From 8d889cdc7ff83213c8f63d7915af3063ed0f3596 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 29 Apr 2019 11:26:43 +0200 Subject: [PATCH] new file: c/Cube/Cube-4.4.3-gompi-2019.03.eb new file: c/Cube/Cube-4.4.3-intel-2017a.eb new file: c/Cube/Cube-4.4.3-intel-2018a.eb new file: c/Cube/Cube-4.4.3-intel-2019.02.eb new file: c/CubeGUI/CubeGUI-4.4.3-gompi.2019.03.eb new file: c/CubeGUI/CubeGUI-4.4.3-intel-2017a.eb new file: c/CubeGUI/CubeGUI-4.4.3-intel-2018a.eb new file: c/CubeGUI/CubeGUI-4.4.3-intel-2019.02.eb new file: c/CubeLib/CubeLib-4.4.3-gompi-2019.03.eb new file: c/CubeLib/CubeLib-4.4.3-intel-2017a.eb new file: c/CubeLib/CubeLib-4.4.3-intel-2018a.eb new file: c/CubeLib/CubeLib-4.4.3-intel-2019.02.eb new file: c/CubeW/CubeW-4.4.2-gompi-2019.03.eb new file: c/CubeW/CubeW-4.4.2-intel-2017a.eb new file: c/CubeW/CubeW-4.4.2-intel-2018a.eb new file: c/CubeW/CubeW-4.4.2-intel-2019.02.eb new file: g/gompi/gompi-2019.03.eb new file: q/Qualimap/Qualimap-2.2.1-intel-2017a.eb modified: r/R/R-3.5.3-intel-2017a.eb modified: t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb new file: t/Trilinos/Trilinos-12.14.1-thyra_test.patch deleted: q/Qualimap/Qualimap-2.2.1.eb deleted: r/R/Makevars deleted: r/R/R-3.5.3-intel-2017a.old --- c/Cube/Cube-4.4.3-gompi-2019.03.eb | 23 + c/Cube/Cube-4.4.3-intel-2017a.eb | 23 + c/Cube/Cube-4.4.3-intel-2018a.eb | 23 + c/Cube/Cube-4.4.3-intel-2019.02.eb | 23 + c/CubeGUI/CubeGUI-4.4.3-gompi.2019.03.eb | 32 ++ c/CubeGUI/CubeGUI-4.4.3-intel-2017a.eb | 34 ++ c/CubeGUI/CubeGUI-4.4.3-intel-2018a.eb | 34 ++ c/CubeGUI/CubeGUI-4.4.3-intel-2019.02.eb | 34 ++ c/CubeLib/CubeLib-4.4.3-gompi-2019.03.eb | 27 + c/CubeLib/CubeLib-4.4.3-intel-2017a.eb | 29 + c/CubeLib/CubeLib-4.4.3-intel-2018a.eb | 27 + c/CubeLib/CubeLib-4.4.3-intel-2019.02.eb | 27 + c/CubeW/CubeW-4.4.2-gompi-2019.03.eb | 27 + c/CubeW/CubeW-4.4.2-intel-2017a.eb | 27 + c/CubeW/CubeW-4.4.2-intel-2018a.eb | 27 + c/CubeW/CubeW-4.4.2-intel-2019.02.eb | 27 + g/gompi/gompi-2019.03.eb | 22 + ...2.2.1.eb => Qualimap-2.2.1-intel-2017a.eb} | 13 +- r/R/Makevars | 2 - r/R/R-3.5.3-intel-2017a.eb | 29 +- r/R/R-3.5.3-intel-2017a.old | 540 ------------------ .../Trilinos-12.14.1-intel-2017c-Py-2.7.eb | 10 +- t/Trilinos/Trilinos-12.14.1-thyra_test.patch | 10 + 23 files changed, 513 insertions(+), 557 deletions(-) create mode 100644 c/Cube/Cube-4.4.3-gompi-2019.03.eb create mode 100644 c/Cube/Cube-4.4.3-intel-2017a.eb create mode 100644 c/Cube/Cube-4.4.3-intel-2018a.eb create mode 100644 c/Cube/Cube-4.4.3-intel-2019.02.eb create mode 100644 c/CubeGUI/CubeGUI-4.4.3-gompi.2019.03.eb create mode 100644 c/CubeGUI/CubeGUI-4.4.3-intel-2017a.eb create mode 100644 c/CubeGUI/CubeGUI-4.4.3-intel-2018a.eb create mode 100644 c/CubeGUI/CubeGUI-4.4.3-intel-2019.02.eb create mode 100644 c/CubeLib/CubeLib-4.4.3-gompi-2019.03.eb create mode 100644 c/CubeLib/CubeLib-4.4.3-intel-2017a.eb create mode 100644 c/CubeLib/CubeLib-4.4.3-intel-2018a.eb create mode 100644 c/CubeLib/CubeLib-4.4.3-intel-2019.02.eb create mode 100644 c/CubeW/CubeW-4.4.2-gompi-2019.03.eb create mode 100644 c/CubeW/CubeW-4.4.2-intel-2017a.eb create mode 100644 c/CubeW/CubeW-4.4.2-intel-2018a.eb create mode 100644 c/CubeW/CubeW-4.4.2-intel-2019.02.eb create mode 100644 g/gompi/gompi-2019.03.eb rename q/Qualimap/{Qualimap-2.2.1.eb => Qualimap-2.2.1-intel-2017a.eb} (73%) delete mode 100644 r/R/Makevars delete mode 100644 r/R/R-3.5.3-intel-2017a.old create mode 100644 t/Trilinos/Trilinos-12.14.1-thyra_test.patch diff --git a/c/Cube/Cube-4.4.3-gompi-2019.03.eb b/c/Cube/Cube-4.4.3-gompi-2019.03.eb new file mode 100644 index 00000000..b92f2bb1 --- /dev/null +++ b/c/Cube/Cube-4.4.3-gompi-2019.03.eb @@ -0,0 +1,23 @@ +# IT4Innovations 2019 + +easyblock = "Toolchain" + +name = 'Cube' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'gompi', 'version': '2019.03'} + +dependencies = [ + ('CubeW', '4.4.2'), + ('CubeLib', '4.4.3'), + ('CubeGUI', '4.4.3'), +] + +moduleclass = 'perf' diff --git a/c/Cube/Cube-4.4.3-intel-2017a.eb b/c/Cube/Cube-4.4.3-intel-2017a.eb new file mode 100644 index 00000000..eee5860c --- /dev/null +++ b/c/Cube/Cube-4.4.3-intel-2017a.eb @@ -0,0 +1,23 @@ +# IT4Innovations 2019 + +easyblock = "Toolchain" + +name = 'Cube' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +dependencies = [ + ('CubeW', '4.4.2'), + ('CubeLib', '4.4.3'), + ('CubeGUI', '4.4.3'), +] + +moduleclass = 'perf' diff --git a/c/Cube/Cube-4.4.3-intel-2018a.eb b/c/Cube/Cube-4.4.3-intel-2018a.eb new file mode 100644 index 00000000..69441c46 --- /dev/null +++ b/c/Cube/Cube-4.4.3-intel-2018a.eb @@ -0,0 +1,23 @@ +# IT4Innovations 2019 + +easyblock = "Toolchain" + +name = 'Cube' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +dependencies = [ + ('CubeW', '4.4.2'), + ('CubeLib', '4.4.3'), + ('CubeGUI', '4.4.3'), +] + +moduleclass = 'perf' diff --git a/c/Cube/Cube-4.4.3-intel-2019.02.eb b/c/Cube/Cube-4.4.3-intel-2019.02.eb new file mode 100644 index 00000000..be7bbeff --- /dev/null +++ b/c/Cube/Cube-4.4.3-intel-2019.02.eb @@ -0,0 +1,23 @@ +# IT4Innovations 2019 + +easyblock = "Toolchain" + +name = 'Cube' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2019.02'} + +dependencies = [ + ('CubeW', '4.4.2'), + ('CubeLib', '4.4.3'), + ('CubeGUI', '4.4.3'), +] + +moduleclass = 'perf' diff --git a/c/CubeGUI/CubeGUI-4.4.3-gompi.2019.03.eb b/c/CubeGUI/CubeGUI-4.4.3-gompi.2019.03.eb new file mode 100644 index 00000000..c1e9b33b --- /dev/null +++ b/c/CubeGUI/CubeGUI-4.4.3-gompi.2019.03.eb @@ -0,0 +1,32 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'gompi', 'version': '2019.03'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubegui-%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7', '', True), + ('CubeLib', '4.4.3') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeGUI/CubeGUI-4.4.3-intel-2017a.eb b/c/CubeGUI/CubeGUI-4.4.3-intel-2017a.eb new file mode 100644 index 00000000..3c2f0a02 --- /dev/null +++ b/c/CubeGUI/CubeGUI-4.4.3-intel-2017a.eb @@ -0,0 +1,34 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubegui-%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7', '', True), + ('CubeLib', '4.4.3') +] + +configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeGUI/CubeGUI-4.4.3-intel-2018a.eb b/c/CubeGUI/CubeGUI-4.4.3-intel-2018a.eb new file mode 100644 index 00000000..15a0385e --- /dev/null +++ b/c/CubeGUI/CubeGUI-4.4.3-intel-2018a.eb @@ -0,0 +1,34 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubegui-%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7', '', True), + ('CubeLib', '4.4.3') +] + +configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeGUI/CubeGUI-4.4.3-intel-2019.02.eb b/c/CubeGUI/CubeGUI-4.4.3-intel-2019.02.eb new file mode 100644 index 00000000..a1c213d3 --- /dev/null +++ b/c/CubeGUI/CubeGUI-4.4.3-intel-2019.02.eb @@ -0,0 +1,34 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2019.02'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubegui-%(version)s.tar.gz'] + +dependencies = [ + ('Qt', '4.8.7', '', True), + ('CubeLib', '4.4.3') +] + +configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeLib/CubeLib-4.4.3-gompi-2019.03.eb b/c/CubeLib/CubeLib-4.4.3-gompi-2019.03.eb new file mode 100644 index 00000000..97cdf272 --- /dev/null +++ b/c/CubeLib/CubeLib-4.4.3-gompi-2019.03.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'gompi', 'version': '2019.03'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubelib-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeLib/CubeLib-4.4.3-intel-2017a.eb b/c/CubeLib/CubeLib-4.4.3-intel-2017a.eb new file mode 100644 index 00000000..a11fb0fc --- /dev/null +++ b/c/CubeLib/CubeLib-4.4.3-intel-2017a.eb @@ -0,0 +1,29 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubelib-%(version)s.tar.gz'] + +configopts = '--enable-platform-mic --with-qt-specs=linux-icc-64 --with-frontend-compiler-suite=intel' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeLib/CubeLib-4.4.3-intel-2018a.eb b/c/CubeLib/CubeLib-4.4.3-intel-2018a.eb new file mode 100644 index 00000000..6248539e --- /dev/null +++ b/c/CubeLib/CubeLib-4.4.3-intel-2018a.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubelib-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeLib/CubeLib-4.4.3-intel-2019.02.eb b/c/CubeLib/CubeLib-4.4.3-intel-2019.02.eb new file mode 100644 index 00000000..d4ac38db --- /dev/null +++ b/c/CubeLib/CubeLib-4.4.3-intel-2019.02.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.4.3' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2019.02'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubelib-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeW/CubeW-4.4.2-gompi-2019.03.eb b/c/CubeW/CubeW-4.4.2-gompi-2019.03.eb new file mode 100644 index 00000000..6c925abb --- /dev/null +++ b/c/CubeW/CubeW-4.4.2-gompi-2019.03.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeW' +version = '4.4.2' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'gompi', 'version': '2019.03'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubew-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeW/CubeW-4.4.2-intel-2017a.eb b/c/CubeW/CubeW-4.4.2-intel-2017a.eb new file mode 100644 index 00000000..62b8dfc0 --- /dev/null +++ b/c/CubeW/CubeW-4.4.2-intel-2017a.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeW' +version = '4.4.2' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubew-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeW/CubeW-4.4.2-intel-2018a.eb b/c/CubeW/CubeW-4.4.2-intel-2018a.eb new file mode 100644 index 00000000..d622ffb7 --- /dev/null +++ b/c/CubeW/CubeW-4.4.2-intel-2018a.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeW' +version = '4.4.2' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubew-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/c/CubeW/CubeW-4.4.2-intel-2019.02.eb b/c/CubeW/CubeW-4.4.2-intel-2019.02.eb new file mode 100644 index 00000000..b961a0ba --- /dev/null +++ b/c/CubeW/CubeW-4.4.2-intel-2019.02.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2019 + +easyblock = 'EB_Score_minus_P' + +name = 'CubeW' +version = '4.4.2' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """Cube, which is used as performance report explorer for Scalasca and + Score-P, is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system + resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree + can be collapsed or expanded to achieve the desired level of granularity.""" + +toolchain = {'name': 'intel', 'version': '2019.02'} +toolchainopts = {'optarch': False} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/'] +sources = ['cubew-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + + +moduleclass = 'perf' diff --git a/g/gompi/gompi-2019.03.eb b/g/gompi/gompi-2019.03.eb new file mode 100644 index 00000000..bbf41874 --- /dev/null +++ b/g/gompi/gompi-2019.03.eb @@ -0,0 +1,22 @@ +# IT4Innovations 2019 + +easyblock = "Toolchain" + +name = 'gompi' +version = '2019.03' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': ''} + +gccver = '6.3.0-2.27' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC and binutils + ('OpenMPI', '4.0.0', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' diff --git a/q/Qualimap/Qualimap-2.2.1.eb b/q/Qualimap/Qualimap-2.2.1-intel-2017a.eb similarity index 73% rename from q/Qualimap/Qualimap-2.2.1.eb rename to q/Qualimap/Qualimap-2.2.1-intel-2017a.eb index e5ea829a..7dda3157 100644 --- a/q/Qualimap/Qualimap-2.2.1.eb +++ b/q/Qualimap/Qualimap-2.2.1-intel-2017a.eb @@ -1,6 +1,6 @@ # IT4Innovations 2019 -easyblock = "CmdCp" +easyblock = "Tarball" name = 'Qualimap' version = '2.2.1' @@ -13,21 +13,18 @@ description = """Qualimap 2 is a platform-independent application written in toolchain = {'name': 'intel', 'version': '2017a'} -sources = ['qualimap_v2.2.1.zip'] +sources = ['qualimap_v%(version)s.zip'] source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads'] dependencies = [ - ('Java', '1.8.0_121', '', True), ('R', '3.5.3'), ] -cmds_map = [('.*', "./compile.sh")] - -files_to_copy = [(['output/bazel'], 'bin')] +modextrapaths = {"PATH": '.'} sanity_check_paths = { - 'files': ['bin/bazel'], - 'dirs': [], + 'files': ['qualimap'], + 'dirs': ['lib', 'scripts', 'species'], } moduleclass = 'bio' diff --git a/r/R/Makevars b/r/R/Makevars deleted file mode 100644 index 12172cf4..00000000 --- a/r/R/Makevars +++ /dev/null @@ -1,2 +0,0 @@ -# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' -PKG_CXXFLAGS = -wd308 diff --git a/r/R/R-3.5.3-intel-2017a.eb b/r/R/R-3.5.3-intel-2017a.eb index 439f0aa2..0feefdf3 100644 --- a/r/R/R-3.5.3-intel-2017a.eb +++ b/r/R/R-3.5.3-intel-2017a.eb @@ -707,9 +707,7 @@ exts_list = [ ('cgdsr', '1.2.10', { 'checksums': ['43bc02fb33c371464f9407d5e5e6419527e9360e3e394343862cca0aebe1d0f7'], }), - ('R.utils', '2.6.0', { - 'checksums': ['5d64993d1209b512a4e97f2edecdbc185f4a369ee5fa2e334ed2cf017486470e'], - }), + ('R.utils', '2.8.0'), ('R.matlab', '3.6.1', { 'checksums': ['1032579fd152d419eaf1f69bf6035fba7a71ef26e76136c48a6fc619e3887804'], }), @@ -2091,7 +2089,30 @@ exts_list = [ ('rtracklayer', '1.42.2'), ('BSgenome', '1.50.0'), ('gsmoothr', '0.1.7'), - ('limma', '3.14.4'), + ('limma', '3.38.3'), + ('edgeR', '3.24.3'), + ('DNAcopy', '1.56.0'), + ('AnnotationDbi', '1.44.0'), + ('annotate', '1.60.1'), + ('genefilter', '1.64.0'), + ('affyio', '1.52.0'), + ('BiocManager', '1.30.4'), + ('preprocessCore', '1.44.0'), + ('affy', '1.60.0'), + ('vsn', '3.50.0'), + ('Ringo', '1.46.0'), + ('R.filesets', '2.13.0'), + ('R.devices', '2.16.0'), + ('aroma.light', '3.12.0'), + ('PSCBS', '0.64.0'), + ('aroma.core', '3.1.3'), + ('R.huge', '0.9.0'), + ('aroma.apd', '0.6.0'), + ('aroma.affymetrix', '3.1.1'), + ('truncnorm', '1.0-8'), + ('Rsolnp', '1.16'), + ('Repitools', '1.28.0'), + ('rtracklayer', '1.42.2'), ] moduleclass = 'lang' diff --git a/r/R/R-3.5.3-intel-2017a.old b/r/R/R-3.5.3-intel-2017a.old deleted file mode 100644 index ddd36ce6..00000000 --- a/r/R/R-3.5.3-intel-2017a.old +++ /dev/null @@ -1,540 +0,0 @@ -# IT4Innovations 2019 - -name = 'R' -version = '3.5.3' - -homepage = 'http://www.r-project.org/' -description = """R is a free software environment for statistical computing and graphics.""" - -toolchain = {'name': 'intel', 'version': '2017a'} - -sources = [SOURCE_TAR_GZ] -source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] - -preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' -configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" -# Actually use Tcl/Tk -configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' -# Enable graphics capabilities for plotting. -configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" -# some recommended packages may fail in a parallel build (e.g. Matrix), -# and we're installing them anyway below -configopts += " --with-recommended-packages=no" - -dependencies = [ - ('cairo', '1.14.8', '', True), - ('libreadline', '7.0', '', True), - ('ncurses', '6.0', '', True), - ('bzip2', '1.0.6', '', True), - ('XZ', '5.2.3', '', True), - ('zlib', '1.2.11', '', True), - ('SQLite', '3.17.0', '', True), - ('PCRE', '8.40', '', True), - ('libpng', '1.6.29', '', True), # for plotting in R - ('libjpeg-turbo', '1.5.1', '', True), # for plottting in R - ('LibTIFF', '4.0.7', '', True), - # Java bindings are built if Java is found, might as well provide it - ('Java', '1.8.0_144', '', True), - ('Tcl', '8.6.6', '', True), # for tcltk - ('Tk', '8.6.6', '', True), # for tcltk - ('cURL', '7.53.1', '', True), # for RCurl - ('libxml2', '2.9.4', '', True), # for XML - ('GDAL', '2.1.3', '-Python-2.7.13', True), # for rgdal - ('PROJ', '4.9.3'), # for rgdal - ('GMP', '6.1.2', '', True), # for igraph - ('NLopt', '2.4.2'), # for nloptr - ('FFTW', '3.3.6'), # for fftw - ('libsndfile', '1.0.28'), # for seewave - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.0.2h'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { - 'source_urls': [ - # package archive - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', - 'http://cran.r-project.org/src/contrib/', # current version of packages - # mirror alternative for current packages - 'http://cran.freestatistics.org/src/contrib', - 'http://www.bioconductor.org/packages/release/bioc/src/contrib/' - ], - 'source_tmpl': name_tmpl, -} - -# !! order of packages is important !! -# packages updated on May 11th 2017 -exts_list = [ - # default libraries, only here to sanity check their presence - 'base', - 'datasets', - 'graphics', - 'grDevices', - 'grid', - 'methods', - 'splines', - 'stats', - 'stats4', - 'tools', - 'utils', - # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', ext_options), - ('abind', '1.4-5', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', dict(ext_options.items() + - [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.4-1', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '4.1.1', ext_options), - ('bootstrap', '2017.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.5', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.6', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-25', ext_options), - ('mime', '0.5', ext_options), - ('markdown', '0.8', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-10', ext_options), - ('mclust', '5.3', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.4', ext_options), - ('som', '0.3-5.1', ext_options), - ('SuppDists', '1.1-9.4', ext_options), - ('stabledist', '0.7-1', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-6', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-3', ext_options), - ('BH', '1.62.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.9', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('backports', '1.0.5', ext_options), - ('checkmate', '1.8.2', ext_options), - ('Rcpp', '0.12.10', ext_options), - ('cubature', '1.3-8', ext_options), - ('DEoptimR', '1.0-8', ext_options), - ('digest', '0.6.12', ext_options), - ('fastmatch', '1.1-0', ext_options), - ('ffbase', '0.12.3', ext_options), - ('iterators', '1.0.8', ext_options), - ('maps', '3.1.1', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.4-0', ext_options), - ('subplex', '1.2-2', ext_options), - ('stringi', '1.1.5', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.2.0', ext_options), - ('evaluate', '0.10', ext_options), - ('logspline', '2.1.9', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.9-4', ext_options), - ('plotrix', '3.6-5', ext_options), - ('randomForest', '4.6-12', ext_options), - ('scatterplot3d', '0.3-40', ext_options), - ('SparseM', '1.77', ext_options), - ('tripack', '1.3-8', ext_options), - ('irace', '2.3', ext_options), - ('rJava', '0.9-8', ext_options), - ('lattice', '0.20-35', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-28', ext_options), - ('Matrix', '1.2-10', ext_options), - ('png', '0.1-7', ext_options), - ('RcppArmadillo', '0.7.800.2.0', ext_options), - ('plyr', '1.8.4', ext_options), - ('pROC', '1.9.1', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.11', ext_options), - ('fail', '1.3', ext_options), - ('rlecuyer', '0.3-4', ext_options), - ('snow', '0.4-2', ext_options), - ('MASS', '7.3-47', ext_options), - ('tree', '1.0-37', ext_options), - ('pls', '2.6-0', ext_options), - ('class', '7.3-14', ext_options), - ('e1071', '1.6-8', ext_options), - ('nnet', '7.3-12', ext_options), - ('nlme', '3.1-131', ext_options), - ('minqa', '1.2.4', ext_options), - ('RcppEigen', '0.3.3.3.0', ext_options), - ('MatrixModels', '0.4-1', ext_options), - ('quantreg', '5.33', ext_options), - ('mgcv', '1.8-17', ext_options), - ('colorspace', '1.3-2', ext_options), - ('robustbase', '0.92-7', ext_options), - ('sp', '1.2-4', ext_options), - ('zoo', '1.8-0', ext_options), - ('lmtest', '0.9-35', ext_options), - ('vcd', '1.4-3', ext_options), - ('snowfall', '1.84-6.1', ext_options), - ('rpart', '4.1-11', ext_options), - ('survival', '2.41-3', ext_options), - ('mice', '2.30', ext_options), - ('urca', '1.3-0', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.22', ext_options), - ('akima', '0.6-2', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-19', ext_options), - ('mixtools', '1.1.0', ext_options), - ('cluster', '2.0.6', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.19-1', ext_options), - ('codetools', '0.2-15', ext_options), - ('foreach', '1.4.3', ext_options), - ('doMC', '1.3.4', ext_options), - ('DBI', '0.6-1', ext_options), - ('foreign', '0.8-68', ext_options), - ('gam', '1.14-4', ext_options), - ('gamlss.data', '5.0-0', ext_options), - ('gamlss.dist', '5.0-0', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-15', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.23-1', ext_options), - ('quantmod', '0.4-8', ext_options), - ('mnormt', '1.5-5', ext_options), - ('mvtnorm', '1.0-6', ext_options), - ('pcaPP', '1.9-61', ext_options), - ('numDeriv', '2016.8-1', ext_options), - ('lava', '1.5', ext_options), - ('prodlim', '1.6.1', ext_options), - ('pscl', '1.4.9', ext_options), - ('memoise', '1.1.0', ext_options), - ('plogr', '0.1-1', ext_options), - ('RSQLite', '1.1-2', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-4', ext_options), - ('sfsmisc', '1.1-0', ext_options), - ('spatial', '7.3-11', ext_options), - ('VGAM', '1.0-3', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.8-2', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.14', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-40', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.1', ext_options), - ('R.oo', '1.21.0', ext_options), - ('cgdsr', '1.2.6', ext_options), - ('R.utils', '2.5.0', ext_options), - ('R.matlab', '3.6.1', ext_options), - ('gbm', '2.1.3', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-1', ext_options), - ('acepack', '1.4.1', ext_options), - ('reshape2', '1.4.2', ext_options), - ('gtable', '0.2.0', ext_options), - ('munsell', '0.4.3', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.4.1', ext_options), - ('proto', '1.0.0', ext_options), - ('lazyeval', '0.2.0', ext_options), - ('assertthat', '0.2.0', ext_options), - ('tibble', '1.3.0', ext_options), - ('ggplot2', '2.2.1', ext_options), - ('gridExtra', '2.2.1', ext_options), - ('chron', '2.3-50', ext_options), - ('data.table', '1.10.4', ext_options), - ('viridisLite', '0.2.0', ext_options), - ('viridis', '0.4.0', ext_options), - ('yaml', '2.1.14', ext_options), - ('jsonlite', '1.4', ext_options), - ('htmltools', '0.3.6', ext_options), - ('htmlwidgets', '0.8', ext_options), - ('knitr', '1.16', ext_options), - ('htmlTable', '1.9', ext_options), - ('Hmisc', '4.0-3', ext_options), - ('fastcluster', '1.1.22', ext_options), - ('registry', '0.3', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doParallel', '1.0.10', ext_options), - ('gridBase', '0.4-7', ext_options), - ('NMF', '0.20.6', ext_options), - ('irlba', '2.1.2', ext_options), - ('igraph', '1.0.1', ext_options), - ('GeneNet', '1.2.13', ext_options), - ('ape', '4.1', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '3.0.1', ext_options), - ('ROCR', '1.0-7', ext_options), - ('httpuv', '1.3.3', ext_options), - ('R6', '2.2.1', ext_options), - ('rjson', '0.2.15', ext_options), - ('sourcetools', '0.1.6', ext_options), - ('shiny', '1.0.3', ext_options), - ('seqinr', '3.3-6', ext_options), - ('LearnBayes', '2.15', ext_options), - ('deldir', '0.1-14', ext_options), - ('gmodels', '2.16.2', ext_options), - ('expm', '0.999-2', ext_options), - ('spdep', '0.6-13', ext_options), - ('dplyr', '0.5.0', ext_options), - ('vegan', '2.4-3', ext_options), - ('adegenet', '2.0.1', ext_options), - ('prettyunits', '1.0.2', ext_options), - ('progress', '1.1.2', ext_options), - ('rncl', '0.8.2', ext_options), - ('XML', '3.98-1.7', ext_options), - ('crayon', '1.3.2', ext_options), - ('praise', '1.0.0', ext_options), - ('testthat', '1.0.2', ext_options), - ('rprojroot', '1.2', ext_options), - ('rmarkdown', '1.5', ext_options), - ('curl', '2.6', ext_options), - ('openssl', '0.9.6', ext_options), - ('httr', '1.2.1', ext_options), - ('reshape', '0.8.6', ext_options), - ('xml2', '1.1.1', ext_options), - ('bold', '0.4.0', ext_options), - ('triebeard', '0.3.0', ext_options), - ('urltools', '1.6.0', ext_options), - ('httpcode', '0.2.0', ext_options), - ('crul', '0.3.6', ext_options), - ('rredlist', '0.3.0', ext_options), - ('rentrez', '1.0.4', ext_options), - ('rotl', '3.0.3', ext_options), - ('solrium', '0.4.0', ext_options), - ('ritis', '0.5.4', ext_options), - ('worrms', '0.1.0', ext_options), - ('natserv', '0.1.4', ext_options), - ('taxize', '0.8.4', ext_options), - ('tidyr', '0.6.2', ext_options), - ('uuid', '0.1-2', ext_options), - ('RNeXML', '2.0.7', ext_options), - ('phylobase', '0.8.4', ext_options), - ('adephylo', '1.1-10', ext_options), - ('animation', '2.5', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.19', dict(ext_options.items() + \ - [('patches', ['bigmemory-4.5.19_icpc-wd308.patch'])])), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.5-8', ext_options), - ('dismo', '1.1-4', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.4', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '8.10', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.6', ext_options), - ('glmnet', '2.0-10', ext_options), - ('rgl', '0.98.1', ext_options), - ('labdsv', '1.8-0', ext_options), - ('stabs', '0.6-2', ext_options), - ('modeltools', '0.2-21', ext_options), - ('strucchange', '1.5-1', ext_options), - ('TH.data', '1.0-8', ext_options), - ('multcomp', '1.4-6', ext_options), - ('coin', '1.1-3', ext_options), - ('party', '1.2-3', ext_options), - ('mboost', '2.8-0', ext_options), - ('msm', '1.6.4', ext_options), - ('nor1mix', '1.2-2', ext_options), - ('np', '0.60-3', ext_options), - ('polynom', '1.3-9', ext_options), - ('polspline', '1.1.12', ext_options), - ('rms', '5.1-1', ext_options), - ('RWekajars', '3.9.1-3', ext_options), - ('RWeka', '0.4-34', ext_options), - ('slam', '0.1-40', ext_options), - ('tm', '0.7-1', ext_options), - ('TraMineR', '2.0-5', ext_options), - ('chemometrics', '1.4.2', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-6', ext_options), - ('statmod', '1.4.29', ext_options), - ('miscTools', '0.6-22', ext_options), - ('maxLik', '1.3-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('optparse', '1.3.2', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), - ('locfit', '1.5-9.1', ext_options), - ('GGally', '1.3.0', ext_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), - ('matrixStats', '0.52.2', ext_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '3.0', ext_options), - ('nloptr', '1.0.4', ext_options), - ('lme4', '1.1-13', ext_options), - ('pbkrtest', '0.4-7', ext_options), - ('car', '2.1-4', ext_options), - ('flashClust', '1.01-2', ext_options), - ('FactoMineR', '1.35', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-14', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-7', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-10', ext_options), - ('BiasedUrn', '1.07', ext_options), - ('TeachingDemos', '2.10', ext_options), - ('kohonen', '3.0.2', dict(ext_options.items() + \ - [('patches', ['kohonen-3.0.2_icpc-wd308.patch'])])), - ('base64', '2.0', ext_options), - ('doRNG', '1.6.6', ext_options), - ('nleqslv', '3.2', ext_options), - ('Deriv', '3.8.0', ext_options), - ('RGCCA', '2.1.2', ext_options), - ('pheatmap', '1.0.8', ext_options), - ('openxlsx', '4.0.17', ext_options), - ('pvclust', '2.0-0', ext_options), - ('RCircos', '1.2.0', ext_options), - ('lambda.r', '1.1.9', ext_options), - ('futile.options', '1.0.0', ext_options), - ('futile.logger', '1.4.3', ext_options), - ('VennDiagram', '1.6.17', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), - ('forecast', '8.0', dict(ext_options.items() + \ - [('patches', ['forecast-6.1_icpc-wd308.patch'])])), - ('fma', '2.3', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), - ('maptools', '0.9-2', ext_options), - ('tensor', '1.5', ext_options), - ('polyclip', '1.6-1', ext_options), - ('goftest', '1.1-1', ext_options), - ('spatstat.utils', '1.6-0', ext_options), - ('spatstat', '1.51-0', ext_options), - ('rgdal', '1.2-7', ext_options), - ('gdalUtils', '2.0.1.7', ext_options), - ('pracma', '2.0.4', ext_options), - ('RCurl', '1.95-4.8', ext_options), - ('bio3d', '2.3-1', ext_options), - ('AUC', '0.3.0', ext_options), - ('interpretR', '0.2.4', ext_options), - ('cvAUC', '1.1.0', ext_options), - ('SuperLearner', '2.0-21', ext_options), - ('lpSolve', '5.6.13', ext_options), - ('mediation', '4.4.5', ext_options), - ('ModelMetrics', '1.1.0', ext_options), - ('caret', '6.0-76', ext_options), - ('adabag', '4.1', ext_options), - ('parallelMap', '1.3', ext_options), - ('ParamHelpers', '1.10', ext_options), - ('ggvis', '0.4.3', ext_options), - ('mlr', '2.11', ext_options), - ('unbalanced', '2.0', ext_options), - ('RSNNS', '0.4-9', ext_options), - ('abc.data', '1.0', ext_options), - ('abc', '2.1', ext_options), - ('lhs', '0.14', ext_options), - ('tensorA', '0.36', ext_options), - ('EasyABC', '1.5', ext_options), - ('shape', '1.4.2', ext_options), - ('whisker', '0.3-2', ext_options), - ('rstudioapi', '0.6', ext_options), - ('commonmark', '1.2', ext_options), - ('desc', '1.1.0', ext_options), - ('roxygen2', '6.0.1', ext_options), - ('git2r', '0.18.0', ext_options), - ('rversions', '1.0.3', ext_options), - ('withr', '1.0.2', ext_options), - ('devtools', '1.13.0', ext_options), - ('Rook', '1.1-1', ext_options), - ('Cairo', '1.5-9', dict(ext_options.items() + - [('patches', ['Cairo-1.5-9.patch'])])), - ('RMTstat', '0.3', ext_options), - ('Lmoments', '1.2-3', ext_options), - ('distillery', '1.0-2', ext_options), - ('extRemes', '2.0-8', ext_options), - ('pixmap', '0.4-11', ext_options), - ('tkrplot', '0.0-23', ext_options), - ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-10', dict(ext_options.items() + \ - [('patches', ['multicool-0.1-10_icpc-wd308.patch'])])), - ('ks', '1.10.6', ext_options), - ('logcondens', '2.1.5', ext_options), - ('Iso', '0.0-17', ext_options), - ('penalized', '0.9-50', ext_options), - ('clusterRepro', '0.5-1.1', ext_options), - ('randomForestSRC', '2.4.2', ext_options), - ('sm', '2.2-5.4', ext_options), - ('psych', '1.7.5', ext_options), - ('pbivnorm', '0.6.0', ext_options), - ('lavaan', '0.5-23.1097', ext_options), - ('matrixcalc', '1.0-3', ext_options), - ('arm', '1.9-3', ext_options), - ('mi', '1.0', ext_options), - ('visNetwork', '1.0.3', ext_options), - ('rgexf', '0.15.3', ext_options), - ('influenceR', '0.1.0', ext_options), - ('DiagrammeR', '0.9.0', ext_options), - ('sem', '3.1-9', ext_options), - ('jpeg', '0.1-8', ext_options), - ('network', '1.13.0', ext_options), - ('statnet.common', '3.3.0', ext_options), - ('sna', '2.4', ext_options), - ('glasso', '1.8', dict(ext_options.items() + \ - [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), - ('huge', '1.2.7', ext_options), - ('d3Network', '0.5.2.1', ext_options), - ('ggm', '2.3', ext_options), - ('qgraph', '1.4.3', ext_options), - ('diveRsity', '1.9.90', ext_options), - ('doSNOW', '1.0.14', ext_options), - ('phangorn', '2.2.0', ext_options), - ('geepack', '1.2-1', ext_options), - ('lubridate', '1.6.0', ext_options), - ('biom', '0.3.12', ext_options), - ('pim', '2.0.1', ext_options), - ('minpack.lm', '1.2-1', ext_options), - ('rootSolve', '1.7', ext_options), - ('diagram', '1.6.3', ext_options), - ('FME', '1.3.5', ext_options), - ('bmp', '0.2', ext_options), - ('readbitmap', '0.1-4', ext_options), - ('purrr', '0.2.2', ext_options), - ('downloader', '0.4', ext_options), - ('imager', '0.40.2', dict(ext_options.items() + \ - [('patches', ['imager-0.40.2_icpc-wd308.patch'])])), - ('pracma', '2.0.4', ext_options), - ('signal', '0.7-6', ext_options), - ('tuneR', '1.3.2', ext_options), - ('pastecs', '1.3-18', ext_options), - ('audio', '0.1-5', ext_options), - ('fftw', '1.0-4', ext_options), - ('seewave', '2.0.5', ext_options), - ('gsw', '1.0-3', ext_options), - ('oce', '0.9-21', ext_options), - ('ineq', '0.2-13', ext_options), - ('soundecology', '1.3.2', ext_options), - # ('KFAS', '1.2.9', ext_options), - # qualimap dependencies - ('Biobase', '2.42.0', ext_options), - ('NOISeq', '2.26.1', ext_options), -] - -moduleclass = 'lang' diff --git a/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb b/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb index c55898bd..2e907762 100644 --- a/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb +++ b/t/Trilinos/Trilinos-12.14.1-intel-2017c-Py-2.7.eb @@ -16,12 +16,13 @@ source_urls = ['https://github.com/trilinos/Trilinos/archive/'] sources = ['%(namelower)s-release-12-14-1.tar.gz'] patches = [ ('Trilinos-12.14.1-epetra_hdf5.patch'), + ('Trilinos-12.14.1-thyra_test.patch'), # ('Trilinos-12.12.1_fix-CEpetra-LAPACK.patch', 'packages/CTrilinos'), # 'Trilinos-12.12.1_muelu-fix-function-signature.patch', # 'Trilinos-12.12.1_fix-Sundance.patch', ] -configopts = '-DThyraEpetraAdapters_TestThyraDebugHang_MPI_4_DISABLE=ON ' +configopts = '-DThyraEpetraAdapters_THYRADEBUGHANG_ENABLE=OFF ' configopts += '-DEpetraExt_ENABLE_HDF5=OFF ' builddependencies = [ @@ -33,8 +34,8 @@ dependencies = [ ('Py', '2.7', '', True), ('Boost', '1.68.0', versionsuffix), ('SCOTCH', '6.0.6'), - ('SuiteSparse', '5.4.0', '-ParMETIS-4.0.3'), - ('ParMETIS', '4.0.3'), + ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), + ('METIS', '5.1.0', '', True), ('netCDF', '4.6.1'), ('MATIO', '1.5.12', '', ('GCCcore', '6.3.0')), ('GLM', '0.9.9.0', '', ('GCCcore', '6.3.0')), @@ -44,6 +45,9 @@ dependencies = [ # disable TrilinosCouplings package, doesn't build correctly (examples fail to compile) skip_exts = ['TrilinosCouplings'] + +prebuildopts = "find packages/amesos2/test/solvers -type f -exec sed -i.bak 's/-lifcoremt_pic/-lifcoremt_pic -lcamd -lccolamd/g' {} + && " + # workaround for Teuchos.pyc not being found during "make install" # see https://github.com/trilinos/Trilinos/issues/1749 preinstallopts = "cd %(builddir)s/trilinos-%(version)s-Source/packages/PyTrilinos/src/PyTrilinos && " diff --git a/t/Trilinos/Trilinos-12.14.1-thyra_test.patch b/t/Trilinos/Trilinos-12.14.1-thyra_test.patch new file mode 100644 index 00000000..b9cfa0a4 --- /dev/null +++ b/t/Trilinos/Trilinos-12.14.1-thyra_test.patch @@ -0,0 +1,10 @@ +--- packages/thyra/adapters/epetra/test/CMakeLists.txt.orig 2019-04-26 08:08:36.271709024 +0200 ++++ packages/thyra/adapters/epetra/test/CMakeLists.txt 2019-04-26 08:08:17.591718590 +0200 +@@ -12,6 +12,7 @@ + + TRIBITS_ADD_EXECUTABLE_AND_TEST( + TestThyraDebugHang ++ EXCLUDE_IF_NOT_TRUE ${PACKAGE_NAME}_THYRADEBUGHANG_ENABLE + SOURCES + TestThyraDebugHang.cpp + ${TEUCHOS_STD_PARALLEL_UNIT_TEST_MAIN}