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Merge branch 'master' into 'openmpi_slurm'

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# Conflicts:
#   Compiler/openmpi/modulefile
This commit is contained in:
caubet_m
2020-09-18 13:05:12 +02:00
parent b2dc06e2df a454593f55
commit 5352d620fd
77 changed files with 500 additions and 390 deletions
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23
.gitlab/issue_templates/New variant.md
View File

@@ -1,21 +1,10 @@
# 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"

3
Compiler/OpenBLAS/files/variants.rhel6
View File

@@ -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}

60
Compiler/boost/build
View File

@@ -1,44 +1,44 @@
#!/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
:
}

39
Compiler/boost/files/variants
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@@ -1,39 +0,0 @@
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

25
Compiler/boost/files/variants.rhel6 Normal file
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@@ -0,0 +1,25 @@
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

1
Compiler/gsl/files/variants.rhel6
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@@ -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}

1
Compiler/gtest/files/variants.rhel6
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@@ -1,2 +1,3 @@
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

17
Compiler/lapack/build Executable file
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@@ -0,0 +1,17 @@
#!/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:

1
Compiler/lapack/files/variants.rhel6 Normal file
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@@ -0,0 +1 @@
lapack/3.9.0 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} b:cmake/3.15.5

21
Compiler/lapack/modulefile Normal file
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@@ -0,0 +1,21 @@
#%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.
"

12
Compiler/mpich/files/variants
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@@ -1,12 +0,0 @@
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

1
Compiler/mpich/files/variants.merlin Normal file
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@@ -0,0 +1 @@
mpich/3.2.1_merlin unstable gcc/{6.4.0,7.3.0} b:binutils/2.29 b:mxm/3.6.3104

8
Compiler/mpich/files/variants.rhel6 Normal file
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@@ -0,0 +1,8 @@
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}

1
Compiler/openmpi/files/variants.rhel6
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@@ -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

10
Compiler/vtk/5/variants.Linux
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@@ -1,10 +0,0 @@
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

1
Compiler/vtk/6/variants.Linux
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@@ -1 +0,0 @@
vtk/6.3.0 unstable b:cmake/3.6.3 gcc/6.2.0

1
Compiler/vtk/7/variants.Linux
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@@ -1 +0,0 @@
vtk/7.0.0 unstable b:cmake/3.6.3 gcc/6.2.0

1
Compiler/vtk/8/variants.Linux
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@@ -1 +0,0 @@
vtk/8.0.0 unstable b:cmake/3.6.3 gcc/5.4.0

11
Compiler/vtk/files/variants.rhel6 Normal file
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@@ -0,0 +1,11 @@
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}

2
EM/crYOLO/files/variants
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@@ -1,3 +1,5 @@
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

15
EM/crYOLO/modulefile
View File

@@ -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" {

7
EM/relion/README.md
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@@ -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.

3
EM/relion/files/variants
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@@ -1,5 +1,6 @@
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

25
HDF5/H5hut/1.99/variants
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@@ -1,25 +0,0 @@
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

27
HDF5/H5hut/build
View File

@@ -1,6 +1,6 @@
#!/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() {

0
HDF5/H5hut/2/variants.Edison → HDF5/H5hut/files/variants.Edison
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0
HDF5/H5hut/2/variants.macos1014 → HDF5/H5hut/files/variants.macos1014
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2
HDF5/H5hut/files/variants.merlin6 Normal file
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@@ -0,0 +1,2 @@
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

3
HDF5/H5hut/2/variants → HDF5/H5hut/files/variants.rhel6
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@@ -1,3 +1,5 @@
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

20
HDF5/trilinos/12/variants
View File

@@ -1,20 +0,0 @@
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/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
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 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

2
HDF5/trilinos/build
View File

@@ -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"

0
HDF5/trilinos/12/variants.Darwin → HDF5/trilinos/files/variants.Darwin
View File

1
HDF5/trilinos/files/variants.merlin6 Normal file
View File

@@ -0,0 +1 @@
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

22
HDF5/trilinos/files/variants.rhel6 Normal file
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@@ -0,0 +1,22 @@
#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
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/7.4.0 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/{1.10.7,2.1.2,3.0.0} 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

2
Libraries/gmp/build
View File

@@ -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

1
Libraries/gmp/files/variants
View File

@@ -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

1
Libraries/mpc/files/variants
View File

@@ -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

1
Libraries/mpfr/files/variants
View File

@@ -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

29
MPI/amrex/files/variants
View File

@@ -1,29 +0,0 @@
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

2
MPI/amrex/files/variants.merlin6 Normal file
View File

@@ -0,0 +1,2 @@
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

15
MPI/amrex/files/variants.rhel6 Normal file
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@@ -0,0 +1,15 @@
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

3
MPI/boost/files/variants.merlin6 Normal file
View File

@@ -0,0 +1,3 @@
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

3
MPI/boost/files/variants.rhel6
View File

@@ -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

141
MPI/elegant/README.md
View File

@@ -1,55 +1,46 @@
# 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
```
or
```
module load gcc/8.4.0 gsl/2.6 lapack/3.9.0 openmpi/3.1.6
```
## Set used versions
```
SDDS_VERSION=3.6.1
ELEGANT_VERSION=34.2.0
```
## 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=${PREFIX}/bin" )
ARGS+=( "SYSGSL=1")
```
## Prepare base build environment
## Prepare everything
EPICS base configuration
```
mkdir -p "${PREFIX}"
mkdir -p "${RPN_DEFNS%/*}"
cp "${DOWNLOAD_DIR}/defns.rpn" "${RPN_DEFNS}"
cd "${PREFIX}"
tar xvf "${DOWNLOAD_DIR}/epics.base.configure.tar.gz"
cd epics/base
make -e "${ARGS[@]}"
```
## Unpack EPICS extensions and OAG apps configuration
```
ARGS+=( "TOOLS=${PREFIX}/bin")
cd "${PREFIX}"
tar xvf "${DOWNLOAD_DIR}/epics.extensions.configure.tar.gz"
tar xvf "${DOWNLOAD_DIR}/oag.apps.configure.tar.gz"
tar xvf "${DOWNLOAD_DIR}/SDDS.${SDDS_VERSION}.tar.gz"
tar xvf "${DOWNLOAD_DIR}/elegant.${ELEGANT_VERSION}.tar.gz"
```
## Configure EPICS base and OAG applications
```
cd epics/base
make "${ARGS[@]}"
cd "${PREFIX}/oag/apps/configure"
sed -i "s/clean::/clean:/" RULES_PYTHON
make -e "${ARGS[@]}"
make "${ARGS[@]}"
```
>
You have to fix the `clean::` target in `${PREFIX}/oag/apps/configure/PYTHON_RULES`
## Compile SDDS
## Build required tools and libraries from SDDS
```
cd "${PREFIX}"
tar xvf "${DOWNLOAD_DIR}/SDDS.${SDDS_VERSION}.tar.gz"
cd "${PREFIX}/epics/extensions/src/SDDS/"
make -e "${ARGS[@]}" -C fftpack && \
make -e "${ARGS[@]}" -C lzma && \
make -e "${ARGS[@]}" -C matlib && \
make -e "${ARGS[@]}" -C mdbcommon && \
make -e "${ARGS[@]}" -C mdblib && \
make -e "${ARGS[@]}" -C mdbmth && \
make -e "${ARGS[@]}" -C meschach && \
make -e "${ARGS[@]}" -C namelist && \
make -e "${ARGS[@]}" -C pgapack && \
make -e "${ARGS[@]}" -C rpns/code && \
make -e "${ARGS[@]}" -C SDDSlib && \
make -e "${ARGS[@]}" -C SDDSlib clean
make "${ARGS[@]}" MPI=1 -C SDDSlib
sed -i -e "s/\( sddspseudoinverse_SYS_LIB.*\)/\1 gfortran/" SDDSaps/pseudoInverse/Makefile
sed -i -e "s/\( sddsmatrixop_SYS_LIBS.*\)/\1 gfortran/" SDDSaps/pseudoInverse/Makefile
make "${ARGS[@]}" -C png && \
make "${ARGS[@]}"
make "${ARGS[@]}" -C pgapack
make "${ARGS[@]}" -C SDDSlib clean
make "${ARGS[@]}" MPI=1 -C SDDSlib
```
## Compile (P)elegant
## Compile elegant
```
cd "${PREFIX}"
tar xvf "${DOWNLOAD_DIR}/elegant.${ELEGANT_VERSION}.tar.gz"
PATH+=":${PREFIX}/bin"
cd "${PREFIX}/oag/apps/src/elegant"
make -e "${ARGS[@]}"
make clean
make "${ARGS[@]}" Pelegant
make "${ARGS[@]}" STATIC_BUILD=NO
```
## Compile Pelegant
```
cd "${PREFIX}/oag/apps/src/elegant"
make clean
make SYSGSL=1 Pelegant
```

22
MPI/elegant/build Executable file
View File

@@ -0,0 +1,22 @@
#!/usr/bin/env modbuild
pbuild::add_to_group 'MPI'
pbuild::prep() {
:
}
pbuild::configure() {
:
}
pbuild::compile() {
:
}
pbuild::install() {
:
}
# Local Variables:
# mode: sh
# sh-basic-offset: 8
# tab-width: 8
# End:

1
MPI/elegant/files/variants.merlin6 Normal file
View File

@@ -0,0 +1 @@
elegant/2020.2.0_merlin6 unstable gcc/8.4.0 openmpi/3.1.6_slurm gsl/2.6

4
MPI/elegant/files/variants.rhel6 Normal file
View File

@@ -0,0 +1,4 @@
elegant/2020.2.0 unstable gcc/8.4.0 openmpi/3.1.6 gsl/2.6
elegant/32.0.0 deprecated gcc/5.4.0 openmpi/1.10.4
elegant/33.1.2 deprecated gcc/5.4.0 openmpi/1.10.4
elegant/34.2.0 deprecated gcc/7.3.0 mpich/3.2.1

14
MPI/elegant/modulefile
View File

@@ -18,6 +18,14 @@ and ramping machines. The code provides simulation of various collective
effects, such as wakes and coherent synchrotron radiation.
"
setenv RPN_DEFNS $PREFIX/RPN-DEFNS
setenv HOST_ARCH linux-x86_64
setenv EPICS_HOST_ARCH linux-x86_64
setenv RPN_DEFNS $PREFIX/RPN_DEFNS
setenv HOST_ARCH linux-x86_64
setenv EPICS_HOST_ARCH linux-x86_64
append-path PATH $PREFIX/epics/extensions/bin/linux-x86_64
append-path PATH $PREFIX/oag/apps/bin/linux-x86_64
append-path LIBRARY_PATH $PREFIX/epics/extensions/lib/linux-x86_64
append-path C_INCLUDE_PATH $PREFIX/epics/extensions/include
append-path CPLUS_INCLUDE_PATH $PREFIX/epics/extensions/include
append-path PKG_CONFIG_PATH $PREFIX/epics/base/lib

2
MPI/hdf5/build
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env modbuild
pbuild::set_download_url "https://support.hdfgroup.org/ftp/HDF5/releases/$P-${V_MAJOR}.${V_MINOR}/$P-$V/src/hdf5-$V.tar.bz2"
pbuild::set_download_url "https://support.hdfgroup.org/ftp/HDF5/releases/$P-${V_MAJOR}.${V_MINOR}/$P-$V/src/hdf5-${V_PKG}.tar.bz2"
pbuild::add_to_group 'MPI'
pbuild::install_docfiles ACKNOWLEDGMENTS

2
MPI/hdf5/files/variants.merlin6 Normal file
View File

@@ -0,0 +1,2 @@
hdf5/1.10.6_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm

1
MPI/hdf5/files/variants.rhel6
View File

@@ -37,3 +37,4 @@ hdf5/1.10.4 stable gcc/{5.5.0,6.4.0,7.3.0,8.2.0} openmpi/3.1.3
hdf5/1.10.4 stable gcc/7.3.0 mpich/3.3
hdf5/1.10.5 stable gcc/{7.4.0,8.3.0} openmpi/3.1.4
hdf5/1.10.6 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6

24
MPI/parmetis/3/variants
View File

@@ -1,24 +0,0 @@
parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.6.5
parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.8.2
parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.8.4
parmetis/3.2.0 stable gcc/4.7.4 openmpi/1.8.8
parmetis/3.2.0 stable gcc/4.8.3 openmpi/1.6.5
parmetis/3.2.0 stable gcc/4.8.3 openmpi/1.8.2
parmetis/3.2.0 stable gcc/4.8.3 openmpi/1.8.4
parmetis/3.2.0 stable gcc/4.8.4 openmpi/1.6.5
parmetis/3.2.0 stable gcc/4.8.4 openmpi/1.8.2
parmetis/3.2.0 stable gcc/4.8.4 openmpi/1.8.4
parmetis/3.2.0 stable gcc/4.8.5 openmpi/1.8.8
parmetis/3.2.0 stable gcc/4.8.5 openmpi/1.10.2
parmetis/3.2.0 stable gcc/4.9.2 openmpi/1.6.5
parmetis/3.2.0 stable gcc/4.9.2 openmpi/1.8.2
parmetis/3.2.0 stable gcc/4.9.2 openmpi/1.8.4
parmetis/3.2.0 stable gcc/4.9.3 openmpi/1.8.8
parmetis/3.2.0 unstable gcc/5.3.0 openmpi/1.8.8
parmetis/3.2.0 unstable gcc/5.3.0 openmpi/1.10.2
parmetis/3.2.0 unstable gcc/6.1.0 openmpi/1.8.8
parmetis/3.2.0 unstable gcc/6.1.0 openmpi/1.10.2
parmetis/3.2.0 unstable gcc/6.2.0 openmpi/1.10.2
parmetis/3.2.0 unstable gcc/6.2.0 openmpi/1.10.4
parmetis/3.2.0 unstable gcc/6.2.0 openmpi/2.0.1
parmetis/3.2.0 unstable gcc/7.3.0 openmpi/3.0.1

31
MPI/parmetis/4/variants
View File

@@ -1,31 +0,0 @@
parmetis/4.0.3 stable gcc/4.8.2 openmpi/1.6.5 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/4.8.5 openmpi/1.10.2 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/4.9.4 openmpi/1.10.2 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/5.3.0 openmpi/1.10.2 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/5.4.0 openmpi/1.10.2 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/6.1.0 openmpi/1.10.2 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/6.2.0 openmpi/1.10.2 b:cmake/3.4.1
parmetis/4.0.3 unstable gcc/4.8.5 openmpi/1.10.4 b:cmake/3.6.3
parmetis/4.0.3 unstable gcc/4.9.4 openmpi/1.10.4 b:cmake/3.6.3
parmetis/4.0.3 unstable gcc/5.4.0 openmpi/1.10.4 b:cmake/3.6.3
parmetis/4.0.3 unstable gcc/6.2.0 openmpi/1.10.4 b:cmake/3.6.3
parmetis/4.0.3 unstable gcc/6.2.0 openmpi/2.0.1 b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.3.0 openmpi/1.10.7 b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.3.0 openmpi/2.1.2 b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.0.0 b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.0.1 b:cmake/3.9.6
parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.1.2 b:cmake/3.9.6
parmetis/4.0.3 stable gcc/7.3.0 openmpi/3.1.3 b:cmake/3.9.6
parmetis/4.0.3 stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.9.6
parmetis/4.0.3 stable clang-macos/9.0.0 openmpi/1.10.7 b:cmake/3.6.3
parmetis/4.0.3 stable clang-macos/9.0.0 openmpi/2.1.2 b:cmake/3.6.3
parmetis/4.0.3 stable clang-macos/9.0.0 openmpi/3.0.0 b:cmake/3.6.3
parmetis/4.0.3 stable intel/17.4 openmpi/1.10.7 b:cmake/3.6.3
parmetis/4.0.3 stable intel/17.4 openmpi/2.1.2 b:cmake/3.6.3
parmetis/4.0.3 stable intel/17.4 openmpi/3.0.0 b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.3.0 mpich/3.3 b:cmake/3.9.6

0
MPI/parmetis/4/variants.Edison → MPI/parmetis/files/variants.Edison
View File

2
MPI/parmetis/files/variants.merlin6 Normal file
View File

@@ -0,0 +1,2 @@
parmetis/4.0.3_slurm unstable gcc/{7.5.0,8.4.0,9.3.0} openmpi/3.1.6_slurm b:cmake/3.15.5

25
MPI/parmetis/files/variants.rhel6 Normal file
View File

@@ -0,0 +1,25 @@
parmetis/3.2.0 stable gcc/{4.7.4,4.8.3,4.8.4,4.9.2} openmpi/{1.6.5,1.8.2,1.8.4}
parmetis/3.2.0 stable gcc/{4.7.4,4.8.5,4.9.3,5.3.0,6.1.0} openmpi/1.8.8
parmetis/3.2.0 stable gcc/{4.8.5,5.3.0,6.1.0,6.2.0} openmpi/1.10.2
parmetis/3.2.0 stable gcc/6.2.0 openmpi/{1.10.4,2.0.1}
parmetis/3.2.0 stable gcc/7.3.0 openmpi/3.0.1
parmetis/4.0.3 stable gcc/4.8.2 openmpi/1.6.5 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/{4.8.5,4.9.4,5.3.0,5.4.0,6.1.0,6.2.0} openmpi/1.10.2 b:cmake/3.4.1
parmetis/4.0.3 stable gcc/{4.8.5,4.9.4,5.4.0,6.2.0} openmpi/1.10.4 b:cmake/3.6.3
parmetis/4.0.3 stable gcc/6.2.0 openmpi/2.0.1 b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.3.0 openmpi/{1.10.7,2.1.2,3.0.0,3.0.1,3.1.2,3.1.3} b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.4.0 openmpi/3.1.4 b:cmake/3.9.6
parmetis/4.0.3 stable intel/17.4 openmpi/{1.10.7,2.1.2,3.0.0} b:cmake/3.6.3
parmetis/4.0.3 stable gcc/7.3.0 mpich/3.3 b:cmake/3.9.6
parmetis/4.0.3 unstable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 b:cmake/3.9.6

15
Programming/Python/build
View File

@@ -48,16 +48,19 @@ pbuild::post_install_Linux() {
}
pbuild::post_install() {
export LD_LIBRARY_PATH+=":${PREFIX}/lib"
export LDFLAGS="-L${OPENSSL_LIBRARY_DIR}"
export PATH="${PREFIX}/bin:${PATH}"
export LD_LIBRARY_PATH="${PREFIX}/lib:${LD_LIBRARY_PATH}"
export CFLAGS="-I${OPENSSL_INCLUDE_DIR} -I${OPENSSL_INCLUDE_DIR}/openssl"
export CPPFLAGS="-I${OPENSSL_INCLUDE_DIR} -I${OPENSSL_INCLUDE_DIR}/openssl"
export LD_LIBRARY_PATH+=":${PREFIX}/lib"
export LDFLAGS="-L${OPENSSL_LIBRARY_DIR}"
ln -fs "${PREFIX}/bin/python${V%%.*}" "${PREFIX}/bin/python"
ln -fs "${PREFIX}/include/python${V%.*}m" "${PREFIX}/include/python"
ln -fs "${PREFIX}/include/python${V%.*}m" "${PREFIX}/include/python${V%.*}"
PATH+=":${PREFIX}/bin"
cd "${BUILDBLOCK_DIR}"
"${PREFIX}/bin/python" 'get-pip.py'
if (( V_MAJOR == 2 || (V_MAJOR == 3 && V_MINOR <= 7) )); then
cd "${BUILDBLOCK_DIR}"
"${PREFIX}/bin/python" 'get-pip.py'
fi
std::info "Building numpy\n"
pip${V_MAJOR} install numpy

7
Programming/Python/files/variants.rhel6
View File

@@ -2,8 +2,15 @@ Python/2.7.11 stable openssl/1.0.2j Tcl/8.6.4 Tk/8.6.4
Python/2.7.12 stable openssl/1.0.2j Tcl/8.6.4 Tk/8.6.4
Python/2.7.14 stable openssl/1.0.2o Tcl/8.6.4 Tk/8.6.4
Python/2.7.16 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4
Python/2.7.17 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4
# commented, problems to build ssl module
#Python/2.7.18 unstable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4
Python/3.4.0 deprecated openssl/1.0.2m Tcl/8.6.4 Tk/8.6.4
Python/3.4.3 stable openssl/1.0.2m Tcl/8.6.4 Tk/8.6.4
Python/3.6.3 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4
# commented, problems to build ssl module
#Python/3.6.11 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4
Python/3.7.3 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4
Python/3.7.4 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4
Python/3.7.8 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4
Python/3.8.4 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4

3
Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md
View File

@@ -2,7 +2,8 @@
IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6)
export TMPDIR=/opt/tmp/bliven_s
export TMPDIR=/opt/tmp/$USER
export XDG_CACHE_HOME=/opt/tmp/$USER/.cache
CONDA_COPY_ALWAYS=1 conda env create --file cryolo.yml
conda activate cryolo

4
Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml → Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-cpu.yml
View File

@@ -1,4 +1,4 @@
name: cryolo-1.5.6-gpu
name: cryolo-1.6.1-cpu
channels:
- defaults
dependencies:
@@ -11,4 +11,4 @@ dependencies:
- intel-openmp==2019.4
- pip
- pip:
- cryolo[gpu]==1.5.6
- cryolo[cpu]==1.6.1

14
Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml Normal file
View File

@@ -0,0 +1,14 @@
name: cryolo-1.6.1-gpu
channels:
- defaults
dependencies:
- python=3.6
- pyqt=5
- cudnn=7.1.2
- numpy==1.14.5
- cython
- wxPython==4.0.4
- intel-openmp==2019.4
- pip
- pip:
- cryolo[gpu]==1.6.1

12
Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml
View File

@@ -6,5 +6,15 @@ channels:
dependencies:
- python=3.6
- ldapuserdir
- cython # for pyslurm
# python development
- conda-build
- cython # for pyslurm
- black
- flake8
- mypy
- mypy_extensions
- typing_extensions
- tox
- tox-conda
- pytest
- bpython

20
Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md Normal file
View File

@@ -0,0 +1,20 @@
# scicat-client
The scicat-client environment is used in the datacatalog module. Contact
Spencer Bliven, Stephan Egli, or Leo Sala for more info.
## Installing
First, create the conda environment
conda env create -f scicat_client.yml
Next, install scicat_client. Eventually this should be done automatically
through conda, but for now it needs to be installed from source.
git clone git@github.com:paulscherrerinstitute/scicat_client.git
cd scicat_client
conda activate scicat_client-0.1.0
python setup.py install

18
Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml Normal file
View File

@@ -0,0 +1,18 @@
# Clean environment based on pure conda-forge packages
name: scicat_client-0.1.0
channels:
- conda-forge
- http://conda-pkg.intranet.psi.ch
dependencies:
- python=3.8
- requests
# development tools
- conda-build
- black
- flake8
- mypy
- mypy_extensions
- typing_extensions
- tox
- tox-conda
- pytest

14
Programming/anaconda/files/admintools/conda_setup.sh Normal file
View File

@@ -0,0 +1,14 @@
# simulate `conda init` type hook
# Expects CONDA_EXE and CONDA_PREFIX to be set
__conda_setup="$("${CONDA_EXE:-conda}" 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "${CONDA_PREFIX:?CONDA_PREFIX not set}/etc/profile.d/conda.sh" ]; then
. "${CONDA_PREFIX}/etc/profile.d/conda.sh"
else
export PATH="${CONDA_PREFIX}/bin:$PATH"
fi
fi
unset __conda_setup

27
Programming/anaconda/files/admintools/kernelwrapper.sh Executable file
View File

@@ -0,0 +1,27 @@
#!/bin/bash
dbgecho() {
DBGLOG=/tmp/kernelwrapper-${USER}.log
if [[ $DEBUG_JUPYTER_WRAPPER == 1 ]]; then
echo "$1" >> $DBGLOG
fi
}
DATE=$(date +%Y-%m-%dT%H:%M)
dbgecho "$DATE: $@"
# ensure that module commands are available
dbgecho "sourcing profile.bash"
source /opt/psi/config/profile.bash
dbgecho "sourcing conda.sh"
source /opt/psi/Programming/anaconda/2019.07/conda/etc/profile.d/conda.sh &>> $DBGLOG
dbgecho "Running activate"
conda activate $1
# undefine module command since it causes error in the notebook when using
# shell escapes
unset -f module
shift
exec "$@"

3
Programming/anaconda/modulefile
View File

@@ -57,7 +57,8 @@ switch [module-info mode] {
# but we need to prevent conflicts with a conda from a different source.
# puts stderr "DEBUG: Using conda from $P/$V\n"
puts stdout "source \"$PREFIX/conda/etc/profile.d/conda.sh\";\n"
#puts stdout "source \"$PREFIX/conda/etc/profile.d/conda.sh\";\n"
puts stdout "source $PREFIX/admintools/conda_setup.sh;\n"
# Activate base? No: anaconda should just provide the conda tool
#puts stdout "conda activate;\n"

1
Programming/gcc/build
View File

@@ -36,7 +36,6 @@ pbuild::pre_configure() {
pbuild::add_configure_args "--with-mpc=${MPC_PREFIX}"
pbuild::add_configure_args "--enable-lto"
pbuild::add_configure_args "--disable-multilib"
pbuild::add_configure_args "--with-build-config=bootstrap-debug"
pbuild::add_configure_args "--with-pkgversion='PSI Environment Module'"
pbuild::add_configure_args "--with-build-config=bootstrap-debug"
}

4
Programming/gcc/files/variants.rhel6
View File

@@ -24,11 +24,15 @@ gcc/7.1.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3
gcc/7.2.0 stable b:gmp/6.1.2 b:mpfr/3.1.5 b:mpc/1.0.3-2
gcc/7.3.0 stable b:gmp/6.1.2 b:mpfr/4.0.0 b:mpc/1.1.0
gcc/7.4.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.1-1 b:mpc/1.1.0-2
gcc/7.5.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4
gcc/8.1.0 stable b:gmp/6.1.2 b:mpfr/4.0.1 b:mpc/1.1.0
gcc/8.2.0 stable b:gmp/6.1.2 b:mpfr/4.0.1 b:mpc/1.1.0
gcc/8.3.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 b:mpc/1.1.0-3
gcc/8.4.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4
gcc/9.1.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 b:mpc/1.1.0-3
gcc/9.2.0 stable b:gmp/6.1.2-1 b:mpfr/4.0.2 b:mpc/1.1.0-3 b:isl/0.21
gcc/9.3.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4
gcc/10.1.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4

20
Tools/datacatalog/README.md Normal file
View File

@@ -0,0 +1,20 @@
# Datacatalog
## Overview
This module provides tools to interface with the Data Catalog (discovery.psi.ch).
## Installation
Run `./build <VERSION>` to install the latest version. This downloads the
latest versions of the datasetIngestor, datasetRetriever, and datasetArchiver
tools. Note that the downloads are not versioned, so make sure that the current
variant matches the installed binaries.
The `scicat_client` script is also installed. This is maintained as an anaconda
environment, then symlinked into the datacatalog pmodule. Anaconda hard-codes
the correct python interpreter, so all dependencies should resolve even though
the conda module is not activated. See
Programming/anaconda/2019.07/conda-env-defs/scicat_client for environment
installation details.

21
Tools/datacatalog/README.md_template
View File

@@ -1,21 +0,0 @@
# The Mellanox MXM communication library
## Overview
The Mellanox MXM communication library provides support for the Mellanox MXM interface for InfiniBand.
## Installation
For the module we use a RPM distributed by HP.
1. Create new directory `/opt/psi/System/mxm/VERSION_merlin`
1. Download RPM from https://downloads.linux.hpe.com/sdr/repo/mlnx_ofed/RedHatEnterpriseServer/
1. Unpack RPM with `rpm2cpio RPM | cpio -i --make-dirs` somewhere
1. copy all files from `opt/mellanox/mxm` to the module directory
1. adapt directories in `lib/pkg-config/mxm.pc`
1. add new variant to `files/variants`
1. run the build-script to install the modulefile and to set the release
> **Note:** The shared library `libmxm.so`provided by the RPMs for RHEL 6 cannot be used to compile other software.
They requiry GLIBC >= 2.14, but on RHEL 6 only 2.12 is installed!

3
Tools/datacatalog/build
View File

@@ -25,5 +25,8 @@ pbuild::install() {
/usr/bin/curl -o "$PREFIX/bin/datasetArchiver" https://intranet.psi.ch/pub/Daas/WebHome/datasetArchiver
chmod +x "$PREFIX/bin/datasetArchiver"
# Hardcoded; could be made version-specific in the future if needed
ln -s "${PMODULES_ROOT}/Programming/anaconda/2019.07/conda/envs/scicat_client-0.1.0/bin/scicat_client" "$PREFIX/bin/scicat_client"
}

1
Tools/emacs/build
View File

@@ -35,5 +35,4 @@ pbuild::post_install_Darwin() {
}
pbuild::add_to_group 'Tools'
pbuild::make_all

1
Tools/emacs/files/variants
View File

@@ -1,3 +1,4 @@
emacs/25.1 stable b:libungif/4.1.4 b:tiff/4.0.3
emacs/25.3 stable b:libungif/4.1.4 b:tiff/4.0.9
emacs/26.1 stable b:libungif/4.1.4 b:tiff/4.0.9 b:nettle/3.4 gnutls/3.5.19
emacs/26.3 stable b:libungif/4.1.4 b:tiff/4.0.9 b:nettle/3.4 gnutls/3.5.19

1
Tools/gnuplot/files/variants
View File

@@ -4,3 +4,4 @@ gnuplot/5.2.0 stable
gnuplot/5.2.4 stable
gnuplot/5.2.6 stable
gnuplot/5.2.7 stable
gnuplot/5.2.8 stable

4
Tools/openssl/files/variants
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@@ -1,4 +0,0 @@
openssl/1.0.2h deprecated
openssl/1.0.2j stable
openssl/1.0.2o stable
openssl/1.0.2r stable

5
Tools/openssl/files/variants.rhel6 Normal file
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@@ -0,0 +1,5 @@
openssl/1.0.2h deprecated
openssl/1.0.2j deprecated
openssl/1.0.2o deprecated
openssl/1.0.2r stable
openssl/1.1.1g unstable