompleter for modules. That autocompleter has to create a cache first. It seems there is a timeout on that, controlled by this line. It might be that creation of this cache is indeed slow. Could be that it simply needs to crawl through a lot of CVMFS paths, which could be slow. Could be that going through the build dir is slow - I think the bot is building in a writeable overlay, which I believe may be a bit slow (also to read?).

We could try to increase that TIMEOUT. Or skip the test. Or ignore the test failures...

The only thing I can't really explain is why we haven't seen it with other IPython's. But... details...

@bedroge
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bedroge commented Oct 26, 2023

@casparvl This sounded somewhat familiar, and it seems I have run into this as well a few years ago:
#95
I also had the impression that it was caused by slow I/O (due to CVMFS and/or fuse-overlayfs?); rerunning the same installation on the same machine often solved the issue (maybe because the files were then in the CVMFS cache?).

@casparvl
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I reproduced this issue now also interactively, by running the container with:

./eessi_container --save <somepath> --access rw

and using the default EASYBUILD_INSTALLPATH set by configure_easybuild. Thus, we're installing in the writable overlay, and this reproduces the issue.

I'll adapt my docs in this pr so that building in the writeable overlay is explained (instead of in /tmp what we suggest now). It might be slower, but a more exact replica of what the bot does. Since the goal is to reproduce build failures, we should stick to that as close as possible.

@boegel boegel changed the base branch from 2023.06 to pilot.eessi-hpc.org-2023.06 November 21, 2023 21:18
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casparvl commented Feb 9, 2024

I'm going to close this. We have ESPResSo now in the software.eessi.io, added here. It's probably not worth it to still try to push this to the pilot repository.

@casparvl casparvl closed this Feb 9, 2024
TopRichard pushed a commit to TopRichard/bot-software-layer1 that referenced this pull request Jun 3, 2024
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4 participants