{vis}[foss/2023] IMOD v4.12.62 w/ CUDA 12.1.1 by ThomasHoffmann77 · Pull Request #20555 · easybuilders/easybuild-easyconfigs

ThomasHoffmann77 · 2024-05-17T15:02:27Z

(created using eb --new-pr)

boegel · 2024-05-22T12:58:03Z

easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

+# download manually from mercurial repository and create source tarball:
+# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
+# get lunch 
+# cd IMOD
+# hg update -r IMOD_4-12-62
+# rm .hg* -rf
+# cd ..
+# find IMOD -print|sort| tar -czf IMOD-`cat IMOD/.version`.tar.gz -T -


let's use download_instructions here, see for example #19884

@boegel how to use EasyBuild's sources archive?
https://bio3d.colorado.edu/imod/COPYRIGHT.txt: "... All portions of IMOD, except as noted below, are open source under the General Public License (GPL) version 2.0. ..."

boegel · 2024-05-22T14:45:09Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4006.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/boegel/7af93b650a3b83644c139ff79c4fb9d8 for a full test report.

add download instructions

style

add groff builddependency

easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

set IMOD_JAVADIR in modXXXfooter

github-actions · 2025-01-09T09:02:00Z

Updated software `IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb`

Diff against IMOD-4.11.5-fosscuda-2020b.eb

easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
index 1f1c6e82c8..bf7aeee083 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -1,8 +1,8 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04
 easyblock = 'ConfigureMake'
 
 name = 'IMOD'
-version = '4.11.5'
+version = '4.12.62'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://bio3d.colorado.edu/imod/'
 description = """IMOD is a set of image processing, modeling and display
@@ -13,94 +13,120 @@ 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."""
 
-toolchain = {'name': 'fosscuda', 'version': '2020b'}
-toolchainopts = {'pic': True, 'openmp': True}
-# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
-cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6']
-
-# download manually from mercurial repository and create source tarball:
-# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
-# get lunch 
-# cd IMOD
-# hg update -r IMOD_4-11-5
-# cd ..
-# tar czf IMOD-4.11.5.tar.gz IMOD
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}  # openmp leads to segfault with xftoxg tool
+
+download_instructions = f"""{name} requires manual download from  mercurial repository:
+ hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
+ cd IMOD
+ hg update -r IMOD_%s
+ rm .hg* -rf
+ cd ..
+ find IMOD -print|sort| tar -czf IMOD-`cat IMOD/.version`.tar.gz -T -
+""" % version.replace('.', '-')
+
 sources = [SOURCE_TAR_GZ]
-# can't include a valid checksum, since tarball has to be created manually
-patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch']
+patches = [
+    'IMOD-4.11.12_hdf1.12.patch',
+    'IMOD-4.12.17_tiltalign_include.patch',
+    # replace hardcoded CUDA compute capabilitites in machines/rhlinux. set as CUDACC:
+    'IMOD-4.12.58_cudacc.patch',
+]
 checksums = [
-    # can't include a valid checksum for source tarball, since it has to be created manually
-    None,  # IMOD-4.11.5.tar.gz
-    '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971',  # IMOD-4.11.5_fix-csvtohtml-py3.patch
+    # IMOD-4.12.62.tar.gz: 
+    None,  # can't include a valid checksum for source tarball, since it has to be created manually
+    # IMOD-4.11.12_hdf1.12.patch:
+    '19e5bff97b997c600f157dd56eddae96a7f34fef528e7f40e76ea8e19144810e',
+    # IMOD-4.12.17_tiltalign_include.patch: 
+    '998c01a4f78b0d48dbffc530fcb12faaa892b1d322bce4f1643df20799845ab7',
+    # IMOD-4.12.58_cudacc.patch:
+    '9563b1ac9ab1569689d7db4380301f330290d9695988f8b31e7ea08d2601ee25',
 ]
 
+builddependencies = [('groff', '1.22.4')]
+
 dependencies = [
-    ('LibTIFF', '4.1.0'),
-    ('Qt5', '5.14.2'),
+    ('LibTIFF', '4.5.0'),
+    ('Qt5', '5.15.10'),
     ('Java', '11', '', SYSTEM),
-    ('HDF5', '1.10.7'),
-    ('Python', '3.8.6'),
+    ('HDF5', '1.14.0'),
+    ('Python', '3.11.3'),
+    ('libGLU', '9.0.3'),
+    ('tcsh', '6.24.10'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('UCX-CUDA', '1.14.1', versionsuffix),
 ]
 
 # parallel build sometimes fails
 parallel = 1
 
-# replace hardcoded CUDA compute capabilitites in machines/rhlinux. 
-local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|'
-local_cuda_replace += '   awk \'{'
-local_cuda_replace += '          printf "-arch sm_"$1; '
-local_cuda_replace += '          for (i=1;i<=NF; i++){printf(" -gencode=arch=compute_%s,code=sm_%s",$i,$i) } '
-local_cuda_replace += '   }\''
-local_cudaarch_sed = 'sed -i "s/-arch sm_35/`' + local_cuda_replace + '`/g" machines/rhlinux &&'
-
 # modify all qmake pro files in order to pass CFLAGS
-local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&"
+_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; && "
 
 # exports required for configure and build
-local_exports = 'export QTDIR=$EBROOTQT5 &&'
-local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&'
-local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&'
-local_exports += 'export CUDA_DIR=$CUDA_HOME &&'
+_exports = 'export QTDIR=$EBROOTQT5 && '
+_exports += "export CUDACC='%(cuda_cc_cmake)s' && "
+_exports += 'export HDF5_DIR=$EBROOTHDF5 && '
+_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` && '
+_exports += 'export CUDA_DIR=$CUDA_HOME && '
 #  readw_or_imod.f and others with gfortran10: 
 #     Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2))
 #     => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0.
-local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&'  # required for gfortran10
+_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" && '  # required for gfortran10
+
+# rename pysrc/pip.py to pysrc/PIP.py
+_renamePip = """sed -i 's/from pip/from PIP/g' pysrc/* &&"""
+_renamePip += """mv pysrc/pip.py pysrc/PIP.py &&"""
+_renamePip += """sed -i 's/pip.py/PIP.py/g' pysrc/Makefile &&"""
+
+_useTcsh = 'sed -i "s|#!/bin/csh -f|#!/usr/bin/env tcsh|g;s|#! /bin/csh -f|#!/usr/bin/env tcsh|g" '
+_useTcsh += ' %(builddir)s/IMOD/{manpages/convert,setup,setup2,machines/rhlinux,packMacApps} &&'
 
-preconfigopts = local_exports
-preconfigopts += local_cudaarch_sed
-preconfigopts += local_qmake_pass_cflags
+preconfigopts = _exports
+preconfigopts += _renamePip
+preconfigopts += _qmake_pass_cflags
+preconfigopts += _useTcsh
 
 # IMOD's configure script is named setup and does not know the parameter --prefix, but -i. 
 # CFLAGs are passed with -flags.
 configure_cmd = './setup '
+configure_cmd += '-c gnu '  # htf it finds icc?
 configure_cmd += '-flags "$CFLAGS" '    # inject CFLAGS
 configure_cmd += '-i %(installdir)s '  # set installdir
-configure_cmd += ' #'  # avoid passing unknown arg --prefix
+configure_without_installdir = True
 
-prebuildopts = local_exports
+prebuildopts = _exports
 
 # create some missing directories required for installation process:
-preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&'
+preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p && '
 
 # patch hardcoded /usr/bin/python to use Python included as dependency
 preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && "
+preinstallopts += "export PYTHONPATH=%(builddir)s/IMOD/pysrc:$PYTHONPATH && "
 preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && "
 preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && "
 
+modextrapaths = {'PYTHONPATH': 'pylib'}
+
 modextravars = {
     'IMOD_DIR': "%(installdir)s",
     'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug',
-    'IMOD_JAVADIR': '$JAVA_HOME',
     'FOR_DISABLE_STACK_TRACE': '1',
 }
+
+modluafooter = """
+setenv("IMOD_JAVADIR", os.getenv("JAVA_HOME"))
+"""
+
+modtclfooter = """
+setenv IMOD_JAVADIR $::env(JAVA_HOME)
+"""
+
+
 modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.'
-# Observed problems with alias on a tcl based module system. Use bin/subm python script instead.
-# modaliases = {
-#     'subm': 'submfg $* &'
-# }
 sanity_check_paths = {
     'files': ['VERSION', 'bin/subm'],
     'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
 }
-
+sanity_check_commands = [('xftoxg', '-h')]
 moduleclass = 'vis'

Diff against IMOD-4.11.5-foss-2020b.eb

easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
index d3a1580f52..bf7aeee083 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -1,8 +1,8 @@
-# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04
 easyblock = 'ConfigureMake'
 
 name = 'IMOD'
-version = '4.11.5'
+version = '4.12.62'
+versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://bio3d.colorado.edu/imod/'
 description = """IMOD is a set of image processing, modeling and display
@@ -13,81 +13,120 @@ 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."""
 
-toolchain = {'name': 'foss', 'version': '2020b'}
-toolchainopts = {'pic': True, 'openmp': True}
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}  # openmp leads to segfault with xftoxg tool
+
+download_instructions = f"""{name} requires manual download from  mercurial repository:
+ hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
+ cd IMOD
+ hg update -r IMOD_%s
+ rm .hg* -rf
+ cd ..
+ find IMOD -print|sort| tar -czf IMOD-`cat IMOD/.version`.tar.gz -T -
+""" % version.replace('.', '-')
 
-# download manually from mercurial repository and create source tarball:
-# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
-# get lunch 
-# cd IMOD
-# hg update -r IMOD_4-11-5
-# cd ..
-# tar czf IMOD-4.11.5.tar.gz IMOD
 sources = [SOURCE_TAR_GZ]
-patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch']
+patches = [
+    'IMOD-4.11.12_hdf1.12.patch',
+    'IMOD-4.12.17_tiltalign_include.patch',
+    # replace hardcoded CUDA compute capabilitites in machines/rhlinux. set as CUDACC:
+    'IMOD-4.12.58_cudacc.patch',
+]
 checksums = [
-    # can't include a valid checksum for source tarball, since it has to be created manually
-    None,  # IMOD-4.11.5.tar.gz
-    '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971',  # IMOD-4.11.5_fix-csvtohtml-py3.patch
+    # IMOD-4.12.62.tar.gz: 
+    None,  # can't include a valid checksum for source tarball, since it has to be created manually
+    # IMOD-4.11.12_hdf1.12.patch:
+    '19e5bff97b997c600f157dd56eddae96a7f34fef528e7f40e76ea8e19144810e',
+    # IMOD-4.12.17_tiltalign_include.patch: 
+    '998c01a4f78b0d48dbffc530fcb12faaa892b1d322bce4f1643df20799845ab7',
+    # IMOD-4.12.58_cudacc.patch:
+    '9563b1ac9ab1569689d7db4380301f330290d9695988f8b31e7ea08d2601ee25',
 ]
 
+builddependencies = [('groff', '1.22.4')]
+
 dependencies = [
-    ('LibTIFF', '4.1.0'),
-    ('Qt5', '5.14.2'),
+    ('LibTIFF', '4.5.0'),
+    ('Qt5', '5.15.10'),
     ('Java', '11', '', SYSTEM),
-    ('HDF5', '1.10.7'),
-    ('Python', '3.8.6'),
+    ('HDF5', '1.14.0'),
+    ('Python', '3.11.3'),
+    ('libGLU', '9.0.3'),
+    ('tcsh', '6.24.10'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('UCX-CUDA', '1.14.1', versionsuffix),
 ]
 
 # parallel build sometimes fails
 parallel = 1
 
 # modify all qmake pro files in order to pass CFLAGS
-local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&"
+_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; && "
 
 # exports required for configure and build
-local_exports = 'export QTDIR=$EBROOTQT5 &&'
-local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&'
-local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&'
+_exports = 'export QTDIR=$EBROOTQT5 && '
+_exports += "export CUDACC='%(cuda_cc_cmake)s' && "
+_exports += 'export HDF5_DIR=$EBROOTHDF5 && '
+_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` && '
+_exports += 'export CUDA_DIR=$CUDA_HOME && '
 #  readw_or_imod.f and others with gfortran10: 
 #     Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2))
 #     => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0.
-local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&'  # required for gfortran10
+_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" && '  # required for gfortran10
 
-preconfigopts = local_exports
-preconfigopts += local_qmake_pass_cflags
+# rename pysrc/pip.py to pysrc/PIP.py
+_renamePip = """sed -i 's/from pip/from PIP/g' pysrc/* &&"""
+_renamePip += """mv pysrc/pip.py pysrc/PIP.py &&"""
+_renamePip += """sed -i 's/pip.py/PIP.py/g' pysrc/Makefile &&"""
+
+_useTcsh = 'sed -i "s|#!/bin/csh -f|#!/usr/bin/env tcsh|g;s|#! /bin/csh -f|#!/usr/bin/env tcsh|g" '
+_useTcsh += ' %(builddir)s/IMOD/{manpages/convert,setup,setup2,machines/rhlinux,packMacApps} &&'
+
+preconfigopts = _exports
+preconfigopts += _renamePip
+preconfigopts += _qmake_pass_cflags
+preconfigopts += _useTcsh
 
 # IMOD's configure script is named setup and does not know the parameter --prefix, but -i. 
 # CFLAGs are passed with -flags.
 configure_cmd = './setup '
+configure_cmd += '-c gnu '  # htf it finds icc?
 configure_cmd += '-flags "$CFLAGS" '    # inject CFLAGS
 configure_cmd += '-i %(installdir)s '  # set installdir
-configure_cmd += ' #'  # avoid passing unknown arg --prefix
+configure_without_installdir = True
 
-prebuildopts = local_exports
+prebuildopts = _exports
 
 # create some missing directories required for installation process:
 preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p && '
 
 # patch hardcoded /usr/bin/python to use Python included as dependency
 preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && "
+preinstallopts += "export PYTHONPATH=%(builddir)s/IMOD/pysrc:$PYTHONPATH && "
 preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && "
 preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && "
 
+modextrapaths = {'PYTHONPATH': 'pylib'}
+
 modextravars = {
     'IMOD_DIR': "%(installdir)s",
     'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug',
-    'IMOD_JAVADIR': '$JAVA_HOME',
     'FOR_DISABLE_STACK_TRACE': '1',
 }
+
+modluafooter = """
+setenv("IMOD_JAVADIR", os.getenv("JAVA_HOME"))
+"""
+
+modtclfooter = """
+setenv IMOD_JAVADIR $::env(JAVA_HOME)
+"""
+
+
 modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.'
-# Observed problems with alias on a tcl based module system. Use bin/subm python script instead.
-# modaliases = {
-#     'subm': 'submfg $* &'
-# }
 sanity_check_paths = {
     'files': ['VERSION', 'bin/subm'],
     'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
 }
-
+sanity_check_commands = [('xftoxg', '-h')]
 moduleclass = 'vis'

Diff against IMOD-4.7.15_RHEL6-64_CUDA6.0.eb

easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
index a1c29d2be5..bf7aeee083 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -1,13 +1,10 @@
-# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
-# authors:
-# * Pablo Escobar Lopez (sciCORE - University of Basel - SIB Swiss Institute of Bioinformatics)
-# * Benjamin Roberts (Landcare Research NZ Ltd)
+easyblock = 'ConfigureMake'
 
 name = 'IMOD'
-version = '4.7.15'
-versionsuffix = '_RHEL6-64_CUDA6.0'
+version = '4.12.62'
+versionsuffix = '-CUDA-%(cudaver)s'
 
-homepage = 'http://bio3d.colorado.edu/imod/'
+homepage = 'https://bio3d.colorado.edu/imod/'
 description = """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
@@ -16,14 +13,120 @@ 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."""
 
-toolchain = SYSTEM
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'pic': True}  # openmp leads to segfault with xftoxg tool
 
-source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/']
-sources = ['%(namelower)s_%(version)s%(versionsuffix)s.csh']
+download_instructions = f"""{name} requires manual download from  mercurial repository:
+ hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
+ cd IMOD
+ hg update -r IMOD_%s
+ rm .hg* -rf
+ cd ..
+ find IMOD -print|sort| tar -czf IMOD-`cat IMOD/.version`.tar.gz -T -
+""" % version.replace('.', '-')
+
+sources = [SOURCE_TAR_GZ]
+patches = [
+    'IMOD-4.11.12_hdf1.12.patch',
+    'IMOD-4.12.17_tiltalign_include.patch',
+    # replace hardcoded CUDA compute capabilitites in machines/rhlinux. set as CUDACC:
+    'IMOD-4.12.58_cudacc.patch',
+]
+checksums = [
+    # IMOD-4.12.62.tar.gz: 
+    None,  # can't include a valid checksum for source tarball, since it has to be created manually
+    # IMOD-4.11.12_hdf1.12.patch:
+    '19e5bff97b997c600f157dd56eddae96a7f34fef528e7f40e76ea8e19144810e',
+    # IMOD-4.12.17_tiltalign_include.patch: 
+    '998c01a4f78b0d48dbffc530fcb12faaa892b1d322bce4f1643df20799845ab7',
+    # IMOD-4.12.58_cudacc.patch:
+    '9563b1ac9ab1569689d7db4380301f330290d9695988f8b31e7ea08d2601ee25',
+]
+
+builddependencies = [('groff', '1.22.4')]
 
 dependencies = [
-    ('CUDA', '6.0.37'),
-    ('Java', '1.7.0_80'),
+    ('LibTIFF', '4.5.0'),
+    ('Qt5', '5.15.10'),
+    ('Java', '11', '', SYSTEM),
+    ('HDF5', '1.14.0'),
+    ('Python', '3.11.3'),
+    ('libGLU', '9.0.3'),
+    ('tcsh', '6.24.10'),
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('UCX-CUDA', '1.14.1', versionsuffix),
 ]
 
+# parallel build sometimes fails
+parallel = 1
+
+# modify all qmake pro files in order to pass CFLAGS
+_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; && "
+
+# exports required for configure and build
+_exports = 'export QTDIR=$EBROOTQT5 && '
+_exports += "export CUDACC='%(cuda_cc_cmake)s' && "
+_exports += 'export HDF5_DIR=$EBROOTHDF5 && '
+_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` && '
+_exports += 'export CUDA_DIR=$CUDA_HOME && '
+#  readw_or_imod.f and others with gfortran10: 
+#     Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2))
+#     => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0.
+_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" && '  # required for gfortran10
+
+# rename pysrc/pip.py to pysrc/PIP.py
+_renamePip = """sed -i 's/from pip/from PIP/g' pysrc/* &&"""
+_renamePip += """mv pysrc/pip.py pysrc/PIP.py &&"""
+_renamePip += """sed -i 's/pip.py/PIP.py/g' pysrc/Makefile &&"""
+
+_useTcsh = 'sed -i "s|#!/bin/csh -f|#!/usr/bin/env tcsh|g;s|#! /bin/csh -f|#!/usr/bin/env tcsh|g" '
+_useTcsh += ' %(builddir)s/IMOD/{manpages/convert,setup,setup2,machines/rhlinux,packMacApps} &&'
+
+preconfigopts = _exports
+preconfigopts += _renamePip
+preconfigopts += _qmake_pass_cflags
+preconfigopts += _useTcsh
+
+# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. 
+# CFLAGs are passed with -flags.
+configure_cmd = './setup '
+configure_cmd += '-c gnu '  # htf it finds icc?
+configure_cmd += '-flags "$CFLAGS" '    # inject CFLAGS
+configure_cmd += '-i %(installdir)s '  # set installdir
+configure_without_installdir = True
+
+prebuildopts = _exports
+
+# create some missing directories required for installation process:
+preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p && '
+
+# patch hardcoded /usr/bin/python to use Python included as dependency
+preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && "
+preinstallopts += "export PYTHONPATH=%(builddir)s/IMOD/pysrc:$PYTHONPATH && "
+preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && "
+preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && "
+
+modextrapaths = {'PYTHONPATH': 'pylib'}
+
+modextravars = {
+    'IMOD_DIR': "%(installdir)s",
+    'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug',
+    'FOR_DISABLE_STACK_TRACE': '1',
+}
+
+modluafooter = """
+setenv("IMOD_JAVADIR", os.getenv("JAVA_HOME"))
+"""
+
+modtclfooter = """
+setenv IMOD_JAVADIR $::env(JAVA_HOME)
+"""
+
+
+modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.'
+sanity_check_paths = {
+    'files': ['VERSION', 'bin/subm'],
+    'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
+}
+sanity_check_commands = [('xftoxg', '-h')]
 moduleclass = 'vis'

jfgrimm · 2025-06-17T13:08:40Z

closing in favour of #21753

{vis}[foss/2023] IMOD v4.12.62 w/ CUDA 12.1.1

42bd13f

boegel reviewed May 22, 2024

View reviewed changes

boegel added the update label May 22, 2024

boegel added this to the 4.x milestone May 22, 2024

ThomasHoffmann77 mentioned this pull request May 24, 2024

RELION5 draft for tomo support; 2nd try jfgrimm/easybuild-easyconfigs#6

Open

20 tasks

ThomasHoffmann77 added 2 commits May 24, 2024 11:53

Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

dc7e2c7

add download instructions

Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

7105b2f

style

ThomasHoffmann77 requested a review from boegel May 31, 2024 08:17

Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

1c13f4a

add groff builddependency

cjroberts reviewed Jan 8, 2025

View reviewed changes

easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb Outdated Show resolved Hide resolved

Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

a28e154

set IMOD_JAVADIR in modXXXfooter

jfgrimm closed this Jun 17, 2025

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

{vis}[foss/2023] IMOD v4.12.62 w/ CUDA 12.1.1#20555

{vis}[foss/2023] IMOD v4.12.62 w/ CUDA 12.1.1#20555
ThomasHoffmann77 wants to merge 5 commits intoeasybuilders:developfrom
ThomasHoffmann77:20240517170220_new_pr_IMOD41262

ThomasHoffmann77 commented May 17, 2024

Uh oh!

boegel May 22, 2024

Uh oh!

ThomasHoffmann77 May 24, 2024

Uh oh!

boegel commented May 22, 2024

Uh oh!

Uh oh!

github-actions bot commented Jan 9, 2025

Uh oh!

jfgrimm commented Jun 17, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

ThomasHoffmann77 commented May 17, 2024

Uh oh!

boegel May 22, 2024

Choose a reason for hiding this comment

Uh oh!

ThomasHoffmann77 May 24, 2024

Choose a reason for hiding this comment

Uh oh!

boegel commented May 22, 2024

Uh oh!

Uh oh!

github-actions bot commented Jan 9, 2025

Updated software IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

Uh oh!

jfgrimm commented Jun 17, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Updated software `IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb`