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Merge branch 'master' into 251-build-modules-with-gcc-10-4-0

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gsell
2022-12-13 10:07:08 +01:00
parent 9efd4e6e23 a4f6d90ada
commit 4b11bcaddc
17 changed files with 242 additions and 22 deletions
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26
Compiler/H5root/1/variants
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@@ -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

20
Compiler/gsl/files/variants.rhel6 Normal file
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@@ -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

14
EM/IMOD/README.md Normal file
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@@ -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).

43
EM/IMOD/build Executable file
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@@ -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"
}

2
EM/IMOD/files/variants Normal file
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IMOD/4.9.5 stable
IMOD/4.11.20 unstable cuda/10.1.105

45
EM/IMOD/modulefile Normal file
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@@ -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 <spencer.bliven@psi.ch> / Dmitry Ozerov <dmitry.ozerov@psi.ch>"
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
}
}

24
EM/MotionCor2/README.md
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@@ -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 |

21
EM/MotionCor2/bin/MotionCor2 Executable file
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@@ -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 ${CUDA_VERSION} ]; then
echo 'MotionCor2 requires the cuda module. Run `module load cuda/<version>`' >&2
exit 1
fi
CUDA=$(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 "$EXE" "$@"

1
EM/MotionCor2/build
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@@ -18,5 +18,6 @@ pbuild::compile() {
pbuild::install() {
cp $BUILDBLOCK_DIR/files/LICENSE $PREFIX/
cp -r $BUILDBLOCK_DIR/bin $PREFIX/
}

3
EM/MotionCor2/files/variants
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@@ -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

8
EM/ctffind4/README Normal file
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@@ -0,0 +1,8 @@
# ctffind4
## Installation
./build
Installs the pre-build binaries.

36
EM/ctffind4/build Executable file
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@@ -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"
}

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EM/ctffind4/files/variants Normal file
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@@ -0,0 +1,2 @@
ctffind4/4.1.8 stable
ctffind4/4.1.14 stable

10
EM/ctffind4/modulefile Normal file
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@@ -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 <spencer.bliven@psi.ch>"
module-help "
Mindell, JA, Grigorieff N. 2003. Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 142:334-47.
"

6
Libraries/ucx/files/variants.merlin6
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@@ -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

2
MPI/hdf5/files/variants.rhel6
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@@ -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

1
Programming/gcc/files/variants.rhel6
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@@ -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