Commit 5352d620 authored by caubet_m's avatar caubet_m

Merge branch 'master' into 'openmpi_slurm'

# Conflicts:
#   Compiler/openmpi/modulefile
parents b2dc06e2 a454593f
# New module variant
[//]: # (open an issue for each version and System)
* **Name:**
* **Group:**
* **with:**
* **System:**
* **Overlay**
| **Name** | **Version** | **Group** | **with** | **System** | **Overlay** |
|----------|-------------|-----------|------------|------------|-------------|
| | | | | | default |
[//]: # (if you do not have hierarchival dependencies use the check-list below
- [ ] build
- [ ] tested
- [ ] released
[//]: # (otherwise use check-lists like the one below for each variant)
- [ ] version X.Y.Z with WITH1
- [ ] build
- [ ] tested
- [ ] released
/label ~"New variant"
......@@ -6,3 +6,6 @@ OpenBLAS/0.2.20_omp stable gcc/7.3.0
OpenBLAS/0.2.20 stable intel/17.4
OpenBLAS/0.3.7 stable gcc/{7.4.0,8.3.0,9.2.0}
OpenBLAS/0.3.9 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0}
OpenBLAS/0.3.10 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0}
#!/usr/bin/env modbuild
pbuild::set_download_url "https://netcologne.dl.sourceforge.net/project/${P}/${P}/$V/${P}_${V_PKG//./_}.tar.gz"
#pbuild::set_download_url "https://dl.bintray.com/boostorg/release/${V_PKG}/source/${P}_${V_PKG//./_}.tar.gz"
#pbuild::set_download_url "https://netcologne.dl.sourceforge.net/project/$P/$P/$V/$P_${V_MAJOR}_${V_MINOR}_${V_PATCHLVL}.tar.gz"
pbuild::set_download_url "https://dl.bintray.com/boostorg/release/${V_PKG}/source/${P}_${V_PKG//./_}.tar.gz"
pbuild::add_to_group 'Compiler'
BOOST_BUILD_PATH="${BUILD_DIR}"
pbuild::configure() {
cd "${SRC_DIR}"
"${SRC_DIR}"/bootstrap.sh \
--prefix="${PREFIX}" \
--with-libraries=all \
--with-python-root="${PYTHON_PREFIX}" \
|| exit 1
TOOLSET=''
pbuild::pre_configure() {
case "${COMPILER}" in
gcc )
TOOLSET=gcc
;;
* )
std::die 1 "Unsupported compiler!"
;;
esac
}
pbuild::compile() {
cd "${SRC_DIR}"
./b2 \
--build-type=minimal \
--build-dir="${BUILD_DIR}" \
--layout=system \
cd "${SRC_DIR}"
./bootstrap.sh \
--prefix="${PREFIX}" \
--with-toolset=${TOOLSET} \
--without-libraries=python \
|| exit 1
./b2 \
--build-dir="${BUILD_DIR}" \
--layout=system \
--without-python \
--without-mpi \
variant=release \
link=shared,static \
threading=multi \
stage
toolset=${TOOLSET} \
variant=release \
link=shared,static \
threading=multi \
install -j 3 \
|| exit 1
}
pbuild::install() {
cd "${SRC_DIR}"
./b2 \
--build-type=minimal \
--build-dir="${BUILD_DIR}" \
--layout=system \
--without-mpi \
variant=release \
link=shared,static \
threading=multi \
install
:
}
boost/1.55.0 stable gcc/4.7.4 b:Python/3.4.0
boost/1.55.0 stable gcc/4.8.3 b:Python/3.4.0
boost/1.55.0 stable gcc/4.8.4 b:Python/3.4.0
boost/1.55.0 stable gcc/4.8.5 b:Python/2.7.11
boost/1.55.0 stable gcc/4.9.2 b:Python/3.4.0
boost/1.57.0 stable gcc/4.8.2 b:Python/3.4.0
boost/1.58.0 stable gcc/4.8.4 b:Python/3.4.0
boost/1.58.0 stable gcc/4.8.5 b:Python/2.7.11
boost/1.58.0 stable gcc/4.9.3 b:Python/2.7.11
boost/1.58.0 stable gcc/6.3.0 b:Python/2.7.12
boost/1.61.0 stable gcc/4.8.5 b:Python/2.7.11
boost/1.61.0 stable gcc/6.2.0 b:Python/2.7.11
boost/1.62.0 stable gcc/4.8.5 Python/2.7.12
boost/1.62.0 stable gcc/4.9.4 Python/2.7.12
boost/1.62.0 stable gcc/5.4.0 Python/2.7.12
boost/1.62.0 stable gcc/6.2.0 Python/2.7.12
boost/1.62.0 stable gcc/6.3.0 Python/2.7.12
boost/1.62.0 stable gcc/7.1.0 Python/2.7.12
boost/1.63.0 stable gcc/6.3.0 Python/2.7.12
boost/1.64.0 stable gcc/5.4.0 Python/2.7.12
boost/1.66.0 stable gcc/5.5.0 b:Python/2.7.12
boost/1.66.0 stable gcc/6.4.0 b:Python/2.7.12
boost/1.66.0 stable gcc/7.3.0 b:Python/2.7.12
boost/1.66.0 stable clang-macos/9.0.0 b:Python/2.7.12
boost/1.66.0 stable intel/17.4 b:Python/2.7.12
boost/1.67.0 stable gcc/5.5.0 b:Python/2.7.14
boost/1.67.0 stable gcc/6.4.0 b:Python/2.7.14
boost/1.67.0 stable gcc/7.3.0 b:Python/2.7.14
boost/1.67.0 stable clang-macos/9.0.0 b:Python/2.7.14
boost/1.67.0 stable intel/17.4 b:Python/2.7.14
boost/1.68.0 stable gcc/7.3.0 b:Python/2.7.14
boost/1.68.0 stable gcc/8.2.0 b:Python/2.7.14
boost/1.55.0 deprecated gcc/{4.7.4,4.8.3,4.8.4,4.9.2} b:Python/3.4.0
boost/1.55.0 deprecated gcc/4.8.5 b:Python/2.7.11
boost/1.57.0 deprecated gcc/4.8.2 b:Python/3.4.0
boost/1.58.0 deprecated gcc/4.8.4 b:Python/3.4.0
boost/1.58.0 deprecated gcc/{4.8.5,4.9.3} b:Python/2.7.11
boost/1.61.0 deprecated gcc/{4.8.5,6.2.0} b:Python/2.7.11
boost/1.62.0 deprecated gcc/{4.8.5,4.9.4,5.4.0,6.2.0,6.3.0,7.1.0} Python/2.7.12
boost/1.63.0 deprecated gcc/6.3.0 Python/2.7.12
boost/1.64.0 deprecated gcc/5.4.0 Python/2.7.12
boost/1.66.0 stable gcc/{5.5.0,6.4.0,7.3.0} b:Python/2.7.14
boost/1.66.0 stable intel/17.4 b:Python/2.7.12
boost/1.67.0 stable gcc/{5.5.0,6.4.0,7.3.0} b:Python/2.7.14
boost/1.67.0 stable intel/17.4 b:Python/2.7.14
boost/1.68.0 stable gcc/{7.3.0,8.2.0} b:Python/2.7.14
boost/1.73.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} b:zlib/1.2.11
......@@ -13,3 +13,4 @@ gsl/2.5 stable gcc/{6.3.0,7.3.0,7.4.0,8.3.0,9.1.0}
gsl/2.5 stable intel/19.4
gsl/2.6 stable gcc/{7.4.0,8.3.0,9.1.0,9.2.0}
gsl/2.6 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0}
gtest/1.7.0 stable gcc/{5.4.0,6.4.0,7.3.0,7.4.0} b:cmake/3.10.3
gtest/1.8.1 stable gcc/{5.5.0,6.4.0,7.4.0,8.3.0,9.2.0} b:cmake/3.10.3
gtest/1.10.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} b:cmake/3.15.5
#!/usr/bin/env modbuild
pbuild::set_download_url "https://github.com/Reference-LAPACK/$P/archive/v${V_PKG}.tar.gz"
pbuild::add_configure_args '-DCBLAS=ON'
pbuild::add_configure_args '-DLAPACKE=ON'
pbuild::add_to_group 'Compiler'
pbuild::install_docfiles \
'README.md' \
'LICENSE'
# Local Variables:
# mode: sh
# sh-basic-offset: 8
# tab-width: 8
# End:
lapack/3.9.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} b:cmake/3.15.5
#%Module1.0
module-whatis "Linear Algebra PACKage"
module-url "http://www.netlib.org/lapack/"
module-license "See $PREFIX/share/doc/openmpi/LICENSE"
module-maintainer "Achim Gsell <achim.gsell@psi.ch>"
module-help "
LAPACK is written in Fortran 90 and provides routines for solving
systems of simultaneous linear equations, least-squares solutions
of linear systems of equations, eigenvalue problems, and singular
value problems. The associated matrix factorizations (LU, Cholesky,i
QR, SVD, Schur, generalized Schur) are also provided, as are related
computations such as reordering of the Schur factorizations and
estimating condition numbers. Dense and banded matrices are handled,
but not general sparse matrices. In all areas, similar functionality
is provided for real and complex matrices, in both single and double
precision.
This modules also includes the C-bindings in the library liblapack.a
and the BLAS library libcblas.a.
"
mpich/3.2.1 stable gcc/4.8.5
mpich/3.2.1 stable gcc/5.5.0
mpich/3.2.1 stable gcc/6.4.0
mpich/3.2.1 stable gcc/7.3.0
mpich/3.2.1 stable gcc/8.2.0
mpich/3.2.1_merlin unstable gcc/6.4.0 b:binutils/2.29 b:mxm/3.6.3104
mpich/3.2.1_merlin unstable gcc/7.3.0 b:binutils/2.29 b:mxm/3.6.3104
mpich/3.2.1 stable intel/17.4
mpich/3.3 stable gcc/7.3.0
mpich/3.3 stable gcc/7.4.0
mpich/3.3 stable gcc/8.3.0
mpich/3.2.1_merlin unstable gcc/{6.4.0,7.3.0} b:binutils/2.29 b:mxm/3.6.3104
mpich/3.1.4 deprecated gcc/{4.7.4,4.8.4,4.9.2,5.1.0}
mpich/3.1.4 deprecated intel/15.2
mpich/3.2.1 stable gcc/{4.8.5,5.5.0,6.4.0,7.3.0,8.2.0}
mpich/3.2.1 stable intel/17.4
mpich/3.3 stable gcc/{7.3.0,7.4.0,8.3.0}
mpich/3.3.2 unstable gcc/{7.5.0,8.4.0,9.3.0}
......@@ -38,6 +38,7 @@ openmpi/3.1.2 stable gcc/{7.3.0,8.2.0}
openmpi/3.1.2 stable intel/18.4
openmpi/3.1.3 stable gcc/{4.8.5,5.5.0,6.4.0,6.5.0,7.3.0,8.2.0,8.3.0}
openmpi/3.1.4 stable gcc/{7.4.0,8.3.0,9.1.0,9.2.0}
openmpi/3.1.6 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0}
openmpi/4.0.0 stable gcc/{5.5,6.4,6.5,7.3,7.4,8.2,8.3}.0
......
vtk/5.10.1 stable b:cmake/2.8.12.2 gcc/4.7.4
vtk/5.10.1 stable b:cmake/2.8.12.2 gcc/4.8.3
vtk/5.10.1 stable b:cmake/3.1.3 gcc/4.8.4
vtk/5.10.1 stable b:cmake/3.4.1 gcc/4.8.5
vtk/5.10.1 stable b:cmake/3.1.3 gcc/4.9.2
vtk/5.10.1 stable b:cmake/3.6.3 gcc/4.9.4
vtk/5.10.1 stable b:cmake/3.6.3 gcc/5.3.0
vtk/5.10.1 stable b:cmake/3.6.3 gcc/6.2.0
vtk/5.10.1 unstable b:cmake/3.1.3 intel/15.3
vtk/6.3.0 unstable b:cmake/3.6.3 gcc/6.2.0
vtk/7.0.0 unstable b:cmake/3.6.3 gcc/6.2.0
vtk/8.0.0 unstable b:cmake/3.6.3 gcc/5.4.0
vtk/5.10.1 deprecated b:cmake/2.8.12.2 gcc/{4.7.4,4.8.3}
vtk/5.10.1 deprecated b:cmake/3.1.3 gcc/{4.8.4,4.9.2}
vtk/5.10.1 deprecated b:cmake/3.1.3 intel/15.3
vtk/5.10.1 deprecated b:cmake/3.6.3 gcc/{4.8.5,4.9.4,5.3.0}
vtk/7.0.0 deprecated b:cmake/3.6.3 gcc/6.2.0
vtk/8.0.0 deprecated b:cmake/3.6.3 gcc/5.4.0
vtk/8.2.0 unstable b:cmake/3.15.5 gcc/{7.5.0,8.4.0,9.3.0}
crYOLO/1.2.3 unstable cuda/9.0.176
crYOLO/1.5.6_gpu unstable anaconda/2019.07
crYOLO/1.6.1_gpu unstable anaconda/2019.07
crYOLO/1.6.1_cpu unstable anaconda/2019.07
......@@ -26,19 +26,28 @@ convolutional neural networks and utilizes the popular You Only Look Once
set shelltype [module-info shelltype]
switch -- $shelltype {
"sh" {
puts stdout "source \"\${ANACONDA_PREFIX}\"/admintools/conda_setup.sh;\n"
}
default {
puts stderr "Shells of type '$shelltype' are NOT supported!"
}
}
#set useflag [string map {{:} {}} $USEFLAGS]
#puts stderr "conda activate cryolo-${V_PKG}-${USEFLAGS%\n"
# Determine useflags and construct conda env name
set list [split $V "_"]
set version [lindex ${list} 0]
set useflags [lrange ${list} 1 end]
set flavour [lindex $useflags 0]
set env_to_activate [string tolower ${P}]-${version}-${flavour}
#puts stderr "P/V: $P/$V"
#puts stderr "USEFLAG: [lindex $useflags 0]"
#puts stderr "$env_to_activate"
switch [module-info mode] {
"load" {
# Relies on the anaconda module being loaded since we need to update the path
puts stdout "conda activate cryolo-1.5.6-gpu;\n"
puts stdout "conda activate $env_to_activate;\n"
}
"unload" -
"remove" {
......
......@@ -3,8 +3,9 @@
## Installation
Relion is installed from git. The ./build script should work for both stable
(tags) and unstable (branches) versions.
(tags) and unstable (branches) versions. It should be run on Merlin6 from an
admin account.
Currently only gcc/7.4.0 is used. Better performance is reported with
intel icc and MKL, but this would require additional openmpi variants.
Currently only gcc/7.4.0 is used. Better performance is reported with intel icc
and MKL, but this would require additional openmpi variants.
relion/2.1.b1 stable gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44
relion/3.0_beta stable gcc/4.9.4 openmpi/2.0.1 cuda/8.0.44
relion/3.0.8 unstable gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
relion/3.0.8 stable gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
relion/3.1-beta unstable gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/9.2.148 b:cmake/3.14.0 b:tiff/4.0.9
relion/3.1.0 unstable gcc/7.5.0 openmpi/4.0.4_slurm cuda/10.0.130 b:cmake/3.15.5 b:tiff/4.0.9 b:git/2.22.0
H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.6.5 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.6.5 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.2 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.2 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.4 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.7.4 openmpi/1.8.4 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.6.5 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.6.5 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.2 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.2 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.4 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.8.3 openmpi/1.8.4 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.6.5 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.6.5 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.2 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.2 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.4 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.8.4 openmpi/1.8.4 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.8.5 openmpi/1.8.8 hdf5/1.8.12 b:libtool b:autoconf b:automake
H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.6.5 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.6.5 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.2 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.2 hdf5/1.8.14
H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.4 hdf5/1.8.12
H5hut/1.99.13 stable gcc/4.9.2 openmpi/1.8.4 hdf5/1.8.14
#!/usr/bin/env modbuild
pbuild::set_download_url "http://amas.web.psi.ch/Downloads/$P/$P-$V.tar.gz"
pbuild::set_download_url "http://amas.web.psi.ch/Downloads/$P/$P-${V_PKG}.tar.gz"
pbuild::add_to_group 'HDF5'
pbuild::install_docfiles 'AUTHORS' 'COPYING'
......@@ -8,32 +8,27 @@ if [[ ${V_MAJOR} == 1 ]]; then
pbuild::compile_in_sourcetree
fi
pbuild::pre_configure() {
: ./autogen.sh
pbuild::post_prep() {
./autogen.sh
}
pbuild::configure() {
pbuild::pre_configure() {
pbuild::add_configure_args "--enable-parallel"
pbuild::add_configure_args "--enable-debug"
pbuild::add_configure_args "--enable-shared"
pbuild::add_configure_args "--with-hdf5=$HDF5_PREFIX"
pbuild::add_configure_args "--with-pic"
if (( V_MAJOR >= 2 )); then
: config_args+=" --enable-python"
: pbuild::add_configure_args "--enable-python"
fi
case "${COMPILER}" in
"clang-macos" )
:
;;
* )
config_args+='--enable-fortran'
pbuild::add_configure_args '--enable-fortran'
;;
esac
"${SRC_DIR}"/configure \
--prefix="${PREFIX}" \
--enable-parallel \
--enable-debug \
--enable-shared \
--with-hdf5=$HDF5_PREFIX \
--with-pic \
${config_args} \
|| exit 1
}
pbuild::compile() {
......
H5hut/2.0.0rc6_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm hdf5/1.10.6_slurm b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.12 b:parmetis/4.0.3_slurm
H5hut/1.99.13 deprecated gcc/{4.7.4,4.8.3,4.8.4,4.9.2} openmpi/{1.6.5,1.8.2,1.8.4} hdf5/{1.8.12,1.8.14}
H5hut/2.0.0rc2 deprecated gcc/4.8.5 openmpi/1.10.2 hdf5/1.8.17 b:automake/1.14 b:autoconf/2.69 b:libtool/2.4.2 b:Python/2.7.12 b:parmetis/4.0.3
H5hut/2.0.0rc3 deprecated gcc/5.4.0 openmpi/1.10.4 hdf5/1.8.17 b:automake/1.14 b:autoconf/2.69 b:libtool/2.4.2 b:Python/2.7.12 b:parmetis/4.0.3
......@@ -19,4 +21,5 @@ H5hut/2.0.0rc5 stable gcc/7.3.0 openmpi/3.1.3 hdf5/1.10.4 b:automake/1.16.1 b:
H5hut/2.0.0rc6 stable gcc/7.3.0 openmpi/3.1.3 hdf5/1.10.4 b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.12 b:parmetis/4.0.3
H5hut/2.0.0rc6 stable gcc/7.4.0 openmpi/3.1.4 hdf5/1.10.5 b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.12 b:parmetis/4.0.3
H5hut/2.0.0rc6 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 hdf5/1.10.6 b:automake/1.16.1 b:autoconf/2.69 b:libtool/2.4.6-1 b:Python/2.7.12 b:parmetis/4.0.3
......@@ -2,7 +2,7 @@
pbuild::set_download_url \
"https://github.com/$P/$P/tarball/$P-release-${V//./-}" \
"$P-$V.tar.gz"
"$P-${V_PKG}.tar.gz"
pbuild::set_sha256sum \
"trilinos-12.12.1.tar.gz:c8f2029fa36230b9f384c56139aaa33111227bcf653e73f7daf3c9efdecc1d2d"
......
trilinos/12.18.1_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm hdf5/1.10.6_slurm b:cmake/3.15.5 b:OpenBLAS/0.3.10 b:parmetis/4.0.3_slurm
trilinos/12.2.1 unstable gcc/4.8.2 openmpi/1.6.5 hdf5/1.8.12 b:cmake/3.6.3 b:OpenBLAS/0.2.9 b:parmetis/4.0.3
#trilinos/11.10.2 deprecated b:cmake/2.8.12.2 gcc/{4.7.4,4.8.3,4.8.4,9.2.0} openmpi/{1.6.5,1.8.2,1.8.4} OpenBLAS/0.2.9 parmetis/3.2.0
#trilinos/11.12.1 deprecated b:cmake/2.8.12.2 gcc/{4.7.4,4.8.3,4.8.4,9.2.0} openmpi/{1.6.5,1.8.2,1.8.4} OpenBLAS/0.2.9 parmetis/3.2.0
#trilinos/11.14.1 deprecated b:cmake/3.1.3 gcc/{4.7.4,4.8.3,4.8.4,9.2.0} openmpi/{1.6.5,1.8.2,1.8.4} OpenBLAS/0.2.9 parmetis/3.2.0
#trilinos/11.14.3 deprecated b:cmake/3.4.1 gcc/4.8.5 openmpi/1.10.2 b:OpenBLAS/0.2.9 b:parmetis/3.2.0
#trilinos/11.14.3 deprecated b:cmake/3.4.1 gcc/6.2.0 openmpi/{1.10.2,1.10.4,2.0.1} b:OpenBLAS/0.2.9 b:parmetis/3.2.0
trilinos/12.2.1 deprecated gcc/4.8.2 openmpi/1.6.5 hdf5/1.8.12 b:cmake/3.6.3 b:OpenBLAS/0.2.9 b:parmetis/4.0.3
trilinos/12.8.1 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3
trilinos/12.10.1 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3
......@@ -6,15 +12,11 @@ trilinos/12.10.1 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.
trilinos/12.10.1-1 stable gcc/{5.4.0,6.2.0} openmpi/1.10.4 hdf5/1.8.18 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3
trilinos/12.10.1-2 stable gcc/5.4.0 openmpi/1.10.4 hdf5/1.8.18 b:cmake/3.6.3 b:OpenBLAS/0.2.19 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.3.0 openmpi/{1.10.7,2.1.2,3.0.0,3.1.2,3.1.3} hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.3.0 openmpi/1.10.7 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.3.0 openmpi/2.1.2 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.3.0 openmpi/3.0.0 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.3.0 openmpi/3.1.2 hdf5/1.10.3 b:cmake/3.9.6 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.3.0 openmpi/3.1.3 hdf5/1.10.4 b:cmake/3.9.6 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.4.0 openmpi/3.1.4 hdf5/1.10.5 b:cmake/3.10.3 b:OpenBLAS/0.3.7 b:parmetis/4.0.3
trilinos/12.12.1 stable gcc/7.3.0 mpich/3.3 hdf5/1.10.4 b:cmake/3.9.6 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable intel/17.4 openmpi/1.10.7 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable intel/17.4 openmpi/2.1.2 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable intel/17.4 openmpi/3.0.0 hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.12.1 stable intel/17.4 openmpi/{1.10.7,2.1.2,3.0.0} hdf5/1.10.1 b:cmake/3.6.3 b:OpenBLAS/0.2.20 b:parmetis/4.0.3
trilinos/12.18.1 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 hdf5/1.10.6 b:cmake/3.15.5 b:OpenBLAS/0.3.10 b:parmetis/4.0.3
......@@ -10,5 +10,3 @@ declare -rx CPP=/usr/bin/cpp
pbuild::add_configure_args "--disable-shared"
pbuild::add_configure_args "--with-pic"
pbuild::make_all
......@@ -4,3 +4,4 @@ gmp/6.1.0 stable
gmp/6.1.1 stable
gmp/6.1.2 stable
gmp/6.1.2-1 stable
gmp/6.2.0 stable
......@@ -6,3 +6,4 @@ mpc/1.1.0 stable b:gmp/6.1.2 b:mpfr/4.0.0
mpc/1.1.0-1 stable b:gmp/6.1.2 b:mpfr/4.0.1
mpc/1.1.0-2 stable b:gmp/6.1.2-1 b:mpfr/4.0.1-1
mpc/1.1.0-3 stable b:gmp/6.1.2-1 b:mpfr/4.0.2
mpc/1.1.0-4 stable b:gmp/6.2.0 b:mpfr/4.0.2-1
......@@ -7,3 +7,4 @@ mpfr/4.0.0 stable b:gmp/6.1.2
mpfr/4.0.1 stable b:gmp/6.1.2
mpfr/4.0.1-1 stable b:gmp/6.1.2-1
mpfr/4.0.2 stable b:gmp/6.1.2-1
mpfr/4.0.2-1 stable b:gmp/6.2.0
amrex/18.07_2d stable gcc/7.3.0 openmpi/1.10.7 b:cmake/3.9.6
amrex/18.07_2d stable gcc/7.3.0 openmpi/2.1.5 b:cmake/3.9.6
amrex/18.07_2d stable gcc/7.3.0 openmpi/3.0.0 b:cmake/3.9.6
amrex/18.07_2d stable gcc/7.3.0 openmpi/3.1.2 b:cmake/3.9.6
amrex/18.07_2d stable gcc/7.3.0 openmpi/3.1.3 b:cmake/3.9.6
amrex/18.07_2d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3
amrex/18.07_2d stable gcc/8.2.0 openmpi/1.10.7 b:cmake/3.9.6
amrex/18.07_2d stable gcc/8.2.0 openmpi/2.1.5 b:cmake/3.9.6
amrex/18.07_2d stable gcc/8.2.0 openmpi/3.1.3 b:cmake/3.9.6
amrex/18.07_2d stable gcc/7.3.0 mpich/3.2.1 b:cmake/3.9.6
amrex/18.07_2d stable gcc/8.2.0 mpich/3.2.1 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.3.0 openmpi/1.10.7 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.3.0 openmpi/2.1.5 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.3.0 openmpi/3.0.0 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.3.0 openmpi/3.1.2 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.3.0 openmpi/3.1.3 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3
amrex/18.07_3d stable gcc/8.2.0 openmpi/1.10.7 b:cmake/3.9.6
amrex/18.07_3d stable gcc/8.2.0 openmpi/2.1.5 b:cmake/3.9.6
amrex/18.07_3d stable gcc/8.2.0 openmpi/3.1.3 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.3.0 mpich/3.2.1 b:cmake/3.9.6
amrex/18.07_3d stable gcc/8.2.0 mpich/3.2.1 b:cmake/3.9.6
amrex/18.07_3d_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:cmake/3.15.5
amrex/18.07_2d stable gcc/7.3.0 openmpi/{1.10.7,2.1.5,3.0.0,3.1.2,3.1.3} b:cmake/3.9.6
amrex/18.07_2d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3
amrex/18.07_2d stable gcc/8.2.0 openmpi/{1.10.7,2.1.5,3.1.3} b:cmake/3.9.6
amrex/18.07_2d stable gcc/{7.3.0,8.2.0} mpich/3.2.1 b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.3.0 openmpi/{1.10.7,2.1.5,3.0.0,3.1.2,3.1.3} b:cmake/3.9.6
amrex/18.07_3d stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.10.3
amrex/18.07_3d stable gcc/8.2.0 openmpi/{1.10.7,2.1.5,3.1.3} b:cmake/3.9.6
amrex/18.07_3d stable gcc/{7.3.0,8.2.0} mpich/3.2.1 b:cmake/3.9.6
amrex/18.07_3d unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6 b:cmake/3.15.5
boost/1.70.0_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:zlib/1.2.11
boost/1.73.0_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:zlib/1.2.11
......@@ -16,3 +16,6 @@ boost/1.68.0-1 stable gcc/7.3.0 mpich/3.3 b:zlib/1.2.11
boost/1.70.0 stable gcc/7.3.0 openmpi/3.1.3 b:zlib/1.2.11
boost/1.70.0 stable gcc/7.4.0 openmpi/3.1.4 b:zlib/1.2.11
boost/1.70.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:zlib/1.2.11
boost/1.73.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:zlib/1.2.11
# How to compile (P)elegant
# Building a module for (P)elegant
## Official build instructions
## Home page and official build instructions
>
Go down for PSI build instructions!
Elgant is a software packages produced by the [Accelerator Operations
and Physics Group](https://www.aps.anl.gov/Accelerator-Operations-Physics/Software).
It requires the EPICS build-system and SDDS. The EPICS build-system is completely
based on Makefiles. This makes it a bit harder to compile and more error prone.
Instructions to setup `epics/base`, `epics/extensions` compile `SDDS` and `elegant`. The instructions to build from source are almost at the end of the page:
Instructions to setup `epics/base`, `epics/extensions` and to compile `SDDS` as
well as `elegant` can be found
[here](https://www.aps.anl.gov/Accelerator-Operations-Physics/Software/installationGuide_Linux).
The instructions to build from source are almost at the end of the page.
https://www.aps.anl.gov/Accelerator-Operations-Physics/Software/installationGuide_Linux
Instructions to build [`Pelegant`](https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html)
Instructions to build `Pelegant`:
## Getting required configuration files
https://ops.aps.anl.gov/publish/Pelegant_manual/node2.html
* [file defining constants and some functions](https://ops.aps.anl.gov/cgi-bin/oagLog4.cgi?name=defns.rpn)
* [EPICS base configuration](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.base.configure.tar.gz)
* [EPICS extensions configuration](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.extensions.configure.tar.gz)
* [Configuration files for elegant, spiffe, genesis, and shower](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=oag.apps.configure.tar.gz)
## Get the software
## SDDS and Elegant sources
**Main page**
* https://www1.aps.anl.gov/Accelerator-Operations-Physics/Software
**Configuration files for EPICS build system (base and extensions)**
* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.base.configure.tar.gz
* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=epics.extensions.configure.tar.gz
**Configure files for elegant, spiffe, genesis, and shower**
* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=oag.apps.configure.tar.gz
**SDDS source**
* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=SDDS.3.6.1.tar.gz
**elegant source**
* http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=elegant.34.2.0.tar.gz
* [SDDS 4.3.1 source](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=SDDS.4.3.0.tar.gz)
* [Elegant 2020.2.0 source](http://www.aps.anl.gov/Accelerator_Systems_Division/Accelerator_Operations_Physics/cgi-bin/oagLog4.cgi?name=elegant.2020.2.0.tar.gz)
## Required Modules
```
module load gcc/7.3.0 gsl/2.4 OpenBLAS/0.2.20 mpich/3.2.1
module load gcc/8.4.0 gsl/2.6 OpenBLAS/0.3.10 mpich/3.2.1
```
## Set used versions
or
```
SDDS_VERSION=3.6.1
ELEGANT_VERSION=34.2.0
module load gcc/8.4.0 gsl/2.6 lapack/3.9.0 openmpi/3.1.6
```
## Setup Environment
```
SDDS_VERSION=4.3
ELEGANT_VERSION=2020.2.0
source "${PMODULES_ROOT}/config/modbuild.conf"
DOWNLOAD_DIR="${PMODULES_DISTFILESDIR}/elegant"
PREFIX="${PMODULES_ROOT}/MPI/elegant/${ELEGANT_VERSION}/${MPI}/${MPI_VERSION}/${COMPILER}/${COMPILER_VERSION}"
......@@ -59,81 +50,67 @@ export HOST_ARCH=linux-x86_64
export EPICS_HOST_ARCH=linux-x86_64
export RPN_DEFNS="${PREFIX}/RPN_DEFNS/defns.rpn"
export PERLLIB="${PREFIX}/lib/perl"
```
```
PATH+=":$PREFIX/epics/extensions/bin/${EPICS_HOST_ARCH}"
ARGS=()
ARGS+=( "GNU_BIN=$GCC_DIR/bin" )
ARGS+=( "LD=/usr/bin/ld" )
ARGS+=( "AR=/usr/bin/ar -rc" )
ARGS+=( "RANLIB=/usr/bin/ranlib" )
ARGS+=( "EPICS_BASE=${PREFIX}" )
ARGS+=( "INSTALL_LOCATION=${PREFIX}" )
ARGS+=( "INSTALL_LIB=${PREFIX}/lib" )
ARGS+=( "INSTALL_SHRLIB=${PREFIX}/lib" )
ARGS+=( "INSTALL_TCLLIB=${PREFIX}/lib" )
ARGS+=( "INSTALL_BIN=${PREFIX}/bin" )
ARGS+=( "SYSGSL=1")
```
## Prepare base build environment
## Prepare everything