New architecture to separate software-building and analysis steps

Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.

Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.

Also, some of the software versions were also updated after some checks
with their webpages.

This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).

1 files changed, 72 insertions, 0 deletions

diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk
new file mode 100755
index 0000000..fef25c7
--- /dev/null
+++ b/reproduce/software/make/atlas-multiple.mk
@@ -0,0 +1,72 @@
+# Rules to build ATLAS shared libraries in multi-threaded mode on GNU/Linux
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be run during the initial `./configure' script. It is
+# not included into the reproduction pipe after that.
+#
+# ------------------------------------------------------------------------
+#
+# Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This Makefile is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+ORIGLDFLAGS := $(LDFLAGS)
+
+include Make.inc
+
+all: libatlas.so libf77blas.so libptf77blas.so libstcblas.so libptcblas.so \
+   libblas.so libcblas.so liblapack.so.3.6.1 libptlapack.so.3.6.1 liblapack.so.3
+
+libatlas.so: libatlas.a
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname $@ -o $@ \
+	   --whole-archive libatlas.a --no-whole-archive -lc $(LIBS)
+
+libf77blas.so : libf77blas.a libatlas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libf77blas.so.3 \
+	   -o $@ --whole-archive libf77blas.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -latlas
+
+libptf77blas.so : libptf77blas.a libatlas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libblas.so.3 \
+	   -o $@ --whole-archive libptf77blas.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -latlas
+
+libstcblas.so : libcblas.a libatlas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libstcblas.so \
+	   -o $@ --whole-archive libcblas.a -L. -latlas -lblas
+
+libptcblas.so : libptcblas.a libatlas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libcblas.so \
+	   -o $@ --whole-archive libptcblas.a -L. -latlas -lblas
+
+libblas.so: libptf77blas.so
+	ln -s $< $@
+
+libcblas.so: libptcblas.so
+	ln -s $< $@
+
+liblapack.so.3.6.1 : liblapack.a libstcblas.so libf77blas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libstlapack.so.3 \
+	   -o $@ --whole-archive liblapack.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -lstcblas -lf77blas
+
+libptlapack.so.3.6.1 : libptlapack.a libcblas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname liblapack.so.3 \
+	   -o $@ --whole-archive libptlapack.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -lcblas -lblas
+
+liblapack.so.3: libptlapack.so.3.6.1
+	ln -s $< $@