update LAMMPS easyblock for LAMMPS/23Jun22 #2213

ocaisa · 2020-10-28T14:57:56Z

This easyblock supports the patch release 22Oct20 of LAMMPS, which is rc2 for the next stable release. ~~Unfortunately it is not currently backwards compatible so is a WIP until we figure that out.~~

UPDATE:
This now supports the latest stable version of LAMMPS (23Jun2022)

at https://docs.lammps.org/Build_extras.html#available-architecture-settings

rarensu · 2021-11-24T14:43:03Z

Dependency YAFF is not compatible with the newer h5py yet. I turned the YAFF extension off rather than try to deal with downgrades or other hacky nonsense. Eventually YAFF will catch up and we can turn it back on.

arkdavy · 2022-03-18T14:42:32Z

Hi. I have updated the easyblock, and it builds now both 3Mar20 and 29Sep21 releases (and, therefore, 22Oct20 should also work). I could submit my changes to this PR, but not sure how to do that. So, could you check the attached easyblock? (which needs to be renamed to 'lammps.py')

lammps.zip

ocaisa · 2022-03-23T08:53:01Z

Sorry, I did take an initial look at this but I haven't had time to incorporate it yet (and won't for at least another two weeks). The one point I would raise is that it is likely that your version comparisons is not working correctly. LAMMPS has unfortunate versions which looseversion is unlikely to get right. At least it is predictable though, I think we will need to implement a version mapping function that will translate 29Oct2020 to 2020.10.29 to ensure we get that right.

ocaisa · 2022-03-23T12:26:43Z

For version translation, something like this would work:

import re
def translate_version(version):
    items = [x for x in re.split('(\d+)', version) if x]
    if len(items) != 3:
        raise ValueError("Version %s does not have 3 elements" % version)
    month_map = {"JAN": '01', "FEB": '02', "MAR": '03', "APR": '04', "MAY": '05', "JUN": '06', "JUL": '07', "AUG": '08', "SEP": '09', "OCT": '10', "NOV": '11', "DEC": '12'}
    return items[2] + month_map[items[1].upper()] + items[0]

arkdavy · 2022-03-23T12:41:57Z

Thanks for the hint and for the function template!

I thought LoosVersion would work with any format, but let me add and test this function into lammps.py. I will just re-attach an updated version later.

ocaisa · 2022-03-23T14:21:07Z

I tested it out just to be sure:

[ocaisa@xlnode1 ~]$ python -c "from distutils.version import LooseVersion; print(LooseVersion('28Sep2021') > LooseVersion('29Sep2020'))"
False

arkdavy · 2022-03-23T16:09:21Z

yeah, I have also seen it! So, the function you suggested did work, and here is an updated file
lammps.txt

ocaisa · 2022-05-13T13:37:03Z

I tested this for the 3Mar2020 release and it gives an identical configure command to the existing easyblock.

…ld-easyblocks into lammps_allow_disable_cuda

ocaisa · 2022-05-13T15:38:01Z

Test report by @ocaisa

Overview of tested easyconfigs (in order)

FAIL (build issue) LAMMPS-29Sep2021-foss-2021b-CUDA-11.4.1-kokkos.eb (partial log available at https://gist.github.com/fa2578689b743bcf733111fb0a330919)

Build succeeded for 0 out of 1 (1 easyconfigs in total)
login1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz, Python 3.6.8
See https://gist.github.com/1ec5f32d0fc83df84676d43d43daad5b for a full test report.

Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com>

branfosj · 2022-07-22T07:19:40Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

*FAIL (unhandled exception: list index out of range)Traceback (most recent call last):
File "/rds/projects/2017/branfosj-rse/easybuild/src/easybuild-framework/easybuild/main.py", line 128, in build_and_install_software
(ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
File "/rds/projects/2017/branfosj-rse/easybuild/src/easybuild-framework/easybuild/framework/easyblock.py", line 4077, in build_and_install_one
result = app.run_all_steps(run_test_cases=run_test_cases)
File "/rds/projects/2017/branfosj-rse/easybuild/src/easybuild-framework/easybuild/framework/easyblock.py", line 3960, in run_all_steps
self.run_step(step_name, step_methods)
File "/rds/projects/2017/branfosj-rse/easybuild/src/easybuild-framework/easybuild/framework/easyblock.py", line 3795, in run_step
step_method(self)()
File "/dev/shm/branfosj/tmp-up-EL8/included-easyblocks-hwqtmlmr/easybuild/easyblocks/lammps.py", line 392, in configure_step
python_lib = glob.glob("%s/lib/libpython%s.so" % (python_dir, python_short_version))[0]
IndexError: list index out of range
** LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb

Build succeeded for 0 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/0e3a26dfd88506ed161ba7952f4ed277 for a full test report.

branfosj · 2022-07-22T07:24:42Z

easybuild/easyblocks/l/lammps.py

+        python_dir = get_software_root('Python')
+        if python_dir:
+            python_short_version = '.'.join(get_software_version('Python').split('.')[:2])
+            python_lib = glob.glob("%s/lib*/libpython%s.so" % (python_dir, python_short_version))[0]


For Python 3.7 (2019b) the library is libpython3.7m.so, which is why I see #2213 (comment)

Goes off to recall how to include an optional m

python -c "import sysconfig; print(sysconfig.get_config_var('abiflags'))"

Is from https://github.com/easybuilders/easybuild-easyblocks/blob/develop/easybuild/easyblocks/p/python.py#L511 - i.e. how we check for the right library in the Python easyblock.

Urgh, I should have waited before committing 9f9591b, will fix now

ocaisa · 2022-07-22T08:42:54Z

Test report by @ocaisa

Overview of tested easyconfigs (in order)

*FAIL (unhandled exception: list index out of range)Traceback (most recent call last):
File "/home/ocaisa/EasyBuild_Git/easybuild-framework/easybuild/main.py", line 128, in build_and_install_software
(ec_res['success'], app_log, err) = build_and_install_one(ec, init_env)
File "/home/ocaisa/EasyBuild_Git/easybuild-framework/easybuild/framework/easyblock.py", line 4077, in build_and_install_one
result = app.run_all_steps(run_test_cases=run_test_cases)
File "/home/ocaisa/EasyBuild_Git/easybuild-framework/easybuild/framework/easyblock.py", line 3960, in run_all_steps
self.run_step(step_name, step_methods)
File "/home/ocaisa/EasyBuild_Git/easybuild-framework/easybuild/framework/easyblock.py", line 3795, in run_step
step_method(self)()
File "/tmp/eb-bqftmjfd/included-easyblocks-op9r_ga4/easybuild/easyblocks/lammps.py", line 396, in configure_step
python_lib_path = glob.glob(os.path.join(python_dir, 'lib', python_lib))[0]
IndexError: list index out of range
** LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb

Build succeeded for 0 out of 1 (1 easyconfigs in total)
login1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz, Python 3.6.8
See https://gist.github.com/7f862cf2aee83149e0a2634337f62759 for a full test report.

ocaisa · 2022-07-22T09:11:30Z

Test report by @ocaisa

Overview of tested easyconfigs (in order)

SUCCESS LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
login1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz, Python 3.6.8
See https://gist.github.com/27188bbeef5491ac93404649392c9193 for a full test report.

branfosj · 2022-07-22T10:47:35Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

FAIL (build issue) LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb (partial log available at https://gist.github.com/8677715c2349553cce8a22afc6d6171d)
SUCCESS LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb
FAIL (build issue) LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb (partial log available at https://gist.github.com/77cbeacdf59e60d144fddb215080d152)

Build succeeded for 1 out of 3 (3 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/c9baaff78aca40aa2edbed877b5d5378 for a full test report.

ocaisa · 2022-07-22T10:58:12Z

@branfosj Both of those builds are failing on the same issue:

fatal error: Python.h: No such file or directory

Could that be true? Am I picking up the wrong Python include path?

ocaisa · 2022-07-22T11:06:10Z

Urgh, yeah, the files are in a subdirectory...grr

branfosj · 2022-07-22T11:09:12Z

Failed runs with Python 3.7.4, the relevant parts are:

-DPython_EXECUTABLE=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.7.4-GCCcore-8.3.0/bin/python
-DPYTHON_EXECUTABLE=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.7.4-GCCcore-8.3.0/bin/python
-DPYTHON_LIBRARY=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.7.4-GCCcore-8.3.0/lib64/libpython3.7m.so
-DPYTHON_INCLUDE_DIR=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.7.4-GCCcore-8.3.0/include

Success with Python 3.8.2:

-DPython_EXECUTABLE=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.8.2-GCCcore-9.3.0/bin/python
-DPYTHON_EXECUTABLE=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.8.2-GCCcore-9.3.0/bin/python
-DPYTHON_LIBRARY=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.8.2-GCCcore-9.3.0/lib64/libpython3.8.so
-DPYTHON_INCLUDE_DIR=/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.8.2-GCCcore-9.3.0/include

Location of Python.h:

/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.7.4-GCCcore-8.3.0/include/python3.7m/Python.h
/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.8.2-GCCcore-9.3.0/include/python3.8/Python.h

Ah, in the actual build lines

2019b the only Python include is:

-I/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.7.4-GCCcore-8.3.0/include

but for 2020a we've gained an extra include path:

-I/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.8.2-GCCcore-9.3.0/include 
-I/rds/projects/2017/branfosj-rse/easybuild/EL8-cas/software/Python/3.8.2-GCCcore-9.3.0/include/python3.8

However, I am not seeing information in the log as to what caused that extra include to appear for 2020a.

ocaisa · 2022-07-22T11:15:24Z

@branfosj Should be fixed with 616caf7

ocaisa · 2022-07-22T11:36:47Z

Test report by @ocaisa

Overview of tested easyconfigs (in order)

SUCCESS LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
login1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz, Python 3.6.8
See https://gist.github.com/49eb971aa1b5687655e880b407f5dd84 for a full test report.

branfosj · 2022-07-22T12:13:08Z

Test report by @branfosj

Overview of tested easyconfigs (in order)

SUCCESS LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb
SUCCESS LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb
SUCCESS LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb

Build succeeded for 3 out of 3 (3 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/2ec0691ff9de57f49aa0a2abcdc390e4 for a full test report.

branfosj

lgtm

branfosj · 2022-07-22T12:33:08Z

Going in, thanks @ocaisa!

Alan O'Cais added 2 commits October 28, 2020 15:55

Update LAMMPS easyblock for LAMMPS/22Oct20

f1c688c

Update lammps.py

e539ee8

boegel added the update label Nov 11, 2020

boegel added this to the 4.x milestone Nov 11, 2020

Update lammps.py

9dfe1c6

ocaisa changed the title ~~Update LAMMPS easyblock for LAMMPS/22Oct20~~ Update LAMMPS easyblock for LAMMPS/29Oct20 Jan 27, 2021

ocaisa added 3 commits November 12, 2021 15:14

Update to latest list of archs

733c669

at https://docs.lammps.org/Build_extras.html#available-architecture-settings

Update lammps.py

2953b83

Update lammps.py

c95b0b8

rarensu mentioned this pull request Nov 24, 2021

{chem}[fosscuda/2020b] LAMMPS-29Sep with CUDA (via kokkos) easybuilders/easybuild-easyconfigs#14414

Closed

migueldiascosta mentioned this pull request Jan 4, 2022

{chem}[foss/2020b] LAMMPS v29Sep2021 easybuilders/easybuild-easyconfigs#14653

Closed

arkdavy mentioned this pull request Jan 21, 2022

{chem}[GCCcore/11.2.0,foss/2021b] LAMMPS v29Sep2021 (with and without cuda) easybuilders/easybuild-easyconfigs#14815

Closed

Alan O'Cais added 3 commits May 13, 2022 14:45

Integrate input from @arkdavy

cc85c80

Appease hound

2928b9b

Fix escape sequence

47f016b

ocaisa marked this pull request as ready for review May 13, 2022 13:29

Merge branch 'develop' into lammps_allow_disable_cuda

5b78c9f

Alan O'Cais added 4 commits May 13, 2022 15:42

Fix escape sequence

16c24ff

Merge branch 'lammps_allow_disable_cuda' of github.com:ocaisa/easybui…

0c7f739

…ld-easyblocks into lammps_allow_disable_cuda

Spacing for hound

9b12cfb

Fix lint error

1b992fe

ocaisa and others added 3 commits July 21, 2022 11:42

Update easybuild/easyblocks/l/lammps.py

2ff4064

Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com>

Address review

97d4342

Update lammps.py

424a623

branfosj reviewed Jul 22, 2022

View reviewed changes

ocaisa added 5 commits July 22, 2022 10:03

Be forgiving if you can't find Python libs

9f9591b

Tidy up Python library detection

c7c7d96

Appease the hound

97afdf2

Make sure to provide full path

3227c2f

Missing import

3331661

ocaisa added 2 commits July 22, 2022 10:48

Forgot to strip the newline

de8936d

Error out if Python is not included as a dep

f5a9c29

Provide correct Python include folder

616caf7

branfosj approved these changes Jul 22, 2022

View reviewed changes

branfosj modified the milestones: 4.x, next release (4.6.1?) Jul 22, 2022

branfosj merged commit c5d76b0 into easybuilders:develop Jul 22, 2022

ocaisa deleted the lammps_allow_disable_cuda branch July 22, 2022 12:40

ocaisa mentioned this pull request Jul 25, 2022

{chem}[foss/2021a,foss/2021b] LAMMPS v23Jun2022 w/ Python 3.9.5 + 3.9.6 and CUDA easybuilders/easybuild-easyconfigs#15900

Merged

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boegel changed the title ~~Update LAMMPS easyblock for LAMMPS/23Jun22~~ update LAMMPS easyblock for LAMMPS/23Jun22 Aug 3, 2022

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update LAMMPS easyblock for LAMMPS/23Jun22 #2213

update LAMMPS easyblock for LAMMPS/23Jun22 #2213

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branfosj commented Jul 22, 2022

update LAMMPS easyblock for LAMMPS/23Jun22 #2213

update LAMMPS easyblock for LAMMPS/23Jun22 #2213

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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