{phys}[intel/2019b] BLOCK v1.5.3 w/ Python 2.7.16 #16642

nicholascheng94 · 2022-11-15T04:21:17Z

(created using eb --new-pr)

nicholascheng94 · 2022-11-15T04:40:03Z

Test report by @nicholascheng94
SUCCESS
Build succeeded for 1 out of 1 (2 easyconfigs in total)
sms - Linux CentOS Linux 7.6.1810, x86_64, AMD EPYC 7601 32-Core Processor, Python 2.7.5
See https://gist.github.com/fc4977d7ba1a4b545656917138e8c564 for a full test report.

boegelbot · 2022-11-15T15:25:31Z

@nicholascheng94: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/3467443012
Output from first failing test suite run:

FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 873, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>20(1[89]|[2-9][0-9])[ab]).*\.eb$' easyconfigs:

found 2 variants of 'Boost' dependency in easyconfigs using '2019b' toolchain generation
* version: 1.55.0; versionsuffix: -Python-2.7.16 as dep for set(['BLOCK-1.5.3-intel-2019b-Python-2.7.16.eb'])
* version: 1.71.0; versionsuffix:  as dep for set(['Boost.Python-1.71.0-gompi-2019b.eb', 'RheoTool-5.0-foss-2019b.eb', 'TopHat-2.1.2-iimpi-2019b.eb', 'Portcullis-1.2.2-foss-2019b-Python-3.7.4.eb', 'PETSc-3.12.4-intel-2019b-Python-2.7.16.eb', 'BLAST+-2.9.0-gompi-2019b.eb', 'Siesta-4.1-MaX-1.0-intel-2019b.eb', 'PyCUDA-2019.1.2-intelcuda-2019b-Python-3.7.4.eb', 'OpenFOAM-v1912-intel-2019b.eb', 'BUSCO-4.0.5-foss-2019b-Python-3.7.4.eb', 'CGAL-4.14.1-foss-2019b-Python-3.7.4.eb', 'SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb', 'FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb', 'ABySS-2.1.5-foss-2019b.eb', 'Trinity-2.9.1-foss-2019b-Python-3.7.4.eb', 'STEAK-2019.09.12-foss-2019b-Python-2.7.16.eb', 'decona-0.1.2-foss-2019b-Python-3.7.4.eb', 'SLEPc-3.12.2-foss-2019b-Python-3.7.4.eb', 'CGAL-4.14.1-intel-2019b-Python-3.7.4.eb', 'Alpha-20200430-foss-2019b-Python-2.7.16.eb', 'prokka-1.14.5-gompi-2019b.eb', 'RMBlast-2.10.0-gompi-2019b.eb', 'MITObim-1.9.1-gompi-2019b.eb', 'ELSI-2.5.0-intel-2019b.eb', 'RStudio-Server-1.2.5042-foss-2019b-Java-11.eb', 'petsc4py-3.12.0-foss-2019b-Python-3.7.4.eb', 'Kent_tools-401-gompi-2019b.eb', 'SHAPEIT4-4.2.0-foss-2019b.eb', 'PyFR-1.9.0-intelcuda-2019b-Python-3.7.4.eb', 'RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb', 'CoordgenLibs-3.0.1-gompi-2019b.eb', 'FreeFEM-4.5-foss-2019b-Python-3.7.4.eb', 'Boost.Python-1.71.0-iimpi-2019b.eb', 'ABRicate-0.9.9-gompi-2019b.eb', 'PETSc-3.12.4-intel-2019b-Python-3.7.4.eb', 'FLAIR-1.5.1-20200630-foss-2019b-Python-3.7.4.eb', 'MIRA-4.0.2-gompi-2019b.eb', 'BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb', 'AUGUSTUS-3.3.3-foss-2019b.eb', 'FuSeq-1.1.2-gompi-2019b.eb', 'metaerg-1.2.3-intel-2019b-Python-2.7.16.eb', 'polymake-4.0r1-foss-2019b.eb', 'OpenFOAM-7-foss-2019b-20200508.eb', 'OrthoFinder-2.3.8-foss-2019b-Python-2.7.16.eb', 'OpenFOAM-v1912-foss-2019b.eb', 'FSL-6.0.4-foss-2019b-Python-3.7.4.eb', 'BLAST+-2.9.0-iimpi-2019b.eb', 'DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb', 'Kraken2-2.0.8-beta-gompi-2019b-Perl-5.30.0.eb', 'Armadillo-9.900.1-foss-2019b.eb', 'libosmium-2.15.6-foss-2019b-Python-3.7.4.eb', 'Salmon-1.1.0-gompi-2019b.eb', 'PSI4-1.3.2-intel-2019b-Python-3.7.4.eb', 'pIRS-2.0.2-gompi-2019b.eb', 'OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb', 'maeparser-1.3.0-gompi-2019b.eb', 'OpenFOAM-7-foss-2019b.eb', 'Cufflinks-2.2.1-gompi-2019b.eb', 'Blender-2.81-intel-2019b-Python-3.7.4.eb', 'OrthoFinder-2.3.11-intel-2019b-Python-3.7.4.eb', 'manta-1.6.0-gompi-2019b-Python-2.7.16.eb', 'PyCUDA-2019.1.2-fosscuda-2019b-Python-3.7.4.eb', 'MariaDB-10.4.13-gompi-2019b.eb', 'OpenFOAM-2.3.1-intel-2019b.eb', 'FLAIR-1.5-foss-2019b-Python-3.7.4.eb', 'Amber-18-fosscuda-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16.eb', 'Salmon-1.0.0-gompi-2019b.eb', 'PETSc-3.12.4-foss-2019b-Python-3.7.4.eb', 'Arrow-0.16.0-intel-2019b-Python-3.7.4.eb', 'variant_tools-3.1.3-foss-2019b-Python-3.7.4.eb', 'RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb', 'OpenImageIO-2.0.12-iimpi-2019b.eb', 'MOABS-1.3.9.6-gompi-2019b.eb', 'BLAST+-2.11.0-gompi-2019b.eb', 'RMBlast-2.9.0-gompi-2019b.eb', 'TopHat-2.1.2-gompi-2019b.eb', 'LiBis-20200428-foss-2019b-Python-3.7.4.eb', 'RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb', 'FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb', 'gmsh-4.5.6-intel-2019b-Python-2.7.16.eb', 'Boost.Python-1.71.0-iimpic-2019b.eb', 'antiSMASH-5.1.2-foss-2019b-Python-3.7.4.eb', 'libzeep-5.0.1-gompi-2019b.eb', 'Trinity-2.10.0-foss-2019b-Python-3.7.4.eb', 'gmsh-4.5.6-foss-2019b-Python-3.7.4.eb', 'pyABC-0.10.4-foss-2019b-Python-3.7.4.eb', 'OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb', 'AUGUSTUS-3.3.3-intel-2019b.eb', 'PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb', 'Sailfish-0.10.1-gompi-2019b.eb', 'hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb', 'STAR-Fusion-1.8.1-foss-2019b-Python-3.7.4.eb', 'OpenFOAM-6-foss-2019b.eb', 'Amber-18-foss-2019b-AmberTools-19-patchlevel-12-17-Python-2.7.16.eb', 'Boost.Python-1.71.0-gompic-2019b.eb', 'FEniCS-2019.1.0-foss-2019b-Python-3.7.4.eb', 'Trinity-2.9.1-foss-2019b-Python-2.7.16.eb', 'OpenFOAM-v1906-foss-2019b.eb', 'slepc4py-3.12.0-foss-2019b-Python-3.7.4.eb', 'scikit-cuda-0.5.3-fosscuda-2019b-Python-3.7.4.eb', 'Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb', 'SLEPc-3.12.2-intel-2019b-Python-3.7.4.eb', 'OpenImageIO-2.0.12-gompi-2019b.eb', 'Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb', 'SHAPEIT4-4.1.3-foss-2019b.eb', 'Arrow-0.16.0-foss-2019b-Python-3.7.4.eb', 'SLEPc-3.12.2-intel-2019b-Python-2.7.16.eb', 'Blender-2.81-foss-2019b-Python-3.7.4.eb'])


======================================================================
FAIL: test_pr_patch_descr (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1199, in test_pr_patch_descr
    self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches))
AssertionError: No description found in patches: easybuild/easyconfigs/b/BLOCK/BLOCK-1.5.3.patch

======================================================================
FAIL: test_pr_sha256_checksums (test.easyconfigs.easyconfigs.EasyConfigTest)
Make sure changed easyconfigs have SHA256 checksums in place.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 953, in test_pr_sha256_checksums
    self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues))
AssertionError: No checksum issues:
Checksums missing for one or more sources/patches in BLOCK-1.5.3-intel-2019b-Python-2.7.16.eb: found 1 sources + 1 patches vs 0 checksums
Checksums missing for one or more sources/patches in Boost-1.55.0-intel-2019b-Python-2.7.16.eb: found 1 sources + 0 patches vs 0 checksums

======================================================================
FAIL: test_style_conformance (test.easyconfigs.styletests.StyleTest)
Check the easyconfigs for style
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/styletests.py", line 68, in test_style_conformance
    self.assertEqual(result, 0, error_msg)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/base/testing.py", line 116, in assertEqual
    raise AssertionError("%s:\nDIFF%s:\n%s" % (msg, limit, ''.join(diff[:self.ASSERT_MAX_DIFF])))
AssertionError: There shouldn't be any code style errors (and/or warnings), found 2:
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/b/BLOCK/BLOCK-1.5.3-intel-2019b-Python-2.7.16.eb:32:21: W292 no newline at end of file
/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/easybuild/easyconfigs/b/Boost/Boost-1.55.0-intel-2019b-Python-2.7.16.eb:23:22: W292 no newline at end of file

: 2 != 0:
DIFF:
- 2

----------------------------------------------------------------------
Ran 15712 tests in 828.741s

FAILED (failures=4)
ERROR: Not all tests were successful

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Please talk to my owner @boegel if you notice you me acting stupid),
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lexming · 2022-11-18T01:15:12Z

easybuild/easyconfigs/b/BLOCK/BLOCK-1.5.3-intel-2019b-Python-2.7.16.eb

+
+dependencies = [
+    ('Python', '2.7.16'),
+    ('Boost', '1.55.0', versionsuffix),


Our repository of easyconfigs restricts the versions allow for each dependency to one per toolchain. This is necessary to keep the size of our repository in check.

In this case, this means that all easyconfigs in intel/2019b depending on Boost can only depend on v1.71.0 of Boost. Please update this dependency accordingly.

Suggested change

('Boost', '1.55.0', versionsuffix),

('Boost', '1.71.0', versionsuffix),

lexming · 2022-11-18T01:16:18Z

easybuild/easyconfigs/b/BLOCK/BLOCK-1.5.3.patch

@@ -0,0 +1,94 @@
+--- input.h.orig	2020-05-13 14:26:17.364524313 +0800


Please add a header to the patch file describing its purpose and author.

lexming · 2022-11-18T01:17:08Z

easybuild/easyconfigs/b/BLOCK/BLOCK-1.5.3-intel-2019b-Python-2.7.16.eb

+toolchainopts = {'cstd': 'c++11'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://www.sunqm.net/pyscf/files/src/']


It is necessary to add the checksums of all sources and files. You can do so with the command eb --inject-checksums

lexming

@nicholascheng94 I've been also working on Block v1.5.3 as well, but in a more recent toolchain. See #16711.

I made a PR to your fork with my suggested changes. Please check nicholascheng94#1 and, if you agree with the changes, merge it to automatically update this PR.

This is the list changes compared to your easyconfig:

use sources from new repo in https://github.com/pyscf/Block
add missing checksums (with eb --inject-checksums)
use Python only as builddependency (it is not needed to execute block.spin_adapted)
use version of Boost provided in this toolchain (see {phys}[intel/2019b] BLOCK v1.5.3 w/ Python 2.7.16 #16642 (comment))
build both the MPI and serial versions of Boost
add sanity check commands

rename BLOCK to Block and update with latest sources for v1.5.3

boegelbot · 2023-05-10T07:26:01Z

@nicholascheng94: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/4934117301
Output from first failing test suite run:

FAIL: test__parse_easyconfig_Block-1.5.3-intel-2019b.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for easyconfig Block-1.5.3-intel-2019b.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1544, in innertest
    template_easyconfig_test(self, spec_path)
  File "test/easyconfigs/easyconfigs.py", line 1402, in template_easyconfig_test
    self.assertTrue(res, error_msg)
AssertionError: Invalid checksum for patch file Block-1.5.3_use-eb-environment.patch in Block-1.5.3-intel-2019b.eb: {'Block-1.5.3_use-eb-environment.patch': '7c954ac4b12fe99c51290a4c19788dc175a109339fe821a90394af34bc974a76'}

======================================================================
FAIL: test_pr_patch_descr (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1232, in test_pr_patch_descr
    self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches))
AssertionError: No description found in patches: easybuild/easyconfigs/b/Block/BLOCK-1.5.3.patch

----------------------------------------------------------------------
Ran 16993 tests in 645.459s

FAILED (failures=2)
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 me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

nicholascheng94 · 2023-05-10T07:29:10Z

Thanks @lexming ! So sorry for the delay... was not working on using this software anymore so had not the time to get back on this.

boegel · 2024-01-13T17:53:55Z

Closing this since intel/2019b is no longer supported, see https://docs.easybuild.io/policies/toolchains

We have an easyconfig for Block with a more recent toolchain, see #19493

nicholascheng94 added 2 commits November 15, 2022 12:21

adding easyconfigs: BLOCK-1.5.3-intel-2019b-Python-2.7.16.eb

3b9d719

add patch file

05bb765

lexming requested changes Nov 18, 2022

View reviewed changes

rename BLOCK to Block and update with latest sources for v1.5.3

dbab014

lexming mentioned this pull request Nov 23, 2022

rename BLOCK to Block and update with latest sources for v1.5.3 nicholascheng94/easybuild-easyconfigs#1

Merged

lexming reviewed Nov 23, 2022

View reviewed changes

boegel added the new label Dec 13, 2022

boegel added this to the 4.x milestone Dec 13, 2022

Merge pull request #1 from lexming/block-2019b

e385514

rename BLOCK to Block and update with latest sources for v1.5.3

boegel closed this Jan 13, 2024

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{phys}[intel/2019b] BLOCK v1.5.3 w/ Python 2.7.16 #16642

{phys}[intel/2019b] BLOCK v1.5.3 w/ Python 2.7.16 #16642

nicholascheng94 commented Nov 15, 2022

nicholascheng94 commented Nov 15, 2022

boegelbot commented Nov 15, 2022

lexming Nov 18, 2022

lexming Nov 18, 2022

lexming Nov 18, 2022

lexming left a comment

boegelbot commented May 10, 2023

nicholascheng94 commented May 10, 2023

boegel commented Jan 13, 2024

	('Boost', '1.55.0', versionsuffix),
	('Boost', '1.71.0', versionsuffix),

		@@ -0,0 +1,94 @@
		--- input.h.orig 2020-05-13 14:26:17.364524313 +0800

{phys}[intel/2019b] BLOCK v1.5.3 w/ Python 2.7.16 #16642

{phys}[intel/2019b] BLOCK v1.5.3 w/ Python 2.7.16 #16642

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nicholascheng94 commented Nov 15, 2022

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boegelbot commented May 10, 2023

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boegel commented Jan 13, 2024