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{2023.06}[foss/2021a] RStudio-Server V1.4.1717-Java-11-R V4.1.0 #299

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{2023.06}[foss/2021a] RStudio-Server V1.4.1717-Java-11-R V4.1.0 #299

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b4b5611
{2023.06}[foss/2021a] RStudio-Server V1.4.1717-Java-11-R V4.1.0
Jul 6, 2023
374e772
added reference to java easyblock 2557
Jul 6, 2023
0389a21
Merge branch '2023.06' of https://github.com/EESSI/software-layer int…
Jul 10, 2023
3ecc814
Merge branch '2023.06' of https://github.com/EESSI/software-layer int…
Jul 12, 2023
56d95b9
added the Xvfb parse_hook
Jul 12, 2023
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10 changes: 10 additions & 0 deletions eb_hooks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -199,6 +199,15 @@ def parse_hook_ucx_eprefix(ec, eprefix):
raise EasyBuildError("UCX-specific hook triggered for non-UCX easyconfig?!")


def parse_hook_xvfb_cp_permissions(ec, eprefix):
"""Add user write permission to xvfb-run before copying it in the postinstallcmds."""
if ec.name == 'Xvfb':
ec['postinstallcmds'] = ["chmod u+wx xvfb-run && cp -a xvfb-run %(installdir)s/bin/"]
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@TopRichard Can you clarify why this is needed?

If there's a problem here, I'm not sure why we didn't see it outside of EESSI...

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@boegel Xvfb is a dependency, and so it was set to avoid a failure.

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I got that part, but I don't see why we would see this problem with Xvfb outside of EESSI.

I'm seeing it too in #328 where I'm trying to get R installed (just to break down this PR a bit), so I'll take a closer look.

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@boegel I debugged that issue some time ago, see #299 (comment) and the messages below that one. TLDR (if I remember correctly): it's a combination of our writable overlay + setting the installation dir as read-only (and xvfb-run is shipped as "patch" in the EB installation dir).

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@laraPPr laraPPr Sep 19, 2023 •
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I'm also running into the same issue with #335

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@boegel Could the issue with Xvfb be related to the version of XZ? That is the only difference I can discern in EESSI.

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It's (I believe) somehow related to the fact we now have write-only installations and the writable overlay. We should probably create an upstream PR to reverse the order of statements in the Xvfb postinstallcmds, which is what the hook update here is doing (or we just move forward with the hook update here).

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OK, I understand this a bit better now. The cp -a xvfb-run fails in our particular build environment in which we use fuse-overlayfs (but not in a regular build environment when the file is just copied from one filesystem to another) because of the read-only permissions on the EasyBuild installation (where xvfb-run comes from).

I strongly prefer fixing this centrally in EasyBuild, so I've opened a pull request for it: easybuilders/easybuild-easyconfigs#18834

I'm also fixing the chmod u+x, which should actually be chmod a+x, so exec permissions on xvfb-run in the installation directory are set for all users, not just for the account used to perform the installation.

print_msg("Using custom postinstallcmds for %s: %s", ec.name, ec['postinstallcmds'])
else:
raise EasyBuildError("Xvfb-specific hook triggered for non-Xvfb easyconfig?!")


def pre_configure_hook(self, *args, **kwargs):
"""Main pre-configure hook: trigger custom functions based on software name."""
if self.name in PRE_CONFIGURE_HOOKS:
Expand Down Expand Up @@ -265,6 +274,7 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs):
'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
'Qt5': parse_hook_qt5_check_qtwebengine_disable,
'UCX': parse_hook_ucx_eprefix,
'Xvfb': parse_hook_xvfb_cp_permissions,
}

POST_PREPARE_HOOKS = {
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3 changes: 3 additions & 0 deletions eessi-2023.06-eb-4.7.2-2021a.yml
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Expand Up @@ -13,3 +13,6 @@ easyconfigs:
# see https://github.com/easybuilders/easybuild-easyconfigs/pull/18087
options:
from-pr: 18087
- RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb:
options:
include-easyblocks-from-pr: 2557