{vis}[foss/2023a] IMOD v5.1.3 w/ CUDA 12.1.1

[ThomasHoffmann77]

(created using eb --new-pr)

[sassy-crick]

@ThomasHoffmann77 You might want to sync your PR with development, something like this:

eb --sync-pr-with-develop NUMBER_OF_PR

[github-actions]

Updated software IMOD-5.0.1-foss-2023a-CUDA-12.1.1.eb

Diff against IMOD-5.1.0-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/i/IMOD/IMOD-5.1.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-5.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/i/IMOD/IMOD-5.0.1-foss-2023a-CUDA-12.1.1.eb
index e7947f8353..fca8c8b39b 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-5.1.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-5.0.1-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'IMOD'
-version = '5.1.0'
+version = '5.0.1'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://bio3d.colorado.edu/imod/'
@@ -16,18 +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_instructions = f"""
-To generate the source tarball for %(name)s:
-  hg clone --debug http://bio3d.colorado.edu/%(namelower)s/nightlyBuilds/%(name)s
-  get lunch
-  cd %(name)s
-  hg update -r %(name)s_{version.replace('.', '-')}
-  cd ..
-  tar czf %(name)s-%(version)s.tar.gz IMOD
-"""
-
+# 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',
@@ -35,7 +32,7 @@ patches = [
     'IMOD-4.12.58_cudacc.patch',
 ]
 checksums = [
-    # IMOD-5.1.0.tar.gz: 
+    # 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',
@@ -59,24 +56,17 @@ dependencies = [
 ]
 
 # parallel build sometimes fails
-maxparallel = 1
+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 = ' && '.join([
-    'export QTDIR=$EBROOTQT5',
-    'export CUDACC="%(cuda_cc_cmake)s"',
-    'export HDF5_DIR="$EBROOTHDF5"',
-    'export QMAKESPEC="$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC`"',
-    'export CUDA_DIR="$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.
-    'export CFLAGS="$CFLAGS -fallow-argument-mismatch"',  # required for gfortran10 and newer
-])
-
+_exports = 'export QTDIR=$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.
@@ -97,9 +87,11 @@ 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'
-configopts = '-c gnu -flags "$CFLAGS"'
-prefix_opt = '-i '
+configure_cmd = './setup '
+configure_cmd += '-c gnu '  # htf it finds icc?
+configure_cmd += '-flags "$CFLAGS" '    # inject CFLAGS
+configure_cmd += '-i %(installdir)s '  # set installdir
+configure_without_installdir = True
 
 prebuildopts = _exports
 
@@ -120,14 +112,10 @@ modextravars = {
     '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': ['lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
+    'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
 }
-
 sanity_check_commands = [('xftoxg', '-h')]
-
-modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.'
-
 moduleclass = 'vis'

Updated software IMOD-5.1.0-foss-2023a-CUDA-12.1.1.eb

Diff against IMOD-5.0.1-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/i/IMOD/IMOD-5.0.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-5.0.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/i/IMOD/IMOD-5.1.0-foss-2023a-CUDA-12.1.1.eb
index fca8c8b39b..e7947f8353 100644
--- a/easybuild/easyconfigs/i/IMOD/IMOD-5.0.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/i/IMOD/IMOD-5.1.0-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'IMOD'
-version = '5.0.1'
+version = '5.1.0'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://bio3d.colorado.edu/imod/'
@@ -16,15 +16,18 @@ 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"""
+To generate the source tarball for %(name)s:
+  hg clone --debug http://bio3d.colorado.edu/%(namelower)s/nightlyBuilds/%(name)s
+  get lunch
+  cd %(name)s
+  hg update -r %(name)s_{version.replace('.', '-')}
+  cd ..
+  tar czf %(name)s-%(version)s.tar.gz IMOD
+"""
+
 sources = [SOURCE_TAR_GZ]
+
 patches = [
     'IMOD-4.11.12_hdf1.12.patch',
     'IMOD-4.12.17_tiltalign_include.patch',
@@ -32,7 +35,7 @@ patches = [
     'IMOD-4.12.58_cudacc.patch',
 ]
 checksums = [
-    # IMOD-4.12.62.tar.gz: 
+    # IMOD-5.1.0.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',
@@ -56,17 +59,24 @@ dependencies = [
 ]
 
 # parallel build sometimes fails
-parallel = 1
+maxparallel = 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 && '
+_exports = ' && '.join([
+    'export QTDIR=$EBROOTQT5',
+    'export CUDACC="%(cuda_cc_cmake)s"',
+    'export HDF5_DIR="$EBROOTHDF5"',
+    'export QMAKESPEC="$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC`"',
+    'export CUDA_DIR="$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.
+    'export CFLAGS="$CFLAGS -fallow-argument-mismatch"',  # required for gfortran10 and newer
+])
+
 #  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.
@@ -87,11 +97,9 @@ 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 "$CFLAGS" '    # inject CFLAGS
-configure_cmd += '-i %(installdir)s '  # set installdir
-configure_without_installdir = True
+configure_cmd = './setup'
+configopts = '-c gnu -flags "$CFLAGS"'
+prefix_opt = '-i '
 
 prebuildopts = _exports
 
@@ -112,10 +120,14 @@ modextravars = {
     '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'],
+    'dirs': ['lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
 }
+
 sanity_check_commands = [('xftoxg', '-h')]
+
+modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.'
+
 moduleclass = 'vis'

[jfgrimm]

Doing a bit of work on this locally, will add some more suggestions soon

[jfgrimm]

is this command needed? doesn't work for me, and seems to be fine without it

Suggested change

get lunch

[ThomasHoffmann77]

that's rather a comment than a command. I could also be deleted or be replaced by "drink coffee or tee" or by "wait"

[jfgrimm]

ahhh makes more sense

[jfgrimm]

@boegelbot: please test @ jsc-zen3
CORE_CNT=16

[jfgrimm]

Test report by @jfgrimm
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
node056.viking2.yor.alces.network - Linux Rocky Linux 8.9, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/be9f3611e43e297089844fc6eef4c69a for a full test report.

[boegelbot]

@jfgrimm: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21753 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21753 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 6861

Test results coming soon (I hope)...

Details

- notification for comment with ID 2980815287 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/4f6f29b139d7b3d2bf609a844fc960f2 for a full test report.

edit: forgot that the source needs manual downloading

[jfgrimm]

Test report by @jfgrimm
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node056.viking2.yor.alces.network - Linux Rocky Linux 8.9, x86_64, AMD EPYC 7643 48-Core Processor, Python 3.6.8
See https://gist.github.com/jfgrimm/0cf3e2859887f07e627e3135102b0a1a for a full test report.