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Added README to combine guidance for accelerated & non-accelerated benchmarks... 

Added README to combine guidance for accelerated & non-accelerated benchmarks relevant to D7.5, removed older
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cp2k/CP2K_Build_README.txt deleted 100644 → 0
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Build instructions for CP2K.
2016-10-26
===== 1. Get the code =====
Download a CP2K release from https://sourceforge.net/projects/cp2k/files/ or follow instructions at
https://www.cp2k.org/download to check out the relevant branch of the CP2K SVN repository. These
build instructions and the accompanying benchmark run instructions have been tested with release
4.1.
===== 2. Prerequisites & Libraries =====
GNU make and Python 2.x are required for the build process, as are a Fortran 2003 compiler and
matching C compiler, e.g. gcc/gfortran (gcc >=4.6 works, later version is recommended).
CP2K can benefit from a number of external libraries for improved performance. It is advised to use
vendor-optimized versions of these libraries. If these are not available on your machine, there
exist freely available implementations of these libraries including but not limited to those listed
below.
Required:
---------
The minimum set of libraries required to build a CP2K executable that will run the UEABS benchmarks
is:
1. LAPACK & BLAS, as provided by, for example:
netlib : http://netlib.org/lapack & http://netlib.org/blas
MKL : part of your Intel MKL installation, if available
LibSci : installed on Cray platforms
ATLAS : http://math-atlas.sf.net
OpenBLAS : http://www.openblas.net
clBLAS : http://gpuopen.com/compute-product/clblas/
2. SCALAPACK & BLACS, as provided by, for example:
netlib : http://netlib.org/scalapack/
MKL : part of your Intel MKL installation, if available
LibSci : installed on Cray platforms
3. LIBINT, available from https://www.cp2k.org/static/downloads/libint-1.1.4.tar.gz
(see build instructions in section 2.1 below)
Optional:
---------
The following libraries are optional but give a significant performance benefit:
4. FFTW3, available from http://www.fftw.org or provided as an interface by MKL
5. ELPA, available from https://www.cp2k.org/static/downloads/elpa-2016.05.003.tar.gz
6. libgrid, available from inside the distribution at cp2k/tools/autotune_grid
7. libxsmm, available from https://www.cp2k.org/static/downloads/libxsmm-1.4.4.tar.gz
More information can be found in the INSTALL file in the CP2K distribution.
2.1 Building LIBINT
-------------------
The following commands will uncompress and install the LIBINT library required for the UEABS
benchmarks:
tar xzf libint-1.1.4
cd libint-1.1.4
./configure CC=cc CXX=CC --prefix=some_path_other_than_this_directory
make
make install
The environment variables CC and CXX are optional and can be used to specify the C and C++ compilers
to use for the build (the example above is configured to use the compiler wrappers cc and CC used on
Cray systems). By default the build process only creates static libraries (ending in .a). If you
want to be able to link dynamically to LIBINT when building CP2K you can pass the flag
--enable-shared to ./configure in order to produce shared libraries (ending in .so). In that case
you will need to ensure that the library is located in place that is accessible at runtime and that
the LD_LIBRARY_PATH environment variable includes the LIBINT installation directory.
For more build options see ./configure --help.
===== 3. Building CP2K =====
If you have downloaded a tarball of the release, uncompress the file by running
tar xf cp2k-4.1.tar.bz2.
If necessary you can find additional information about building CP2K in the INSTALL file located in
the root directory of the CP2K distribution.
==== 3.1 Create or choose an arch file ====
Before compiling the choice of compilers, the library locations and compilation and linker flags
need to be specified. This is done in an arch (architecture) file. Example arch files for a number
of common architecture examples can be found inside cp2k/arch. The names of these files match the
pattern architecture.version (e.g., Linux-x86-64-gfortran.sopt). The case "version=psmp" corresponds
to the hybrid MPI + OpenMP version that you should build to run the UEABS benchmarks.
In most cases you need to create a custom arch file, either from scratch or by modifying an existing
one that roughly fits the cpu type, compiler, and installation paths of libraries on your
system. You can also consult https://dashboard.cp2k.org, which provides sample arch files as part of
the testing reports for some platforms (click on the status field for a platform, and search for
'ARCH-file' in the resulting output).
As a guided example, the following should be included in your arch file if you are compiling with
GNU compilers:
(a) Specification of which compiler and linker commands to use:
CC = gcc
FC = mpif90
LD = mpif90
CP2K is primarily a Fortran code, so only the Fortran compiler needs to be MPI-enabled.
(b) Specification of the DFLAGS variable, which should include:
-D__parallel (to build parallel CP2K executable)
-D__SCALAPACK (to link to ScaLAPACK)
-D__LIBINT (to link to LIBINT)
-D__MKL (if relying on MKL to provide ScaLAPACK and/or an FFTW interface)
-D__HAS_NO_SHARED_GLIBC (for convenience on HPC systems, see INSTALL file)
Additional DFLAGS needed to link to performance libraries, such as -D__FFTW3 to link to FFTW3,
are listed in the INSTALL file.
(c) Specification of compiler flags:
Required (for gfortran):
FCFLAGS = $(DFLAGS) -ffree-form -fopenmp
Recommended additional flags (for gfortran):
FCFLAGS += -O3 -ffast-math -funroll-loops
If you want to link any libraries containing header files you should pass the path to the
directory containing these to FCFLAGS in the format -I/path_to_include_dir.
(d) Specification of linker flags:
LDFLAGS = $(FCFLAGS)
(e) Specification of libraries to link to:
Required (LIBINT):
-L/home/z01/z01/UEABS/CP2K/libint/1.1.4/lib -lderiv -lint
If you use MKL to provide ScaLAPACK and/or an FFTW interface the LIBS variable should be used
to pass the relevant flags provided by the MKL Link Line Advisor (https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor),
which you should use carefully in order to generate the right options for your system.
(f) AR = ar -r
As an example, a simple arch file is shown below for ARCHER (http://www.archer.ac.uk), a Cray system
that uses compiler wrappers cc and ftn to compile C and Fortran code respectively, and which has
LIBINT installed in /home/z01/z01/user/cp2k/libs/libint/1.1.4. On Cray systems the compiler wrappers
automatically link in Cray's LibSci library which provides ScaLAPACK, hence there is no need for
explicit specification of the library location and library names in LIBS or relevant include paths
in FCFLAGS. This would not be the case if MKL was used instead.
#=============================================================================================
#
# Ensure the following environment modules are loaded before starting the build:
#
# PrgEnv-gnu
# cray-libsci
#
CC = cc
CPP =
FC = ftn
LD = ftn
AR = ar -r
DFLAGS = -D__parallel \
-D__SCALAPACK \
-D__LIBINT \
-D__HAS_NO_SHARED_GLIBC
CFLAGS = $(DFLAGS)
FCFLAGS = $(DFLAGS) -ffree-form -fopenmp
FCFLAGS += -O3 -ffast-math -funroll-loops
LDFLAGS = $(FCFLAGS)
LIBS = -L/home/z01/z01/user/cp2k/libint/1.1.4/lib -lderiv -lint
#=============================================================================================
==== 3.2 Compile ===
Change directory to cp2k-4.1/makefiles
There is no configure stage. If the arch file for your machine is called
SomeArchitecture_SomeCompiler.psmp, then issue the following command to compile:
make ARCH=SomeArchitecture_SomeCompiler VERSION=psmp
or, if you are able to run in parallel with N threads:
make -j N ARCH=SomeArchitecture_SomeCompiler VERSION=psmp
There is also no "make install" stage. If everything goes fine, you'll find the executable cp2k.psmp
in the directory cp2k-4.1/exe/SomeArchitecture_SomeCompiler
cp2k/CP2K_Download_README.txt deleted 100644 → 0
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CP2K can be downloaded from : http://www.cp2k.org/download
It is free for all users under GPL license,
see Obtaining CP2K section in the download page.
In UEABS(2IP) the 2.3 branch was used that can be downloaded from :
http://sourceforge.net/projects/cp2k/files/cp2k-2.3.tar.bz2
Data files are compatible with at least 2.4 branch.
Tier-0 data set requires the libint-1.1.4 library. If libint version 1
is not available on your machine, libint can be downloaded from :
http://sourceforge.net/projects/libint/files/v1-releases/libint-1.1.4.tar.gz
cp2k/CP2K_Run_README.txt deleted 100644 → 0
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Run instructions for CP2K.
2016-10-26
After building the hybrid MPI+OpenMP version of CP2K you have an executable
called cp2k.psmp. The general way to run the benchmarks is:
export OMP_NUM_THREADS=##
parallel_launcher launcher_options path_to_cp2k.psmp -i inputfile -o logfile
Where:
o The parallel_launcher is mpirun, mpiexec, or some variant such as aprun on
Cray systems or srun when using Slurm.
o The launcher_options include the parallel placement in terms of total numbers
of nodes, MPI ranks/tasks, tasks per node, and OpenMP threads per task (which
should be equal to the value given to OMP_NUM_THREADS)
You can try any combination of tasks per node and OpenMP threads per task to
investigate absolute performance and scaling on the machine of interest.
For tier-1 systems the best performance is usually obtained with pure MPI,while
for tier-0 systems the best performance is typically obtained using 1 MPI task
per node with the number of threads being equal to the number of cores per node.
More information in the form of a README and an example job script is included
in each benchmark tar file.
The run walltime is reported near the end of logfile:
grep "CP2K " logfile | awk -F ' ' '{print $7}'
cp2k/README.md 0 → 100644
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## Overview
This README together with the provided benchmark input files, CP2K build configuration ("arch") files and other details provided in each subdirectory corresponding to a machine specify how the CP2K benchmarking results presented in the PRACE-5IP deliverable D7.5 ("Evaluation of Accelerated and Non-accelerated Benchmarks") were obtained and provide general guidance on building CP2K and running the UEABS benchmarks.
In short, the procedure followed to generate CP2K UEABS benchmark results for the D7.5 deliverable on a given machine was:
1. Compile Libint
2. Compile Libxc
3. Compile FFTW library (or use MKL's FFTW3 interface)
4. Compile CP2K and link to Libint, Libxc, FFTW, LAPACK, BLAS, SCALAPACK and BLACS, and to relevant CUDA libraries if building for GPU
5. Run the benchmarks, namely:
- Test Case A: H2O-1024
- Test Case B: LiH-HFX (adjusting the MAX_MEMORY input parameter to take into account available on-node memory)
- Test Case C: H2O-DFT-LS
Gcc/gfortran was used to compile the libraries and CP2K itself, with the exception of the Frioul machine on which the Intel compiler was used to compile for the Knights Landing processor. In general it is recommended to use an MPI library built using the same compiler used to build CP2K. General information about building CP2K and libraries it depends on can be found in INSTALL.md included in the CP2K source distribution.
The reported walltime for a given run is obtained by querying the resulting .log file for CP2K's internal timing, as follows:
```
grep "CP2K " *.log
```
### Optional
Optional performance libraries including ELPA, libgrid, and libsmm/libxsmm can and should be built and linked to when compiling a CP2K executable for maximum performance for production usage. This was not done for the results presented in deliverable D7.5 due to the effort and complexity involved in doing so for the range of machines on which benchmark results were generated, which included PRACE Tier-0 production machines as well as pre-production prototypes. Information about these libraries can be found in INSTALL.md included in the CP2K source distribution.
## 1. Compile Libint
The Libint library can be obtained from <http://sourceforge.net/projects/libint/files/v1-releases/libint-1.1.4.tar.gz>
The specific commands used to build version 1.1.4 of Libint using GCC on a number of different machines can be found in the machine-specific subdirectories accompanying this README. By default the build process only creates static (.a) libraries. If you want to be able to link dynamically to Libint when building CP2K you can pass the flag
--enable-shared to ./configure in order to produce shared libraries (.so).
If you can, it is easiest to build Libint on the same processor architecture on which you will run CP2K. This typically correspond to being to compile directly on the relevant compute nodes of the machine. If this is not possible and if you are forced instead to compile on nodes with a different processor architecture to the compute nodes on which CP2K will eventually run, see the section below on cross-compiling Libint.
More information about Libint can be found inside the CP2K distribution base directory in
```
/tools/hfx_tools/libint_tools/README_LIBINT
```
### Cross-compiling Libint for compute nodes
If you are forced to cross-compile Libint for compute nodes on nodes that have a different processor architecture, follow these instructions. They assume you will be able to call a parallel application launcher like ``mpirun`` or ``mpiexec`` during your build process in order to run compiled code.
In ``/src/lib/`` edit the files ``MakeRules`` and ``MakeRules.in``.
On the last line of each file, replace
```
cd $(LIBSRCLINK); $(TOPOBJDIR)/src/bin/$(NAME)/$(COMPILER)
```
with
```
cd $(LIBSRCLINK); $(PARALLEL_LAUNCHER_COMMAND) $(TOPOBJDIR)/src/bin/$(NAME)/$(COMPILER)
```
Then run
```
export PARALLEL_LAUNCHER_COMMAND="mpirun -n 1"
```
replacing ``mpirun`` with a different parallel application launcher such as ``mpiexec`` (or ``aprun`` if applicable). When proceeding with the configure stage, include the configure flag ``cross-compiling=yes``.
## 2. Compile Libxc
The Libxc library can be obtained from <https://tddft.org/programs/libxc/download/previous/>. Version 4.2.3 was used for deliverable D7.5.
The specific commands used to build Libxc using GCC on a number of different machines can be found in the machine-specific subdirectories accompanying this README.
## 3. Compile FFTW
If FFTW (FFTW3) is not already available preinstalled on your system it can be obtained from <http://www.fftw.org/download.html>
The specific commands used to build FFTW using GCC on a number of different machines can be found in the machine-specific subdirectories accompanying this README.
Alternatively, you can use MKL's FFTW3 interface.
## 4. Compile CP2K
The CP2K source code can be downloaded from <https://github.com/cp2k/cp2k/releases/>. Version 6.1 of CP2K was used to generate the results reported in D7.5.
The general procedure is to create a custom so-called arch (architecture) file inside the ``arch`` directory in the CP2K distribution, which includes examples for a number of common architectures. The arch file specifies build parameters such as the choice of compilers, library locations and compilation and linker flags. Building the hybrid MPI + OpenMP ("psmp") version of CP2K (most convenient for running benchmarks) in accordance with a given arch file is then accomplished by entering the ``makefiles`` directory in the distribution and running
```
make -j number_of_cores_available_to_you ARCH=arch_file_name VERSION=psmp
```
If the build is successful, the resulting executable ``cp2k.psmp`` can be found inside ``/exe/arch_file_name/`` in the CP2K base directory.
Detailed information about arch file and library options and overall build procedure can be found in the ``INSTALL.md`` readme file. You can also consult https://dashboard.cp2k.org, which provides sample arch files as part of
the testing reports for some platforms (click on the status field for a platform, and search for 'ARCH-file' in the resulting output).
Specific arch files used to build CP2K for deliverable D7.5 can be found in the machine-specific subdirectories in this repository.
### Linking to MKL
If you are linking to Intel's MKL library to provide LAPACK, BLAS, SCALAPACK and BLACS (and possibly FFTW3) you should choose linking options using the [MKL Link Line Advisor tool](https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor), carefully selecting the options relevant on your machine environment.
### Building a CUDA-enabled version of CP2K
See the ``PizDaint`` subdirectory for an example arch file that enables GPU acceleration with CUDA. The ``-arch`` NVIDIA flag should be adjusted to choose the right option for the particular Nvidia GPU architecture in question. For example ``-arch sm35`` matches the Tesla K40 and K80 GPU architectures.
## Running the UEABS benchmarks
### Test Case A: H2O-1024
### Test Case B: LiH-HFX
### Test Case C: H2O-DFT-LS
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