From 42bd13f41d02bc8888d8bd305c8bbb09ae249556 Mon Sep 17 00:00:00 2001
From: thoffman <thoffman@embl.de>
Date: Fri, 17 May 2024 17:02:21 +0200
Subject: [PATCH 1/5] {vis}[foss/2023] IMOD v4.12.62 w/ CUDA 12.1.1

---
 .../i/IMOD/IMOD-4.11.12_hdf1.12.patch         |  36 ++++++
 .../IMOD/IMOD-4.12.17_tiltalign_include.patch |  13 ++
 .../i/IMOD/IMOD-4.12.58_cudacc.patch          |  22 ++++
 .../IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb    | 121 ++++++++++++++++++
 4 files changed, 192 insertions(+)
 create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.12_hdf1.12.patch
 create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.12.17_tiltalign_include.patch
 create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.12.58_cudacc.patch
 create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.12_hdf1.12.patch b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.12_hdf1.12.patch
new file mode 100644
index 000000000000..94c463f639ce
--- /dev/null
+++ b/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;
diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.17_tiltalign_include.patch b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.17_tiltalign_include.patch
new file mode 100644
index 000000000000..3e649ece83f2
--- /dev/null
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.17_tiltalign_include.patch
@@ -0,0 +1,13 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/08
+diff -ru IMOD/flib/beadtrack/beadtrack.cpp IMOD_tiltalign_include/flib/beadtrack/beadtrack.cpp
+--- IMOD/flib/beadtrack/beadtrack.cpp	2023-08-25 12:38:55.864116440 +0200
++++ IMOD_tiltalign_include/flib/beadtrack/beadtrack.cpp	2023-08-25 17:13:50.646567630 +0200
+@@ -21,7 +21,7 @@
+ #include "btfuncs.h"
+ #include "tafuncs.h"
+ #include "arraymaxes.h"
+-#include "mapsepgroups.h"
++#include "../tiltalign/mapsepgroups.h"
+ #include "cgpixels.h"
+ #include "tltcntrl.h"
+ 
diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.58_cudacc.patch b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.58_cudacc.patch
new file mode 100644
index 000000000000..dfe81d1da235
--- /dev/null
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.58_cudacc.patch
@@ -0,0 +1,22 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/01
+# replace hardcoded CUDA compute capabilitites in machines/rhlinux. 
+# Allow to be set by env $CUDACC
+diff -ru IMOD/machines/rhlinux IMOD_cudacc/machines/rhlinux
+--- IMOD/machines/rhlinux	2024-01-29 12:33:58.000000000 +0100
++++ IMOD_cudacc/machines/rhlinux	2024-01-31 12:47:19.481617766 +0100
+@@ -604,10 +604,11 @@
+ if ($?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 ($cudamajor >= 12) set cuda_arch_opts = '-arch sm_50'
++    #if ($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 ($cudamajor >= 12) set cuda_arch_opts = '-arch sm_50'
++    set cuda_arch_opts = `echo "$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"
diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
new file mode 100644
index 000000000000..54961cdcf025
--- /dev/null
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -0,0 +1,121 @@
+easyblock = 'ConfigureMake'
+
+name = 'IMOD'
+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
+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': '2023a'}
+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_4-12-62
+# rm .hg* -rf
+# cd ..
+# find IMOD -print|sort| tar -czf IMOD-`cat IMOD/.version`.tar.gz -T -
+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',
+]
+
+# can't include a valid checksum, since tarball has to be created manually
+dependencies = [
+    ('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:$PYTHONPATH && "
+preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && "
+preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && "
+
+modextrapaths = {'PYTHONPATH': 'pylib'}
+
+modextravars = {
+    'IMOD_DIR': "%(installdir)s",
+    'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug',
+    'IMOD_JAVADIR': '$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'

From dc7e2c7380f68de1bfeec623bde41a3aec531e31 Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Fri, 24 May 2024 11:53:19 +0200
Subject: [PATCH 2/5] Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

add download instructions
---
 .../IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
index 54961cdcf025..fb38aee0ba3c 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -16,14 +16,15 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado."""
 toolchain = {'name': 'foss', 'version': '2023a'}
 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_4-12-62
-# rm .hg* -rf
-# cd ..
-# find IMOD -print|sort| tar -czf IMOD-`cat IMOD/.version`.tar.gz -T -
+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',

From 7105b2f0e0c3f94052bf4fe7bd76c4eedf304b96 Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Fri, 24 May 2024 12:27:25 +0200
Subject: [PATCH 3/5] Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

style
---
 .../easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
index fb38aee0ba3c..dcf2424b8639 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -92,7 +92,7 @@ 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	
+configure_without_installdir = True
 
 prebuildopts = _exports
 

From 1c13f4a943a4d1d9c9976b7f059bad46642d9292 Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Mon, 10 Jun 2024 11:21:10 +0200
Subject: [PATCH 4/5] Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

add groff builddependency
---
 .../easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb  | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
index dcf2424b8639..7646bba732dc 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -43,7 +43,8 @@ checksums = [
     '9563b1ac9ab1569689d7db4380301f330290d9695988f8b31e7ea08d2601ee25',
 ]
 
-# can't include a valid checksum, since tarball has to be created manually
+builddependencies = [('groff', '1.22.4')]
+
 dependencies = [
     ('LibTIFF', '4.5.0'),
     ('Qt5', '5.15.10'),

From a28e1546adbd3966437b183419956301539a4108 Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Thu, 9 Jan 2025 10:01:28 +0100
Subject: [PATCH 5/5] Update IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb

set IMOD_JAVADIR in modXXXfooter
---
 .../i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb     | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
index 7646bba732dc..bf7aeee0834b 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.12.62-foss-2023a-CUDA-12.1.1.eb
@@ -111,9 +111,18 @@ 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.'
 sanity_check_paths = {
     'files': ['VERSION', 'bin/subm'],