Bugfix: Slepc stand alone test by RikkiButler20 · Pull Request #28593 · spack/spack

RikkiButler20 · 2022-01-25T19:21:57Z

Fixes 27983

The test fails due to an undefined reference in the example file.

RikkiButler20 · 2022-01-25T22:39:01Z

@vsoch Can you try running the slepc test with these changes?

vsoch · 2022-01-25T23:07:14Z

Yeah it will be a bit - need to install again.

vsoch

Sorry for the delay! Here are the updated results:

$ bin/spack test results -l -- slepc
==> Results for test suite '4gcvbws2pgx7po4fyiifp4anj6x242do', spec matching 'slepc':
==>   slepc-3.16.1-grefsgc PASSED
==> Testing package slepc-3.16.1-grefsgc
==> [2022-01-26-17:29:46.086647] test: compile hello example
==> [2022-01-26-17:29:46.086841] '/tmp/spack/lib/spack/env/gcc/gcc' '-I/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/slepc-3.16.1-grefsgch7dxpgm6qpq67b57j7bstmu6e/include' '-L/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/slepc-3.16.1-grefsgch7dxpgm6qpq67b57j7bstmu6e/lib' '-L/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/petsc-3.16.3-nrvqhfypucpihegzafnzrry7yp2zrcs7/lib' '-L/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/openmpi-4.1.2-pltxvyjtqoqayz22kln2ndul42hyi5c3/lib' '/home/vanessa/.spack/test/4gcvbws2pgx7po4fyiifp4anj6x242do/slepc-3.16.1-grefsgc/data/slepc/hello.c' '-o' 'hello' '-lslepc' '-lpetsc' '-lmpi'
PASSED
==> [2022-01-26-17:29:46.266905] test: run hello example
==> [2022-01-26-17:29:46.267276] './hello'
Hello world
PASSED

var/spack/repos/builtin/packages/slepc/package.py

RikkiButler20 · 2022-02-04T19:00:49Z

@spackbot run pipeline

spackbot-app · 2022-02-04T19:00:52Z

I've started that pipeline for you!

vsoch

I saw results before, and I'm not anymore I think.

==>   slepc-3.16.1-grefsgc PASSED
==> Testing package slepc-3.16.1-grefsgc
==> [2022-02-07-10:20:57.860398] Warning: Skipping slepc test: failed to find test1.c

RikkiButler20 · 2022-02-07T21:21:03Z

@vsoch Did you re-install slepc?

vsoch · 2022-02-07T22:06:48Z

No - I didn't know I needed to do that. Will try again after that.

vsoch

$ bin/spack test results -l -- slepc
==> Results for test suite '25bdyqjyjmxjfl6cex33eftlnnp5uba7', spec matching 'slepc':
==>   slepc-3.16.2-d2cvd32 PASSED
==> Testing package slepc-3.16.2-d2cvd32
==> [2022-02-07-15:42:26.991939] Installing /tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/slepc-3.16.2-d2cvd32q46ai5azr3fp7m5avxl32srdx/.spack/test to /home/vanessa/.spack/test/25bdyqjyjmxjfl6cex33eftlnnp5uba7/slepc-3.16.2-d2cvd32/cache/slepc
==> [2022-02-07-15:42:27.015149] test: compile test1 example
==> [2022-02-07-15:42:27.015358] '/tmp/spack/lib/spack/env/gcc/gcc' '-I/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/slepc-3.16.2-d2cvd32q46ai5azr3fp7m5avxl32srdx/include' '-L/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/slepc-3.16.2-d2cvd32q46ai5azr3fp7m5avxl32srdx/lib' '-L/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/petsc-3.16.4-tuhalwfgo4mi3d6acbukidnytrhbk3vk/lib' '-L/tmp/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/openmpi-4.1.2-pltxvyjtqoqayz22kln2ndul42hyi5c3/lib' '/home/vanessa/.spack/test/25bdyqjyjmxjfl6cex33eftlnnp5uba7/slepc-3.16.2-d2cvd32/cache/slepc/src/eps/tests/test1.c' '-o' 'test1' '-lslepc' '-lpetsc' '-lmpi' '-lm'
PASSED
==> [2022-02-07-15:42:27.237853] test: run test1 example
==> [2022-02-07-15:42:27.238229] './test1'

Generalized Symmetric Eigenproblem, N=2025 (45x45 grid)

 All requested eigenvalues computed up to the required tolerance:
     29.73524

PASSED

Remove unneeded file

var/spack/repos/builtin/packages/slepc/package.py

tldahlgren · 2022-02-12T00:26:51Z

var/spack/repos/builtin/packages/slepc/package.py

        self.run_test(exe=cc_exe,
                      options=['-I{0}'.format(self.prefix.include),
-                               '-L', self.prefix.lib, '-l', 'slepc',
-                               '-L', self.spec['petsc'].prefix.lib, '-l', 'petsc',
-                               '-L', self.spec['mpi'].prefix.lib, '-l', 'mpi',
-                               '-o', exe, join_path(test_dir, 'hello.c')],
+                               '-L{0}'.format(self.prefix.lib),
+                               '-L{0}'.format(self.spec['petsc'].prefix.lib),
+                               '-L{0}'.format(self.spec['mpi'].prefix.lib),
+                               join_path(test_dir, 'test1.c'), '-o', exe,
+                               '-lslepc', '-lpetsc', '-lmpi', '-lm'],
                      purpose='test: compile {0} example'.format(exe),
                      work_dir=test_dir)


Is this needed anymore? I would think the make you introduced at line 175 already takes care of this.

Without it, I get this error: ./test1: error while loading shared libraries: libparpack.so.2: cannot open shared object file

@balay I am unable to build the example using the makefile. I get the error that I posted above.

var/spack/repos/builtin/packages/slepc/package.py

joseeroman · 2022-02-17T18:54:56Z

I have been having a look at this. I think the problem is due to how SLEPc's configure is invoked from spack. In particular, the line

                    '--with-arpack-lib=%s' % spec['arpack-ng'].libs.joined()

There are two issues:

First, the option --with-arpack-libshould be a comma-separated list. It seems that spack is not adding the commas.
Second, rather than a list of libraries, it should be a list of flags such as -Wl,-rpath,/path/to/arpack,-lparpack,-larpack. But then commas are used for two different purposes.

SLEPc's configure checks that a program is correctly linked, but does not run it, that is why it fails later when trying to run an example.

This problem does not appear when using --with-arpack-dir, so I guess the change #28654 is worse than before.

Any comments? @balay Should I change SLEPc's configure to accept a list separated with spaces instead of commas?

alalazo · 2023-02-20T16:49:38Z

What is the status of this PR?

joseeroman · 2023-02-20T17:05:01Z

What is the status of this PR?

I changed upstream SLEPc. Since version 3.18 the configure script accepts a quoted string for --with-arpack-lib instead of comma-separated list. I don't know if that change has fixed the issue with the standalone test.

tldahlgren · 2024-10-29T01:14:43Z

Closing this PR since the stand-alone test API used here was deprecated and the package is now successfully using the new API (for this test).

RikkiButler20 added update-package e4s bugfix Something wasn't working, here's a fix stand-alone-tests Stand-alone (or smoke) tests for installed packages labels Jan 25, 2022

RikkiButler20 self-assigned this Jan 25, 2022

spackbot-app bot added the commands label Jan 25, 2022

spackbot-app bot requested review from balay and joseeroman January 25, 2022 19:22

Change the order of the options

95ae6d0

RikkiButler20 force-pushed the bugfix/slepc-stand-alone branch from bf5768f to 95ae6d0 Compare January 25, 2022 19:23

RikkiButler20 removed the commands label Jan 25, 2022

RikkiButler20 removed request for balay and joseeroman January 25, 2022 19:23

RikkiButler20 marked this pull request as draft January 25, 2022 19:23

Fix style error

2503a79

RikkiButler20 requested a review from vsoch January 26, 2022 23:31

vsoch reviewed Jan 27, 2022

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RikkiButler20 marked this pull request as ready for review January 27, 2022 22:02

RikkiButler20 and others added 5 commits January 27, 2022 17:07

Use tty.warn

835202f

Copy & run test from src/eps/tests

ed91d0f

Merge branch 'develop' into bugfix/slepc-stand-alone

422e073

Fix style errors

d13123a

Run the example

4363292

RikkiButler20 requested a review from vsoch February 7, 2022 17:19

vsoch reviewed Feb 7, 2022

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RikkiButler20 requested review from balay and tldahlgren February 7, 2022 23:13

Use the makefile

08a4814

Remove unneeded file

tldahlgren reviewed Feb 12, 2022

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tldahlgren requested changes Feb 12, 2022

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RikkiButler20 added 3 commits February 14, 2022 09:15

Move if file exists check

2f7834e

Check each step of running the example

a0091ee

Fix style errors

1ebc2e6

tldahlgren closed this Oct 29, 2024

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