{vis}[foss/2022a] IMOD v4.12.17 /w CUDA 11.7.0

easybuild/easyconfigs/i/IMOD/IMOD-4.11.12_hdf1.12.patch

@@ -0,0 +1,36 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/08
+# add H5O_INFO_BASIC (better _ALL?)
+# H5Oget_info_by_idx3 API changed for HDF5 version >= 1.12.0
+# https://stackoverflow.com/questions/62157364/why-is-hdf5-giving-a-too-few-arguments-error-here
+# https://support.hdfgroup.org/ftp/HDF5/prev-releases/ReleaseFiles/hdf5-1.12.0-RELEASE.txt
+diff -ru IMOD/libiimod/iihdf.c IMOD_hdf5/libiimod/iihdf.c
+--- IMOD/libiimod/iihdf.c	2022-02-24 19:07:06.000000000 +0100
++++ IMOD_hdf5/libiimod/iihdf.c	2023-08-24 18:31:53.029981337 +0200
+@@ -774,7 +774,7 @@
+   }
+
+   /* Find out if there are attributes */
+-  if (!retval && H5Oget_info(groupID, &objInfo) < 0)
++  if (!retval && H5Oget_info(groupID, &objInfo, H5O_INFO_BASIC) < 0)
+     retval = IIERR_IO_ERROR;
+   if (!retval)
+     gdptr->numAttributes = (int)objInfo.num_attrs;
+@@ -820,8 +820,7 @@
+     }
+
+     /* Get the info */
+-    if (H5Oget_info_by_idx(groupID, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)ind,
+-                           &objInfo, H5P_DEFAULT) < 0) {
++    if (H5Oget_info_by_idx(groupID, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)ind, &objInfo, H5P_DEFAULT, H5O_INFO_BASIC) < 0) {
+       retval = IIERR_IO_ERROR;
+       break;
+     }
+@@ -931,7 +930,7 @@
+             sMaxGroupNum = B3DMAX(sMaxGroupNum, groupNum);
+           }
+           dsData.dsetID = dsetID;
+-          if (H5Oget_info(dsetID, &objInfo) < 0)
++          if (H5Oget_info(dsetID, &objInfo, H5O_INFO_BASIC) < 0)
+             retval = IIERR_IO_ERROR;
+           if (!retval)
+             dsData.numAttributes = (int)objInfo.num_attrs;

easybuild/easyconfigs/i/IMOD/IMOD-4.12.17-foss-2022a-CUDA-11.7.0.eb

@@ -0,0 +1,110 @@
+easyblock = 'ConfigureMake'
+
+name = 'IMOD'
+version = '4.12.17'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+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
+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."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'pic': True}  # openmp leads to segfault with xftoxg tool
+
+# 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_4-12-17
+# cd ..
+# tar czf IMOD-4.12.17.tar.gz IMOD
+sources = [SOURCE_TAR_GZ]
+patches = [
+    'IMOD-4.11.12_hdf1.12.patch',
+    'IMOD-4.12.17_tiltalign_include.patch',
+    'IMOD-4.12.17_rename_pip.patch',
+    # replace hardcoded CUDA compute capabilitites in machines/rhlinux. set as CUDACC
+    'IMOD-4.12.17_cudacc.patch',
+]
+checksums = [
+    {'IMOD-4.12.17.tar.gz': '63978ef981d04ab0b9d5de406dcb8ebeebd1832b75423cd00be3d190352bd820'},
+    {'IMOD-4.11.12_hdf1.12.patch': '19e5bff97b997c600f157dd56eddae96a7f34fef528e7f40e76ea8e19144810e'},
+    {'IMOD-4.12.17_tiltalign_include.patch': '998c01a4f78b0d48dbffc530fcb12faaa892b1d322bce4f1643df20799845ab7'},
+    {'IMOD-4.12.17_rename_pip.patch': '1075b8b4023cd0738e418690fec9dea95991c6bc5b5eefa707ebfc6a56a60893'},
+    {'IMOD-4.12.17_cudacc.patch': 'fa0a1db35073bff8a99bf6fb48f8c5f0710f307d6b15f2378ed431803ae630d1'},
+]
+
+# can't include a valid checksum, since tarball has to be created manually
+dependencies = [
+    ('LibTIFF', '4.3.0'),
+    ('Qt5', '5.15.5'),
+    ('Java', '11', '', SYSTEM),
+    ('HDF5', '1.12.2'),
+    ('Python', '3.10.4'),
+    ('libGLU', '9.0.2'),
+    ('tcsh', '6.24.01'),
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('UCX-CUDA', '1.12.1', 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="$CFLAGS -fallow-argument-mismatch" && '  # required for gfortran10
+
+preconfigopts = _exports
+preconfigopts += _qmake_pass_cflags
+preconfigopts += 'sed -i "s|#!/bin/csh -f|#!/usr/bin/env tcsh|g;s|#! /bin/csh -f|#!/usr/bin/env tcsh|g" '
+preconfigopts += ' %(builddir)s/IMOD/{manpages/convert,setup,setup2,machines/rhlinux,packMacApps} &&'
+
+# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. 
+# CFLAGs are passed with -flags.
+configure_cmd = './setup '
+configure_cmd += '-c gnu '  # htf it finds icc?
+configure_cmd += '-flags "$CFLAGS" '    # inject CFLAGS
+configure_cmd += '-i %(installdir)s '  # set installdir
+configure_cmd += ' #'  # avoid passing unknown arg --prefix
+
+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',
+}
+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'

easybuild/easyconfigs/i/IMOD/IMOD-4.12.17_cudacc.patch

@@ -0,0 +1,20 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11
+# replace hardcoded CUDA compute capabilitites in machines/rhlinux. 
+# Allow to be set by env $CUDACC
+diff -ru IMOD/machines/rhlinux IMOD_cuda_cc/machines/rhlinux
+--- IMOD/machines/rhlinux	2023-08-25 12:38:55.000000000 +0200
++++ IMOD_cuda_cc/machines/rhlinux	2023-11-06 16:24:33.990693005 +0100
+@@ -541,9 +541,10 @@
+ if ($?CUDA_DIR) then
+     set cudavers = `nvcc --version | sed -n -e '/[,.]/s// /g' -e '/^.*release/s///p'`
+     @ cudamajor = $cudavers[1]
+-    if ($cudamajor >= 4) set cuda_arch_opts = '-arch sm_20'
+-    if ($cudamajor >= 9) set cuda_arch_opts = '-arch sm_30'
+-    if ($cudamajor >= 11) set cuda_arch_opts = '-arch sm_35'
++    #if ($cudamajor >= 4) set cuda_arch_opts = '-arch sm_20'
++    #if ($cudamajor >= 9) set cuda_arch_opts = '-arch sm_30'
++    #if ($cudamajor >= 11) set cuda_arch_opts = '-arch sm_35'
++    set cuda_arch_opts = `echo "$CUDACC" | awk -F ';' '{for (i=1;i<=NF;i++) printf "-gencode=arch=compute_%s,code=sm_%s " , $i, $i}'`  
+     set cudalibdir = "$CUDA_DIR/lib"
+     if ($cudamajor > 2 && $m64bit == true) set cudalibdir = "$CUDA_DIR/lib64"
+     set nvcc_flags = "$cuda_arch_opts $nvcc_flags -DUNIX -Xcompiler -fno-strict-aliasing -O3"