Containerization of Environ build #9

lattice737 · 2024-06-24T03:03:21Z

A Dockerfile build of QE with Environ to mitigate "works on my machine" problems by automating the source downloads, dependency installations, and compilation steps in a partitioned, self-contained environment treated as an independent OS. I've arbitrarily chosen an Ubuntu OS, but best practice for a distributed library is to offer multiple OS Dockerfiles. I included SSSP pseudopotential file downloads and Python installation just as a convenience factor; I don't know how helpful those really are for regular Environ use--maybe they could be useful for demos.

I've included instructions in the comments at the start of the file, which should be friendly for folks who are unfamiliar with Docker. I'll include them here for completeness:

Use containerized installation
0) Install Docker (https://docs.docker.com/engine/install/) or Docker Desktop (https://www.docker.com/products/docker-desktop/)
1) Clone repo:     git clone https://github.com/environ-developers/Environ.git && cd Environ
2) Build image:    docker build -t environ-sandbox . && docker image ls
3) Run container:  docker run -i -p 8000:80 environ-sandbox && docker ps
4) Access container:
   a) Docker Desktop
   b) CLI: docker exec -it <container ID> bash

I only attempted to install PW, and total image build time is usually about 5 min for me. After that, it's plug and play. I tried to run a few examples, but it took a long time, and I noticed a few exceptions and warnings I didn't understand:

# ./run_example.sh

/app/q-e/Environ/examples/qe/pw/sccs : starting

This example shows how to use pw.x to calculate the solvation energy 
and other solvent related quantites for a water molecule in water
using a fully self consistent dielectric defined on the electronic
density according to 

   O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136, 064102 (2012) 

Two equivalent calculations are performed, using two different 
algorithms to obtain the self consistent dielectic as described in 

G. Fisicaro, L. Genovese, O. Andreussi, N. Marzari and S. Goedecker,
               J. Chem. Phys. 144, 014103 (2016)

  executables directory: /app/q-e/bin
  pseudo directory:      /app/q-e/pseudo
  temporary directory:   /app/q-e/tempdir
  checking that needed directories and files exist...
Downloading O.pbe-rrkjus.UPF to /app/q-e/pseudo...
Downloading H.pbe-rrkjus.UPF to /app/q-e/pseudo... done

  running pw.x as:   /app/q-e/bin/pw.x  -nk 1 -nd 1 -nb 1 -nt 1  --environ

  cleaning /app/q-e/tempdir... done
  running the relax calculation in vacuum with direct solver
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG
 done
  cleaning /app/q-e/tempdir... done
  running the relax calculation in water with fixed-point solver
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_OVERFLOW_FLAG
STOP 1
Error condition encountered during test: exit status = 1
Aborting

I wasn't sure if they were necessarily due to the build or maybe some other issue. I could not run the tests due to a syntax error in the driver:

# ./run-pw.sh
./run-pw.sh: line 35: [: =: unary operator expected

I'm not sure if the test suite and examples are up to date and/or possibly incompatible with the OS or installation configurations I set. I'm hoping you see something I don't and we can tweak this one instance to be used by everyone (or at least the Linux-friendly audience). That in mind, feel free to edit yourself if you would build differently--this is just my best guess (haha).

Anyway, I noticed quite a few questions about installation in the support group, so I'm hoping this helps at least one person with that. It seems to me that is a barrier for some users, so I think there may be a considerable benefit to this approach.

Replicate Environ, QE compilation; Include helpful tools: pseudos, python; Configure for custom options; additional testing needed--occasional warnings with tests, examples

lattice737 · 2024-06-24T18:28:05Z

I was running tests wrongly before. Test results:

Using executable: /app/q-e/Environ/tests/..//tests/run-pw.sh.
Test id: 240625.
Benchmark: GIT.

pw_confine - pw.in (arg(s): confine-sccs.in): Passed.
pw_confine - pw.in (arg(s): confine-ss.in): Passed.
pw_confine - pw.in (arg(s): confine-system.in): Passed.
pw_dielectric - neutral.in (arg(s): dielectric-sccs-default.in): Passed.
pw_dielectric - neutral.in (arg(s): dielectric-sccs-iter-aux.in): Passed.
pw_dielectric - neutral.in (arg(s): dielectric-sccs-psd.in): Passed.
pw_dielectric - neutral.in (arg(s): dielectric-ss-default.in): **FAILED**.
f1
    ERROR: absolute error 1.03e-02 greater than 1.00e-03. (Test: 0.0018.  Benchmark: 0.0121.)

pw_dielectric - neutral.in (arg(s): dielectric-ss-iter-aux.in): **FAILED**.
f1
    ERROR: absolute error 1.05e-02 greater than 1.00e-03. (Test: 0.0017.  Benchmark: 0.0122.)

pw_dielectric - charged.in (arg(s): dielectric-sccs-default.in): Passed.
pw_dielectric - charged.in (arg(s): dielectric-sccs-iter-aux.in): Passed.
pw_dielectric - charged.in (arg(s): dielectric-sccs-psd.in): Passed.
pw_dielectric - charged.in (arg(s): dielectric-ss-default.in): **FAILED**.
f1
    ERROR: absolute error 6.40e-03 greater than 1.00e-03. (Test: 0.3552.  Benchmark: 0.3488.)

pw_dielectric - charged.in (arg(s): dielectric-ss-iter-aux.in): **FAILED**.
f1
    ERROR: absolute error 6.40e-03 greater than 1.00e-03. (Test: 0.355.  Benchmark: 0.3486.)

pw_dielectric - neutral.in (arg(s): dielectric-sys-default.in): Passed.
pw_dielectric - neutral.in (arg(s): dielectric-sys-iter-aux.in): Passed.
pw_dielectric - charged.in (arg(s): dielectric-sys-default.in): Passed.
pw_dielectric - charged.in (arg(s): dielectric-sys-iter-aux.in): Passed.
pw_electrolyte - pw.in (arg(s): electrolyte-lmpb-sccs-stern_full.in): Passed.
pw_electrolyte - pw.in (arg(s): electrolyte-lmpb-sccs-stern_ions.in): Passed.
pw_electrolyte - pw.in (arg(s): electrolyte-lmpb-ss-stern_full.in): Passed.
pw_electrolyte - pw.in (arg(s): electrolyte-lmpb-ss-stern_ions.in): Passed.
pw_electrolyte - pw.in (arg(s): electrolyte-lpb-sccs.in): Passed.
pw_electrolyte - pw.in (arg(s): electrolyte-lpb-ss.in): Passed.
pw_externals - isolated.in (arg(s): externals_0d_vacuum_default.in): Passed.
pw_externals - isolated.in (arg(s): externals_2d_vacuum_default.in): Passed.
pw_externals - isolated.in (arg(s): externals_0d_dielectric_default.in): Passed.
pw_externals - isolated.in (arg(s): externals_2d_dielectric_default.in): Passed.
pw_externals - slab.in (arg(s): externals_0d_vacuum_default.in): Passed.
pw_externals - slab.in (arg(s): externals_2d_vacuum_default.in): Passed.
pw_externals - slab.in (arg(s): externals_0d_dielectric_default.in): Passed.
pw_externals - slab.in (arg(s): externals_2d_dielectric_default.in): Passed.
pw_field-aware - pw.in (arg(s): fa-ss.in): Passed.
pw_gcs - pw.in (arg(s): gcs-solvent.in): Passed.
pw_gcs - pw.in (arg(s): gcs-vacuum.in): Passed.
pw_ms - pw.in (arg(s): ms-solvent.in): Passed.
pw_ms - pw.in (arg(s): ms-vacuum.in): Passed.
pw_mt - neutral.in (arg(s): dielectric-default.in): Passed.
pw_mt - charged.in (arg(s): dielectric-default.in): Passed.
pw_mt - isolated.in (arg(s): externals_0d_vacuum_default.in): Passed.
pw_mt - isolated.in (arg(s): externals_0d_dielectric_default.in): Passed.
pw_periodic - neutral.in (arg(s): periodic-vacuum-default.in): Passed.
pw_periodic - charged.in (arg(s): periodic-vacuum-default.in): Passed.
pw_periodic - neutral.in (arg(s): periodic-dielectric-default.in): Passed.
pw_periodic - charged.in (arg(s): periodic-dielectric-default.in): Passed.
pw_regions - pw.in (arg(s): insphere-default.in): Passed.
pw_regions - pw.in (arg(s): outslab-default.in): Passed.
pw_slab - neutral.in (arg(s): periodic-vacuum-default.in): Passed.
pw_slab - neutral.in (arg(s): periodic-dielectric-default.in): Passed.
pw_slab - charged.in (arg(s): periodic-vacuum-default.in): Passed.
pw_slab - charged.in (arg(s): periodic-dielectric-default.in): Passed.
pw_solvent-aware - pw.in (arg(s): local-sccs.in): Passed.
pw_solvent-aware - pw.in (arg(s): sa-sccs.in): Passed.
pw_solvent-aware - pw.in (arg(s): local-ss.in): **FAILED**.
f1
    ERROR: absolute error 6.40e-03 greater than 1.00e-03. (Test: 0.0439.  Benchmark: 0.0503.)

pw_solvent-aware - pw.in (arg(s): sa-ss.in): **FAILED**.
f1
    ERROR: absolute error 7.10e-03 greater than 1.00e-03. (Test: 0.0439.  Benchmark: 0.051.)

pw_spin - radical.in (arg(s): vacuum-pcc.in): Passed.
pw_spin - radical.in (arg(s): dielectric-pcc.in): Passed.
pw_surface - pw.in (arg(s): surface-sccs-default.in): Passed.
pw_surface - pw.in (arg(s): surface-sccs-fft.in): Passed.
pw_surface - pw.in (arg(s): surface-ss-default.in): **FAILED**.
f1
    ERROR: absolute error 3.e-03 greater than 1.00e-03. (Test: 0.0305.  Benchmark: 0.0338.)

pw_surface - pw.in (arg(s): surface-ss-fft.in): **FAILED**.
f1
    ERROR: absolute error 3.10e-03 greater than 1.00e-03. (Test: 0.0307.  Benchmark: 0.08.)

pw_surface - pw.in (arg(s): surface-sys-default.in): Passed.
pw_surface - pw.in (arg(s): surface-sys-fft.in): Passed.
pw_volume - pw.in (arg(s): volume-sccs-default.in): Passed.
pw_volume - pw.in (arg(s): volume-ss-default.in): **FAILED**.
f1
    ERROR: absolute error 2.64e-02 greater than 1.00e-03. (Test: 0.0305.  Benchmark: 0.0569.)

pw_volume - pw.in (arg(s): volume-sys-default.in): Passed.
pw_water - neutral.in (arg(s): water-neutral-sccs-default.in): Passed.
pw_water - neutral.in (arg(s): water-neutral-ss-default.in): **FAILED**.
f1
    ERROR: absolute error 3.00e-03 greater than 1.00e-03. (Test: 0.1444.  Benchmark: 0.1414.)

pw_water - cation.in (arg(s): water-cation-sccs-default.in): Passed.
pw_water - cation.in (arg(s): water-cation-ss-default.in): **FAILED**.
f1
    ERROR: absolute error 3.50e-03 greater than 1.00e-03. (Test: 0.58.  Benchmark: 0.3423.)

pw_water - anion.in (arg(s): water-anion-sccs-default.in): Passed.
pw_water - anion.in (arg(s): water-anion-ss-default.in): **FAILED**.
f1
    ERROR: absolute error 1.10e-02 greater than 1.00e-03. (Test: 0.018.  Benchmark: 0.007.)

All done. ERROR: only 59 out of 71 tests passed.
Failed tests in:
	/app/q-e/Environ/tests/pw_dielectric/
	/app/q-e/Environ/tests/pw_solvent-aware/
	/app/q-e/Environ/tests/pw_surface/
	/app/q-e/Environ/tests/pw_volume/
	/app/q-e/Environ/tests/pw_water/

Run tests and examples; Add flags for optional pseudo download, run tests/examples; Use v22.04 distro with additional deps; Add env variables, refactor for legibility; 58/71 tests passing, 8/10 examples run

lattice737 · 2024-06-24T21:39:03Z

Included openmpi (and other goodies) in the build and also ran examples:

# grep -E ": starting|: done" /app/examples.log
/app/q-e/Environ/examples/qe/pw/sccs : starting
/app/q-e/Environ/examples/qe/pw/sccs : done
/app/q-e/Environ/examples/qe/pw/sscs : starting
/app/q-e/Environ/examples/qe/pw/sscs : done
/app/q-e/Environ/examples/qe/pw/pbc : starting
/app/q-e/Environ/examples/qe/pw/pbc : done
/app/q-e/Environ/examples/qe/pw/slab : starting
/app/q-e/Environ/examples/qe/pw/slab : done
/app/q-e/Environ/examples/qe/pw/helmholtz : starting
/app/q-e/Environ/examples/qe/pw/helmholtz : done
/app/q-e/Environ/examples/qe/pw/helmholtz_linpb : starting
/app/q-e/Environ/examples/qe/pw/helmholtz_linpb : done
/app/q-e/Environ/examples/qe/pw/helmholtz_linpb : done
/app/q-e/Environ/examples/qe/pw/helmholtz_linpb : done
/app/q-e/Environ/examples/qe/pw/helmholtz_linpb : done
/app/q-e/Environ/examples/qe/pw/helmholtz_linpb : done
/app/q-e/Environ/examples/qe/pw/mott_schottky : starting
/app/q-e/Environ/examples/qe/pw/mott_schottky : done
/app/q-e/Environ/examples/qe/pw/ms_gcs : starting
/app/q-e/Environ/examples/qe/pw/ms_gcs : done
/app/q-e/Environ/examples/qe/pw/solvent_aware : starting

but I ran into an error running the solvent-aware examples:

/app/q-e/Environ/examples/qe/pw/solvent_aware : starting

This example shows how to use pw.x to simulate a 10xH20 water cluster 
immersed in continuum solvent. By setting the solvent_radius inside the 
BOUNDARY namelist, one activates the solvent-aware interface, see 

O. Andreussi, N.G. Hörmann, F. Nattino, G. Fisicaro, S. Goedecker, and
        N. Marzari, J. Chem. Theory Comput. 15, 1996 (2019).

This feature prevents dielectric from getting inside the cluster.


  executables directory: /app/q-e/bin
  pseudo directory:      /app/q-e/pseudo
  temporary directory:   /app/q-e/tempdir
  checking that needed directories and files exist... done

  running pw.x as:   /app/q-e/bin/pw.x  -nk 1 -nd 1 -nb 1 -nt 1  --environ

  cleaning /app/q-e/tempdir... done
Error condition encountered during test: exit status = 137
Aborting

Configure docker image building, artifact loading; Unset Dockerfile flags for CI

`mpirun --allow-run-as-root` and OMPI environment vars not honored at runtime

lattice737 · 2024-06-25T20:13:32Z

Examples

10/10 examples actually do run successfully with the containerized build. I think my other session running all the examples just timed out:

/app/q-e/Environ/examples/qe/pw/solvent_aware : starting
/app/q-e/Environ/examples/qe/pw/solvent_aware : done
/app/q-e/Environ/examples/qe/pw/field_aware : starting
/app/q-e/Environ/examples/qe/pw/field_aware : done

Continuous Integration

I also configured a CI action that builds environ on commits to master and develop, running tests on pull requests, merges with master, and pushes with v#.# tags. This will help to identify commits that break the build.

CI Issues

I can't seem to run the tests in parallel with CI for some reason. All the tests fail, and the error is about missing values against benchmarks, which is usually connected to an OMPI warning not to run as root. Even with the override flag and environment variables, I can't seem to run mpi with root, which is necessary for Docker containers. For now, CI tests will be run serially 🥲

...
pw_water - anion.in (arg(s): water-anion-ss-default.in): **FAILED**.
Different sets of data extracted from benchmark and test.
    Data only in benchmark: e1, f1, n1.

All done. ERROR: only 0 out of 71 tests passed.
...

I wanted to include a job that runs examples, but they take forever! Are there some "essential" examples that we can run in this pipeline? Or maybe it's unnecessary to automate examples like this?

lattice737 · 2024-06-26T14:16:01Z

Feature Summary

Containerized parallel build of QE PW with Environ using gfortran and OpenMPI on Ubuntu OS
a. Option to download SSSP efficiency/precision pseudopotentials
b. Option to run tests in parallel during build (logs to /app/tests.log)
c. Option to run examples during build (logs to /app/examples.log)
d. Python and pipx included
Automatic CI on commit pushes (master and develop branches only)
a. Compiles Environ on all commits
b. Runs tests with build when:
- Branch merged with master
- Commit includes version tag (e.g. v3.1)
- Pull request updated (this could be refined, but I figured it's better to start broad)

Performance

Examples: 10/10 completed
Tests: 59/71 passed

Future Directions

cmake build
All package installations (i.e. make all)
Additional architecture support (i.e. QE-supported architectures)
Additional compiler support (e.g. ifx)
Specific configuration builds (by request)--potentially useful for specific use cases and replicability

olivieroandreussi and others added 3 commits June 21, 2024 12:03

Bring back parallel gather in get_dvtot

b3f62cd

Update README.md

e5af4e4

Write Dockerfile

90ed29d

Replicate Environ, QE compilation; Include helpful tools: pseudos, python; Configure for custom options; additional testing needed--occasional warnings with tests, examples

Update Dockerfile

59dea32

Run tests and examples; Add flags for optional pseudo download, run tests/examples; Use v22.04 distro with additional deps; Add env variables, refactor for legibility; 58/71 tests passing, 8/10 examples run

lattice737 added 23 commits June 24, 2024 20:47

Develop build action as production-grade build test

ca78f8e

Configure docker image building, artifact loading; Unset Dockerfile flags for CI

Unset tests flag in Dockerfile

3fa3951

Update ci.yml

9b32d23

Add print statements

4a2dcbd

Remove sed, add needs

d6680da

Update builderx version

3381acb

Add buildx setup step, fix buildx push ref

dba1406

Debug bad image reference

ba5a74b

Correct exec flags

91f6034

Refactor ci

3681e21

Remove exec interactivity

dc58012

Use run-action to run tests

d17d133

Add ompi env variables to test job

61833ac

Use env for OMPI vars, set fail exit code condition

7c1e702

Set ompi vars inline, add fi

4cef6e8

Use -e flags, exit status 1 for any failed tests

da6b144

Set env variables inline, grep silently

7300b50

Set env variables for step and command

f9a099a

Run tests serially

7b579c9

Display env variables

f647c8b

Use root flag with mpirun

a6bd521

Run tests serially for now

37b7df8

`mpirun --allow-run-as-root` and OMPI environment vars not honored at runtime

Configure ci triggers--merges, pushes to master, develop

27f9118

olivieroandreussi merged commit 2ff991f into environ-developers:develop Jul 4, 2024

jerrypgreenberg mentioned this pull request Dec 6, 2024

seg fault runnig QE with Environ #15

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Containerization of Environ build #9

Containerization of Environ build #9

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Containerization of Environ build #9

Containerization of Environ build #9

Conversation

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Examples

Continuous Integration

CI Issues

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Feature Summary

Performance

Future Directions

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