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f146dbdb02
modified: i/IMOD/IMOD-4.11.1-fosscuda-2020b.eb new file: v/vaspkit/vaspkit-1.3.5-foss-2022a.eb
112 lines
4.7 KiB
Plaintext
112 lines
4.7 KiB
Plaintext
# IT4Innovations 2022
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# JK
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# Had to fix some arch-specifying files in the source code!
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# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04
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easyblock = 'ConfigureMake'
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name = 'IMOD'
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version = '4.11.1'
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homepage = 'https://bio3d.colorado.edu/imod/'
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description = """IMOD is a set of image processing, modeling and display
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programs used for tomographic reconstruction and for 3D reconstruction of EM
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serial sections and optical sections. The package contains tools for assembling
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and aligning data within multiple types and sizes of image stacks, viewing 3-D
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data from any orientation, and modeling and display of the image files. IMOD
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was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim
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Kremer, Quanren Xiong, and John Heumann at the University of Colorado."""
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toolchain = {'name': 'fosscuda', 'version': '2020b'}
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toolchainopts = {'pic': True, 'openmp': True}
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# download manually from mercurial repository and create source tarball:
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# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
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# get lunch ????? co to je
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# cd IMOD
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# hg update -r IMOD_4-11-1
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# cd ..
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# tar czf IMOD-4.11.1.tar.gz IMOD
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sources = [SOURCE_TAR_GZ]
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patches = ['IMOD-4.11.5_fix-csvtohtml-py3.patch']
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checksums = [
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'4a2a51641a3169d1066faa8011caa90196fa1aef71da5d93cfafcf0703f8bcc6', # IMOD-4.11.1.tar.gz
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'8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch
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]
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# can't include a valid checksum, since tarball has to be created manually
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dependencies = [
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('LibTIFF', '4.1.0'),
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('Qt5', '5.14.2'),
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('Java', '11', '', True),
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('HDF5', '1.10.7'),
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('Python', '3.8.6'),
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]
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# parallel build sometimes fails
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parallel = 1
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# replace hardcoded CUDA compute capabilitites in machines/rhlinux.
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local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|'
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local_cuda_replace += ' awk \'{'
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local_cuda_replace += ' printf "-arch sm_"$1; '
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local_cuda_replace += ' for (i=1;i<=NF; i++){printf(" -gencode=arch=compute_%s,code=sm_%s",$i,$i) } '
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local_cuda_replace += ' }\''
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local_cudaarch_sed = 'sed -i "s/-arch sm_35/`' + local_cuda_replace + '`/g" machines/rhlinux &&'
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# modify all qmake pro files in order to pass CFLAGS
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local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&"
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# exports required for configure and build
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local_exports = 'export QTDIR=$EBROOTQT5 &&'
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local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&'
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local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&'
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local_exports += 'export CUDA_DIR=$CUDA_HOME &&'
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# readw_or_imod.f and others with gfortran10:
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# Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2))
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# => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0.
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local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10
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preconfigopts = local_exports
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preconfigopts += local_cudaarch_sed
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preconfigopts += local_qmake_pass_cflags
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preconfigopts += "mv pysrc/pip.py pysrc/imodpip.py &&"
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preconfigopts += "sed -i 's/pip.py/imodpip.py/' pysrc/Makefile &&"
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preconfigopts += "sed -i 's/from pip/from imodpip/' pysrc/* &&"
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# IMOD's configure script is named setup and does not know the parameter --prefix, but -i.
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# CFLAGs are passed with -flags.
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configure_cmd = './setup '
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configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS
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configure_cmd += '-i %(installdir)s ' # set installdir
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configure_cmd += ' #' # avoid passing unknown arg --prefix
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prebuildopts = local_exports
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# create some missing directories required for installation process:
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preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&'
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# patch hardcoded /usr/bin/python to use Python included as dependency
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preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && "
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preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && "
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preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && "
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modextravars = {
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'IMOD_DIR': "%(installdir)s",
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'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug',
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'IMOD_JAVADIR': '$JAVA_HOME',
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'FOR_DISABLE_STACK_TRACE': '1',
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}
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modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.'
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# Observed problems with alias on a tcl based module system. Use bin/subm python script instead.
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# modaliases = {
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# 'subm': 'submfg $* &'
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# }
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sanity_check_paths = {
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'files': ['VERSION', 'bin/subm'],
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'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
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}
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moduleclass = 'vis'
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