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precommit: Switch from markdownlint to mdformat
This commit is contained in:
Ole Schütt
Ole Schütt
parent
f95d3a4a5d
commit
786bc82ff9
35 changed files with 266 additions and 579 deletions
13
INSTALL.md
13
INSTALL.md
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@ -197,7 +197,7 @@ the FFTW3 threading library libfftw3_threads (or libfftw3_omp) is required.
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- The version 5.1.0 (or later) of LIBXC can be downloaded from <https://www.tddft.org/programs/libxc>
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- CP2K does not make use of fourth derivates such that LIBXC may be configured
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with './configure --disable-lxc \<other LIBXC configuration flags\>'.
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with './configure --disable-lxc \<other LIBXC configuration flags>'.
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- During the installation, the directories `$(LIBXC_DIR)/lib`
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and `$(LIBXC_DIR)/include` are created.
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- Add `-D__LIBXC` to DFLAGS, `-I$(LIBXC_DIR)/include` to FCFLAGS
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@ -333,8 +333,7 @@ should work out of the box on Nvidia hardware as well.
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- Add `GPUVER=Mi50, Mi60, Mi100, Mi250`
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- Add `OFFLOAD_CC = hipcc`
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- Add `-lamdhip64` to the `LIBS` variable
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- Add `OFFLOAD_FLAGS = '-fopenmp -m64 -pthread -fPIC -D__GRID_HIP -O2
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--offload-arch=gfx908 --rocm-path=$(ROCM_PATH)'` where `ROCM_PATH` is the path
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- Add `OFFLOAD_FLAGS = '-fopenmp -m64 -pthread -fPIC -D__GRID_HIP -O2 --offload-arch=gfx908 --rocm-path=$(ROCM_PATH)'` where `ROCM_PATH` is the path
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where the rocm sdk resides. Architectures Mi250 (gfx90a), Mi100 (gfx908),
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Mi50 (gfx906) the hip backend for the grid library supports nvidia hardware
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as well. It uses the same code and can be used to validate the backend in case
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@ -429,13 +428,13 @@ Alternatively, <https://dashboard.cp2k.org> provides sample arch files as part o
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the testing reports (click on the status field, search for 'ARCH-file').
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- With -DNDEBUG assertions may be stripped ("compiled out").
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- NDEBUG is the ANSI-conforming symbol name (not __NDEBUG).
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- NDEBUG is the ANSI-conforming symbol name (not \_\_NDEBUG).
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- Regular release builds may carry assertions for safety.
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Conventionally, there are six versions:
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| Acronym | Meaning |
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|---------|----------------------------------|
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| Acronym | Meaning |
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| ------- | -------------------------------- |
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| sdbg | OpenMP + debug settings |
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| sopt | OpenMP + OMP_NUM_THREADS=1 |
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| ssmp | OpenMP |
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@ -589,4 +588,4 @@ can be generated using the cp2k executable, see <https://manual.cp2k.org/trunk/g
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## 8. Happy computing
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The CP2K team.
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The CP2K team.
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32
README.md
32
README.md
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@ -22,7 +22,7 @@ To clone the current master (development version):
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git clone --recursive https://github.com/cp2k/cp2k.git cp2k
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```
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Note the ``--recursive`` flag that is needed because CP2K uses git submodules.
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Note the `--recursive` flag that is needed because CP2K uses git submodules.
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To clone a release version v*x.y*:
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@ -41,29 +41,29 @@ For building CP2K from scratch see the [installation instructions](./INSTALL.md)
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## Links
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* [CP2K.org](https://www.cp2k.org)
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- [CP2K.org](https://www.cp2k.org)
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for showcases of scientific work, tutorials, exercises, presentation slides, etc.
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* [The manual](https://manual.cp2k.org/)
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- [The manual](https://manual.cp2k.org/)
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with descriptions of all the keywords for the CP2K input file
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* [The dashboard](https://dashboard.cp2k.org)
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- [The dashboard](https://dashboard.cp2k.org)
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to get an overview of the currently tested architectures
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* [The Google group](https://groups.google.com/group/cp2k) to get help if you
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- [The Google group](https://groups.google.com/group/cp2k) to get help if you
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could not find an answer in one of the previous links
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* [Acknowledgements](https://www.cp2k.org/funding) for list of institutions and
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- [Acknowledgements](https://www.cp2k.org/funding) for list of institutions and
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grants that help to fund the development of CP2K
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## Directory organization
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* [`arch`](./arch): Collection of definitions for different architectures and compilers
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* [`benchmarks`](./benchmarks): Inputs for benchmarks
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* [`data`](./data): Simulation parameters e.g. basis sets and pseudopotentials
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* [`exts`](./exts): Access to external libraries via GIT submodules
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* [`src`](./src): The source code
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* [`tests`](./tests): Inputs for tests and regression tests
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* [`tools`](./tools): Mixed collection of useful scripts related to cp2k
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- [`arch`](./arch): Collection of definitions for different architectures and compilers
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- [`benchmarks`](./benchmarks): Inputs for benchmarks
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- [`data`](./data): Simulation parameters e.g. basis sets and pseudopotentials
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- [`exts`](./exts): Access to external libraries via GIT submodules
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- [`src`](./src): The source code
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- [`tests`](./tests): Inputs for tests and regression tests
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- [`tools`](./tools): Mixed collection of useful scripts related to cp2k
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Additional directories created during build process:
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* `lib`: Libraries built during compilation
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* `obj`: Objects and other intermediate compilation-time files
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* `exe`: Where the executables will be located
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- `lib`: Libraries built during compilation
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- `obj`: Objects and other intermediate compilation-time files
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- `exe`: Where the executables will be located
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@ -85,7 +85,7 @@ dependencies is
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- CP2K_DEV_OPTIONS = OFF : enable developer options. the main purpose is for
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debugging
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- CP2K_USE_GRID_GPU = ON : turn on of gpu support for collocate integrate
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- CP2K_USE_PW_GPU = ON, turn on or off gpu fft support
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- CP2K_USE_DBM_GPU = ON turn on or off dbm gpu support
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@ -120,17 +120,17 @@ with cray-libsci for instance)
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The following list gives several examples of cmake command lines. Just add
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`-DCP2K_USE_SIRIUS=ON` to add support of SIRIUS in cp2k
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```shell cmake -DCP2K_INSTALL_PREFIX=/myprefix ..```
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`shell cmake -DCP2K_INSTALL_PREFIX=/myprefix ..`
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then
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```shell make```
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`shell make`
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- MKL
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the command line is
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```shell cmake -DCP2K_INSTALL_PREFIX=/myprefix -DCP2K_BLAS_VENDOR=MKL
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````shell cmake -DCP2K_INSTALL_PREFIX=/myprefix -DCP2K_BLAS_VENDOR=MKL
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-DCP2K_SCALAPACK_VENDOR=MKL ..```
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- Cray environments (with cray-libsci)
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@ -177,3 +177,4 @@ from time to time. Update to ROCM 5.3.x or above to solve the issue.
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present. '-DCP2k_BLAS_VENDOR=OpenBLAS' will also help cmake to find OpenBLAS if
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it is used. Detecting the scalapack library might also fail if the user
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environment is not properly set up.
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````
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@ -21,13 +21,11 @@ for the MM part of a QM/MM calculation.
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The best configurations are shown below.
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Click the links under "Detailed Results" to see more detail.
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<!-- markdownlint-disable MD013 -->
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| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
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| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | --------------------------------- | ---------------- |
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| HECToR | Cray XE6 | 21/1/2014 | 13196 | 403.928 | 512 cores | 2 OMP threads per MPI task | [hector-h2o-64](https://www.cp2k.org/performance:hector-h2o-64) |
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| ARCHER | Cray XC30 | 9/1/2014 | 13473 | 197.117 | 576 cores | 1 OMP thread per MPI task | [archer-h2o-64](https://www.cp2k.org/performance:archer-h2o-64) |
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| Magnus | Cray XC40 | 6/11/2014 | 14377 | 150.493 | 384 cores | 1 OMP thread per MPI task | [magnus-h2o-64](https://www.cp2k.org/performance:magnus-h2o-64) |
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| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
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| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | --------------------------------- | --------------------------------------------------------------------- |
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| HECToR | Cray XE6 | 21/1/2014 | 13196 | 403.928 | 512 cores | 2 OMP threads per MPI task | [hector-h2o-64](https://www.cp2k.org/performance:hector-h2o-64) |
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| ARCHER | Cray XC30 | 9/1/2014 | 13473 | 197.117 | 576 cores | 1 OMP thread per MPI task | [archer-h2o-64](https://www.cp2k.org/performance:archer-h2o-64) |
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| Magnus | Cray XC40 | 6/11/2014 | 14377 | 150.493 | 384 cores | 1 OMP thread per MPI task | [magnus-h2o-64](https://www.cp2k.org/performance:magnus-h2o-64) |
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| Piz Daint | Cray XC30 | 12/05/2015 | 15268 | 207.972 | 192 cores | 1 OMP thread per MPI task, no GPU | [piz-daint-h2o-64](https://www.cp2k.org/performance:piz-daint-h2o-64) |
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| Cirrus | SGI ICE XA | 24/11/2016 | 7566 | 166.192 | 1152 cores | 9 OMP threads per MPI task | [cirrus-h2o-64](https://www.cp2k.org/performance:cirrus-h2o-64) |
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| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 119.820 | 640 cores | 10 OMP thread per MPI task | [noctua-h2o-64](https://www.cp2k.org/performance:noctua-h2o-64) |
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<!-- markdownlint-enable MD013 -->
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| Cirrus | SGI ICE XA | 24/11/2016 | 7566 | 166.192 | 1152 cores | 9 OMP threads per MPI task | [cirrus-h2o-64](https://www.cp2k.org/performance:cirrus-h2o-64) |
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| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 119.820 | 640 cores | 10 OMP thread per MPI task | [noctua-h2o-64](https://www.cp2k.org/performance:noctua-h2o-64) |
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@ -14,17 +14,17 @@ Generalized Hybrid Orbital (GHO) method.
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## Files description
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``CBD_PHY.inp`` - CP2K input file.
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`CBD_PHY.inp` - CP2K input file.
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``CBD_PHY.prmtop`` - Amber forcefield for MM atoms. The Amber03 forcefield and
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`CBD_PHY.prmtop` - Amber forcefield for MM atoms. The Amber03 forcefield and
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the TIP3P water model are used.
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``CBD_PHY.pdb`` - Atomic input coordinates.
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`CBD_PHY.pdb` - Atomic input coordinates.
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## Results
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### MD Energy file
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<!-- markdownlint-disable MD013 -->
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```cp2k-output
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# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
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0 0.000000 239.300084734 300.000000000 -1095.757596412 -856.457511678 0.000000000
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@ -34,14 +34,11 @@ the TIP3P water model are used.
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4 4.000000 237.524625019 297.774184180 -1087.284636223 -849.760011204 26.518459213
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5 5.000000 245.799648725 308.148217747 -1101.835669561 -856.036020836 27.761591604
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```
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<!-- markdownlint-enable MD013 -->
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### Best Configurations
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The best configurations are shown below.
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<!-- markdownlint-disable MD013 -->
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | -----------| ---------------- | --------------- | --------------------------------- |
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| ARCHER | Cray XC30 | 07/06/2020 | 6e0731f | 358.478 | 576 | 6 OMP threads per MPI task |
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<!-- markdownlint-enable MD013 -->
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | ---------- | ---------------- | --------------- | -------------------------- |
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| ARCHER | Cray XC30 | 07/06/2020 | 6e0731f | 358.478 | 576 | 6 OMP threads per MPI task |
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@ -20,20 +20,19 @@ See also <https://doi.org/10.1021/acs.jctc.9b00424>.
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## Files description
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``ClC-19.inp`` - ClC with 19 QM atoms.
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`ClC-19.inp` - ClC with 19 QM atoms.
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``ClC-253.inp`` - ClC with 253 QM atoms.
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`ClC-253.inp` - ClC with 253 QM atoms.
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``ClC.prmtop`` - Amber forcefield for MM atoms. The Amber14 forcefield and
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`ClC.prmtop` - Amber forcefield for MM atoms. The Amber14 forcefield and
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the TIP3P water model are used.
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``ClC.pdb`` - Atomic input coordinates.
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`ClC.pdb` - Atomic input coordinates.
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## Results
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### MD Energy file for ClC-19
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<!-- markdownlint-disable MD013 -->
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```cp2k-output
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# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
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0 0.000000 215.076797492 300.000000000 -596.086687006 -381.009889515 0.000000000
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@ -58,13 +57,12 @@ the TIP3P water model are used.
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### Best Configuration for ClC-19
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | -----------| ---------------- | --------------- | --------------------------------- |
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| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 225.171 | 384 | 4 OMP threads per MPI task |
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | ---------- | ---------------- | --------------- | -------------------------- |
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| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 225.171 | 384 | 4 OMP threads per MPI task |
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### Best Configuration for ClC-253
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | -----------| ---------------- | --------------- | --------------------------------- |
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| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 937.151 | 576 | 6 OMP threads per MPI task |
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<!-- markdownlint-enable MD013 -->
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | ---------- | ---------------- | --------------- | -------------------------- |
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| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 937.151 | 576 | 6 OMP threads per MPI task |
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@ -17,17 +17,17 @@ See also <https://doi.org/10.1021/acs.jctc.9b00424>.
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## Files description
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``MQAE.inp`` - CP2K input file.
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`MQAE.inp` - CP2K input file.
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``MQAE.prmtop`` - Amber forcefield for MM atoms. The Amber14 forcefield and
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`MQAE.prmtop` - Amber forcefield for MM atoms. The Amber14 forcefield and
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the SPCE water model are used.
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``MQAE.pdb`` - Atomic input coordinates.
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`MQAE.pdb` - Atomic input coordinates.
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## Results
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### MD Energy file
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<!-- markdownlint-disable MD013 -->
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```cp2k-output
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# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
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0 0.000000 10.239105709 300.000000000 -191.999316391 -181.760210683 0.000000000
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@ -42,7 +42,6 @@ the SPCE water model are used.
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The best configurations are shown below.
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | -----------| ---------------- | --------------- | --------------------------------- |
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| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 72.439 | 384 | 6 OMP threads per MPI task |
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<!-- markdownlint-enable MD013 -->
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| Machine Name | Architecture | Date | Commit No. | Fastest time (s) | Number of Cores | Number of Threads |
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| ------------ | ------------ | ---------- | ---------- | ---------------- | --------------- | -------------------------- |
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| ARCHER | Cray XC30 | 16/06/2020 | 6e0731f | 72.439 | 384 | 6 OMP threads per MPI task |
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|
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@ -35,13 +35,11 @@ initial guess of the electronic density is made based on Atomic Orbitals.
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The best configurations are shown below.
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Click the links under "Detailed Results" to see more detail.
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<!-- markdownlint-disable MD013 -->
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| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
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| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | --------------------------------- | ---------------- |
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| HECToR | Cray XE6 | 21/1/2014 | 13196 | 39.066 | 512 cores | 2 OMP threads per MPI task | [hector-h2o-64](https://www.cp2k.org/performance:hector-h2o-64) |
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| ARCHER | Cray XC30 | 8/1/2014 | 13473 | 18.11 | 576 cores | 1 OMP thread per MPI task | [archer-h2o-64](https://www.cp2k.org/performance:archer-h2o-64) |
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| Magnus | Cray XC40 | 22/10/2014 | 14377 | 17.275 | 384 cores | 1 OMP thread per MPI task | [magnus-h2o-64](https://www.cp2k.org/performance:magnus-h2o-64) |
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| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
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| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | --------------------------------- | --------------------------------------------------------------------- |
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| HECToR | Cray XE6 | 21/1/2014 | 13196 | 39.066 | 512 cores | 2 OMP threads per MPI task | [hector-h2o-64](https://www.cp2k.org/performance:hector-h2o-64) |
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| ARCHER | Cray XC30 | 8/1/2014 | 13473 | 18.11 | 576 cores | 1 OMP thread per MPI task | [archer-h2o-64](https://www.cp2k.org/performance:archer-h2o-64) |
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| Magnus | Cray XC40 | 22/10/2014 | 14377 | 17.275 | 384 cores | 1 OMP thread per MPI task | [magnus-h2o-64](https://www.cp2k.org/performance:magnus-h2o-64) |
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| Piz Daint | Cray XC30 | 12/05/2015 | 15268 | 19.885 | 192 cores | 1 OMP thread per MPI task, no GPU | [piz-daint-h2o-64](https://www.cp2k.org/performance:piz-daint-h2o-64) |
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| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 15.560 | 1152 cores | 9 OMP threads per MPI task | [cirrus-h2o-64](https://www.cp2k.org/performance:cirrus-h2o-64) |
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| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 13.3 | 640 cores | 10 OMP threads per MPI task | [noctua-h2o-64](https://www.cp2k.org/performance:noctua-h2o-64) |
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<!-- markdownlint-enable MD013 -->
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| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 15.560 | 1152 cores | 9 OMP threads per MPI task | [cirrus-h2o-64](https://www.cp2k.org/performance:cirrus-h2o-64) |
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| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 13.3 | 640 cores | 10 OMP threads per MPI task | [noctua-h2o-64](https://www.cp2k.org/performance:noctua-h2o-64) |
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@ -41,16 +41,14 @@ the number of atoms scales cubically with `NREP`.
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The best configurations are shown below.
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Click the links under "Detailed Results" to see more detail.
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<!-- markdownlint-disable MD013 -->
|
||||
| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
|
||||
| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | ---------------------------------- | ---------------- |
|
||||
| HECToR | Cray XE6 | 16/1/2014 | 13196 | 98.256 | 65536 | 8 OMP threads per MPI task | [hector-h2o-dft-ls](https://www.cp2k.org/performance:hector-h2o-dft-ls) |
|
||||
| ARCHER | Cray XC30 | 8/1/2014 | 13473 | 28.476 | 49152 | 4 OMP threads per MPI task | [archer-h2o-dft-ls](https://www.cp2k.org/performance:archer-h2o-dft-ls) |
|
||||
| Magnus | Cray XC40 | 3/12/2014 | 14377 | 30.921 | 24576 | 2 OMP threads per MPI task | [magnus-h2o-dft-ls](https://www.cp2k.org/performance:magnus-h2o-dft-ls) |
|
||||
| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
|
||||
| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | ---------------------------------- | ----------------------------------------------------------------------------- |
|
||||
| HECToR | Cray XE6 | 16/1/2014 | 13196 | 98.256 | 65536 | 8 OMP threads per MPI task | [hector-h2o-dft-ls](https://www.cp2k.org/performance:hector-h2o-dft-ls) |
|
||||
| ARCHER | Cray XC30 | 8/1/2014 | 13473 | 28.476 | 49152 | 4 OMP threads per MPI task | [archer-h2o-dft-ls](https://www.cp2k.org/performance:archer-h2o-dft-ls) |
|
||||
| Magnus | Cray XC40 | 3/12/2014 | 14377 | 30.921 | 24576 | 2 OMP threads per MPI task | [magnus-h2o-dft-ls](https://www.cp2k.org/performance:magnus-h2o-dft-ls) |
|
||||
| Piz Daint | Cray XC30 | 12/05/2015 | 15268 | 27.900 | 32768 | 2 OMP threads per MPI task, no GPU | [piz-daint-h2o-dft-ls](https://www.cp2k.org/performance:piz-daint-h2o-dft-ls) |
|
||||
| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 543.032 | 2016 | 2 OMP threads per MPI task | [cirrus-h2o-dft-ls](https://www.cp2k.org/performance:cirrus-h2o-dft-ls) |
|
||||
| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 37.730 | 10240 | 10 OMP threads per MPI task | [noctua-h2o-dft-ls](https://www.cp2k.org/performance:noctua-h2o-dft-ls) |
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 543.032 | 2016 | 2 OMP threads per MPI task | [cirrus-h2o-dft-ls](https://www.cp2k.org/performance:cirrus-h2o-dft-ls) |
|
||||
| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 37.730 | 10240 | 10 OMP threads per MPI task | [noctua-h2o-dft-ls](https://www.cp2k.org/performance:noctua-h2o-dft-ls) |
|
||||
|
||||
### Weak Scaling on Piz Daint, CSCS
|
||||
|
||||
|
|
@ -67,26 +65,24 @@ Following results were obtained in the following conditions:
|
|||
while the cells marked with an `X` crashed with out-of-memory errors, and the
|
||||
cells left empty weren't measured.
|
||||
|
||||
| nodes / NREP | NREP=1 | NREP=2 | NREP=3 | NREP=4 | NREP=6 | NREP=8 | NREP=9 |
|
||||
| ------------- | ----- | ----- | ----- | ----- | ----- | ----- | ----- |
|
||||
| 1 node | 7.4 | 60.3 | X | | | | |
|
||||
| 2 nodes | 7.4 | 35.0 | 269.4 | X | | | |
|
||||
| 4 nodes | 9.9 | 22.7 | 149.8 | X | | | |
|
||||
| 6 nodes | 12.1 | 19.7 | 113.0 | X | | | |
|
||||
| 8 nodes | 11.4 | 16.4 | 90.2 | 253.4 | X | | |
|
||||
| 12 nodes | 15.5 | 21.7 | 71.5 | 193.8 | X | | |
|
||||
| 16 nodes | 15.5 | 20.8 | 61.5 | 159.2 | X | | |
|
||||
| 24 nodes | 22.0 | 24.7 | 51.8 | 130.2 | X | | |
|
||||
| 32 nodes | 15.9 | 20.4 | 42.8 | 101.8 | 352.9 | X | |
|
||||
| 36 nodes | 21.9 | 25.6 | 44.0 | 99.8 | 333.0 | X | |
|
||||
| 48 nodes | 24.5 | 34.1 | 42.0 | 84.1 | 277.9 | X | |
|
||||
| 64 nodes | 24.9 | 29.0 | 40.4 | 79.7 | 257.5 | X | |
|
||||
| 128 nodes | 26.3 | 32.8 | 36.6 | 62.5 | 181.9 | 400.6 | X |
|
||||
| nodes / NREP | NREP=1 | NREP=2 | NREP=3 | NREP=4 | NREP=6 | NREP=8 | NREP=9 |
|
||||
| ------------ | ------ | ------ | ------ | ------ | ------ | ------ | ------ |
|
||||
| 1 node | 7.4 | 60.3 | X | | | | |
|
||||
| 2 nodes | 7.4 | 35.0 | 269.4 | X | | | |
|
||||
| 4 nodes | 9.9 | 22.7 | 149.8 | X | | | |
|
||||
| 6 nodes | 12.1 | 19.7 | 113.0 | X | | | |
|
||||
| 8 nodes | 11.4 | 16.4 | 90.2 | 253.4 | X | | |
|
||||
| 12 nodes | 15.5 | 21.7 | 71.5 | 193.8 | X | | |
|
||||
| 16 nodes | 15.5 | 20.8 | 61.5 | 159.2 | X | | |
|
||||
| 24 nodes | 22.0 | 24.7 | 51.8 | 130.2 | X | | |
|
||||
| 32 nodes | 15.9 | 20.4 | 42.8 | 101.8 | 352.9 | X | |
|
||||
| 36 nodes | 21.9 | 25.6 | 44.0 | 99.8 | 333.0 | X | |
|
||||
| 48 nodes | 24.5 | 34.1 | 42.0 | 84.1 | 277.9 | X | |
|
||||
| 64 nodes | 24.9 | 29.0 | 40.4 | 79.7 | 257.5 | X | |
|
||||
| 128 nodes | 26.3 | 32.8 | 36.6 | 62.5 | 181.9 | 400.6 | X |
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
| nodes / NREP | NREP=6 | NREP=8 | NREP=9 | NREP=10 | NREP=11 | NREP=12 | NREP=13 | NREP=14 | NREP=16 | NREP=18 | NREP=19 | NREP=20 |
|
||||
| ------------- | ----- | ----- | ----- | ------- | ------- | ------- | ------- | ------- | ------- | ------- | ------- | ------- |
|
||||
| 256 nodes | 132.6 | 262.3 | 359.2 | 498.8 | 647.1 | X | | | | | | |
|
||||
| 512 nodes | 106.0 | 212.5 | 290.2 | 409.2 | 534.0 | 732.3 | 875.2 | 1030.1 | X | | | |
|
||||
| 1024 nodes | 98.1 | 168.9 | | 284.7 | | 510.8 | | 786.5 | 1161.1 | 1607.3 | 1872.8 | X |
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
| nodes / NREP | NREP=6 | NREP=8 | NREP=9 | NREP=10 | NREP=11 | NREP=12 | NREP=13 | NREP=14 | NREP=16 | NREP=18 | NREP=19 | NREP=20 |
|
||||
| ------------ | ------ | ------ | ------ | ------- | ------- | ------- | ------- | ------- | ------- | ------- | ------- | ------- |
|
||||
| 256 nodes | 132.6 | 262.3 | 359.2 | 498.8 | 647.1 | X | | | | | | |
|
||||
| 512 nodes | 106.0 | 212.5 | 290.2 | 409.2 | 534.0 | 732.3 | 875.2 | 1030.1 | X | | | |
|
||||
| 1024 nodes | 98.1 | 168.9 | | 284.7 | | 510.8 | | 786.5 | 1161.1 | 1607.3 | 1872.8 | X |
|
||||
|
|
|
|||
|
|
@ -29,7 +29,7 @@ avoid recomputing any integrals on-the-fly, improving performance.
|
|||
## Benchmark Requirements
|
||||
|
||||
To run these this benchmark, CP2K needs to be compiled with libint support
|
||||
(-D__LIBINT), and it is advantageous to have a OMP/MPI hybrid code (cp2k.psmp).
|
||||
(-D\_\_LIBINT), and it is advantageous to have a OMP/MPI hybrid code (cp2k.psmp).
|
||||
|
||||
## How to Run the Benchmark
|
||||
|
||||
|
|
@ -41,7 +41,7 @@ To run these this benchmark, CP2K needs to be compiled with libint support
|
|||
cp LiH_bulk_3-RESTART.wfn B88.wfn
|
||||
```
|
||||
|
||||
2. run `input_bulk_HFX_3.inp` on a number of nodes (about 30min on 2048 cores)
|
||||
1. run `input_bulk_HFX_3.inp` on a number of nodes (about 30min on 2048 cores)
|
||||
|
||||
The obtained energies should be similar to (obtained on 2048 MPI x 8 OMP cores):
|
||||
|
||||
|
|
@ -108,18 +108,16 @@ BASIS_SET OPT1
|
|||
The best configurations are shown below. Click the links under
|
||||
"Detailed Results" to see more detail.
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of cores | Number of threads | Detailed results |
|
||||
| ------------:| ------------:| ----------:| ------------:| ----------------:| ---------------:| ----------------------------------:| ----------------:|
|
||||
| HECToR | Cray XE6 | 21/1/2014 | 13196(*) | 121.362 | 65536 | 8 OMP threads per MPI task | [hector-lih-hfx](https://www.cp2k.org/performance:hector-lih-hfx) |
|
||||
| ARCHER | Cray XC30 | 9/1/2014 | 13473(*) | 51.172 | 49152 | 6 OMP threads per MPI task | [archer-lih-hfx](https://www.cp2k.org/performance:archer-lih-hfx) |
|
||||
| Magnus | Cray XC40 | 10/11/2014 | 14377(*) | 62.075 | 24576 | 4 OMP threads per MPI task | [magnus-lih-hfx](https://www.cp2k.org/performance:magnus-lih-hfx) |
|
||||
| Piz Daint | Cray XC30 | 12/05/2015 | 15268 | 66.051 | 32768 | 4 OMP threads per MPI task, no GPU | [piz-daint-lih-hfx](https://www.cp2k.org/performance:piz-daint-lih-hfx) |
|
||||
| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 483.676 | 2016 | 6 OMP threads per MPI task | [cirrus-lih-hfx](https://www.cp2k.org/performance:cirrus-lih-hfx) |
|
||||
| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 131.290 | 10240 | 4 OMP threads per MPI task | [noctua-lih-hfx](https://www.cp2k.org/performance:noctua-lih-hfx) |
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of cores | Number of threads | Detailed results |
|
||||
| -----------: | -----------: | ---------: | -----------: | ---------------: | --------------: | ---------------------------------: | ----------------------------------------------------------------------: |
|
||||
| HECToR | Cray XE6 | 21/1/2014 | 13196(\*) | 121.362 | 65536 | 8 OMP threads per MPI task | [hector-lih-hfx](https://www.cp2k.org/performance:hector-lih-hfx) |
|
||||
| ARCHER | Cray XC30 | 9/1/2014 | 13473(\*) | 51.172 | 49152 | 6 OMP threads per MPI task | [archer-lih-hfx](https://www.cp2k.org/performance:archer-lih-hfx) |
|
||||
| Magnus | Cray XC40 | 10/11/2014 | 14377(\*) | 62.075 | 24576 | 4 OMP threads per MPI task | [magnus-lih-hfx](https://www.cp2k.org/performance:magnus-lih-hfx) |
|
||||
| Piz Daint | Cray XC30 | 12/05/2015 | 15268 | 66.051 | 32768 | 4 OMP threads per MPI task, no GPU | [piz-daint-lih-hfx](https://www.cp2k.org/performance:piz-daint-lih-hfx) |
|
||||
| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 483.676 | 2016 | 6 OMP threads per MPI task | [cirrus-lih-hfx](https://www.cp2k.org/performance:cirrus-lih-hfx) |
|
||||
| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 131.290 | 10240 | 4 OMP threads per MPI task | [noctua-lih-hfx](https://www.cp2k.org/performance:noctua-lih-hfx) |
|
||||
|
||||
(*) Prior to r14945, a bug resulted in an underestimation of the number of ERIs
|
||||
(\*) Prior to r14945, a bug resulted in an underestimation of the number of ERIs
|
||||
which should be computed (by roughly 50% for this benchmark. Therefore these
|
||||
results cannot be compared directly with later ones.
|
||||
|
||||
|
|
@ -128,12 +126,12 @@ results cannot be compared directly with later ones.
|
|||
Running on ORNL's Cray XT5 (Jaguar) the following runtime has been obtained in a
|
||||
setup using 8 OMP threads per node (8 cores per node / 16 Gb per node).
|
||||
|
||||
| Cores | Full CP2K[s] | HFX[s] | local HFX[s] | Mem/node[Mb] |
|
||||
| -----:| ------------:| -------:| ------------:| ------------:|
|
||||
| 1024 | 6569.07 | 6488.24 | 6406.99 | 14845.00 |
|
||||
| 2048 | 1369.92 | 1314.86 | 1259.82 | 13468.00 |
|
||||
| 4096 | 722.24 | 670.18 | 631.11 | 7293.00 |
|
||||
| 8192 | 402.18 | 352.21 | 317.59 | 4306.00 |
|
||||
| 16384 | 274.41 | 213.88 | 172.88 | 2801.00 |
|
||||
| 32768 | 201.71 | 135.47 | 85.29 | 2046.00 |
|
||||
| 65536 | 255.97 | 117.33 | 41.43 | 1673.00 |
|
||||
| Cores | Full CP2K\[s\] | HFX\[s\] | local HFX\[s\] | Mem/node\[Mb\] |
|
||||
| ----: | -------------: | -------: | -------------: | -------------: |
|
||||
| 1024 | 6569.07 | 6488.24 | 6406.99 | 14845.00 |
|
||||
| 2048 | 1369.92 | 1314.86 | 1259.82 | 13468.00 |
|
||||
| 4096 | 722.24 | 670.18 | 631.11 | 7293.00 |
|
||||
| 8192 | 402.18 | 352.21 | 317.59 | 4306.00 |
|
||||
| 16384 | 274.41 | 213.88 | 172.88 | 2801.00 |
|
||||
| 32768 | 201.71 | 135.47 | 85.29 | 2046.00 |
|
||||
| 65536 | 255.97 | 117.33 | 41.43 | 1673.00 |
|
||||
|
|
|
|||
|
|
@ -18,8 +18,8 @@ To run the benchmark, CP2K needs to be compiled with libint support (`-D__LIBINT
|
|||
|
||||
## Results on Piz Dora, CSCS
|
||||
|
||||
| Input File | Configuration | Total Number of Cores| Runtime [s] |
|
||||
| ---------- | -------------------------:| --------------------:| ------------:|
|
||||
| GW.inp | 16 nodes x 36 MPI x 1 OMP | 576 | 305 |
|
||||
| Input File | Configuration | Total Number of Cores | Runtime \[s\] |
|
||||
| ---------- | ------------------------: | --------------------: | ------------: |
|
||||
| GW.inp | 16 nodes x 36 MPI x 1 OMP | 576 | 305 |
|
||||
|
||||
The timings have been obtained on CRAY-XC40 (PizDora@CSCS)
|
||||
|
|
|
|||
|
|
@ -16,17 +16,16 @@
|
|||
|
||||
1. run `H2O-128-PBE-TZ.inp`: this will generate the file `H2O-128-PBE-TZ-RESTART.wfn`,
|
||||
necessary for the benchmark run.
|
||||
2. run `H2O-128-RI-dRPA-TZ.inp` for the RI-RPA benchmark.
|
||||
1. run `H2O-128-RI-dRPA-TZ.inp` for the RI-RPA benchmark.
|
||||
|
||||
## Results
|
||||
|
||||
### Results on Piz Daint, CSCS
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
| Input File | Date | CP2K Git SHA | Number of nodes | Node Configuration | Runtime |
|
||||
| ---------------------- | ---------- | ------------:| ---------------:| ------------------- | ------- |
|
||||
| H2O-128-PBE-TZ.inp | 2019-08-19 | 4519a8ad7 | 4 nodes | 12 MPI x 1 OMP | ~2 min |
|
||||
| H2O-128-RI-dRPA-TZ.inp | 2019-08-19 | 4519a8ad7 | 128 nodes | 2 MPI x 6 OMP | 80 min |
|
||||
| H2O-128-RI-dRPA-TZ.inp | 2019-12-03 | 78cea8eee | 1024 nodes | 2 MPI x 6 OMP | 487 sec |
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
|
||||
*) The timings have been obtained on CRAY-XC50 (PizDaint@CSCS, GPU partition)
|
||||
| Input File | Date | CP2K Git SHA | Number of nodes | Node Configuration | Runtime |
|
||||
| ---------------------- | ---------- | -----------: | --------------: | ------------------ | ------- |
|
||||
| H2O-128-PBE-TZ.inp | 2019-08-19 | 4519a8ad7 | 4 nodes | 12 MPI x 1 OMP | ~2 min |
|
||||
| H2O-128-RI-dRPA-TZ.inp | 2019-08-19 | 4519a8ad7 | 128 nodes | 2 MPI x 6 OMP | 80 min |
|
||||
| H2O-128-RI-dRPA-TZ.inp | 2019-12-03 | 78cea8eee | 1024 nodes | 2 MPI x 6 OMP | 487 sec |
|
||||
|
||||
\*) The timings have been obtained on CRAY-XC50 (PizDaint@CSCS, GPU partition)
|
||||
|
|
|
|||
|
|
@ -23,16 +23,16 @@ are taken from [cp2k/data](../../../data) directory.
|
|||
|
||||
1. run `H2O-32-PBE-TZ.inp`: this will generate the file `H2O-32-PBE-TZ-RESTART.wfn`,
|
||||
necessary for the two benchmark runs.
|
||||
2. run `H2O-32-RI-MP2-TZ.inp` for the RI-MP2 benchmark.
|
||||
3. and/or run `H2O-32-RI-dRPA-TZ.inp` for the RI-RPA benchmark.
|
||||
1. run `H2O-32-RI-MP2-TZ.inp` for the RI-MP2 benchmark.
|
||||
1. and/or run `H2O-32-RI-dRPA-TZ.inp` for the RI-RPA benchmark.
|
||||
|
||||
## Results
|
||||
|
||||
### Results on Piz Dora, CSCS
|
||||
|
||||
| Input File | Configuration | Total Number of Cores| Runtime [s] |
|
||||
| ---------- | -------------------------:| --------------------:| ------------:|
|
||||
| RI-MP2.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 392 |
|
||||
| RI-RPA.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 221 |
|
||||
| Input File | Configuration | Total Number of Cores | Runtime \[s\] |
|
||||
| ---------- | ------------------------: | --------------------: | ------------: |
|
||||
| RI-MP2.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 392 |
|
||||
| RI-RPA.inp | 16 nodes x 16 MPI x 1 OMP | 256 | 221 |
|
||||
|
||||
*) The timings have been obtained on CRAY-XC40 (PizDora@CSCS)
|
||||
\*) The timings have been obtained on CRAY-XC40 (PizDora@CSCS)
|
||||
|
|
|
|||
|
|
@ -24,8 +24,8 @@ RI-MP2 run, and can be found in the [cp2k/data](../../../data) directory.
|
|||
|
||||
1. run `H2O-64-PBE-TZ.inp`: this will generate the file `H2O-64-PBE-TZ-RESTART.wfn`,
|
||||
necessary for the two benchmark runs.
|
||||
2. run `H2O-64-RI-MP2-TZ.inp` for the RI-MP2 benchmark.
|
||||
3. and/or run `H2O-64-RI-dRPA-TZ.inp` for the RI-RPA benchmark.
|
||||
1. run `H2O-64-RI-MP2-TZ.inp` for the RI-MP2 benchmark.
|
||||
1. and/or run `H2O-64-RI-dRPA-TZ.inp` for the RI-RPA benchmark.
|
||||
|
||||
## Results
|
||||
|
||||
|
|
@ -34,33 +34,30 @@ RI-MP2 run, and can be found in the [cp2k/data](../../../data) directory.
|
|||
The best configurations are shown below.
|
||||
Click the links under "Detailed Results"to see more detail.
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
|
||||
| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | ---------------------------------- | ---------------- |
|
||||
| HECToR | Cray XE6 | 13/01/2014 | 13196 | 141.633 | 49152 | 8 OMP threads per MPI task | [hector-h2o-64-ri-mp2](https://www.cp2k.org/performance:hector-h2o-64-ri-mp2) |
|
||||
| ARCHER | Cray XC30 | 09/01/2014 | 13473 | 83.945 | 36864 | 4 OMP threads per MPI task | [archer-h2o-64-ri-mp2](https://www.cp2k.org/performance:archer-h2o-64-ri-mp2) |
|
||||
| Magnus | Cray XC40 | 04/11/2014 | 14377 | 63.891 | 24576 | 6 OMP threads per MPI task | [magnus-h2o-64-ri-mp2](https://www.cp2k.org/performance:magnus-h2o-64-ri-mp2) |
|
||||
| Machine Name | Architecture | Date | SVN Revision | Fastest time (s) | Number of Cores | Number of Threads | Detailed Results |
|
||||
| ------------ | ------------ | ---------- | ------------ | ---------------- | --------------- | ---------------------------------- | ----------------------------------------------------------------------------------- |
|
||||
| HECToR | Cray XE6 | 13/01/2014 | 13196 | 141.633 | 49152 | 8 OMP threads per MPI task | [hector-h2o-64-ri-mp2](https://www.cp2k.org/performance:hector-h2o-64-ri-mp2) |
|
||||
| ARCHER | Cray XC30 | 09/01/2014 | 13473 | 83.945 | 36864 | 4 OMP threads per MPI task | [archer-h2o-64-ri-mp2](https://www.cp2k.org/performance:archer-h2o-64-ri-mp2) |
|
||||
| Magnus | Cray XC40 | 04/11/2014 | 14377 | 63.891 | 24576 | 6 OMP threads per MPI task | [magnus-h2o-64-ri-mp2](https://www.cp2k.org/performance:magnus-h2o-64-ri-mp2) |
|
||||
| Piz Daint | Cray XC30 | 12/05/2015 | 15268 | 48.15 | 32768 | 8 OMP threads per MPI task, no GPU | [piz-daint-h2o-64-ri-mp2](https://www.cp2k.org/performance:piz-daint-h2o-64-ri-mp2) |
|
||||
| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 303.571 | 2016 | 1 OMP thread per MPI task | [cirrus-h2o-64-ri-mp2](https://www.cp2k.org/performance:cirrus-h2o-64-ri-mp2) |
|
||||
| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 82.571 | 10240 | 2 OMP threads per MPI task | [noctua-h2o-64-ri-mp2](https://www.cp2k.org/performance:noctua-h2o-64-ri-mp2) |
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
| Cirrus | SGI ICE XA | 24/11/2016 | 17566 | 303.571 | 2016 | 1 OMP thread per MPI task | [cirrus-h2o-64-ri-mp2](https://www.cp2k.org/performance:cirrus-h2o-64-ri-mp2) |
|
||||
| Noctua | Cray CS500 | 25/09/2019 | 9f58d81 | 82.571 | 10240 | 2 OMP threads per MPI task | [noctua-h2o-64-ri-mp2](https://www.cp2k.org/performance:noctua-h2o-64-ri-mp2) |
|
||||
|
||||
### Results on Monte Rosa, CSCS
|
||||
|
||||
| Input File | Configuration | Total Number of Cores| Runtime |
|
||||
| --------------------- | -------------------:| --------------------:| -------:|
|
||||
| H2O-64-PBE-TZ.inp | 128 MPI x 2 OMP | 256 | 50 s |
|
||||
| H2O-64-RI-MP2-TZ.inp | 1024 MPI x 2 OMP | 2048 | ~18 min |
|
||||
| H2O-64-RI-dRPA-TZ.inp | 1024 MPI x 2 OMP | 2048 | ~12 min |
|
||||
| Input File | Configuration | Total Number of Cores | Runtime |
|
||||
| --------------------- | ---------------: | --------------------: | ------: |
|
||||
| H2O-64-PBE-TZ.inp | 128 MPI x 2 OMP | 256 | 50 s |
|
||||
| H2O-64-RI-MP2-TZ.inp | 1024 MPI x 2 OMP | 2048 | ~18 min |
|
||||
| H2O-64-RI-dRPA-TZ.inp | 1024 MPI x 2 OMP | 2048 | ~12 min |
|
||||
|
||||
*) The timings have been obtained on CRAY-XE6 (MonteRosa@CSCS)
|
||||
\*) The timings have been obtained on CRAY-XE6 (MonteRosa@CSCS)
|
||||
|
||||
### Results on Piz Daint, CSCS
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
| Input File | Date | CP2K Git SHA | Number of nodes | Node Configuration | Runtime |
|
||||
| --------------------- | ---------- | ------------:| ---------------:| ------------------- | ------- |
|
||||
| H2O-64-PBE-TZ.inp | 2019-08-07 | 4519a8ad7 | 4 nodes | 12 MPI x 1 OMP | 69 s |
|
||||
| H2O-64-RI-dRPA-TZ.inp | 2019-08-07 | 4519a8ad7 | 128 nodes | 2 MPI x 6 OMP | 455 s |
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
|
||||
*) The timings have been obtained on CRAY-XC50 (PizDaint@CSCS, GPU partition)
|
||||
| Input File | Date | CP2K Git SHA | Number of nodes | Node Configuration | Runtime |
|
||||
| --------------------- | ---------- | -----------: | --------------: | ------------------ | ------- |
|
||||
| H2O-64-PBE-TZ.inp | 2019-08-07 | 4519a8ad7 | 4 nodes | 12 MPI x 1 OMP | 69 s |
|
||||
| H2O-64-RI-dRPA-TZ.inp | 2019-08-07 | 4519a8ad7 | 128 nodes | 2 MPI x 6 OMP | 455 s |
|
||||
|
||||
\*) The timings have been obtained on CRAY-XC50 (PizDaint@CSCS, GPU partition)
|
||||
|
|
|
|||
|
|
@ -23,11 +23,11 @@ linear algebra routines as displayed at the end of the cp2k output.
|
|||
|
||||
On rosa the total run times are approximately:
|
||||
|
||||
| Input file | Number cores | Runtime |
|
||||
| ------------- | ------------:| ---------------------:|
|
||||
| H2O-256.inp | 576 cores | 5 min |
|
||||
| H2O-1024.inp | 576 cores | 40 min |
|
||||
| H2O-4096.inp | 2304 cores | 15 min |
|
||||
| Input file | Number cores | Runtime |
|
||||
| ------------- | -----------: | --------------------: |
|
||||
| H2O-256.inp | 576 cores | 5 min |
|
||||
| H2O-1024.inp | 576 cores | 40 min |
|
||||
| H2O-4096.inp | 2304 cores | 15 min |
|
||||
| H2O-65536.inp | | doesn't run so far... |
|
||||
|
||||
Runs performed with cp2k from 30.01.09 (no libdbcsr routines used), compiled
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ nodes, SB + K20X, +- 8Gb mem used per node
|
|||
```
|
||||
|
||||
### MD Energy File
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
|
||||
```shell
|
||||
> cat pao_ml_md-1.ener
|
||||
# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
|
||||
|
|
@ -64,7 +64,6 @@ nodes, SB + K20X, +- 8Gb mem used per node
|
|||
19 9.500000 105.405738067 286.181305486 -554932.815285468 -554827.409547401 365.768221021
|
||||
20 10.000000 102.522367308 278.352824576 -554929.882289568 -554827.359922261 364.275226861
|
||||
```
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
|
||||
### Timings
|
||||
|
||||
|
|
|
|||
|
|
@ -2,5 +2,5 @@
|
|||
|
||||
The purpose of these tests is to give a quick idea of the performance of a
|
||||
system, when only a single node is available.
|
||||
The tests should run in < 5 minutes on a modern node,
|
||||
The tests should run in \< 5 minutes on a modern node,
|
||||
and require less than 16Gb of memory.
|
||||
|
|
|
|||
|
|
@ -5,11 +5,10 @@ This directory contains NNP models from the following paper:
|
|||
Committee neural network potentials control generalization errors
|
||||
and enable active learning
|
||||
Christoph Schran, Kyrstof Brezina, and Ondrej Marsalek
|
||||
J. Chem. Phys. 153, 2020, DOI: [10.1063/5.0016004](
|
||||
https://doi.org/10.1063/5.0016004)
|
||||
J. Chem. Phys. 153, 2020, DOI: [10.1063/5.0016004](https://doi.org/10.1063/5.0016004)
|
||||
arXiv: [2006.01541](https://arxiv.org/abs/2006.01541)
|
||||
|
||||
## Contents
|
||||
|
||||
* `nnp-1/2/3/4/5/6/7/8`
|
||||
All parameters of the C-NNP model from generation 4 of the active learning procedure.
|
||||
- `nnp-1/2/3/4/5/6/7/8`
|
||||
All parameters of the C-NNP model from generation 4 of the active learning procedure.
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ written in C. For the time being only features required by [DBT](../dbt/) are im
|
|||
|
||||
## Storage
|
||||
|
||||
The DBM uses [coordinate lists](https://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_(COO))
|
||||
The DBM uses [coordinate lists](<https://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_(COO)>)
|
||||
as internal storage format.
|
||||
An existing block is represented by the following data structure:
|
||||
|
||||
|
|
@ -18,7 +18,7 @@ typedef struct {
|
|||
```
|
||||
|
||||
To allow for efficient OpenMP parallelism the blocks are
|
||||
[sharded](https://en.wikipedia.org/wiki/Shard_(database_architecture)) via round-robin:
|
||||
[sharded](<https://en.wikipedia.org/wiki/Shard_(database_architecture)>) via round-robin:
|
||||
|
||||
```C
|
||||
const int ishard = row % matrix->nshards;
|
||||
|
|
@ -45,7 +45,6 @@ The last stage of the multiplication are the backends for specific hardware, e.g
|
|||
They are passed batches of task for processing. Each task describes a single block
|
||||
multiplication. A simplest backend implementation looks like this:
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
```C
|
||||
for (int itask = 0; itask < ntasks; itask++) {
|
||||
const dbm_task_t task = batch[itask];
|
||||
|
|
@ -58,7 +57,6 @@ for (int itask = 0; itask < ntasks; itask++) {
|
|||
dgemm(transa, transb, task.m, task.n, task.k, alpha, data_a, lda, data_b, ldb, 1.0, data_c, ldc);
|
||||
}
|
||||
```
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
|
||||
## MiniApp
|
||||
|
||||
|
|
|
|||
|
|
@ -50,7 +50,6 @@ The `grid_collocate_miniapp.x` binary allows to run individual .task files.
|
|||
By default `grid_collocate_pgf_product_cpu` is called. When the `--batch` flag
|
||||
is set then `grid_collocate_task_list` is called instead.
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
```shell
|
||||
$ cd cp2k/src/grid
|
||||
$ make
|
||||
|
|
@ -60,7 +59,6 @@ Usage: grid_base_ref_miniapp.x [--batch <cycles-per-block>] <cycles> <task-file>
|
|||
$ ./grid_collocate_miniapp.x --batch 10 100 sample_tasks/collocate_ortho_density_l2200.task
|
||||
Task: sample_tasks/collocate_ortho_density_l2200.task Batched: yes Cycles: 1.000000e+02 Max value: 1.579830e+02 Max diff: 1.705303e-13 Time: 1.884854e-03 sec
|
||||
```
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
|
||||
## Unit Test
|
||||
|
||||
|
|
@ -69,7 +67,6 @@ The `grid_collocate_unittest.x` binary runs the .task files from the
|
|||
Beware that this is merely a smoke test.
|
||||
The cp2k regtest suite provides much more thorough testing.
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
```shell
|
||||
$ cd cp2k/src/grid
|
||||
$ make
|
||||
|
|
@ -83,4 +80,3 @@ Task: ../../src/grid/sample_tasks/collocate_ortho_density_l0000.task Batche
|
|||
Task: ../../src/grid/sample_tasks/collocate_ortho_non_periodic.task Batched: yes Cycles: 1.000000e+00 Max value: 4.483815e-01 Max diff: 0.000000e+00 Time: 1.882868e-02 sec
|
||||
All tests have passed :-)
|
||||
```
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
|
|
|
|||
|
|
@ -23,7 +23,7 @@ Python interpreter instances due to side effects in the library.
|
|||
|
||||
## Known Issues
|
||||
|
||||
* If libcp2k is built with MPI support, you may get an MPI initialization error
|
||||
- If libcp2k is built with MPI support, you may get an MPI initialization error
|
||||
depending on your MPI implementation/configuration. In that case MPI must be
|
||||
initialized first by using Mpi4py and the Fortran MPI communicator handler
|
||||
must be passed down the CP2K via the respective `...comm` functions.
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
# Fist EAM Regression Tests
|
||||
|
||||
The potentials for Ag, Pt and Au listed here are converted from the [LAMMPS distribution](http://lammps.sandia.gov).
|
||||
The mixed file is generated by multiplication of Za(R)*Zb(R)/R as prescribed in
|
||||
The mixed file is generated by multiplication of Za(R)\*Zb(R)/R as prescribed in
|
||||
Foiles et al., PRB 33 (1986) 7983.
|
||||
Note that the grid is quite loose, so `EMAX_SPLINE` is set to a high value (D. Passerone).
|
||||
|
|
|
|||
|
|
@ -5,27 +5,23 @@ The only prerequisite is to [install Docker](https://docs.docker.com/get-docker/
|
|||
|
||||
## Production Images
|
||||
|
||||
1. Build the container image:
|
||||
1. Build the container image:
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
```shell
|
||||
docker build -f Dockerfile.prod_psmp --build-arg GIT_COMMIT_SHA=$(git rev-parse HEAD) -t cp2k_prod_psmp ../../
|
||||
```
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
```shell
|
||||
docker build -f Dockerfile.prod_psmp --build-arg GIT_COMMIT_SHA=$(git rev-parse HEAD) -t cp2k_prod_psmp ../../
|
||||
```
|
||||
|
||||
2. Go to the directory with your input files:
|
||||
1. Go to the directory with your input files:
|
||||
|
||||
```shell
|
||||
cd ../../benchmarks/QS_single_node
|
||||
```
|
||||
```shell
|
||||
cd ../../benchmarks/QS_single_node
|
||||
```
|
||||
|
||||
3. Run the container:
|
||||
1. Run the container:
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
```shell
|
||||
docker run --shm-size=1g -ti -v "$(pwd)":/mnt cp2k_prod_psmp mpiexec -genv OMP_NUM_THREADS=2 -np 16 cp2k dbcsr.inp
|
||||
```
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
```shell
|
||||
docker run --shm-size=1g -ti -v "$(pwd)":/mnt cp2k_prod_psmp mpiexec -genv OMP_NUM_THREADS=2 -np 16 cp2k dbcsr.inp
|
||||
```
|
||||
|
||||
## Test Images
|
||||
|
||||
|
|
|
|||
|
|
@ -10,11 +10,11 @@ The driver script `doxyify.sh` will process CP2K source code (`*.F` files) proce
|
|||
one file at a time. The following steps are carried out for each `*.F` file:
|
||||
|
||||
1. Run `remove_double_ampersands.pl` - removes any any double ampersand characters
|
||||
2. Run `fixcomments.pl` - does the addition of missing comments or updating of
|
||||
1. Run `fixcomments.pl` - does the addition of missing comments or updating of
|
||||
existing comments
|
||||
3. Run `remove_extra_comments.pl` - removes any extra comment lines which arise
|
||||
1. Run `remove_extra_comments.pl` - removes any extra comment lines which arise
|
||||
from application of `fixcomments.pl`
|
||||
4. Finally, overwrite the original `*.F` file with the updated version
|
||||
1. Finally, overwrite the original `*.F` file with the updated version
|
||||
|
||||
To run the script, you should execute it with the name of the source file you
|
||||
want to process:
|
||||
|
|
|
|||
|
|
@ -27,16 +27,16 @@ files. It has been tested on emacs 2.1, 2.3 and 2.4.
|
|||
|
||||
### Key Bindings
|
||||
|
||||
| character | |
|
||||
| ------------- |---------------|
|
||||
| `<tab>` | `cp2k-indent-line`
|
||||
| C-j | `newline-and-indent`
|
||||
| C-c ; | `comment-region`
|
||||
| C-M-a | `cp2k-beginning-of-block`
|
||||
| C-M-e | `cp2k-end-of-block`
|
||||
| C-c C-c | `outline-toggle-children`
|
||||
| C-c C-a | `show-all`
|
||||
| C-c C-t | `show-subtree`
|
||||
| character | |
|
||||
| --------- | ------------------------- |
|
||||
| `<tab>` | `cp2k-indent-line` |
|
||||
| C-j | `newline-and-indent` |
|
||||
| C-c ; | `comment-region` |
|
||||
| C-M-a | `cp2k-beginning-of-block` |
|
||||
| C-M-e | `cp2k-end-of-block` |
|
||||
| C-c C-c | `outline-toggle-children` |
|
||||
| C-c C-a | `show-all` |
|
||||
| C-c C-t | `show-subtree` |
|
||||
|
||||
## Installation
|
||||
|
||||
|
|
|
|||
|
|
@ -2,6 +2,6 @@
|
|||
|
||||
For more information on
|
||||
|
||||
* obtaining and using the Vim editor plugin for CP2K, see [CP2K Tools:vim](https://www.cp2k.org/tools:vim)
|
||||
* creating the Vim editor plugin file cp2k.vim (together with the manual),
|
||||
- obtaining and using the Vim editor plugin for CP2K, see [CP2K Tools:vim](https://www.cp2k.org/tools:vim)
|
||||
- creating the Vim editor plugin file cp2k.vim (together with the manual),
|
||||
see [How to generate the CP2K input reference manual](https://manual.cp2k.org/trunk/generate_manual_howto.html)
|
||||
|
|
|
|||
|
|
@ -19,10 +19,10 @@ between ranks for the OpenMP threads.
|
|||
Because of the above-mentioned complexity, a script for planning
|
||||
MPI/OpenMP-hybrid execution (`plan.sh`) is available. Here is a first example
|
||||
for running the PSMP-binary on an SMP-enabled (Hyperthreads) dual-socket system
|
||||
with 24 cores per processor/socket (96 hardware threads in total). At
|
||||
first, a run with 48 ranks and 2 threads per core comes to the mind
|
||||
(`48x2`). However, for instance 16 ranks with 6 threads per rank can
|
||||
be better for performance (`16x6`). To easily place the ranks, Intel MPI
|
||||
with 24 cores per processor/socket (96 hardware threads in total). At
|
||||
first, a run with 48 ranks and 2 threads per core comes to the mind
|
||||
(`48x2`). However, for instance 16 ranks with 6 threads per rank can
|
||||
be better for performance (`16x6`). To easily place the ranks, Intel MPI
|
||||
is used:
|
||||
|
||||
```bash
|
||||
|
|
@ -40,7 +40,7 @@ not necessary and not recommended to build a rather complicated
|
|||
to log the pinning and thread affinization at the startup of an application,
|
||||
`I_MPI_DEBUG=4` can be used with no performance penalty. The recommended
|
||||
`I_MPI_PIN_ORDER=bunch` ensures that ranks per node are split as even as
|
||||
possible with respect to sockets (e.g., 36 ranks on a 2x20-core system
|
||||
possible with respect to sockets (e.g., 36 ranks on a 2x20-core system
|
||||
are put in 2x18 ranks instead of 20+16 ranks).
|
||||
|
||||
To achieve a similar placement with OpenMPI, ranks are mapped to "execution
|
||||
|
|
@ -55,7 +55,7 @@ mpirun -np 16 --map-by slot:PE=3 \
|
|||
exe/Linux-x86-64-intelx/cp2k.psmp workload.inp
|
||||
```
|
||||
|
||||
**NOTE**: Intel MPI's `I_MPI_PIN_ORDER=bunch` to balance the number of
|
||||
**NOTE**: Intel MPI's `I_MPI_PIN_ORDER=bunch` to balance the number of
|
||||
ranks between sockets (see above) appears hard to achieve with OpenMPI
|
||||
therefore an undersubscribed system may not be recommended. To display and
|
||||
to log the pinning and thread affinization at the startup of an application,
|
||||
|
|
@ -69,9 +69,8 @@ to multiple nodes of the above-mentioned system.
|
|||
To configure the plan-script, the metric of the compute nodes can be given for
|
||||
future invocations so that only the node-count is required as an argument. The
|
||||
script's help output (`-h` or `--help`) initially shows the "system metric" of
|
||||
the computer the script is invoked on. For a system with 48 cores (two
|
||||
sockets, SMP/HT enabled), setting up the "system metric" looks like (`plan.sh
|
||||
[num-nodes] [ncores-per-node] [nthreads-per-core] [nsockets-per-node]`):
|
||||
the computer the script is invoked on. For a system with 48 cores (two
|
||||
sockets, SMP/HT enabled), setting up the "system metric" looks like (`plan.sh [num-nodes] [ncores-per-node] [nthreads-per-core] [nsockets-per-node]`):
|
||||
|
||||
```bash
|
||||
./plan.sh 1 48 2 2
|
||||
|
|
@ -80,7 +79,7 @@ sockets, SMP/HT enabled), setting up the "system metric" looks like (`plan.sh
|
|||
The script is storing the arguments (except for the node-count) as default
|
||||
values for the next plan (file: `$HOME/.xconfigure-cp2k-plan`). This allows to
|
||||
supply the system-type once, and to plan with varying node-counts in a
|
||||
convenient fashion. Planning for 8 nodes of the above kind yields the
|
||||
convenient fashion. Planning for 8 nodes of the above kind yields the
|
||||
following output (`plan.sh 8`):
|
||||
|
||||
```text
|
||||
|
|
@ -102,8 +101,8 @@ The first group of the output displays POT-style (trivial) MPI/OpenMP
|
|||
configurations (penalty denotes potential communication overhead), however the
|
||||
second group (if present) shows rank/thread combinations with the total
|
||||
rank-count hitting a square number (penalty denotes waste of compute due to not
|
||||
filling each node). For the given example, 8 ranks per node with
|
||||
12 threads per rank is chosen (`8x12`) and MPI-executed:
|
||||
filling each node). For the given example, 8 ranks per node with
|
||||
12 threads per rank is chosen (`8x12`) and MPI-executed:
|
||||
|
||||
```bash
|
||||
mpirun -perhost 8 -host node1,node2,node3,node4,node5,node6,node7,node8 \
|
||||
|
|
@ -112,8 +111,7 @@ mpirun -perhost 8 -host node1,node2,node3,node4,node5,node6,node7,node8 \
|
|||
exe/Linux-x86-64-intelx/cp2k.psmp workload.inp
|
||||
```
|
||||
|
||||
**NOTE**: For Intel MPI as well as OpenMPI, mpirun's host-list (`mpirun
|
||||
-host`) is setup with unique node-names, and this is the only style that is
|
||||
**NOTE**: For Intel MPI as well as OpenMPI, mpirun's host-list (`mpirun -host`) is setup with unique node-names, and this is the only style that is
|
||||
explained in this article. There is a competing style where nodes names are
|
||||
duplicated for the sake of enumerating available ranks (or "execution slots"
|
||||
in case of OpenMPI), which is not exercised in this article.
|
||||
|
|
|
|||
|
|
@ -4,23 +4,25 @@ The precommit system consists of the following tools that analyze and format the
|
|||
source code:
|
||||
|
||||
- [doxify](../doxify/)
|
||||
to add Doxygen templates.
|
||||
to add Doxygen templates.
|
||||
- [prettify](../prettify/)
|
||||
to format Fortran files.
|
||||
to format Fortran files.
|
||||
- [analyze_src](../conventions/analyze_src.py)
|
||||
to check copyright banners and a few other things.
|
||||
to check copyright banners and a few other things.
|
||||
- [ast.parse](https://docs.python.org/3/library/ast.html)
|
||||
to check Python syntax.
|
||||
to check Python syntax.
|
||||
- [clang-format](https://clang.llvm.org/docs/ClangFormat.html)
|
||||
to format C and Cuda files.
|
||||
to format C and Cuda files.
|
||||
- [black](https://github.com/psf/black)
|
||||
to format Python scripts.
|
||||
to format Python scripts.
|
||||
- [shfmt](https://github.com/mvdan/sh)
|
||||
to format Shell scripts.
|
||||
to format Shell scripts.
|
||||
- [shellcheck](https://github.com/koalaman/shellcheck)
|
||||
to analyze Shell scripts.
|
||||
- [markdownlint](https://github.com/DavidAnson/markdownlint)
|
||||
to analyze Markdown files.
|
||||
to analyze Shell scripts.
|
||||
- [mdformat](https://github.com/executablebooks/mdformat) with [gfm plugin](https://github.com/hukkin/mdformat-gfm)
|
||||
to format Markdown scripts.
|
||||
- [cmake-format](https://github.com/cheshirekow/cmake_format)
|
||||
to format CMake scripts.
|
||||
|
||||
In contrast to the [CP2K-CI](https://github.com/cp2k/cp2k-ci) these tools
|
||||
process each file individually, which makes them much more lightweight.
|
||||
|
|
|
|||
|
|
@ -13,7 +13,6 @@ apt-get install -qq --no-install-recommends \
|
|||
git \
|
||||
less \
|
||||
nano \
|
||||
npm \
|
||||
python3 \
|
||||
python3-pip \
|
||||
python3-wheel \
|
||||
|
|
@ -22,14 +21,9 @@ apt-get install -qq --no-install-recommends \
|
|||
wget
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
# Install markdownlint-cli and dependencies.
|
||||
# https://github.com/DavidAnson/markdownlint
|
||||
# https://github.com/igorshubovych/markdownlint-cli
|
||||
npm install .
|
||||
ln -s /opt/cp2k-precommit/node_modules/markdownlint-cli/markdownlint.js /usr/bin/markdownlint
|
||||
|
||||
# Install black, flask, gunicorn, and dependencies.
|
||||
# https://github.com/psf/black
|
||||
# Install Python packages. Upgrade via:
|
||||
# pip3 install black flask gunicorn mdformat-gfm cmake-format
|
||||
# pip3 freeze > requirements.txt
|
||||
pip3 install --quiet -r requirements.txt
|
||||
|
||||
# Install shfmt.
|
||||
|
|
|
|||
257
tools/precommit/package-lock.json
generated
257
tools/precommit/package-lock.json
generated
|
|
@ -1,257 +0,0 @@
|
|||
{
|
||||
"name": "cp2k-precommit",
|
||||
"version": "1.0.0",
|
||||
"lockfileVersion": 1,
|
||||
"requires": true,
|
||||
"dependencies": {
|
||||
"argparse": {
|
||||
"version": "1.0.10",
|
||||
"resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.10.tgz",
|
||||
"integrity": "sha512-o5Roy6tNG4SL/FOkCAN6RzjiakZS25RLYFrcMttJqbdd8BWrnA+fGz57iN5Pb06pvBGvl5gQ0B48dJlslXvoTg==",
|
||||
"requires": {
|
||||
"sprintf-js": "~1.0.2"
|
||||
}
|
||||
},
|
||||
"balanced-match": {
|
||||
"version": "1.0.0",
|
||||
"resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.0.tgz",
|
||||
"integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c="
|
||||
},
|
||||
"brace-expansion": {
|
||||
"version": "1.1.11",
|
||||
"resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz",
|
||||
"integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==",
|
||||
"requires": {
|
||||
"balanced-match": "^1.0.0",
|
||||
"concat-map": "0.0.1"
|
||||
}
|
||||
},
|
||||
"commander": {
|
||||
"version": "2.9.0",
|
||||
"resolved": "https://registry.npmjs.org/commander/-/commander-2.9.0.tgz",
|
||||
"integrity": "sha1-nJkJQXbhIkDLItbFFGCYQA/g99Q=",
|
||||
"requires": {
|
||||
"graceful-readlink": ">= 1.0.0"
|
||||
}
|
||||
},
|
||||
"concat-map": {
|
||||
"version": "0.0.1",
|
||||
"resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz",
|
||||
"integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s="
|
||||
},
|
||||
"deep-extend": {
|
||||
"version": "0.5.1",
|
||||
"resolved": "https://registry.npmjs.org/deep-extend/-/deep-extend-0.5.1.tgz",
|
||||
"integrity": "sha512-N8vBdOa+DF7zkRrDCsaOXoCs/E2fJfx9B9MrKnnSiHNh4ws7eSys6YQE4KvT1cecKmOASYQBhbKjeuDD9lT81w=="
|
||||
},
|
||||
"entities": {
|
||||
"version": "2.0.3",
|
||||
"resolved": "https://registry.npmjs.org/entities/-/entities-2.0.3.tgz",
|
||||
"integrity": "sha512-MyoZ0jgnLvB2X3Lg5HqpFmn1kybDiIfEQmKzTb5apr51Rb+T3KdmMiqa70T+bhGnyv7bQ6WMj2QMHpGMmlrUYQ=="
|
||||
},
|
||||
"esprima": {
|
||||
"version": "4.0.1",
|
||||
"resolved": "https://registry.npmjs.org/esprima/-/esprima-4.0.1.tgz",
|
||||
"integrity": "sha512-eGuFFw7Upda+g4p+QHvnW0RyTX/SVeJBDM/gCtMARO0cLuT2HcEKnTPvhjV6aGeqrCB/sbNop0Kszm0jsaWU4A=="
|
||||
},
|
||||
"fs.realpath": {
|
||||
"version": "1.0.0",
|
||||
"resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz",
|
||||
"integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8="
|
||||
},
|
||||
"get-stdin": {
|
||||
"version": "5.0.1",
|
||||
"resolved": "https://registry.npmjs.org/get-stdin/-/get-stdin-5.0.1.tgz",
|
||||
"integrity": "sha1-Ei4WFZHiH/TFJTAwVpPyDmOTo5g="
|
||||
},
|
||||
"glob": {
|
||||
"version": "7.1.6",
|
||||
"resolved": "https://registry.npmjs.org/glob/-/glob-7.1.6.tgz",
|
||||
"integrity": "sha512-LwaxwyZ72Lk7vZINtNNrywX0ZuLyStrdDtabefZKAY5ZGJhVtgdznluResxNmPitE0SAO+O26sWTHeKSI2wMBA==",
|
||||
"requires": {
|
||||
"fs.realpath": "^1.0.0",
|
||||
"inflight": "^1.0.4",
|
||||
"inherits": "2",
|
||||
"minimatch": "^3.0.4",
|
||||
"once": "^1.3.0",
|
||||
"path-is-absolute": "^1.0.0"
|
||||
}
|
||||
},
|
||||
"graceful-readlink": {
|
||||
"version": "1.0.1",
|
||||
"resolved": "https://registry.npmjs.org/graceful-readlink/-/graceful-readlink-1.0.1.tgz",
|
||||
"integrity": "sha1-TK+tdrxi8C+gObL5Tpo906ORpyU="
|
||||
},
|
||||
"ignore": {
|
||||
"version": "5.1.8",
|
||||
"resolved": "https://registry.npmjs.org/ignore/-/ignore-5.1.8.tgz",
|
||||
"integrity": "sha512-BMpfD7PpiETpBl/A6S498BaIJ6Y/ABT93ETbby2fP00v4EbvPBXWEoaR1UBPKs3iR53pJY7EtZk5KACI57i1Uw=="
|
||||
},
|
||||
"inflight": {
|
||||
"version": "1.0.6",
|
||||
"resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz",
|
||||
"integrity": "sha1-Sb1jMdfQLQwJvJEKEHW6gWW1bfk=",
|
||||
"requires": {
|
||||
"once": "^1.3.0",
|
||||
"wrappy": "1"
|
||||
}
|
||||
},
|
||||
"inherits": {
|
||||
"version": "2.0.4",
|
||||
"resolved": "https://registry.npmjs.org/inherits/-/inherits-2.0.4.tgz",
|
||||
"integrity": "sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ=="
|
||||
},
|
||||
"ini": {
|
||||
"version": "1.3.8",
|
||||
"resolved": "https://registry.npmjs.org/ini/-/ini-1.3.8.tgz",
|
||||
"integrity": "sha512-JV/yugV2uzW5iMRSiZAyDtQd+nxtUnjeLt0acNdw98kKLrvuRVyB80tsREOE7yvGVgalhZ6RNXCmEHkUKBKxew=="
|
||||
},
|
||||
"js-yaml": {
|
||||
"version": "3.13.1",
|
||||
"resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-3.13.1.tgz",
|
||||
"integrity": "sha512-YfbcO7jXDdyj0DGxYVSlSeQNHbD7XPWvrVWeVUujrQEoZzWJIRrCPoyk6kL6IAjAG2IolMK4T0hNUe0HOUs5Jw==",
|
||||
"requires": {
|
||||
"argparse": "^1.0.7",
|
||||
"esprima": "^4.0.0"
|
||||
}
|
||||
},
|
||||
"jsonc-parser": {
|
||||
"version": "2.2.1",
|
||||
"resolved": "https://registry.npmjs.org/jsonc-parser/-/jsonc-parser-2.2.1.tgz",
|
||||
"integrity": "sha512-o6/yDBYccGvTz1+QFevz6l6OBZ2+fMVu2JZ9CIhzsYRX4mjaK5IyX9eldUdCmga16zlgQxyrj5pt9kzuj2C02w=="
|
||||
},
|
||||
"linkify-it": {
|
||||
"version": "2.2.0",
|
||||
"resolved": "https://registry.npmjs.org/linkify-it/-/linkify-it-2.2.0.tgz",
|
||||
"integrity": "sha512-GnAl/knGn+i1U/wjBz3akz2stz+HrHLsxMwHQGofCDfPvlf+gDKN58UtfmUquTY4/MXeE2x7k19KQmeoZi94Iw==",
|
||||
"requires": {
|
||||
"uc.micro": "^1.0.1"
|
||||
}
|
||||
},
|
||||
"lodash.differencewith": {
|
||||
"version": "4.5.0",
|
||||
"resolved": "https://registry.npmjs.org/lodash.differencewith/-/lodash.differencewith-4.5.0.tgz",
|
||||
"integrity": "sha1-uvr7yRi1UVTheRdqALsK76rIVLc="
|
||||
},
|
||||
"lodash.flatten": {
|
||||
"version": "4.4.0",
|
||||
"resolved": "https://registry.npmjs.org/lodash.flatten/-/lodash.flatten-4.4.0.tgz",
|
||||
"integrity": "sha1-8xwiIlqWMtK7+OSt2+8kCqdlph8="
|
||||
},
|
||||
"markdown-it": {
|
||||
"version": "10.0.0",
|
||||
"resolved": "https://registry.npmjs.org/markdown-it/-/markdown-it-10.0.0.tgz",
|
||||
"integrity": "sha512-YWOP1j7UbDNz+TumYP1kpwnP0aEa711cJjrAQrzd0UXlbJfc5aAq0F/PZHjiioqDC1NKgvIMX+o+9Bk7yuM2dg==",
|
||||
"requires": {
|
||||
"argparse": "^1.0.7",
|
||||
"entities": "~2.0.0",
|
||||
"linkify-it": "^2.0.0",
|
||||
"mdurl": "^1.0.1",
|
||||
"uc.micro": "^1.0.5"
|
||||
}
|
||||
},
|
||||
"markdownlint": {
|
||||
"version": "0.20.4",
|
||||
"resolved": "https://registry.npmjs.org/markdownlint/-/markdownlint-0.20.4.tgz",
|
||||
"integrity": "sha512-jpfaPgjT0OpeBbemjYNZbzGG3hCLcAIvrm/pEY3+q/szDScG6ZonDacqySVRJAv9glbo8y4wBPJ0wgW17+9GGA==",
|
||||
"requires": {
|
||||
"markdown-it": "10.0.0"
|
||||
}
|
||||
},
|
||||
"markdownlint-cli": {
|
||||
"version": "0.23.2",
|
||||
"resolved": "https://registry.npmjs.org/markdownlint-cli/-/markdownlint-cli-0.23.2.tgz",
|
||||
"integrity": "sha512-OSl5OZ8xzGN6z355cqRkiq67zPi3reJimklaF72p0554q85Dng5ToOjjSB9tDKZebSt85jX8cp+ruoQlPqOsPA==",
|
||||
"requires": {
|
||||
"commander": "~2.9.0",
|
||||
"deep-extend": "~0.5.1",
|
||||
"get-stdin": "~5.0.1",
|
||||
"glob": "~7.1.2",
|
||||
"ignore": "~5.1.4",
|
||||
"js-yaml": "~3.13.1",
|
||||
"jsonc-parser": "~2.2.0",
|
||||
"lodash.differencewith": "~4.5.0",
|
||||
"lodash.flatten": "~4.4.0",
|
||||
"markdownlint": "~0.20.4",
|
||||
"markdownlint-rule-helpers": "~0.11.0",
|
||||
"minimatch": "~3.0.4",
|
||||
"minimist": "~1.2.5",
|
||||
"rc": "~1.2.7"
|
||||
}
|
||||
},
|
||||
"markdownlint-rule-helpers": {
|
||||
"version": "0.11.0",
|
||||
"resolved": "https://registry.npmjs.org/markdownlint-rule-helpers/-/markdownlint-rule-helpers-0.11.0.tgz",
|
||||
"integrity": "sha512-PhGii9dOiDJDXxiRMpK8N0FM9powprvRPsXALgkjlSPTwLh6ymH+iF3iUe3nq8KGu26tclFBlLL5xAGy/zb7FA=="
|
||||
},
|
||||
"mdurl": {
|
||||
"version": "1.0.1",
|
||||
"resolved": "https://registry.npmjs.org/mdurl/-/mdurl-1.0.1.tgz",
|
||||
"integrity": "sha1-/oWy7HWlkDfyrf7BAP1sYBdhFS4="
|
||||
},
|
||||
"minimatch": {
|
||||
"version": "3.0.4",
|
||||
"resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.0.4.tgz",
|
||||
"integrity": "sha512-yJHVQEhyqPLUTgt9B83PXu6W3rx4MvvHvSUvToogpwoGDOUQ+yDrR0HRot+yOCdCO7u4hX3pWft6kWBBcqh0UA==",
|
||||
"requires": {
|
||||
"brace-expansion": "^1.1.7"
|
||||
}
|
||||
},
|
||||
"minimist": {
|
||||
"version": "1.2.6",
|
||||
"resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.6.tgz",
|
||||
"integrity": "sha512-Jsjnk4bw3YJqYzbdyBiNsPWHPfO++UGG749Cxs6peCu5Xg4nrena6OVxOYxrQTqww0Jmwt+Ref8rggumkTLz9Q=="
|
||||
},
|
||||
"once": {
|
||||
"version": "1.4.0",
|
||||
"resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz",
|
||||
"integrity": "sha1-WDsap3WWHUsROsF9nFC6753Xa9E=",
|
||||
"requires": {
|
||||
"wrappy": "1"
|
||||
}
|
||||
},
|
||||
"path-is-absolute": {
|
||||
"version": "1.0.1",
|
||||
"resolved": "https://registry.npmjs.org/path-is-absolute/-/path-is-absolute-1.0.1.tgz",
|
||||
"integrity": "sha1-F0uSaHNVNP+8es5r9TpanhtcX18="
|
||||
},
|
||||
"rc": {
|
||||
"version": "1.2.8",
|
||||
"resolved": "https://registry.npmjs.org/rc/-/rc-1.2.8.tgz",
|
||||
"integrity": "sha512-y3bGgqKj3QBdxLbLkomlohkvsA8gdAiUQlSBJnBhfn+BPxg4bc62d8TcBW15wavDfgexCgccckhcZvywyQYPOw==",
|
||||
"requires": {
|
||||
"deep-extend": "^0.6.0",
|
||||
"ini": "~1.3.0",
|
||||
"minimist": "^1.2.0",
|
||||
"strip-json-comments": "~2.0.1"
|
||||
},
|
||||
"dependencies": {
|
||||
"deep-extend": {
|
||||
"version": "0.6.0",
|
||||
"resolved": "https://registry.npmjs.org/deep-extend/-/deep-extend-0.6.0.tgz",
|
||||
"integrity": "sha512-LOHxIOaPYdHlJRtCQfDIVZtfw/ufM8+rVj649RIHzcm/vGwQRXFt6OPqIFWsm2XEMrNIEtWR64sY1LEKD2vAOA=="
|
||||
}
|
||||
}
|
||||
},
|
||||
"sprintf-js": {
|
||||
"version": "1.0.3",
|
||||
"resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.0.3.tgz",
|
||||
"integrity": "sha1-BOaSb2YolTVPPdAVIDYzuFcpfiw="
|
||||
},
|
||||
"strip-json-comments": {
|
||||
"version": "2.0.1",
|
||||
"resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-2.0.1.tgz",
|
||||
"integrity": "sha1-PFMZQukIwml8DsNEhYwobHygpgo="
|
||||
},
|
||||
"uc.micro": {
|
||||
"version": "1.0.6",
|
||||
"resolved": "https://registry.npmjs.org/uc.micro/-/uc.micro-1.0.6.tgz",
|
||||
"integrity": "sha512-8Y75pvTYkLJW2hWQHXxoqRgV7qb9B+9vFEtidML+7koHUFapnVJAZ6cKs+Qjz5Aw3aZWHMC6u0wJE3At+nSGwA=="
|
||||
},
|
||||
"wrappy": {
|
||||
"version": "1.0.2",
|
||||
"resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
|
||||
"integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
{
|
||||
"name": "cp2k-precommit",
|
||||
"version": "1.0.0",
|
||||
"description": "Tools used by the cp2k-precomit system",
|
||||
"main": "index.js",
|
||||
"repository": "",
|
||||
"scripts": {
|
||||
"test": "echo \"Error: no test specified\" && exit 1"
|
||||
},
|
||||
"repository": {
|
||||
"type": "git",
|
||||
"url": ""
|
||||
},
|
||||
"keywords": [],
|
||||
"author": "",
|
||||
"license": "ISC",
|
||||
"dependencies": {
|
||||
"markdownlint-cli": "^0.23.2"
|
||||
}
|
||||
}
|
||||
|
|
@ -204,7 +204,7 @@ def process_file(fn: str, allow_modifications: bool) -> None:
|
|||
run_remote_tool("shellcheck", fn)
|
||||
|
||||
if re.match(r".*\.md$", fn):
|
||||
run_remote_tool("markdownlint", fn)
|
||||
run_remote_tool("mdformat", fn)
|
||||
|
||||
if re.match(r"(.*/CMakeLists.txt)|(.*\.cmake)$", fn):
|
||||
run_remote_tool("cmakeformat", fn)
|
||||
|
|
|
|||
|
|
@ -41,9 +41,10 @@ def shellcheck():
|
|||
|
||||
|
||||
# ======================================================================================
|
||||
@app.route("/markdownlint", methods=["POST"])
|
||||
def markdownlint():
|
||||
return run_tool(["markdownlint"])
|
||||
@app.route("/mdformat", methods=["POST"])
|
||||
@app.route("/markdownlint", methods=["POST"]) # for backwards compatibility
|
||||
def mdformat():
|
||||
return run_tool(["mdformat"])
|
||||
|
||||
|
||||
# ======================================================================================
|
||||
|
|
|
|||
|
|
@ -1,21 +1,23 @@
|
|||
appdirs==1.4.4
|
||||
attrs==21.4.0
|
||||
black==22.3.0
|
||||
black==22.10.0
|
||||
click==8.1.3
|
||||
cmake-format==0.6.13
|
||||
cmakelang==0.6.13
|
||||
Flask==2.1.2
|
||||
Flask==2.2.2
|
||||
gunicorn==20.1.0
|
||||
gyp==0.1
|
||||
itsdangerous==2.1.2
|
||||
Jinja2==3.1.2
|
||||
linkify-it-py==1.0.3
|
||||
markdown-it-py==2.1.0
|
||||
MarkupSafe==2.1.1
|
||||
mdformat==0.7.16
|
||||
mdformat-gfm==0.3.5
|
||||
mdformat_tables==0.4.1
|
||||
mdit-py-plugins==0.3.1
|
||||
mdurl==0.1.2
|
||||
mypy-extensions==0.4.3
|
||||
pathspec==0.9.0
|
||||
pathspec==0.10.1
|
||||
platformdirs==2.5.2
|
||||
regex==2022.4.24
|
||||
six==1.16.0
|
||||
toml==0.10.2
|
||||
tomli==2.0.1
|
||||
typed-ast==1.5.3
|
||||
Werkzeug==2.1.2
|
||||
uc-micro-py==1.0.1
|
||||
Werkzeug==2.2.2
|
||||
|
|
|
|||
|
|
@ -107,37 +107,35 @@ The following table list the licenses of all those packages. While the toolchain
|
|||
does support linking proprietary software packages, like e.g. MKL, these have to
|
||||
be installed separately by the user.
|
||||
|
||||
<!-- markdownlint-disable MD013 -->
|
||||
| Package | License | GPL Compatible |
|
||||
| --------- | --------------------------------------------------------------------------------------- | -------------- |
|
||||
| cmake | [BSD 3-Clause](https://gitlab.kitware.com/cmake/cmake/raw/master/Copyright.txt) | Yes |
|
||||
| cosma | [BSD 3-Clause](https://github.com/eth-cscs/COSMA/blob/master/LICENCE) | Yes |
|
||||
| elpa | [LGPL](https://gitlab.mpcdf.mpg.de/elpa/elpa/blob/master/LICENSE) | Yes |
|
||||
| fftw | [GPL](http://www.fftw.org/doc/License-and-Copyright.html) | Yes |
|
||||
| gcc | [GPL](https://gcc.gnu.org/git/?p=gcc.git;a=blob_plain;f=COPYING;hb=HEAD) | Yes |
|
||||
| gsl | [GPL](https://www.gnu.org/software/gsl/doc/html/gpl.html) | Yes |
|
||||
| hdf5 | [BSD 3-Clause](https://support.hdfgroup.org/ftp/HDF5/releases/COPYING) | Yes |
|
||||
| libint | [GPL](https://github.com/evaleev/libint/blob/master/LICENSE) | Yes |
|
||||
| libvori | LGPL-3 | Yes |
|
||||
| libvdwxc | [GPL](https://gitlab.com/libvdwxc/libvdwxc/blob/master/LICENSE) | Yes |
|
||||
| libxc | [MPL](https://gitlab.com/libxc/libxc/blob/master/COPYING) | Yes |
|
||||
| libxsmm | [BSD 3-Clause](https://github.com/hfp/libxsmm/blob/master/LICENSE.md) | Yes |
|
||||
| mpich | [MPICH](https://github.com/pmodels/mpich/blob/master/COPYRIGHT) | [Yes](https://enterprise.dejacode.com/licenses/public/mpich/#license-conditions) |
|
||||
| openblas | [BSD 3-Clause](https://github.com/xianyi/OpenBLAS/blob/develop/LICENSE) | Yes |
|
||||
| openmpi | [BSD 3-Clause](https://github.com/open-mpi/ompi/blob/master/LICENSE) | Yes |
|
||||
| pexsi | [BSD 3-Clause](https://bitbucket.org/berkeleylab/pexsi/src/master/LICENSE) | Yes |
|
||||
| plumed | [LGPL](https://github.com/plumed/plumed2/blob/master/COPYING.LESSER) | Yes |
|
||||
| ptscotch | [CeCILL-C](https://www.labri.fr/perso/pelegrin/scotch/) | [Yes](https://cecill.info/faq.en.html#gpl) |
|
||||
| quip | [GPL](https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/COPYRIGHT) | Yes |
|
||||
| fox | [BSD 3-Clause](https://github.com/andreww/fox/blob/master/LICENSE) | Yes |
|
||||
| reflapack | [BSD 3-Clause](http://www.netlib.org/lapack/LICENSE.txt) | Yes |
|
||||
| scalapack | [BSD 3-Clause](http://www.netlib.org/scalapack/LICENSE) | Yes |
|
||||
| sirius | [BSD 2-Clause](https://github.com/electronic-structure/SIRIUS/blob/master/LICENSE) | Yes |
|
||||
| spfft | [BSD 3-Clause](https://github.com/eth-cscs/SpFFT/blob/master/LICENSE) | Yes |
|
||||
| spglib | [BSD 3-Clause](https://github.com/atztogo/spglib/blob/master/COPYING) | Yes |
|
||||
| superlu | [BSD 3-Clause](https://github.com/xiaoyeli/superlu/blob/master/License.txt) | Yes |
|
||||
| valgrind | [GPL](https://sourceware.org/git/?p=valgrind.git;a=blob_plain;f=COPYING;hb=HEAD) | Yes |
|
||||
<!-- markdownlint-enable MD013 -->
|
||||
| Package | License | GPL Compatible |
|
||||
| --------- | ---------------------------------------------------------------------------------- | -------------------------------------------------------------------------------- |
|
||||
| cmake | [BSD 3-Clause](https://gitlab.kitware.com/cmake/cmake/raw/master/Copyright.txt) | Yes |
|
||||
| cosma | [BSD 3-Clause](https://github.com/eth-cscs/COSMA/blob/master/LICENCE) | Yes |
|
||||
| elpa | [LGPL](https://gitlab.mpcdf.mpg.de/elpa/elpa/blob/master/LICENSE) | Yes |
|
||||
| fftw | [GPL](http://www.fftw.org/doc/License-and-Copyright.html) | Yes |
|
||||
| gcc | [GPL](https://gcc.gnu.org/git/?p=gcc.git;a=blob_plain;f=COPYING;hb=HEAD) | Yes |
|
||||
| gsl | [GPL](https://www.gnu.org/software/gsl/doc/html/gpl.html) | Yes |
|
||||
| hdf5 | [BSD 3-Clause](https://support.hdfgroup.org/ftp/HDF5/releases/COPYING) | Yes |
|
||||
| libint | [GPL](https://github.com/evaleev/libint/blob/master/LICENSE) | Yes |
|
||||
| libvori | LGPL-3 | Yes |
|
||||
| libvdwxc | [GPL](https://gitlab.com/libvdwxc/libvdwxc/blob/master/LICENSE) | Yes |
|
||||
| libxc | [MPL](https://gitlab.com/libxc/libxc/blob/master/COPYING) | Yes |
|
||||
| libxsmm | [BSD 3-Clause](https://github.com/hfp/libxsmm/blob/master/LICENSE.md) | Yes |
|
||||
| mpich | [MPICH](https://github.com/pmodels/mpich/blob/master/COPYRIGHT) | [Yes](https://enterprise.dejacode.com/licenses/public/mpich/#license-conditions) |
|
||||
| openblas | [BSD 3-Clause](https://github.com/xianyi/OpenBLAS/blob/develop/LICENSE) | Yes |
|
||||
| openmpi | [BSD 3-Clause](https://github.com/open-mpi/ompi/blob/master/LICENSE) | Yes |
|
||||
| pexsi | [BSD 3-Clause](https://bitbucket.org/berkeleylab/pexsi/src/master/LICENSE) | Yes |
|
||||
| plumed | [LGPL](https://github.com/plumed/plumed2/blob/master/COPYING.LESSER) | Yes |
|
||||
| ptscotch | [CeCILL-C](https://www.labri.fr/perso/pelegrin/scotch/) | [Yes](https://cecill.info/faq.en.html#gpl) |
|
||||
| quip | [GPL](https://github.com/libAtoms/QUIP/blob/public/src/libAtoms/COPYRIGHT) | Yes |
|
||||
| fox | [BSD 3-Clause](https://github.com/andreww/fox/blob/master/LICENSE) | Yes |
|
||||
| reflapack | [BSD 3-Clause](http://www.netlib.org/lapack/LICENSE.txt) | Yes |
|
||||
| scalapack | [BSD 3-Clause](http://www.netlib.org/scalapack/LICENSE) | Yes |
|
||||
| sirius | [BSD 2-Clause](https://github.com/electronic-structure/SIRIUS/blob/master/LICENSE) | Yes |
|
||||
| spfft | [BSD 3-Clause](https://github.com/eth-cscs/SpFFT/blob/master/LICENSE) | Yes |
|
||||
| spglib | [BSD 3-Clause](https://github.com/atztogo/spglib/blob/master/COPYING) | Yes |
|
||||
| superlu | [BSD 3-Clause](https://github.com/xiaoyeli/superlu/blob/master/License.txt) | Yes |
|
||||
| valgrind | [GPL](https://sourceware.org/git/?p=valgrind.git;a=blob_plain;f=COPYING;hb=HEAD) | Yes |
|
||||
|
||||
## For Developers
|
||||
|
||||
|
|
@ -156,6 +154,7 @@ be installed separately by the user.
|
|||
on other libraries being already installed and the correct
|
||||
environment variables set. At the end of each script, it should
|
||||
write to __two__ files: `build/setup_PKG` and `install/setup`.
|
||||
|
||||
- The `build/setup_PKG` file contains all the instructions to set
|
||||
the variables used by the `install_cp2k_toolchain.sh` and other
|
||||
`script/install_PKG.sh` scripts in order for them to correctly
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue