diff --git a/.gitlab/issue_templates/New variant.md b/.gitlab/issue_templates/New variant.md index 1c048f7..d884fa4 100644 --- a/.gitlab/issue_templates/New variant.md +++ b/.gitlab/issue_templates/New variant.md @@ -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" diff --git a/Compiler/OpenBLAS/files/variants.rhel6 b/Compiler/OpenBLAS/files/variants.rhel6 index 5e8c3cc..d56d4e6 100644 --- a/Compiler/OpenBLAS/files/variants.rhel6 +++ b/Compiler/OpenBLAS/files/variants.rhel6 @@ -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} diff --git a/Compiler/boost/build b/Compiler/boost/build index e836e3d..5b2d34b 100755 --- a/Compiler/boost/build +++ b/Compiler/boost/build @@ -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 + : } - - diff --git a/Compiler/boost/files/variants b/Compiler/boost/files/variants deleted file mode 100644 index d20237b..0000000 --- a/Compiler/boost/files/variants +++ /dev/null @@ -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 diff --git a/Compiler/boost/files/variants.rhel6 b/Compiler/boost/files/variants.rhel6 new file mode 100644 index 0000000..51cd332 --- /dev/null +++ b/Compiler/boost/files/variants.rhel6 @@ -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 diff --git a/Compiler/gsl/files/variants.rhel6 b/Compiler/gsl/files/variants.rhel6 index c4ea7a2..236f69e 100644 --- a/Compiler/gsl/files/variants.rhel6 +++ b/Compiler/gsl/files/variants.rhel6 @@ -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} diff --git a/Compiler/gtest/files/variants.rhel6 b/Compiler/gtest/files/variants.rhel6 index 639fb93..becc451 100644 --- a/Compiler/gtest/files/variants.rhel6 +++ b/Compiler/gtest/files/variants.rhel6 @@ -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 diff --git a/Compiler/lapack/build b/Compiler/lapack/build new file mode 100755 index 0000000..0665726 --- /dev/null +++ b/Compiler/lapack/build @@ -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: diff --git a/Compiler/lapack/files/variants.rhel6 b/Compiler/lapack/files/variants.rhel6 new file mode 100644 index 0000000..71d6728 --- /dev/null +++ b/Compiler/lapack/files/variants.rhel6 @@ -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 diff --git a/Compiler/lapack/modulefile b/Compiler/lapack/modulefile new file mode 100644 index 0000000..771cee5 --- /dev/null +++ b/Compiler/lapack/modulefile @@ -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 " +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. +" diff --git a/Compiler/mpich/files/variants b/Compiler/mpich/files/variants deleted file mode 100644 index 8ebff5e..0000000 --- a/Compiler/mpich/files/variants +++ /dev/null @@ -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 diff --git a/Compiler/mpich/files/variants.merlin b/Compiler/mpich/files/variants.merlin new file mode 100644 index 0000000..30ac8ad --- /dev/null +++ b/Compiler/mpich/files/variants.merlin @@ -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 diff --git a/Compiler/mpich/files/variants.rhel6 b/Compiler/mpich/files/variants.rhel6 new file mode 100644 index 0000000..ca89e5f --- /dev/null +++ b/Compiler/mpich/files/variants.rhel6 @@ -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} diff --git a/Compiler/openmpi/files/variants.rhel6 b/Compiler/openmpi/files/variants.rhel6 index 646a5db..0f78053 100644 --- a/Compiler/openmpi/files/variants.rhel6 +++ b/Compiler/openmpi/files/variants.rhel6 @@ -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 diff --git a/Compiler/vtk/5/variants.Linux b/Compiler/vtk/5/variants.Linux deleted file mode 100644 index ea19eb6..0000000 --- a/Compiler/vtk/5/variants.Linux +++ /dev/null @@ -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 diff --git a/Compiler/vtk/6/variants.Linux b/Compiler/vtk/6/variants.Linux deleted file mode 100644 index 6f70840..0000000 --- a/Compiler/vtk/6/variants.Linux +++ /dev/null @@ -1 +0,0 @@ -vtk/6.3.0 unstable b:cmake/3.6.3 gcc/6.2.0 diff --git a/Compiler/vtk/7/variants.Linux b/Compiler/vtk/7/variants.Linux deleted file mode 100644 index f4c4034..0000000 --- a/Compiler/vtk/7/variants.Linux +++ /dev/null @@ -1 +0,0 @@ -vtk/7.0.0 unstable b:cmake/3.6.3 gcc/6.2.0 diff --git a/Compiler/vtk/8/variants.Linux b/Compiler/vtk/8/variants.Linux deleted file mode 100644 index 580fb68..0000000 --- a/Compiler/vtk/8/variants.Linux +++ /dev/null @@ -1 +0,0 @@ -vtk/8.0.0 unstable b:cmake/3.6.3 gcc/5.4.0 diff --git a/Compiler/vtk/files/variants.rhel6 b/Compiler/vtk/files/variants.rhel6 new file mode 100644 index 0000000..fe1b334 --- /dev/null +++ b/Compiler/vtk/files/variants.rhel6 @@ -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} + diff --git a/EM/crYOLO/files/variants b/EM/crYOLO/files/variants index 7dc6e35..92b226c 100644 --- a/EM/crYOLO/files/variants +++ b/EM/crYOLO/files/variants @@ -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 diff --git a/EM/crYOLO/modulefile b/EM/crYOLO/modulefile index 596f793..41cf27a 100644 --- a/EM/crYOLO/modulefile +++ b/EM/crYOLO/modulefile @@ -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" { diff --git a/EM/relion/README.md b/EM/relion/README.md index f63b42b..33c92ee 100644 --- a/EM/relion/README.md +++ b/EM/relion/README.md @@ -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. diff --git a/EM/relion/files/variants b/EM/relion/files/variants index 34ef8b8..08cb86b 100644 --- a/EM/relion/files/variants +++ b/EM/relion/files/variants @@ -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 diff --git a/HDF5/H5hut/1.99/variants b/HDF5/H5hut/1.99/variants deleted file mode 100644 index 89a54ed..0000000 --- a/HDF5/H5hut/1.99/variants +++ /dev/null @@ -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 diff --git a/HDF5/H5hut/build b/HDF5/H5hut/build index d167828..75790b4 100755 --- a/HDF5/H5hut/build +++ b/HDF5/H5hut/build @@ -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() { diff --git a/HDF5/H5hut/2/variants.Edison b/HDF5/H5hut/files/variants.Edison similarity index 100% rename from HDF5/H5hut/2/variants.Edison rename to HDF5/H5hut/files/variants.Edison diff --git a/HDF5/H5hut/2/variants.macos1014 b/HDF5/H5hut/files/variants.macos1014 similarity index 100% rename from HDF5/H5hut/2/variants.macos1014 rename to HDF5/H5hut/files/variants.macos1014 diff --git a/HDF5/H5hut/files/variants.merlin6 b/HDF5/H5hut/files/variants.merlin6 new file mode 100644 index 0000000..7fdfd46 --- /dev/null +++ b/HDF5/H5hut/files/variants.merlin6 @@ -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 + diff --git a/HDF5/H5hut/2/variants b/HDF5/H5hut/files/variants.rhel6 similarity index 89% rename from HDF5/H5hut/2/variants rename to HDF5/H5hut/files/variants.rhel6 index ea3b5f2..3838b03 100644 --- a/HDF5/H5hut/2/variants +++ b/HDF5/H5hut/files/variants.rhel6 @@ -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 diff --git a/HDF5/trilinos/12/variants b/HDF5/trilinos/12/variants deleted file mode 100644 index 83b689f..0000000 --- a/HDF5/trilinos/12/variants +++ /dev/null @@ -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 diff --git a/HDF5/trilinos/build b/HDF5/trilinos/build index 3047df6..162f654 100755 --- a/HDF5/trilinos/build +++ b/HDF5/trilinos/build @@ -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" diff --git a/HDF5/trilinos/12/variants.Darwin b/HDF5/trilinos/files/variants.Darwin similarity index 100% rename from HDF5/trilinos/12/variants.Darwin rename to HDF5/trilinos/files/variants.Darwin diff --git a/HDF5/trilinos/files/variants.merlin6 b/HDF5/trilinos/files/variants.merlin6 new file mode 100644 index 0000000..aa8ebf1 --- /dev/null +++ b/HDF5/trilinos/files/variants.merlin6 @@ -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 diff --git a/HDF5/trilinos/files/variants.rhel6 b/HDF5/trilinos/files/variants.rhel6 new file mode 100644 index 0000000..00b8695 --- /dev/null +++ b/HDF5/trilinos/files/variants.rhel6 @@ -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 diff --git a/Libraries/gmp/build b/Libraries/gmp/build index 4f302ba..5f4ffcc 100755 --- a/Libraries/gmp/build +++ b/Libraries/gmp/build @@ -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 - diff --git a/Libraries/gmp/files/variants b/Libraries/gmp/files/variants index bbc09b3..e881a18 100644 --- a/Libraries/gmp/files/variants +++ b/Libraries/gmp/files/variants @@ -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 diff --git a/Libraries/mpc/files/variants b/Libraries/mpc/files/variants index ed9d355..ffdd49b 100644 --- a/Libraries/mpc/files/variants +++ b/Libraries/mpc/files/variants @@ -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 diff --git a/Libraries/mpfr/files/variants b/Libraries/mpfr/files/variants index 2bc2629..a728d5f 100644 --- a/Libraries/mpfr/files/variants +++ b/Libraries/mpfr/files/variants @@ -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 diff --git a/MPI/amrex/files/variants b/MPI/amrex/files/variants deleted file mode 100644 index 6975014..0000000 --- a/MPI/amrex/files/variants +++ /dev/null @@ -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 - diff --git a/MPI/amrex/files/variants.merlin6 b/MPI/amrex/files/variants.merlin6 new file mode 100644 index 0000000..ddd3bae --- /dev/null +++ b/MPI/amrex/files/variants.merlin6 @@ -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 + diff --git a/MPI/amrex/files/variants.rhel6 b/MPI/amrex/files/variants.rhel6 new file mode 100644 index 0000000..e72a265 --- /dev/null +++ b/MPI/amrex/files/variants.rhel6 @@ -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 + diff --git a/MPI/boost/files/variants.merlin6 b/MPI/boost/files/variants.merlin6 new file mode 100644 index 0000000..15aaa7c --- /dev/null +++ b/MPI/boost/files/variants.merlin6 @@ -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 + diff --git a/MPI/boost/files/variants.rhel6 b/MPI/boost/files/variants.rhel6 index afea691..a71432e 100644 --- a/MPI/boost/files/variants.rhel6 +++ b/MPI/boost/files/variants.rhel6 @@ -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 diff --git a/MPI/elegant/README.md b/MPI/elegant/README.md index 8254c23..e6d6c38 100644 --- a/MPI/elegant/README.md +++ b/MPI/elegant/README.md @@ -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 ``` diff --git a/MPI/elegant/build b/MPI/elegant/build new file mode 100755 index 0000000..6cb8745 --- /dev/null +++ b/MPI/elegant/build @@ -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: diff --git a/MPI/elegant/files/variants.merlin6 b/MPI/elegant/files/variants.merlin6 new file mode 100644 index 0000000..f1ac524 --- /dev/null +++ b/MPI/elegant/files/variants.merlin6 @@ -0,0 +1 @@ +elegant/2020.2.0_merlin6 unstable gcc/8.4.0 openmpi/3.1.6_slurm gsl/2.6 diff --git a/MPI/elegant/files/variants.rhel6 b/MPI/elegant/files/variants.rhel6 new file mode 100644 index 0000000..1f30d1c --- /dev/null +++ b/MPI/elegant/files/variants.rhel6 @@ -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 diff --git a/MPI/elegant/modulefile b/MPI/elegant/modulefile index 8d5c272..040d321 100644 --- a/MPI/elegant/modulefile +++ b/MPI/elegant/modulefile @@ -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 $PREFIX/epics/base/lib diff --git a/MPI/hdf5/build b/MPI/hdf5/build index c3d4dd4..b82cc29 100755 --- a/MPI/hdf5/build +++ b/MPI/hdf5/build @@ -1,6 +1,6 @@ #!/usr/bin/env modbuild -pbuild::set_download_url "https://support.hdfgroup.org/ftp/HDF5/releases/$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 diff --git a/MPI/hdf5/files/variants.merlin6 b/MPI/hdf5/files/variants.merlin6 new file mode 100644 index 0000000..f0a10c9 --- /dev/null +++ b/MPI/hdf5/files/variants.merlin6 @@ -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 + diff --git a/MPI/hdf5/files/variants.rhel6 b/MPI/hdf5/files/variants.rhel6 index 3c471fa..8b2a001 100644 --- a/MPI/hdf5/files/variants.rhel6 +++ b/MPI/hdf5/files/variants.rhel6 @@ -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 diff --git a/MPI/parmetis/3/variants b/MPI/parmetis/3/variants deleted file mode 100644 index 20cccdc..0000000 --- a/MPI/parmetis/3/variants +++ /dev/null @@ -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 diff --git a/MPI/parmetis/4/variants b/MPI/parmetis/4/variants deleted file mode 100644 index e1893ac..0000000 --- a/MPI/parmetis/4/variants +++ /dev/null @@ -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 diff --git a/MPI/parmetis/4/variants.Edison b/MPI/parmetis/files/variants.Edison similarity index 100% rename from MPI/parmetis/4/variants.Edison rename to MPI/parmetis/files/variants.Edison diff --git a/MPI/parmetis/files/variants.merlin6 b/MPI/parmetis/files/variants.merlin6 new file mode 100644 index 0000000..a060ecc --- /dev/null +++ b/MPI/parmetis/files/variants.merlin6 @@ -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 + diff --git a/MPI/parmetis/files/variants.rhel6 b/MPI/parmetis/files/variants.rhel6 new file mode 100644 index 0000000..a370896 --- /dev/null +++ b/MPI/parmetis/files/variants.rhel6 @@ -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 diff --git a/Programming/Python/build b/Programming/Python/build index eb53bfa..ad0be5b 100755 --- a/Programming/Python/build +++ b/Programming/Python/build @@ -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${V_MAJOR} install numpy diff --git a/Programming/Python/files/variants.rhel6 b/Programming/Python/files/variants.rhel6 index cf1b0bb..3380dbc 100644 --- a/Programming/Python/files/variants.rhel6 +++ b/Programming/Python/files/variants.rhel6 @@ -2,8 +2,15 @@ Python/2.7.11 stable openssl/1.0.2j Tcl/8.6.4 Tk/8.6.4 Python/2.7.12 stable openssl/1.0.2j Tcl/8.6.4 Tk/8.6.4 Python/2.7.14 stable openssl/1.0.2o Tcl/8.6.4 Tk/8.6.4 Python/2.7.16 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +Python/2.7.17 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +# commented, problems to build ssl module +#Python/2.7.18 unstable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 Python/3.4.0 deprecated openssl/1.0.2m Tcl/8.6.4 Tk/8.6.4 Python/3.4.3 stable openssl/1.0.2m Tcl/8.6.4 Tk/8.6.4 Python/3.6.3 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +# commented, problems to build ssl module +#Python/3.6.11 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4 Python/3.7.3 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 Python/3.7.4 stable b:openssl/1.0.2r b:TclTk/8.6.9 b:xz/5.2.4 +Python/3.7.8 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4 +Python/3.8.4 unstable b:openssl/1.1.1g b:TclTk/8.6.9 b:xz/5.2.4 diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md b/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md index 46e620a..18c111c 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md +++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/README.md @@ -2,7 +2,8 @@ IMPORTANT! DON'T INSTALL WITH AURISTOR. Use an OpenAFS system (e.g. pmod6) - export TMPDIR=/opt/tmp/bliven_s + export TMPDIR=/opt/tmp/$USER + export XDG_CACHE_HOME=/opt/tmp/$USER/.cache CONDA_COPY_ALWAYS=1 conda env create --file cryolo.yml conda activate cryolo diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-cpu.yml similarity index 77% rename from Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml rename to Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-cpu.yml index 42b1fe6..284af71 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo.yml +++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-cpu.yml @@ -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 diff --git a/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml new file mode 100644 index 0000000..ec523e2 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/cryolo/cryolo-gpu.yml @@ -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 diff --git a/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml b/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml index 19d540e..ebab9ed 100644 --- a/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml +++ b/Programming/anaconda/2019.07/conda-env-defs/hpce-tools/hpce-tools.yml @@ -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 diff --git a/Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md new file mode 100644 index 0000000..fa4e98a --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/README.md @@ -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 + + diff --git a/Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml new file mode 100644 index 0000000..b50b0f5 --- /dev/null +++ b/Programming/anaconda/2019.07/conda-env-defs/scicat_client/scicat_client.yml @@ -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 diff --git a/Programming/anaconda/files/admintools/conda_setup.sh b/Programming/anaconda/files/admintools/conda_setup.sh new file mode 100644 index 0000000..6ff904f --- /dev/null +++ b/Programming/anaconda/files/admintools/conda_setup.sh @@ -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 + diff --git a/Programming/anaconda/files/admintools/kernelwrapper.sh b/Programming/anaconda/files/admintools/kernelwrapper.sh new file mode 100755 index 0000000..24268dd --- /dev/null +++ b/Programming/anaconda/files/admintools/kernelwrapper.sh @@ -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 $1 + +# undefine module command since it causes error in the notebook when using +# shell escapes +unset -f module +shift +exec "$@" + diff --git a/Programming/anaconda/modulefile b/Programming/anaconda/modulefile index 899b652..3afbc1c 100644 --- a/Programming/anaconda/modulefile +++ b/Programming/anaconda/modulefile @@ -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 $PREFIX/admintools/conda_setup.sh;\n" # Activate base? No: anaconda should just provide the conda tool #puts stdout "conda activate;\n" diff --git a/Programming/gcc/build b/Programming/gcc/build index 274f9df..623b03f 100755 --- a/Programming/gcc/build +++ b/Programming/gcc/build @@ -36,7 +36,6 @@ pbuild::pre_configure() { pbuild::add_configure_args "--with-mpc=${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" } diff --git a/Programming/gcc/files/variants.rhel6 b/Programming/gcc/files/variants.rhel6 index d7dc1a8..3ddf273 100644 --- a/Programming/gcc/files/variants.rhel6 +++ b/Programming/gcc/files/variants.rhel6 @@ -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 diff --git a/Tools/datacatalog/README.md b/Tools/datacatalog/README.md new file mode 100644 index 0000000..7d08119 --- /dev/null +++ b/Tools/datacatalog/README.md @@ -0,0 +1,20 @@ +# Datacatalog + +## Overview + +This module provides tools to interface with the Data Catalog (discovery.psi.ch). + +## Installation + +Run `./build ` 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. + diff --git a/Tools/datacatalog/README.md_template b/Tools/datacatalog/README.md_template deleted file mode 100644 index 77355fb..0000000 --- a/Tools/datacatalog/README.md_template +++ /dev/null @@ -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! \ No newline at end of file diff --git a/Tools/datacatalog/build b/Tools/datacatalog/build index 0492450..77e2ff3 100755 --- a/Tools/datacatalog/build +++ b/Tools/datacatalog/build @@ -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" } diff --git a/Tools/emacs/build b/Tools/emacs/build index 7261baa..cba9fe2 100755 --- a/Tools/emacs/build +++ b/Tools/emacs/build @@ -35,5 +35,4 @@ pbuild::post_install_Darwin() { } pbuild::add_to_group 'Tools' -pbuild::make_all diff --git a/Tools/emacs/files/variants b/Tools/emacs/files/variants index 75f456e..d084e9d 100644 --- a/Tools/emacs/files/variants +++ b/Tools/emacs/files/variants @@ -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 diff --git a/Tools/gnuplot/files/variants b/Tools/gnuplot/files/variants index 6f27cb7..7a89952 100644 --- a/Tools/gnuplot/files/variants +++ b/Tools/gnuplot/files/variants @@ -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 diff --git a/Tools/openssl/files/variants b/Tools/openssl/files/variants deleted file mode 100644 index 3891bf4..0000000 --- a/Tools/openssl/files/variants +++ /dev/null @@ -1,4 +0,0 @@ -openssl/1.0.2h deprecated -openssl/1.0.2j stable -openssl/1.0.2o stable -openssl/1.0.2r stable diff --git a/Tools/openssl/files/variants.rhel6 b/Tools/openssl/files/variants.rhel6 new file mode 100644 index 0000000..ceb6c27 --- /dev/null +++ b/Tools/openssl/files/variants.rhel6 @@ -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