diff --git a/Compiler/H5root/1/variants b/Compiler/H5root/1/variants index 82c7378..6846a0e 100644 --- a/Compiler/H5root/1/variants +++ b/Compiler/H5root/1/variants @@ -1,11 +1,15 @@ -H5root/1.2.0 stable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/4.7.4 hdf5_serial/1.8.12 b:H5hut_serial/1.99.13 root/5.34.19 -H5root/1.2.0 stable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/4.8.3 hdf5_serial/1.8.12 b:H5hut_serial/1.99.13 root/5.34.19 -H5root/1.3.0 unstable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/4.8.3 hdf5_serial/1.8.12 b:H5hut_serial/1.99.13 root/5.34.19 -H5root/1.3.2rc2 unstable gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 -H5root/1.3.2rc4 unstable gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 -H5root/1.3.2rc4-1 unstable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 -H5root/1.3.2rc5 unstable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 -H5root/1.3.2rc5-1 unstable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 -H5root/1.3.2 stable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 -H5root/1.3.4 stable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 -H5root/1.3.4 unstable b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/7.3.0 b:hdf5_serial/1.10.1 b:H5hut/2.0.0rc4 root/6.12.06 boost/1.66.0 gsl/2.4 +H5root/1.2.0 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/4.7.4 hdf5_serial/1.8.12 b:H5hut_serial/1.99.13 root/5.34.19 +H5root/1.2.0 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/4.8.3 hdf5_serial/1.8.12 b:H5hut_serial/1.99.13 root/5.34.19 +H5root/1.3.0 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/4.8.3 hdf5_serial/1.8.12 b:H5hut_serial/1.99.13 root/5.34.19 +H5root/1.3.1 deprecated gcc/4.8.3 +H5root/1.3.1 deprecated gcc/4.8.4 +H5root/1.3.2rc1 deprecated gcc/5.4.0 +H5root/1.3.2rc2 deprecated gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.2rc3 deprecated gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.2rc4 deprecated gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.2rc4-1 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.2rc5 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.2rc5-1 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.2 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.4 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/5.4.0 b:hdf5_serial/1.8.18 b:H5hut/2.0.0rc3 root/6.08.02 boost/1.62.0 gsl/2.2.1 +H5root/1.3.4 deprecated b:autoconf/2.69 b:automake/1.14 b:libtool/2.4.2 gcc/7.3.0 b:hdf5_serial/1.10.1 b:H5hut/2.0.0rc4 root/6.12.06 boost/1.66.0 gsl/2.4 diff --git a/Compiler/gsl/files/variants.rhel6 b/Compiler/gsl/files/variants.rhel6 new file mode 100644 index 0000000..a18e36f --- /dev/null +++ b/Compiler/gsl/files/variants.rhel6 @@ -0,0 +1,20 @@ +gsl/1.15 deprecated gcc/{4.7.4,4.8.3,4.8.4,4.8.5,4.9.2,4.9.3,4.9.4,5.3.0,5.4.0,6.2.0} + +gsl/1.15 deprecated intel/15.3 + +gsl/1.16 deprecated gcc/{4.8.5,4.9.4,5.4.0,6.2.0} + +gsl/2.2.1 deprecated gcc/{4.8.5,4.9.4,5.4.0,6.2.0,6.3.0} + +gsl/2.4 stable gcc/7.3.0 + +gsl/2.4 deprecated intel/17.4 + +gsl/2.5 stable gcc/{6.3.0,7.3.0,7.4.0,8.3.0,9.1.0} + +gsl/2.5 deprecated intel/19.4 + +gsl/2.6 stable gcc/{7.4.0,7.5.0,8.3.0,8.4.0,8.5.0,9.1.0,9.2.0,9.3.0,9.5.0,10.1.0,10.2.0,10.3.0,11.2.0,12.1.0} + +gsl/2.7 stable gcc/{7.5.0,8.4.0,8.5.0,9.3.0,9.5.0,10.3.0,11.3.0,12.1.0} +gsl/2.7 unstable gcc/10.4.0 diff --git a/EM/IMOD/README.md b/EM/IMOD/README.md new file mode 100644 index 0000000..034c88d --- /dev/null +++ b/EM/IMOD/README.md @@ -0,0 +1,14 @@ +# IMOD + + +## Installation + +IMOD is shipped as a self-expanding installation script. Run `./build` to +install. + +## Known Issues + +The installation includes environment scripts which install into +`$IMOD_DIR/profile.d`. These are sourced in the modulefile. This means that the +module cannot be unloaded cleanly (eg IMOD remains in the PATH after +unloading). diff --git a/EM/IMOD/build b/EM/IMOD/build new file mode 100755 index 0000000..a8940a8 --- /dev/null +++ b/EM/IMOD/build @@ -0,0 +1,43 @@ +#!/usr/bin/env modbuild + +pbuild::add_to_group 'EM' + + +pbuild::prep() { + : ${CUDA_VERSION:?No CUDA_VERSION set} + local cuda="${CUDA_VERSION%.*}" + local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh" + local dst="$PMODULES_DISTFILESDIR/${filename}" + if [ -f "$dst" ]; then + echo "Found cached $dst" >&2 + else + ${curl:-curl} \ + --location \ + --fail \ + --output "$dst" \ + "https://bio3d.colorado.edu/imod/AMD64-RHEL5/$filename" + fi + } + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + : ${CUDA_VERSION:?No CUDA_VERSION set} + local cuda="${CUDA_VERSION%.*}" + local filename="imod_${V_PKG}_RHEL7-64_CUDA${cuda}.sh" + local dst="$PMODULES_DISTFILESDIR/${filename}" + + mkdir -p "$PREFIX/profile.d" + sh "$dst" \ + -yes \ + -dir "$PREFIX" \ + -script "$PREFIX/profile.d" + +} + diff --git a/EM/IMOD/files/variants b/EM/IMOD/files/variants new file mode 100644 index 0000000..196b2cd --- /dev/null +++ b/EM/IMOD/files/variants @@ -0,0 +1,2 @@ +IMOD/4.9.5 stable +IMOD/4.11.20 unstable cuda/10.1.105 diff --git a/EM/IMOD/modulefile b/EM/IMOD/modulefile new file mode 100644 index 0000000..d19b9e2 --- /dev/null +++ b/EM/IMOD/modulefile @@ -0,0 +1,45 @@ +#%Module1.0 + +module-whatis "IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections." +module-url "http://bio3d.colorado.edu/imod/" +module-license "mostly GPLv2.0, with the exceptions, see http://bio3d.colorado.edu/imod/COPYRIGHT.txt" +module-maintainer "Spencer Bliven / Dmitry Ozerov " + +module-help " +IMOD is a set of image processing, modeling and display programs used for tomographic +reconstruction and for 3D reconstruction of EM serial sections and optical sections. +The package contains tools for assembling and aligning data within multiple types and +sizes of image stacks, viewing 3-D data from any orientation, and modeling and display +of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, +Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado. + +The development of IMOD has been supported by grants from the National Center for +Research Resources, the National Institute of General Medical Sciences, and the National +Institute for Biomedical Imaging and Bioengineering. IMOD and virtually all programs +contained within the IMOD package are Copyright (c) 1994-2017 by the Regents of the +University of Colorado. Other contributors are acknowledged in our Copyright and +Credits statement http://bio3d.colorado.edu/imod/COPYRIGHT.txt. + +Original publication: +> Kremer J.R., Mastronarde, D.N., and McIntosh, J.R. (1996) Computer +> visualization of three-dimensional image data using IMOD. J. Struct. Biol. +> 116:71-76. + +For tomographic reconstruction, see also: + +> Mastronarde, D.N. (1997) Dual-axis tomography: an approach with alignment +> methods that preserve resolution. J. Struct. Biol. 120:343-352. + +> Mastronarde, D.N. and Held, S.R. (2017) Automated tilt series alignment and +> tomographic reconstruction in IMOD. J. Struct. Biol. 197:102-113. +" + +switch [module-info mode] { + "load" { + puts stdout "source $PREFIX/profile.d/IMOD-linux.sh" + } + "unload" - + "remove" { + # Could unset IMOD variables here + } +} diff --git a/EM/MotionCor2/README.md b/EM/MotionCor2/README.md index 6bd8089..70296e3 100644 --- a/EM/MotionCor2/README.md +++ b/EM/MotionCor2/README.md @@ -6,18 +6,22 @@ 4. Move all executables to /opt/psi/EM/MotionCor2/$VERSION/bin 5. Move user manual to /opt/psi/EM/MotionCor2/$VERSION/ 6. Fix permissions: chmod 755 /opt/psi/EM/MotionCor2/$VERSION/bin +7. Create bin/MotionCor2 wrapper for each version ## Cuda versions -| MotionCor2 | Cuda Versions | -|------------+-------------------------| -| 1.0.5 | 8.0 9.1 | -| 1.1.0 | 8.0 9.0 9.1 | -| 1.2.0 | 8.0 9.1 9.2 | -| 1.2.6 | 8.0 9.2 10.1 | -| 1.3.0 | 8.0 9.2 10.1 | -| 1.3.1 | 9.2 10.1 10.2 | -| 1.3.2 | 8.0 9.2 10.0 10.1 10.2 | -| 1.4.0 | 9.2 10.0 10.1 10.2 11.0 | +| MotionCor2 | Cuda Versions | +|------------|-----------------------------------------| +| 1.0.5 | 8.0 9.1 | +| 1.1.0 | 8.0 9.0 9.1 | +| 1.2.0 | 8.0 9.1 9.2 | +| 1.2.6 | 8.0 9.2 10.1 | +| 1.3.0 | 8.0 9.2 10.1 | +| 1.3.1 | 9.2 10.1 10.2 | +| 1.3.2 | 8.0 9.2 10.0 10.1 10.2 | +| 1.4.0 | 9.2 10.0 10.1 10.2 11.0 | +| 1.4.5 | 10.0 10.1 10.2 11.1 11.2 11.3 | +| 1.4.7 | 10.2 11.1 11.2 11.3 11.4 11.5 | +| 1.5.0 | 10.1 10.2 11.1 11.2 11.3 11.4 11.5 11.6 | diff --git a/EM/MotionCor2/bin/MotionCor2 b/EM/MotionCor2/bin/MotionCor2 new file mode 100755 index 0000000..c6619dc --- /dev/null +++ b/EM/MotionCor2/bin/MotionCor2 @@ -0,0 +1,21 @@ +#!/bin/bash + +# Script directory. Better than $MOTIONCOR2_HOME/bin since it can be called without loading modules. +BIN="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )" + +if [ -z ${CUDA_VERSION} ]; then + echo 'MotionCor2 requires the cuda module. Run `module load cuda/`' >&2 + exit 1 +fi + +CUDA=$(echo "${CUDA_VERSION}" | sed -r 's/([0-9]+)\.([0-9]+)(\..*)/\1\2/') + +EXE=$(echo "$BIN"/MotionCor2_*_Cuda${CUDA}*) +#echo "Running $EXE" + +if [ ! -x "$EXE" ]; then + echo "MotionCor2/$MOTIONCOR2_VERSION is not compatible with cuda/$CUDA_VERSION" >&2 + exit 1 +fi + +exec "$EXE" "$@" diff --git a/EM/MotionCor2/build b/EM/MotionCor2/build index b9411f5..0dbbe97 100755 --- a/EM/MotionCor2/build +++ b/EM/MotionCor2/build @@ -18,5 +18,6 @@ pbuild::compile() { pbuild::install() { cp $BUILDBLOCK_DIR/files/LICENSE $PREFIX/ + cp -r $BUILDBLOCK_DIR/bin $PREFIX/ } diff --git a/EM/MotionCor2/files/variants b/EM/MotionCor2/files/variants index f871400..5c76d42 100644 --- a/EM/MotionCor2/files/variants +++ b/EM/MotionCor2/files/variants @@ -8,3 +8,6 @@ MotionCor2/1.3.0 stable MotionCor2/1.3.1 stable MotionCor2/1.3.2 stable MotionCor2/1.4.0 stable +MotionCor2/1.4.5 stable +MotionCor2/1.4.7 stable +MotionCor2/1.5.0 stable diff --git a/EM/ctffind4/README b/EM/ctffind4/README new file mode 100644 index 0000000..8044d39 --- /dev/null +++ b/EM/ctffind4/README @@ -0,0 +1,8 @@ +# ctffind4 + +## Installation + + ./build + +Installs the pre-build binaries. + diff --git a/EM/ctffind4/build b/EM/ctffind4/build new file mode 100755 index 0000000..ad8ea2a --- /dev/null +++ b/EM/ctffind4/build @@ -0,0 +1,36 @@ +#!/usr/bin/env modbuild + +# Binary distribution with manual installation. See README.md + +pbuild::add_to_group 'EM' + +pbuild::set_download_url "https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${V_PKG}-linux64.tar.gz&file=1&type=node&id=26" + +#pbuild::prep() { +# local filename="ctffind-${V_PKG}-linux64.tar.gz" +# local dst="$PMODULES_DISTFILESDIR/${filename}" +# if [ -f "$dst" ]; then +# echo "Found cached $dst" >&2 +# else +# ${curl:-curl} \ +# --location \ +# --fail \ +# --output "$dst" \ +# "https://grigoriefflab.umassmed.edu/system/tdf?path=${filename}&file=1&type=node&id=26" +# fi +#} +# + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + mkdir -p "$PREFIX/bin" + mv "$SRC_DIR/"* "$PREFIX/bin" +} + diff --git a/EM/ctffind4/files/variants b/EM/ctffind4/files/variants new file mode 100644 index 0000000..1f3614f --- /dev/null +++ b/EM/ctffind4/files/variants @@ -0,0 +1,2 @@ +ctffind4/4.1.8 stable +ctffind4/4.1.14 stable diff --git a/EM/ctffind4/modulefile b/EM/ctffind4/modulefile new file mode 100644 index 0000000..6098b06 --- /dev/null +++ b/EM/ctffind4/modulefile @@ -0,0 +1,10 @@ +#%Module1.0 + +module-whatis "CTF estimation from electron micrographs" +module-url "https://grigoriefflab.umassmed.edu/ctffind4" +module-license "The Janelia Research Campus Software License 1.2 http://license.janelia.org/license/janelia_license_1_2.html" +module-maintainer "Spencer Bliven " + +module-help " +Mindell, JA, Grigorieff N. 2003. Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 142:334-47. +" diff --git a/Libraries/ucx/files/variants.merlin6 b/Libraries/ucx/files/variants.merlin6 index bd90aa4..df43cb3 100644 --- a/Libraries/ucx/files/variants.merlin6 +++ b/Libraries/ucx/files/variants.merlin6 @@ -1,6 +1,8 @@ ucx/1.9.0_slurm stable cuda/11.1.0 b:doxygen/1.8.14 b:knem/1.1.4 + ucx/1.10.0_slurm stable cuda/11.3.0 b:doxygen/1.8.14 b:knem/1.1.4 b:GDRCopy/2.2.0 ucx/1.10.0-1_slurm stable cuda/11.2.2 b:doxygen/1.8.14 b:knem/1.1.4 b:GDRCopy/2.2.0 + ucx/1.11.0_slurm stable cuda/11.3.0 b:doxygen/1.8.14 b:knem/1.1.4 b:GDRCopy/2.2.0 ucx/1.11.2_slurm stable cuda/11.3.0 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 ucx/1.11.2-1_slurm stable cuda/11.4.3 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 @@ -8,7 +10,9 @@ ucx/1.11.2-2_slurm stable cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b ucx/1.11.2-3_slurm stable cuda/11.1.0 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 ucx/1.12.1_slurm stable cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 -ucx/1.13.1_slurm unstable b:cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 + +ucx/1.13.1_slurm stable b:cuda/11.5.1 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 +ucx/1.13.1-3_slurm unstable b:cuda/11.1.0 b:doxygen/1.9.2 b:knem/1.1.4 b:GDRCopy/2.2.0 ucx/1.9.0_dgx deprecated cuda/11.1.0 b:doxygen/1.8.14 b:knem/1.1.4 ucx/1.10.0-1_dgx deprecated cuda/11.2.2 b:doxygen/1.8.14 b:knem/1.1.4 b:GDRCopy/2.2.0 diff --git a/MPI/hdf5/files/variants.rhel6 b/MPI/hdf5/files/variants.rhel6 index 8d5eb13..1939972 100644 --- a/MPI/hdf5/files/variants.rhel6 +++ b/MPI/hdf5/files/variants.rhel6 @@ -59,4 +59,6 @@ hdf5/1.10.6 stable gcc/{7.5.0,8.4.0,9.3.0,10.1.0} openmpi/3.1.6 hdf5/1.10.7 stable gcc/{7.5.0,8.4.0,9.3.0,10.2.0} openmpi/4.0.5 hdf5/1.10.7 stable gcc/10.3.0 openmpi/4.0.5 +hdf5/1.10.8 unstable gcc/10.4.0 openmpi/4.1.4 + hdf5/1.12.0 stable gcc/{7.5.0,8.4.0,9.3.0,10.2.0} openmpi/4.0.5 diff --git a/Programming/gcc/files/variants.rhel6 b/Programming/gcc/files/variants.rhel6 index 5938bec..09bb8f8 100644 --- a/Programming/gcc/files/variants.rhel6 +++ b/Programming/gcc/files/variants.rhel6 @@ -38,5 +38,6 @@ 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 gcc/10.2.0 stable b:gmp/6.2.0 b:mpfr/4.0.2-1 b:mpc/1.1.0-4 gcc/10.3.0 stable b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 +gcc/10.4.0 stable b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1 gcc/11.2.0 stable b:gcc/10.3.0 b:gmp/6.2.1 b:mpfr/4.1.0 b:mpc/1.2.1