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Commit 209cedf8 authored by Martin Lang's avatar Martin Lang
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Merge branch 'cleanup' into 'develop' 

Remove unused files and directories

See merge request !113
parents 6ec9d24c 4f690c0e
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Dockerfile deleted 100644 → 0
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FROM debian:bullseye
ENV MPSD_OS=linux-debian11
ARG toolchain=foss2021a-mpi # or foss2021a-serial
ENV TERM=xterm-256color
# Get basic packages to setup mpsd mirror
RUN apt-get update && apt-get install -y --no-install-recommends \
ca-certificates \
curl \
gnupg \
wget \
&& rm -rf /var/lib/apt/lists/*
#Set the MPSD mirrors
COPY docker /root/docker
RUN echo "deb http://mpsd-deb-bullseye.desy.de/debian/ bullseye main non-free contrib" > /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian-security/ bullseye-security main contrib non-free" >> /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian/ bullseye-updates main contrib non-free" >> /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian/ bullseye-backports main contrib non-free" >> /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian-mpsd/ mpsd-bullseye/" >> /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian-mpsd/ mpsd-bullseye-nonfree/" >> /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian-mpsd/ mpsd-bullseye-3rdparty/" >> /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian-mpsd/ mpsd-bullseye-backports/" >> /etc/apt/sources.list && \
echo "deb http://mpsd-deb-bullseye.desy.de/debian-mpsd/ mpsd-bullseye-easybuild/" >> /etc/apt/sources.list && \
apt-key add /root/docker/MPSD.asc && \
apt-get -y update
# Convenience tools, if desired for debugging etc
# RUN apt-get -y install wget time nano vim emacs git
# From https://github.com/ax3l/dockerfiles/blob/master/spack/base/Dockerfile:
# install minimal spack dependencies
RUN apt-get install -y --no-install-recommends \
autoconf \
build-essential \
coreutils \
file \
gfortran \
git \
openssh-server \
python-is-python3 \
unzip \
vim \
nano \
rsync \
sudo \
lmod \
automake \
libtool \
linux-headers-$(uname -r) \
&& rm -rf /var/lib/apt/lists/*
# Run the commands to setup spack and install the toolchain
RUN adduser user
USER user
## move the spack-environments repository in to the docker
RUN mkdir -p /home/user/spack-environments/
COPY . /home/user/spack-environments/
WORKDIR /home/user/spack-environments/
## setup the toolchains
# RUN ssh-keygen -b 2048 -t rsa -f /home/user/.ssh/id_rsa -q -N "" && \
# eval `ssh-agent -s` && \
# ssh-add ~/.ssh/id_rsa
RUN gpg --import /home/user/spack-environments/docker/MPSD.asc
RUN /bin/bash /home/user/spack-environments/spack_setup.sh -b ${toolchain}
# If testing toolchains, load the freshly made toolchain and compile octopus and run checks
# If the toolchain variable is 'global' then exit(0) and do nothing else clone octopus, load toolchains and make and test octopus
ENV MODULEPATH=/home/user/spack-environments/lmod/Core:/etc/lmod/modules:/usr/share/lmod/lmod/modulefiles
ENV MPIEXEC=orterun
ENV OMP_NUM_THREADS=1
ENV OCT_TEST_NJOBS=4
ENV OCT_TEST_MPI_NPROCS=2
RUN if [ "${toolchain}" = "global" ]; \
then exit 0; \
else \
git clone https://gitlab.com/octopus-code/octopus /home/user/octopus ; \
fi
# USER root
#TODO module load the toolchain then make octopus
RUN if [ "${toolchain}" = "global" ]; \
then exit 0; \
else \
. /usr/share/lmod/lmod/init/bash ; module load toolchains/${toolchain} && \
cd /home/user/octopus && \
autoreconf -i && \
mkdir _build && \
cd _build && \
echo "sourcing configure with ${MPSD_OCTOPUS_CONFIGURE}" && \
bash "$MPSD_OCTOPUS_CONFIGURE" --prefix=/home/user/octopus/_build/installed && \
make -j 16 && \
make install ; \
fi
RUN if [ "${toolchain}" = "global" ]; \
then exit 0; \
else \
. /usr/share/lmod/lmod/init/bash ; \
module load toolchains/${toolchain} && \
cd /home/user/octopus/_build && \
make check-short | tee /home/user/octopus/_build/check-short.log ; exit 0 ; \
fi
# we add the exit 0 to make sure the container doesn't fail if the tests fail
# the python script bellow determines from the log if the tests failures can be ignored or not
RUN if [ "${toolchain}" = "global" ]; \
then exit 0; \
else \
python /home/user/spack-environments/docker/check_buildlog.py /home/user/octopus/_build/check-short.log ${toolchain}|| /bin/true ; \
fi
CMD /bin/bash -l
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# make targets for making and runing the spack-environments
# image - make ocotpus using "toolchain=foss2021a-mpi"
# image-serial - make octopus using "toolchain=foss2021a-serial"
# no-cache variants do not use docker cache
# run - run the latest container
# run-mount - mounts a folder ../tmps to /tmps in docker ( make sure it exists in host before running)
#
# The docker containers are tagged with the git branch name
gitBranch=`git rev-parse --abbrev-ref HEAD | sed 's/[^a-zA-Z0-9]/-/g'`
image : image-mpi
# Mainstream images
image-mpi: image-foss2021a-mpi
image-serial: image-foss2022a-serial
image-global-packages: image-foss2021a-global-packages
image-cuda-mpi: image-foss2021a-cuda-mpi
# All possible toolchains
image-foss2021a-serial:
docker build --build-arg "toolchain=foss2021a-serial" -f Dockerfile -t spack-environments-serial:${gitBranch} .
image-foss2021a-mpi:
docker build --build-arg "toolchain=foss2021a-mpi" -f Dockerfile -t spack-environments-mpi:${gitBranch} .
image-foss2021a-cuda-mpi:
docker build --build-arg "toolchain=foss2021a-cuda-mpi" -f Dockerfile -t spack-environments-cuda-mpi:${gitBranch} .
image-foss2021a-global-packages :
docker build --build-arg "toolchain=global" -f Dockerfile -t spack-environments-global:${gitBranch} .
image-foss2022a-serial:
docker build --build-arg "toolchain=foss2022a-serial" -f Dockerfile -t spack-environments-serial:${gitBranch} .
image-foss2022a-mpi:
docker build --build-arg "toolchain=foss2022a-mpi" -f Dockerfile -t spack-environments-mpi:${gitBranch} .
image-no-cache :
docker build --no-cache -f Dockerfile -t spack-environments:${gitBranch} .
image-serial-no-cache :
docker build --no-cache --build-arg "toolchain=foss2021a-serial" -f Dockerfile -t spack-environments-serial:${gitBranch} .
run: run-mpi
run-mpi:
docker run -ti -v $PWD:/io spack-environments-mpi:${gitBranch} env TERM=xterm-256color bash -l
run-serial:
docker run -ti -v $PWD:/io spack-environments-serial:${gitBranch} env TERM=xterm-256color bash -l
run-global:
docker run -ti -v $PWD:/io spack-environments-global:${gitBranch} env TERM=xterm-256color bash -l
\ No newline at end of file
bin/template_process deleted 100755 → 0
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#!/usr/bin/perl
# HG: perl one-liner as a program, with a bit
# better error handling
# process template file by substituting environment variables
#
# usage:
#
# export blah=42
# export blubb=2
#
# template_process [-i <var1>[,<var2>] ] <file>
#
# file: (input text file, containing ##blah##-style strings)
#
use strict;
use warnings;
use Getopt::Std;
our ($opt_i);
getopts('i:');
my %IGNORE_EMPTY;
map { $IGNORE_EMPTY{$_}=1 } split (',',$opt_i) if ($opt_i);
my $errorcode=0;
while (<>) {
my $src_line = $_;
my $result = '';
my $previous_match_end = 0;
while ($src_line =~ /##([\w-]+)##/g) {
$result .= substr($src_line, $previous_match_end, $-[0]-$previous_match_end);
my $SUBVAL="error";
if ((exists $ENV{$1}) and ($ENV{$1} ne '')) {
$SUBVAL=$ENV{$1};
} elsif (exists $IGNORE_EMPTY{$1}) {
$SUBVAL='';
} else {
print STDERR "$1 not in env!\n";
$SUBVAL="##!$1_not_in_env!##";
$errorcode|=1;
}
$result .= $SUBVAL;
$previous_match_end = $+[0];
}
$result .= substr($src_line, $previous_match_end);
$_ = $result;
print;
}
exit($errorcode);
bin/update_intel_compilers_yaml deleted 100755 → 0
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#!/usr/bin/python3
import sys
import yaml
# Add flags for the correct gcc to the section of the given compiler in compilers.yaml
# used to add gcc information to intel (and in the future oneapi) compiler
# $script_dir/bin/update_intel_compilers_yaml <path/to/compilers.yaml> "intel@=2021.10.2" \
# "-gcc-name=<path/to/gcc>/bin/gcc" "-gcc-name=<path/to/gcc>/bin/g++" "-gcc-name=<path/to/gcc>/bin/gcc" \
# "12.2.0"
file_name, compiler_spec, cflags, cxxflags, fflags = sys.argv[1:]
with open(file_name) as f:
compilers_yaml = yaml.load(f, Loader=yaml.Loader)
for compiler in compilers_yaml["compilers"]:
if compiler["compiler"]["spec"] == compiler_spec:
compiler["compiler"]["flags"]["cflags"] = cflags
compiler["compiler"]["flags"]["cxxflags"] = cxxflags
compiler["compiler"]["flags"]["fflags"] = fflags
with open(file_name, "w") as f:
yaml.dump(compilers_yaml, stream=f, Dumper=yaml.Dumper)
docker/MPSD.asc deleted 100644 → 0
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# gpg key of mpsd mini-dinstall server 2048R/C2E2FE18
-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: GnuPG v1
mQENBFZUeMABCADUT5PboH5oUzI1Of7aB79D7DfxvKSBiQzHD9ds+OnkWBNpyqWs
WZRWpt3a32WfKRMstDeCh1Xvwy6gDUMTVM+UZhtVJ31weKWrBxYOqaQTdTyIk+39
7xkkV0gJv7votbU1soHXGGGXJPy5X+TuiV809SRaxFgqazC+v0bp+Izx3J0gv0uA
PdYqVQL6NIPMTSHd/cKgWF1HNGdCbYTeTT1O5oTVDV+5HbCEA52BjNGEUJeV5f7s
zwym7ZH1g8vHLqSFdybxYBVi+51gQF9sWlsCOgMu8D560+jaOG6VGNgzv2SVs36i
H/jdUQA2NxkBEE9oBdvtx9mgmH5f84NvhFy/ABEBAAG0OE1QU0QgTWluaS1EaW5z
dGFsbCAoUHNldWRvLXVzZXIpIDxtaW5pLWRpbnN0YWxsQG1wc2RmYWk+iQE3BBMB
CAAhAhsDAh4BAheABQJZqWk1BQsJCAcDBRUKCQgLBRYCAwEAAAoJEGZ8MAHC4v4Y
wL0H/R91k3elMdzstkc2GAskRahwDj2VgwEGfMoY1v8OFoZ6qXQKcviPIbn9dkbM
Ng51CiRhoQnYzEJDyACLZDKB2C99lllk01LQM5ZuZpUaSwzScNZIPUUtAgh+hIU8
rBw4VqflRCfkL4YdP6seVM0dLYoztwtMFNjAzUQquwD7hnlfRWoNta+MBXMzM/KG
OQiQsbFT0k9489zSgXAwaK+TglLvISGttohDa2d0k9sDUBqVUXEbgCnipmbJw3+Y
uPBjkBavrtZOKRBDZqxVVh1GeVnHAWiHrTxdOXqAub6530U2dAOFw4XXVzAgWdl9
sueKz/Ewd10At90OmHEG7RgPlNC5AQ0EVlR4wAEIALrR+/3oaCjANJs5HOtgKWPw
YcQz54dCkwXDWlh0WFwpgiGcNZfvVT/y8ZG8TmZp8BuSi7x1pOfGPbkqF4S7qayD
E09WSPog19Ox7HYAHR9BhQEVuQ8o12FfsAb89vfibmWkqzJr/rFY0nLbWE7qkhO0
7hutS1/jKe/1OPKLQuxqiWlSXucDAm8npr3mobhsqNlN8rYnSZUY9GLuq3Fv+rQt
sX3ngY5PlYt/BbMvV7kxVjl1szHZJ/yJwAxv37I6GLZkTkFKG90iAX8IZg08FT6q
eVxuNe864FdSxCJDm+sdSYNixX334GickFbMzeQvBjDFbdTOsKVhHxYk6yRlK0sA
EQEAAYkBHwQYAQIACQUCVlR4wAIbDAAKCRBmfDABwuL+GLPzCACtU+YGX2U4yu4d
OVovWBoY9Re2EO6KCst8YRYdR44JhaeznEEP7JupzwUdQfdzHfOVzZ/SCHU71RCn
BSuHu/SYW7e8e5nQTq+q6VDLzkIq8cdX1Cw26W7ynvWkk/vDIn6AjQqgUr5x4Q3R
Ppr7/1zn4Gs63QneIPv3TU+MM0liBFSPVjOVEDUgfDtD2pw02GpVRLo8bIJD43rz
4f1n+G5WaUmPgeGpt/KYLUJsJmIuzwezISElC53j7kpjqEeJR0XwnS65QT8lO2g+
lbifQSD7+PermjG9lXaOTXpMjdaxTOg7njf6auseDwlB4O0F1eYdhY1zOv/rkItc
jpXPgC33
=9xdF
-----END PGP PUBLIC KEY BLOCK-----
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# A simple script to check the log file of `make check or `make check-short`
# and report the number of failed tests.
# And if the failed tests are ignorable.
# (errors due to tight thresholds, for example) or needs attention.
import sys
import re
ignored_test_list = {
"foss2021a-mpi": [
"finite_systems_2d/06-gdlib.test",
"finite_systems_3d/30-local_multipoles.test",
"periodic_systems/11-silicon_force.test",
],
"foss2021a-serial": [
"components/07-cholesky serial.test",
"finite_systems_2d/06-gdlib.test",
],
"foss2022a-serial":[
"components/07-cholesky serial.test",
"finite_systems_2d/06-gdlib.test",
],
}
def check_log(log_file):
with open(log_file, "r") as f:
logs = f.readlines()
# extract the last lines that has the format
# |Status: 1 failures
# | Passed: 139 / 142
# | Skipped: 0 / 142
# | Failed: 3 / 142
# |
# | testfile # failed testcases
# | ------------------------------------------------------------------------------
# | finite_systems_2d/06-gdlib.test 1
# | finite_systems_3d/30-local_multipoles.test 2
# | periodic_systems/11-silicon_force.test 1
# |
# |Total run-time of the testsuite: 03:27:12
# and extract the list of failed test files like
# finite_systems_2d/06-gdlib.test,
# finite_systems_3d/30-local_multipoles.test,
# periodic_systems/11-silicon_force.test
# from this example, by scanning from the end of the log file
# starting from the line that has the format
# `Total run-time of the testsuite:`
# and stop when the first line with the format
# `' -------------------------------------`
test_lists = []
reversed_logs = reversed(logs)
while not next(reversed_logs).startswith(
"Total run-time of the testsuite:"
):
pass
while not re.match(r" +-+", (line := next(reversed_logs))):
if not line == "\n": # skip blank lines
test_lists.append(line.split()[0])
if not test_lists:
print("No failed tests")
sys.exit(0)
unexpected_failures = [
test
for test in test_lists
if test not in ignored_test_list[used_toolchain]
]
if unexpected_failures:
print("Found {} unexpected failures".format(len(unexpected_failures)))
print("Unexpected failures : \n" + ", \n".join(unexpected_failures))
print("Built with tool chain : " + used_toolchain)
sys.exit(len(unexpected_failures))
print("All failed tests are ignored")
if __name__ == "__main__":
try:
log_file = sys.argv[1]
except IndexError:
print("Usage: python3 check_buildlog.py log_file toolchain[optional]")
sys.exit(1)
try:
used_toolchain = sys.argv[2]
except IndexError:
print("No toolchain specified, assuming the default foss2021a-mpi")
used_toolchain = "foss2021a-mpi"
check_log(log_file)
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# Compiling `octopus` using the new spack-generated modules
## Load dependencies via modules
```bash
mpsd-modules 24a -m $MPSD_MICROARCH # compilation with "generic" sandybrigde is possible by omitting '-m ...'
module load toolchain/foss2022b-mpi octopus-dependencies/full
```
Optionally list all loaded modules if desired.
```bash
module list
```
## Configure and compile `octopus`
- create octopus build dir (e.g. in octopus dir, `mkdir _build`), and chdir to it
- optionally set `GCC_ARCH=native` (or another target microarchitecture to optimise code for)
- if you are not in a direct subdir of octopus, do `export OCTOPUS_SRC=/path/to/octopus`
- `source $MPSD_OCTOPUS_CONFIGURE [... other-octopus-configure-options ...]`
- `make`
- optionally: (`MPIEXEC="orterun" make check`)
octopus/foss-cuda-mpi-config.sh deleted 100644 → 0
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#!/bin/sh
export CC="mpicc"
MARCH_FLAG="-march=${GCC_ARCH:-native}"
OPTIMISATION_LEVEL="-O3"
export CFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments"
export CXX="mpicxx"
export CXXFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments"
export FC="mpif90"
export FCFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments -ffree-line-length-none -fallow-argument-mismatch -fallow-invalid-boz"
# default to the parent directory unless OCTOPUS_SRC is set
[ "${OCTOPUS_SRC+1}" ] || export OCTOPUS_SRC='..'
# help configure to find the ELPA F90 modules and libraries
try_mpsd_elpa_version=`expr match "$MPSD_ELPA_ROOT" '.*/elpa-\([0-9.]\+\)'`
if [ -n "$try_mpsd_elpa_version" ] ; then
if [ -r $MPSD_ELPA_ROOT/include/elpa_openmp-$try_mpsd_elpa_version/modules/elpa.mod ]; then
export FCFLAGS_ELPA="-I$MPSD_ELPA_ROOT/include/elpa_openmp-$try_mpsd_elpa_version/modules"
export LIBS_ELPA="-lelpa_openmp"
elif [ -r $MPSD_ELPA_ROOT/include/elpa-$try_mpsd_elpa_version/modules/elpa.mod ] ; then
export FCFLAGS_ELPA="-I$MPSD_ELPA_ROOT/include/elpa-$try_mpsd_elpa_version/modules"
fi
fi
unset try_mpsd_elpa_version
# always keep options in the order listed by ``configure --help``
$OCTOPUS_SRC/configure \
--enable-mpi \
--enable-openmp \
--enable-cuda \
--with-libxc-prefix="$MPSD_LIBXC_ROOT" \
--with-libvdwxc-prefix="$MPSD_LIBVDWXC_ROOT" \
--with-blas="-L$MPSD_OPENBLAS_ROOT/lib -lopenblas" \
--with-gsl-prefix="$MPSD_GSL_ROOT" \
--with-fftw-prefix="$MPSD_FFTW_ROOT" \
--with-pfft-prefix="$MPSD_PFFT_ROOT" \
--with-nfft="$MPSD_NFFT_ROOT" \
--with-pnfft-prefix="$MPSD_PNFFT_ROOT" \
--with-berkeleygw-prefix="$MPSD_BERKELEYGW_ROOT" \
--with-sparskit="$MPSD_SPARSKIT_ROOT/lib/libskit.a" \
--with-nlopt-prefix="$MPSD_NLOPT_ROOT" \
--with-blacs="-L$MPSD_NETLIB_SCALAPACK_ROOT/lib -lscalapack" \
--with-scalapack="-L$MPSD_NETLIB_SCALAPACK_ROOT/lib -lscalapack" \
--with-elpa-prefix="$MPSD_ELPA_ROOT" \
--with-cgal="$MPSD_CGAL_ROOT" \
--with-boost="$MPSD_BOOST_ROOT" \
--with-metis-prefix="$MPSD_METIS_ROOT" \
--with-parmetis-prefix="$MPSD_PARMETIS_ROOT" \
--with-psolver-prefix="$MPSD_BIGDFT_PSOLVER_ROOT" \
--with-futile-prefix="$MPSD_BIGDFT_FUTILE_ROOT" \
--with-atlab-prefix="$MPSD_BIGDFT_ATLAB_ROOT" \
--with-dftbplus-prefix="$MPSD_DFTBPLUS_ROOT" \
--with-netcdf-prefix="$MPSD_NETCDF_FORTRAN_ROOT" \
--with-etsf-io-prefix="$MPSD_ETSF_IO_ROOT" \
"$@" | tee 00-configure.log 2>&1
echo "-------------------------------------------------------------------------------" >&2
echo "configure output has been saved to 00-configure.log" >&2
if [ "x${GCC_ARCH-}" = x ] ; then
echo "Microarchitecture optimization: native (set \$GCC_ARCH to override)" >&2
else
echo "Microarchitecture optimization: $GCC_ARCH (from override \$GCC_ARCH)" >&2
fi
echo "-------------------------------------------------------------------------------" >&2
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#!/bin/sh
export CC="mpicc"
MARCH_FLAG="-march=${GCC_ARCH:-native}"
OPTIMISATION_LEVEL="-O3"
export CFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments"
export CXX="mpicxx"
export CXXFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments"
export FC="mpif90"
export FCFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments -ffree-line-length-none -fallow-argument-mismatch -fallow-invalid-boz"
# default to the parent directory unless OCTOPUS_SRC is set
[ "${OCTOPUS_SRC+1}" ] || export OCTOPUS_SRC='..'
# help configure to find the ELPA F90 modules and libraries
try_mpsd_elpa_version=`expr match "$MPSD_ELPA_ROOT" '.*/elpa-\([0-9.]\+\)'`
if [ -n "$try_mpsd_elpa_version" ] ; then
if [ -r $MPSD_ELPA_ROOT/include/elpa_openmp-$try_mpsd_elpa_version/modules/elpa.mod ]; then
export FCFLAGS_ELPA="-I$MPSD_ELPA_ROOT/include/elpa_openmp-$try_mpsd_elpa_version/modules"
export LIBS_ELPA="-lelpa_openmp"
elif [ -r $MPSD_ELPA_ROOT/include/elpa-$try_mpsd_elpa_version/modules/elpa.mod ] ; then
export FCFLAGS_ELPA="-I$MPSD_ELPA_ROOT/include/elpa-$try_mpsd_elpa_version/modules"
fi
fi
unset try_mpsd_elpa_version
# always keep options in the order listed by ``configure --help``
$OCTOPUS_SRC/configure \
--enable-mpi \
--enable-openmp \
--with-libxc-prefix="$MPSD_LIBXC_ROOT" \
--with-libvdwxc-prefix="$MPSD_LIBVDWXC_ROOT" \
--with-blas="-L$MPSD_OPENBLAS_ROOT/lib -lopenblas" \
--with-gsl-prefix="$MPSD_GSL_ROOT" \
--with-fftw-prefix="$MPSD_FFTW_ROOT" \
--with-pfft-prefix="$MPSD_PFFT_ROOT" \
--with-nfft="$MPSD_NFFT_ROOT" \
--with-pnfft-prefix="$MPSD_PNFFT_ROOT" \
--with-berkeleygw-prefix="$MPSD_BERKELEYGW_ROOT" \
--with-sparskit="$MPSD_SPARSKIT_ROOT/lib/libskit.a" \
--with-nlopt-prefix="$MPSD_NLOPT_ROOT" \
--with-blacs="-L$MPSD_NETLIB_SCALAPACK_ROOT/lib -lscalapack" \
--with-scalapack="-L$MPSD_NETLIB_SCALAPACK_ROOT/lib -lscalapack" \
--with-elpa-prefix="$MPSD_ELPA_ROOT" \
--with-cgal="$MPSD_CGAL_ROOT" \
--with-boost="$MPSD_BOOST_ROOT" \
--with-metis-prefix="$MPSD_METIS_ROOT" \
--with-parmetis-prefix="$MPSD_PARMETIS_ROOT" \
--with-psolver-prefix="$MPSD_BIGDFT_PSOLVER_ROOT" \
--with-futile-prefix="$MPSD_BIGDFT_FUTILE_ROOT" \
--with-atlab-prefix="$MPSD_BIGDFT_ATLAB_ROOT" \
--with-dftbplus-prefix="$MPSD_DFTBPLUS_ROOT" \
--with-netcdf-prefix="$MPSD_NETCDF_FORTRAN_ROOT" \
--with-etsf-io-prefix="$MPSD_ETSF_IO_ROOT" \
"$@" | tee 00-configure.log 2>&1
echo "-------------------------------------------------------------------------------" >&2
echo "configure output has been saved to 00-configure.log" >&2
if [ "x${GCC_ARCH-}" = x ] ; then
echo "Microarchitecture optimization: native (set \$GCC_ARCH to override)" >&2
else
echo "Microarchitecture optimization: $GCC_ARCH (from override \$GCC_ARCH)" >&2
fi
echo "-------------------------------------------------------------------------------" >&2
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#!/bin/sh
export CC="gcc"
MARCH_FLAG="-march=${GCC_ARCH:-native}"
OPTIMISATION_LEVEL="-O3"
export CFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments"
export CXX="g++"
export CXXFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments"
export FC="gfortran"
export FCFLAGS="$MARCH_FLAG $OPTIMISATION_LEVEL -g -fno-var-tracking-assignments -ffree-line-length-none -fallow-argument-mismatch -fallow-invalid-boz"
# default to the parent directory unless OCTOPUS_SRC is set
[ "${OCTOPUS_SRC+1}" ] || export OCTOPUS_SRC='..'
# help configure to find the ELPA F90 modules and libraries
try_mpsd_elpa_version=`expr match "$MPSD_ELPA_ROOT" '.*/elpa-\([0-9.]\+\)'`
if [ -n "$try_mpsd_elpa_version" ] ; then
if [ -r $MPSD_ELPA_ROOT/include/elpa_openmp-$try_mpsd_elpa_version/modules/elpa.mod ]; then
export FCFLAGS_ELPA="-I$MPSD_ELPA_ROOT/include/elpa_openmp-$try_mpsd_elpa_version/modules"
export LIBS_ELPA="-lelpa_openmp"
elif [ -r $MPSD_ELPA_ROOT/include/elpa-$try_mpsd_elpa_version/modules/elpa.mod ] ; then
export FCFLAGS_ELPA="-I$MPSD_ELPA_ROOT/include/elpa-$try_mpsd_elpa_version/modules"
fi
fi
unset try_mpsd_elpa_version
# always keep options in the order listed by ``configure --help``
$OCTOPUS_SRC/configure \
--enable-openmp \
--with-libxc-prefix="$MPSD_LIBXC_ROOT" \
--with-libvdwxc-prefix="$MPSD_LIBVDWXC_ROOT" \
--with-blas="-L$MPSD_OPENBLAS_ROOT/lib -lopenblas" \
--with-gsl-prefix="$MPSD_GSL_ROOT" \
--with-fftw-prefix="$MPSD_FFTW_ROOT" \
--with-nfft="$MPSD_NFFT_ROOT" \
--with-netcdf-prefix="$MPSD_NETCDF_ROOT" \
--with-etsf-io-prefix="$MPSD_ETSF_IO_ROOT" \
--with-berkeleygw-prefix="$MPSD_BERKELEYGW_ROOT" \
--with-sparskit="$MPSD_SPARSKIT_ROOT/lib/libskit.a" \
--with-nlopt-prefix="$MPSD_NLOPT_ROOT" \
--with-cgal="$MPSD_CGAL_ROOT" \
--with-boost="$MPSD_BOOST_ROOT" \
--with-metis-prefix="$MPSD_METIS_ROOT" \
--with-psolver-prefix="$MPSD_BIGDFT_PSOLVER_ROOT" \
--with-futile-prefix="$MPSD_BIGDFT_FUTILE_ROOT" \
--with-atlab-prefix="$MPSD_BIGDFT_ATLAB_ROOT" \
--with-dftbplus-prefix="$MPSD_DFTBPLUS_ROOT" \
--with-netcdf-prefix="$MPSD_NETCDF_FORTRAN_ROOT" \
--with-etsf-io-prefix="$MPSD_ETSF_IO_ROOT" \
"$@" | tee 00-configure.log 2>&1
echo "-------------------------------------------------------------------------------" >&2
echo "configure output has been saved to 00-configure.log" >&2
if [ "x${GCC_ARCH-}" = x ] ; then
echo "Microarchitecture optimization: native (set \$GCC_ARCH to override)" >&2
else
echo "Microarchitecture optimization: $GCC_ARCH (from override \$GCC_ARCH)" >&2
fi
echo "-------------------------------------------------------------------------------" >&2
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