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cp2k-feedstock's Introduction

About cp2k-feedstock

Feedstock license: BSD-3-Clause

Home: https://www.cp2k.org

Package license: GPL-2.0-only

Summary: Quantum chemistry and solid state physics software package

Development: https://github.com/cp2k/cp2k

Documentation: https://manual.cp2k.org

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.

Current build status

Azure
VariantStatus
linux_64_blas_implmklmpinompi variant
linux_64_blas_implmklmpiopenmpi variant
linux_64_blas_implopenblasmpinompi variant
linux_64_blas_implopenblasmpiopenmpi variant

Current release info

Name Downloads Version Platforms
Conda Recipe Conda Downloads Conda Version Conda Platforms

Installing cp2k

Installing cp2k from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, cp2k can be installed with conda:

conda install cp2k

or with mamba:

mamba install cp2k

It is possible to list all of the versions of cp2k available on your platform with conda:

conda search cp2k --channel conda-forge

or with mamba:

mamba search cp2k --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search cp2k --channel conda-forge

# List packages depending on `cp2k`:
mamba repoquery whoneeds cp2k --channel conda-forge

# List dependencies of `cp2k`:
mamba repoquery depends cp2k --channel conda-forge

About conda-forge

Powered by NumFOCUS

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating cp2k-feedstock

If you would like to improve the cp2k recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/cp2k-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

  • If the version of a package is not being increased, please add or increase the build/number.
  • If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

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cp2k-feedstock's Issues

re-enable osx build

The Arch file for the OSX MPI build has already been added but it is currrently disabled due to test failures, see #11 (comment)

Number of FAILED  tests 101
Number of WRONG   tests 0
Number of CORRECT tests 2750
Number of NEW     tests 8
Total number of   tests 2859

Most of the runtime failures on osx openmpi seem to be related to invalid memory access (see here )

 ----------------------------------- OT ---------------------------------------

  Step     Update method      Time    Convergence         Total energy    Change
  ------------------------------------------------------------------------------

Program received signal SIGBUS: Access to an undefined portion of a memory object.

Backtrace for this error:

I'd appreciate some help with this

P.S. We may want to revert disabling the -framework Accelerate from 488a594 which was just a test.

linked openblas executable not openmp-ready?

Got this with the latest cp2k 8.1 psmp build on ubuntu linux

OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.

The code seems to run fine but the warning obviously obscures the output

  ----------------------------------- OT ---------------------------------------
  Minimizer      : DIIS                : direct inversion
                                         in the iterative subspace
                                         using   7 DIIS vectors
                                         safer DIIS on
  Preconditioner : FULL_ALL            : diagonalization, state selective
  Precond_solver : DEFAULT
  stepsize       :    0.15000000                  energy_gap     :    0.08000000
  eps_taylor     :   0.10000E-15                  max_taylor     :             4
  ----------------------------------- OT ---------------------------------------

  Step     Update method      Time    Convergence         Total energy    Change
  ------------------------------------------------------------------------------
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
 Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
     1 OT DIIS     0.15E+00  262.7     5.9069E-09      -906.4670015950 -9.06E+02

mpi build requires ssh

When running the MPI build of cp2k on a system without ssh installed, you get

(cp2k) root@instance:~/.condaenvs/envs/cp2k# mpirun --allow-run-as-root cp2k.psmp --help
--------------------------------------------------------------------------
The value of the MCA parameter "plm_rsh_agent" was set to a path
that could not be found:
  plm_rsh_agent: ssh : rsh
Please either unset the parameter, or check that the path is correct

For the regtests on conda-forge, we get around this by adding the options --bind-to-none -mca plm isolated to the mpirun call.

move to standard blas/lapack for OSX?

This is a question rather than a bug:

I noticed that while the CPU% used by the cp2k.ssmp executable follows the value of OMP_NUM_THREADS (e.g. ~200% for 2 threads), the number of threads used by the executable (as reported e.g. by top or the Activity Manager) varies over time and exceeds OMP_NUM_THREADS.
I find the same behavior in the previous cp2k.sopt executable [1] without OpenMP support (~100% CPU but up to 9 threads for the SOPT executable).

This comes from the use of the threaded "Accelerate framework" that I linked against.
However, as one might expect, running 9 threads is not very efficient when all of them are full-on computing and have to share the same resources.

E.g. in a small test, the timings of the cp2k.sopt SOPT executable with setting VECLIB_MAXIMUM_THREADS=1 are about 13% faster than without limiting the number of threads (and things might get worse for OpenMP).

I guess it therefore makes sense to link against the standard blas/lapack libraries instead... even if the accelerate framework binaries might be more optimized for the mac processors (?)
Not sure one can tell people to always use VECLIB_MAXIMUM_THREADS=1 when running the OSX version, they will forget...

[1] Installed via conda install -c conda-forge cp2k=7.1.0=hff491a8_2

OpenMP performance regression in cp2k 9.1?

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

A handful of tests in the serial test suite (with 2 OpenMP threads) started timing out with cpk2 9.2

See output below + discussion in #40 (comment)

In particular, one should give the executable a try locally and see whether it still spends an unreasonable amount of time in multiply_cannon_multrec.

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
$SRC_DIR/regtesting/TEST-Linux-x86-64-conda-ssmp-2022-01-01_12-37-46/xTB/regtest-5/AdeThyvdW.inp.out


Timed out after 400.0125737600001 seconds.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
$SRC_DIR/regtesting/TEST-Linux-x86-64-conda-ssmp-2022-01-01_12-37-46/SE/regtest-3-2/N3-rp_colvar.inp.out


Timed out after 400.0278689349998 seconds.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
$SRC_DIR/regtesting/TEST-Linux-x86-64-conda-ssmp-2022-01-01_12-37-46/SE/regtest-3-4/N3_rp_md.inp.out


Timed out after 400.0097994739999 seconds.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
$SRC_DIR/regtesting/TEST-Linux-x86-64-conda-ssmp-2022-01-01_12-37-46/SE/regtest-3-4/N3_dp_md.inp.out


Timed out after 400.01004742700025 seconds.
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
$SRC_DIR/regtesting/TEST-Linux-x86-64-conda-ssmp-2022-01-01_12-37-46/SE/regtest-3-4/N3_rp_dp_md.inp.out


Timed out after 400.0142775459999 seconds.

------------------------------- Timings --------------------------------
Plot: name="timings", title="Timing Distribution", ylabel="time [s]"
PlotPoint: name="100th_percentile", plot="timings", label="100th %ile", y=400.03, yerr=0.0
PlotPoint: name="99th_percentile", plot="timings", label="99th %ile", y=30.13, yerr=0.0
PlotPoint: name="98th_percentile", plot="timings", label="98th %ile", y=15.45, yerr=0.0
PlotPoint: name="95th_percentile", plot="timings", label="95th %ile", y=8.60, yerr=0.0
PlotPoint: name="90th_percentile", plot="timings", label="90th %ile", y=5.32, yerr=0.0
PlotPoint: name="80th_percentile", plot="timings", label="80th %ile", y=2.67, yerr=0.0

------------------------------- Summary --------------------------------
Number of FAILED  tests 5
Number of WRONG   tests 0
Number of CORRECT tests 2936
Total number of   tests 2941

Installed packages

no applicable

Environment info

not applicable

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