{2025.06-001}[2025b] netCDF 4.9.3 (LAMMPS dependency) by julianmorillo · Pull Request #72 · EESSI/dev.eessi.io-riscv

julianmorillo · 2026-02-27T16:42:00Z

No description provided.

julianmorillo · 2026-02-27T16:43:03Z

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-02-27T16:43:10Z

New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.02/pr_72/300277

date	job status	comment
Feb 27 16:43:08 UTC 2026	submitted	job id `300277` awaits release by job manager
Feb 27 16:44:04 UTC 2026	released	job awaits launch by Slurm scheduler
Feb 27 16:45:13 UTC 2026	running	job `300277` is running
Feb 27 17:03:17 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-300277.out` ✅ no message matching `FATAL:` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2025.06-software-linux-riscv64-generic-riscv-1772211733.tar.zst` size: 0 MiB (22 bytes) entries: 0 modules under 2025.06-001/software/linux/riscv64/generic/modules/all no module files in tarball software under 2025.06-001/software/linux/riscv64/generic/software no software packages in tarball reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod no reprod directories in tarball other under 2025.06-001/software/linux/riscv64/generic no other files in tarball
Feb 27 17:03:17 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job300277.test` does not exist in job directory, or parsing it failed.

julianmorillo · 2026-03-02T16:15:03Z

This is the error in the logs:

[ 22%] Building C object libdap2/CMakeFiles/dap2.dir/getvara.c.o
cd /tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/easybuild_obj/libdap2 && /cvmfs/dev.eessi.io/riscv/versions/2025.06-001/software/linux/riscv64/generic/software/OpenMPI/5.0.8-GCC-14.3.0/bin/mpicc --sysroot=/cvmfs/software.eessi.io/versions/2025.06/compat/linux/riscv64 -DHAVE_CONFIG_H -I/tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/easybuild_obj/include -I/tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/netcdf-c-4.9.3/include -I/tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/netcdf-c-4.9.3/oc2 -I/tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/netcdf-c-4.9.3/libsrc -I/tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/easybuild_obj -O2 -ftree-vectorize -march=rv64gc -mabi=lp64d -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIC -DCURL_STATICLIB=1 -MD -MT libdap2/CMakeFiles/dap2.dir/getvara.c.o -MF CMakeFiles/dap2.dir/getvara.c.o.d -o CMakeFiles/dap2.dir/getvara.c.o -c /tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/netcdf-c-4.9.3/libdap2/getvara.c
In file included from /tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/netcdf-c-4.9.3/libncxml/ncxml_xml2.c:6:
/cvmfs/dev.eessi.io/riscv/versions/2025.06-001/software/linux/riscv64/generic/software/libxml2/2.14.3-GCCcore-14.3.0/include/libxml2/libxml/parser.h:92:27: error: expected ‘:’, ‘,’, ‘;’, ‘}’ or ‘__attribute__’ before ‘XML_DEPRECATED_MEMBER’
   92 |     const char *directory XML_DEPRECATED_MEMBER;
      |                           ^~~~~~~~~~~~~~~~~~~~~
/cvmfs/dev.eessi.io/riscv/versions/2025.06-001/software/linux/riscv64/generic/software/libxml2/2.14.3-GCCcore-14.3.0/include/libxml2/libxml/parser.h:250:25: error: expected ‘:’, ‘,’, ‘;’, ‘}’ or ‘__attribute__’ before ‘XML_DEPRECATED_MEMBER’
  250 |     int replaceEntities XML_DEPRECATED_MEMBER;
      |                         ^~~~~~~~~~~~~~~~~~~~~
/cvmfs/dev.eessi.io/riscv/versions/2025.06-001/software/linux/riscv64/generic/software/libxml2/2.14.3-GCCcore-14.3.0/include/libxml2/libxml/parser.h:1483:42: error: unknown type name ‘xmlCharEncConvImpl’; did you mean ‘xmlCharEncoding’?
 1483 |                                          xmlCharEncConvImpl impl,
      |                                          ^~~~~~~~~~~~~~~~~~
      |                                          xmlCharEncoding
make[2]: *** [libncxml/CMakeFiles/ncxml.dir/build.make:82: libncxml/CMakeFiles/ncxml.dir/ncxml_xml2.c.o] Error 1
make[2]: Leaving directory '/tmp/eessibot/easybuild/build/netCDF/4.9.3/gompi-2025b/easybuild_obj'
make[1]: *** [CMakeFiles/Makefile2:2898: libncxml/CMakeFiles/ncxml.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

julianmorillo · 2026-03-02T17:30:59Z

libxml2 was added as an explicit dependency to netCDF here: easybuilders/easybuild-easyconfigs@3f74f3b

But it is not being considered here: https://github.com/easybuilders/easybuild-easyblocks/blob/c0b3a8983af664f7226eaa9e503840f6b8c3bbf2/easybuild/easyblocks/n/netcdf.py#L71

I think this is causing trouble because the build of netCDF is mixing two libxml2 installations (versions):

The one provided by the EESSI compat layer (2.13.8) in this case
And the one provided by EasyBuild (2.14.3)

julianmorillo · 2026-03-02T17:38:31Z

@bedroge , what do you think?

bedroge · 2026-03-03T08:07:35Z

@bedroge , what do you think?

I think your explanation makes sense. I only wondered why we hadn't seen this with software.eessi.io, but apparently we haven't installed netCDF yet for 2025a/b. Let me try that and see if I can reproduce the issue there, as it makes the debugging a bit easier.

bedroge · 2026-03-03T13:44:27Z

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-03-03T13:44:34Z

New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.03/pr_72/300382

date	job status	comment
Mar 03 13:44:32 UTC 2026	submitted	job id `300382` awaits release by job manager
Mar 03 13:45:37 UTC 2026	released	job awaits launch by Slurm scheduler
Mar 03 13:46:43 UTC 2026	running	job `300382` is running
Mar 03 14:49:51 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-300382.out` ✅ no message matching `FATAL:` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2025.06-software-linux-riscv64-generic-riscv-1772549298.tar.zst` size: 0 MiB (22 bytes) entries: 0 modules under 2025.06-001/software/linux/riscv64/generic/modules/all no module files in tarball software under 2025.06-001/software/linux/riscv64/generic/software no software packages in tarball reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod no reprod directories in tarball other under 2025.06-001/software/linux/riscv64/generic no other files in tarball
Mar 03 14:49:51 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job300382.test` does not exist in job directory, or parsing it failed.

bedroge · 2026-03-03T15:08:55Z

The build passes, but the tests are failing due to this again:

[premier-2:137003] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 1056
[premier-2:137003] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 1231
[premier-2:137003] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 1353
[premier-2:137003] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 2405
[premier-2:137003] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 2460
[premier-2:137003] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 2476
[premier-2:137003] PMIX ERROR: PMIX_ERROR in file server/pmix_server.c at line 4698
--------------------------------------------------------------------------
The gds/shmem2 component attempted to attach to a shared-memory segment at a
particular base address, but was given a different one. Your job will now likely
abort.

  Requested Address: 0x3ffd90000000
  Acquired Address:  0x3afdc1d000

If this problem persists, please consider disabling the gds/shmem2 component by
setting in your environment the following: PMIX_MCA_gds=hash
--------------------------------------------------------------------------

[premier-2:137006] PMIX ERROR: PMIX_ERR_OUT_OF_RESOURCE in file client/pmix_client.c at line 278
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and MPI will try to terminate your MPI job as well)
[premier-2:137006] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
PMIx_Init failed for the following reason:

  PMIX_ERROR

Open MPI requires access to a local PMIx server to execute. Please ensure
that either you are operating in a PMIx-enabled environment, or use "mpirun"
to execute the job.
--------------------------------------------------------------------------

That seems to happen for all build jobs on premier that do something with MPI...

julianmorillo · 2026-03-03T15:50:56Z

Admins suggested me to add:

export PMIX_MCA_gds=hash
export SLURM_MPI_TYPE="pmix"

So adding these exports into site_config.sh script.

julianmorillo · 2026-03-03T15:52:02Z

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-03-03T15:52:11Z

New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.03/pr_72/300401

date	job status	comment
Mar 03 15:52:09 UTC 2026	submitted	job id `300401` awaits release by job manager
Mar 03 15:52:53 UTC 2026	released	job awaits launch by Slurm scheduler
Mar 03 15:53:59 UTC 2026	running	job `300401` is running
Mar 03 16:57:12 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-300401.out` ✅ no message matching `FATAL:` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2025.06-software-linux-riscv64-generic-riscv-1772556914.tar.zst` size: 0 MiB (22 bytes) entries: 0 modules under 2025.06-001/software/linux/riscv64/generic/modules/all no module files in tarball software under 2025.06-001/software/linux/riscv64/generic/software no software packages in tarball reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod no reprod directories in tarball other under 2025.06-001/software/linux/riscv64/generic no other files in tarball
Mar 03 16:57:12 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job300401.test` does not exist in job directory, or parsing it failed.

julianmorillo · 2026-03-03T16:05:18Z

Tested with a simple HelloWorld testcase, and export PMIX_MCA_gds=hash solved the issue:

jmorillo@premier-2:~/mpitutorial/tutorials/mpi-hello-world/code$ export MPICC=/cvmfs/dev.eessi.io/riscv/versions/2025.06-001/software/linux/riscv64/generic/software/OpenMPI/5.0.8-GCC-14.3.0/bin/mpicc
jmorillo@premier-2:~/mpitutorial/tutorials/mpi-hello-world/code$ make
/cvmfs/dev.eessi.io/riscv/versions/2025.06-001/software/linux/riscv64/generic/software/OpenMPI/5.0.8-GCC-14.3.0/bin/mpicc -o mpi_hello_world mpi_hello_world.c
jmorillo@premier-2:~/mpitutorial/tutorials/mpi-hello-world/code$ ls
makefile  mpi_hello_world  mpi_hello_world.c
jmorillo@premier-2:~/mpitutorial/tutorials/mpi-hello-world/code$ export MPIRUN=/cvmfs/dev.eessi.io/riscv/versions/2025.06-001/software/linux/riscv64/generic/software/OpenMPI/5.0.8-GCC-14.3.0/bin/mpirun
jmorillo@premier-2:~/mpitutorial/tutorials/mpi-hello-world/code$ $MPIRUN -n 4 ./mpi_hello_world
[premier-2:219870] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 1056
[premier-2:219870] PMIX ERROR: PMIX_ERROR in file gds_shmem2.c at line 1231
...

jmorillo@premier-2:~/mpitutorial/tutorials/mpi-hello-world/code$ export PMIX_MCA_gds=hash
jmorillo@premier-2:~/mpitutorial/tutorials/mpi-hello-world/code$ $MPIRUN -n 4 ./mpi_hello_world
Hello world from processor premier-2, rank 3 out of 4 processors
Hello world from processor premier-2, rank 0 out of 4 processors
Hello world from processor premier-2, rank 2 out of 4 processors
Hello world from processor premier-2, rank 1 out of 4 processors

bedroge · 2026-03-03T16:10:35Z

Ah, great!

bedroge · 2026-03-03T19:07:49Z

It looks like the sourcing of that site_config script may not work, I think it's related to running in the dev repo. I'll look into it.

bedroge · 2026-03-04T08:07:00Z

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-03-04T08:07:13Z

New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.03/pr_72/300439

date	job status	comment
Mar 04 08:07:11 UTC 2026	submitted	job id `300439` awaits release by job manager
Mar 04 08:08:12 UTC 2026	released	job awaits launch by Slurm scheduler
Mar 04 08:09:17 UTC 2026	running	job `300439` is running
Mar 04 16:12:55 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-300439.out` ✅ no message matching `FATAL:` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2025.06-software-linux-riscv64-generic-riscv-1772615461.tar.zst` size: 0 MiB (22 bytes) entries: 0 modules under 2025.06-001/software/linux/riscv64/generic/modules/all no module files in tarball software under 2025.06-001/software/linux/riscv64/generic/software no software packages in tarball reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod no reprod directories in tarball other under 2025.06-001/software/linux/riscv64/generic no other files in tarball
Mar 04 16:12:55 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job300439.test` does not exist in job directory, or parsing it failed.

bedroge · 2026-03-12T09:54:27Z

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-03-12T09:54:34Z

New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.03/pr_72/301224

date	job status	comment
Mar 12 09:54:32 UTC 2026	submitted	job id `301224` awaits release by job manager
Mar 12 09:55:34 UTC 2026	released	job awaits launch by Slurm scheduler
Mar 12 09:57:06 UTC 2026	running	job `301224` is running
Mar 12 11:01:57 UTC 2026	finished	😢 FAILURE (click triangle for details) Details ✅ job output file `slurm-301224.out` ✅ no message matching `FATAL:` ❌ found message matching `ERROR:` ❌ found message matching `FAILED:` ❌ found message matching `required modules missing:` ❌ no message matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2025.06-software-linux-riscv64-generic-riscv-1773313203.tar.zst` size: 0 MiB (22 bytes) entries: 0 modules under 2025.06-001/software/linux/riscv64/generic/modules/all no module files in tarball software under 2025.06-001/software/linux/riscv64/generic/software no software packages in tarball reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod no reprod directories in tarball other under 2025.06-001/software/linux/riscv64/generic no other files in tarball
Mar 12 11:01:57 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job301224.test` does not exist in job directory, or parsing it failed.

julianmorillo · 2026-03-12T11:43:11Z

@bedroge , 3 tests failing with the same PMIX error as before. We need the sourcing of site_config.sh to work (as it includes the export PMIX_MCA_gds=hash that should prevent the errors). You said it may be related with the fact of running from the dev repo but I was not able to find what the exact problem is...

bedroge · 2026-03-12T11:56:23Z

Oh, right, I forgot about that.

The site config script would not work for this, unfortunately, as the build script sort of wipes the environment again. An alternative would be using Lmod hooks for this, but I couldn't immediately get that to work, as it's looking in a non-existing location in the dev repo. I can try to come up with a fix for that by making a symlink.

bedroge · 2026-03-12T13:31:27Z

EESSI/filesystem-layer#267 should fix this and allow us to use site-specific Lmod hooks for dev.eessi.io.

bedroge · 2026-03-12T15:23:47Z

bot: build repo:dev.eessi.io-riscv-2025.06-001 instance:eessi-bot-riscv for:arch=riscv64/generic

riscv-eessi-io-bot · 2026-03-12T15:23:54Z

New job on instance eessi-bot-riscv for repository dev.eessi.io-riscv-2025.06-001
Building on: generic
Building for: riscv64/generic
Job dir: /home/eessibot/shared/jobs/2026.03/pr_72/301287

date	job status	comment
Mar 12 15:23:52 UTC 2026	submitted	job id `301287` awaits release by job manager
Mar 12 15:24:42 UTC 2026	released	job awaits launch by Slurm scheduler
Mar 12 16:59:27 UTC 2026	running	job `301287` is running
Mar 12 19:14:48 UTC 2026	finished	😁 SUCCESS (click triangle for details) Details ✅ job output file `slurm-301287.out` ✅ no message matching `FATAL:` ✅ no message matching `ERROR:` ✅ no message matching `FAILED:` ✅ no message matching `required modules missing:` ✅ found message(s) matching `No missing installations` ✅ found message matching `.tar.* created!` Artefacts `eessi-2025.06-software-linux-riscv64-generic-riscv-1773342768.tar.zst` size: 2 MiB (2475475 bytes) entries: 57 modules under 2025.06-001/software/linux/riscv64/generic/modules/all `netCDF/4.9.3-gompi-2025b.lua` software under 2025.06-001/software/linux/riscv64/generic/software `netCDF/4.9.3-gompi-2025b` reprod directories under 2025.06-001/software/linux/riscv64/generic/reprod no reprod directories in tarball other under 2025.06-001/software/linux/riscv64/generic no other files in tarball
Mar 12 19:14:48 UTC 2026	test result	🤷 UNKNOWN (click triangle for detailed information) Job test file `_bot_job301287.test` does not exist in job directory, or parsing it failed.
Mar 13 08:04:03 UTC 2026	uploaded	transfer of `eessi-2025.06-software-linux-riscv64-generic-riscv-1773342768.tar.zst` to S3 bucket succeeded

{2025.06-001}[2025b] netCDF 4.9.3 (LAMMPS dependency)

bcb4adc

Merge branch 'main' into netCDF

2d96735

This was referenced Mar 3, 2026

{2025.06}[2025a,2025b] netCDF 4.9.3 EESSI/software-layer#1432

Merged

Make sure that netcdf easyblock picks up the EB-provided libxml2 and bzip2 easybuilders/easybuild-easyblocks#4086

Merged

bedroge reviewed Mar 3, 2026

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Comment thread easystacks/riscv/2025.06-001/eessi-2025.06-eb-5.2.1-2025b.yml Outdated

use commits for easyconfig and easyblock

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julianmorillo and others added 7 commits March 4, 2026 17:09

Merge branch 'main' into netCDF

01b8f65

Merge branch 'main' into netCDF

ef3955f

Merge branch 'main' into netCDF

a96ae63

Merge branch 'main' into netCDF

aa43a53

Merge branch 'main' into netCDF

dcb1666

Merge branch 'main' into netCDF

934e6ac

use latest commits

6693d6b

Merge branch 'main' into netCDF

aed11ba

Merge branch 'main' into netCDF

6a345ff

bedroge approved these changes Mar 13, 2026

View reviewed changes

bedroge added 2025.06-001 bot:deploy labels Mar 13, 2026

Merge branch 'main' into netCDF

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bedroge approved these changes Mar 13, 2026

View reviewed changes

bedroge merged commit cbc5252 into EESSI:main Mar 13, 2026

julianmorillo deleted the netCDF branch March 13, 2026 09:50

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julianmorillo commented Mar 3, 2026 •

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riscv-eessi-io-bot bot commented Mar 12, 2026 •

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riscv-eessi-io-bot bot commented Mar 12, 2026 •

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