{cae}[foss/2022a] Nektar++ v5.2.0 WIB #16953

sassy-crick · 2022-12-20T12:24:01Z

(created using eb --new-pr)

Requires:

PR {lib}[GCCcore/11.2.0,GCCcore/11.3.0] TinyXML v2.6.2 #16992

…+-5.2.0-cmake-flexiblas.patch

sassy-crick · 2022-12-20T15:14:24Z

I have enabled the ctestbut 15 out of the 603 tests are failing with segfaults. This could be my test machine (Tiger CPU) or something else. It might be a good idea to see if that is a problem at other sites too.
Failing tests:

        143 - ADRSolver_Advection3D_m8_DG_hex_nodal (Failed)
        144 - ADRSolver_Advection3D_m12_DG_hex_periodic (Failed)
        145 - ADRSolver_Advection3D_m8_DG_hex (Failed)
        146 - ADRSolver_Advection3D_m8_DG_hex_MF (Failed)
        147 - ADRSolver_Advection3D_m10_DG_hex_VarP (Failed)
        150 - ADRSolver_Advection3D_m12_DG_tet (Failed)
        210 - ADRSolver_Helmholtz3D_Cube_BndFile_Lagrange (Failed)
        223 - ADRSolver_SVV_Prism (Failed)
        313 - IncNavierStokesSolver_Hex_channel_varP (Failed)
        316 - IncNavierStokesSolver_Hex_channel_m6_nodalRestart (Failed)
        345 - IncNavierStokesSolver_Tet_Kovasnay_SVV_DGKer (Failed)
        354 - IncNavierStokesSolver_Tet_channel_varP (Failed)
        371 - IncNavierStokesSolver_Pyr_channel_SVV (Failed)
        512 - StdRegions_StdProject_Diff3D_Hex_Lagrange_P6_Q7 (Failed)
        570 - MultiRegions_Helmholtz2D_CG_P7_Modes_curved_quad (Failed)

added: On Intel Ivy-Bridge I get these failing tests:

        311 - IncNavierStokesSolver_Couette_3DH2D_MVM (Failed)
        321 - IncNavierStokesSolver_SM (Failed)
        322 - IncNavierStokesSolver_SM_base_file (Failed)
        323 - IncNavierStokesSolver_SM_Adj (Failed)
        324 - IncNavierStokesSolver_SM_Adj_base_file (Failed)
        376 - PulseWaveSolver_Junction (Failed)

smoors · 2022-12-21T13:30:36Z

@boegelbot: please test @ generoso

boegelbot · 2022-12-21T13:35:09Z

@smoors: Request for testing this PR well received on login1

PR test command 'EB_PR=16953 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16953 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9869

Test results coming soon (I hope)...

- notification for comment with ID 1361315644 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2022-12-21T13:36:05Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cns2 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/cf1e1e05fb0cd3a2730c7ec30fa93ec6 for a full test report.

smoors · 2022-12-21T13:54:31Z

@sassy-crick why not install the tinyxml dep as a module?

sassy-crick · 2022-12-23T10:43:51Z

@sassy-crick why not install the tinyxml dep as a module?

Thanks to Jasper that is done now and I have added this to the EasyConfig file.

smoors · 2022-12-23T11:42:45Z

@boegelbot: please test @ generoso

boegelbot · 2022-12-23T11:45:11Z

@smoors: Request for testing this PR well received on login1

PR test command 'EB_PR=16953 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_16953 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 9886

Test results coming soon (I hope)...

- notification for comment with ID 1363882959 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2022-12-23T11:46:10Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/0e4983fb57d5998c8d2aac7300397d6d for a full test report.

smoors · 2022-12-23T12:42:55Z

it looks like it needs the static lib, whereas tinyxml is currently installed as shared lib only:

/base/exceptions.py:124 in init): cmd " ninja -j 4 " exited with exit code 1 and output:
ninja: error: 'ThirdParty/dist/lib/libtinyxml.a', needed by 'library/LibUtilities/libLibUtilities.so.5.2.0', missing and no known rule to make it

sassy-crick · 2022-12-23T14:07:52Z

it looks like it needs the static lib, whereas tinyxml is currently installed as shared lib only:

/base/exceptions.py:124 in init): cmd " ninja -j 4 " exited with exit code 1 and output:
ninja: error: 'ThirdParty/dist/lib/libtinyxml.a', needed by 'library/LibUtilities/libLibUtilities.so.5.2.0', missing and no known rule to make it

This is odd as I tested it on a machine which does not have TinyXML installed and the log file reads:

-- Found TinyXML: /rds/general/user/jsassman/home/apps/software/TinyXML/2.6.2-GCCcore-11.3.0/lib/libtinyxml.so

Also, just to be sure I checked again:

[cx1-106-9-3 nektar]$ rpm -qa | grep -i tinyxml
[cx1-106-9-3 nektar]$

As that worked I have updated the file.

Also, for the previous build where I used the OS version, I got:

-- Found TinyXML: /usr/lib/x86_64-linux-gnu/libtinyxml.so

Any idea why it works for me and not for you? Is that a Debian thing? I am a bit puzzled to be honest.

So for me it looks like the dynamic library should work as well.

terjekv · 2023-01-27T08:22:23Z

Test report by @terjekv
FAILED
Build succeeded for 11 out of 12 (1 easyconfigs in total)
ninhursaga.uio.no - Linux RHEL 9.1 (Plow), x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz, 1 x NVIDIA Tesla T4, 525.60.13, Python 3.9.14
See https://gist.github.com/8630d5731624c1c39865cb61b227f92a for a full test report.

Parv621 · 2023-02-21T23:31:56Z

@sassy-crick made me aware of this merge request. Might be good to do the ctests with at least 6 CPU nodes as some of the tests are supposed to run in parallel from 2 to 6 processors. If there are still remaining failed ctests, I would be keen to see their output using --output-on-failure with the ctest command.

sassy-crick · 2023-03-08T18:06:43Z

@boegelbot please test @ jsc-zen2
CORE_CNT=16
EB_ARGS=“--parallel 4”

boegelbot · 2023-03-08T18:07:08Z

@sassy-crick: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=16953 EB_ARGS="“--parallel" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_16953 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2301

Test results coming soon (I hope)...

- notification for comment with ID 1460618718 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

sassy-crick · 2023-03-10T16:55:08Z

@boegelbot please test @ jsc-zen2
CORE_CNT=16
EB_ARGS="--parallel 4"

boegelbot · 2023-03-10T16:57:09Z

@sassy-crick: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=16953 EB_ARGS="--parallel 4" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_16953 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2321

Test results coming soon (I hope)...

- notification for comment with ID 1464092475 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-03-10T17:53:56Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen2g1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/ce0d5fe3662b926b6b9660332e733be1 for a full test report.

Parv621 · 2023-03-16T19:53:22Z

easybuild/easyconfigs/n/Nektar++/Nektar++-5.2.0-foss-2022a.eb

+configopts += '-DCMAKE_C_FLAGS="-DH5_USE_110_API" -DCMAKE_CXX_FLAGS="-DH5_USE_110_API" '
+# Default options, required for a basic build:
+configopts += '-DNEKTAR_USE_HDF5=ON -DNEKTAR_USE_FFTW=ON -DNEKTAR_USE_MPI=ON '
+configopts += '-DTHIRDPARTY_BUILD_GSMPI=ON -DNEKTAR_USE_CCM=ON '


Please add -DNEKTAR_USE_VTK=ON to this

Yazan-Essam · 2023-04-18T02:49:17Z

Ya

Yazan-Essam · 2023-04-18T02:54:02Z

(created using eb --new-pr)

Requires:

PR {lib}[GCCcore/11.2.0,GCCcore/11.3.0] TinyXML v2.6.2 #16992

sassy added 2 commits December 20, 2022 12:23

adding easyconfigs: Nektar++-5.2.0-foss-2022a.eb and patches: Nektar+…

c290b7a

…+-5.2.0-cmake-flexiblas.patch

VTK changed to 9.2.2

08cec01

sassy-crick changed the title ~~{cae}[foss/2022a] Nektar++ v5.2.0~~ {cae}[foss/2022a] Nektar++ v5.2.0 WIB Dec 20, 2022

ctests enabled

b946cab

smoors added the update label Dec 21, 2022

TinyXML added

09a6a4b

Tests changed as suggested by Parv621

5ddc016

Config-flags changed which should ensure all tests are working

62c6759

Parv621 reviewed Mar 16, 2023

View reviewed changes

Yazan-Essam mentioned this pull request Apr 18, 2023

(created using eb --new-pr) Yazan-Essam/Yazan-Rammaha#1

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Yazan-Essam mentioned this pull request Aug 31, 2023

(created using eb --new-pr) #18694

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{cae}[foss/2022a] Nektar++ v5.2.0 WIB #16953

{cae}[foss/2022a] Nektar++ v5.2.0 WIB #16953

sassy-crick commented Dec 20, 2022 •

edited

sassy-crick commented Dec 20, 2022 •

edited

smoors commented Dec 21, 2022

boegelbot commented Dec 21, 2022

boegelbot commented Dec 21, 2022

smoors commented Dec 21, 2022

sassy-crick commented Dec 23, 2022

smoors commented Dec 23, 2022

boegelbot commented Dec 23, 2022

boegelbot commented Dec 23, 2022

smoors commented Dec 23, 2022

sassy-crick commented Dec 23, 2022

terjekv commented Jan 27, 2023

Parv621 commented Feb 21, 2023

sassy-crick commented Mar 8, 2023

boegelbot commented Mar 8, 2023

sassy-crick commented Mar 10, 2023

boegelbot commented Mar 10, 2023

boegelbot commented Mar 10, 2023

Parv621 Mar 16, 2023

Yazan-Essam commented Apr 18, 2023

Yazan-Essam commented Apr 18, 2023

{cae}[foss/2022a] Nektar++ v5.2.0 WIB #16953

Are you sure you want to change the base?

{cae}[foss/2022a] Nektar++ v5.2.0 WIB #16953

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sassy-crick commented Dec 20, 2022 • edited

sassy-crick commented Dec 20, 2022 • edited

smoors commented Dec 21, 2022

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sassy-crick commented Dec 20, 2022 •

edited

sassy-crick commented Dec 20, 2022 •

edited