diff --git a/Custom_EasyBlocks/cpmd.py b/Custom_EasyBlocks/cpmd.py
index 25b38296877dd66301ef190bc1d46b1c8a5f3c3c..8885f4b26da9e8646fc4f11f6e61632d14724894 100644
--- a/Custom_EasyBlocks/cpmd.py
+++ b/Custom_EasyBlocks/cpmd.py
@@ -36,7 +36,8 @@ EasyBuild support for building and installing CPMD, implemented as an easyblock
#the pseudo-fix is to remove installdir/obj as postinstallcmds from the easyconfig file
#the documentation was missing and is now added in a somewhat weird procedure
#to the builddir and subsequently copied to the installdir/doc via postinstallcmds from the easyconfig file
-#the hybrid MPI/OMP version can solely installed through the openmp toolchain option
+#the hybrid version is installed via prefix_opt = '-omp -DEST=' independent of toolchain options in easyconfig file
+#
#the cuda implementation is ignored
#
@@ -68,6 +69,7 @@ class EB_CPMD(ConfigureMake):
"""Custom easyconfig parameters for CPMD."""
extra_vars = {
'base_configuration': [None, "Base configuration from which to start (file name)", CUSTOM],
+ 'MIT' : [None, "Open-Source Version of CPMD (MIT licence)",CUSTOM],
}
return ConfigureMake.extra_options(extra_vars)
@@ -89,7 +91,12 @@ class EB_CPMD(ConfigureMake):
config_file_candidates = []
for confdirname in ["configure", "CONFIGURE"]:
- config_file_prefix = os.path.join(self.builddir, "CPMD", confdirname)
+ if self.cfg['MIT']:
+ cpmdname = 'CPMD-%s' % self.version
+ else:
+ cpmdname = 'CPMD'
+
+ config_file_prefix = os.path.join(self.builddir, cpmdname , confdirname)
if os.path.isdir(config_file_prefix):
break
else:
@@ -149,6 +156,8 @@ class EB_CPMD(ConfigureMake):
(r"^(\s*CC=.*)", r"#\1"),
(r"^(\s*FC=.*)", r"#\1"),
(r"^(\s*LD)=.*", r"\1='$(FC)'"),
+ (r" -openmp ", r" -qopenmp "),
+ (r"-mkl=", r"-qmkl="),
])
except IOError as err:
raise EasyBuildError("Failed to patch %s: %s", selected_base_config, err)
@@ -174,8 +183,8 @@ class EB_CPMD(ConfigureMake):
options = [self.cfg['configopts']]
# enable OpenMP support if desired
- if self.toolchain.options.get('openmp', None) and LooseVersion(self.version) >= LooseVersion('4.0'):
- options.append("-omp")
+# if self.toolchain.options.get('openmp', None) and LooseVersion(self.version) >= LooseVersion('4.0'):
+# options.append("-omp")
# This "option" has to come last as it's the chief argument, coming after
# all flags and so forth.
@@ -240,11 +249,12 @@ class EB_CPMD(ConfigureMake):
if preproc_flag is None:
preproc_flag = ''
+# do not use default='None' for CPPFLAGS
apply_regex_substitutions(makefile, [
- (r"^(\s*CPPFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('CPPFLAGS'))),
- (r"^(\s*CFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('CFLAGS'))),
- (r"^(\s*FFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('FFLAGS'))),
- (r"^(\s*LFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('LDFLAGS'))),
+ (r"^(\s*CPPFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('CPPFLAGS',' '))),
+ (r"^(\s*CFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('CFLAGS',' '))),
+ (r"^(\s*FFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('FFLAGS',' '))),
+ (r"^(\s*LFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('LDFLAGS',' '))),
# Allow to define own XFLAGS
(r"# CPPFLAGS =", r"CPPFLAGS +="),
@@ -259,14 +269,14 @@ class EB_CPMD(ConfigureMake):
])
if self.toolchain.options.get('openmp', None):
apply_regex_substitutions(makefile, [
- (r"^(\s*LFLAGS\s*=.*)", r"\1 {0} {1}".format(os.getenv('LIBLAPACK_MT'), os.getenv('LIBBLAS_MT')))
+ (r"^(\s*LFLAGS\s*=.*)", r"\1 {0} {1}".format(os.getenv('LIBLAPACK_MT',' '), os.getenv('LIBBLAS_MT',' ')))
])
else:
apply_regex_substitutions(makefile, [
- (r"^(\s*LFLAGS\s*=.*)", r"\1 {0} {1}".format(os.getenv('LIBLAPACK'), os.getenv('LIBBLAS')))
+ (r"^(\s*LFLAGS\s*=.*)", r"\1 {0} {1}".format(os.getenv('LIBLAPACK',' '), os.getenv('LIBBLAS',' ')))
])
apply_regex_substitutions(makefile, [
- (r"^(\s*LFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('LIBFFT'))),
+ (r"^(\s*LFLAGS\s*=.*)", r"\1 {0}".format(os.getenv('LIBFFT',' '))),
])
if get_software_root('imkl'):
diff --git a/Golden_Repo/a/Advisor/Advisor-2023.0.0.eb b/Golden_Repo/a/Advisor/Advisor-2023.0.0.eb
index 1de7e199916259e0b69107a6807576df6760a653..e0123c4fd3db076fdaaf22f080f0ec859a1805ff 100644
--- a/Golden_Repo/a/Advisor/Advisor-2023.0.0.eb
+++ b/Golden_Repo/a/Advisor/Advisor-2023.0.0.eb
@@ -18,8 +18,8 @@ checksums = ['5d8ef163f70ee3dc42b13642f321d974f49915d55914ba1ca9177ed29b100b9d']
dontcreateinstalldir = True
modextrapaths = {
- 'PATH': 'advisor/bin64',
- 'MANPATH': 'advisor/man'
+ 'PATH': '%(namelower)s/%(version)s/bin64',
+ 'MANPATH': '%(namelower)s/%(version)s/man'
}
sanity_check_paths = {
diff --git a/Golden_Repo/c/CPMD/CPMD-4.3-intel-para-2022a_MIT.eb b/Golden_Repo/c/CPMD/CPMD-4.3-intel-para-2022a_MIT.eb
new file mode 100644
index 0000000000000000000000000000000000000000..3085814b6d28470fcfc7ead35a9a0db02212c346
--- /dev/null
+++ b/Golden_Repo/c/CPMD/CPMD-4.3-intel-para-2022a_MIT.eb
@@ -0,0 +1,58 @@
+name = 'CPMD'
+version = '4.3'
+versionsuffix = '_MIT'
+
+homepage = 'https://github.com/CPMD-code'
+description = """The CPMD code is a parallelized plane wave / pseudopotential
+implementation of Density Functional Theory, particularly designed for
+ab-initio molecular dynamics. This is version 4.3 released under MIT licence in January 2023.
+"""
+
+toolchain = {'name': 'intel-para', 'version': '2022a'}
+toolchainopts = {'usempi': True}
+
+sources = [
+ {'download_filename': 'archive/refs/tags/%(version)s.tar.gz', 'filename': 'cpmd-4.3MIT.tar.gz'},
+ 'cpmd4.3_manual.pdf',
+]
+
+source_urls = [
+ 'https://github.com/CPMD-code/CPMD',
+]
+
+patches = [
+ 'cppflags.patch',
+ '%(namelower)s-v%(version)s-config.patch'
+]
+
+checksums = [
+ 'e0290f9da0d255f90a612e60662b14a97ca53003f89073c6af84fa7bc8739f65',
+ '2bfe01db05df1cb21cc8eae500da92b7744c786beeef25e6b2c86116ffc2e135',
+ '36c57801d5643c5e07f81ce7d4e973ae2e3100fb61220bccbbe4de3629c20d8c',
+ '45719bf7ca0c567c9c78b3f23201976fceda565d47fea2d1bc998b72fdc53caa',
+]
+
+# the cpmd.py post-cleanup of the results of the configure step
+# is rather error-prone
+
+preconfigopts = 'pwd && chmod u+x scripts/configure.sh && '
+
+prefix_opt = '-DEST='
+
+MIT = True
+
+postinstallcmds = [
+ 'rm -rf %(installdir)s/obj',
+ 'mkdir %(installdir)s/doc',
+ 'cp %(builddir)s/cpmd4.3_manual.pdf %(installdir)s/doc'
+]
+
+
+sanity_check_paths = {
+ 'files': ['bin/cpmd.x', 'lib/libcpmd.a'],
+ 'dirs': ['bin', 'lib'],
+}
+
+modloadmsg = 'MPI-Version: cpmd.x \n'
+
+moduleclass = 'chem'
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new file mode 100644
index 0000000000000000000000000000000000000000..635c4615c89442bc54b385eb71e2704d39c6cdd5
--- /dev/null
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@@ -0,0 +1,131 @@
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diff --git a/Golden_Repo/j/JupyterLab/401html.patch b/Golden_Repo/j/JupyterLab/401html.patch
deleted file mode 100644
index c3e71a800541a396377737132022c67a077d7564..0000000000000000000000000000000000000000
--- a/Golden_Repo/j/JupyterLab/401html.patch
+++ /dev/null
@@ -1,135 +0,0 @@
-diff -Naur jupyterlab-2.2.9.orig/401.html jupyterlab-2.2.9/401.html
---- jupyterlab-2.2.9.orig/401.html 1970-01-01 01:00:00.000000000 +0100
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