Merge pull request #17639 from lexming/20230401113716_new_pr_SoPlex221

{math}[GCC/11.3.0] SoPlex v2.2.1, ZIMPL v3.3.4, SCIP v3.2.1, GOBNILP v1.6.3
easybuilders · Apr 3, 2023 · 129620e · 129620e
2 parents 023544d + e68cd18
commit 129620e
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diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb
@@ -0,0 +1,63 @@
+easyblock = 'Bundle'
+
+name = 'GOBNILP'
+version = '1.6.3'
+_nodots_version = version.replace('.', '')
+_scip_version = '3.2.1'
+_scip_nodots_version = _scip_version.replace('.', '')
+
+homepage = 'https://www.cs.york.ac.uk/aig/sw/gobnilp/'
+description = """GOBNILP (Globally Optimal Bayesian Network learning using Integer Linear
+Programming) is a C program which learns Bayesian networks from complete
+discrete data or from local scores."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+dependencies = [
+    ('SCIP', _scip_version),
+    ('ZIMPL', '3.3.4'),
+    ('SoPlex', '2.2.1'),
+    ('GMP', '6.2.1'),
+    ('libreadline', '8.1'),
+    ('ncurses', '6.3'),
+    ('zlib', '1.2.12'),
+]
+
+default_easyblock = 'MakeCp'
+
+components = [
+    ('LOP', _scip_version, {
+        'source_urls': ['https://github.com/scipopt/scip/archive/refs/tags/'],
+        'sources': ['v%s.tar.gz' % _scip_nodots_version],
+        'patches': ['LOP-%(version)s_standalone-scip-lop-build.patch'],
+        'checksums': [
+            {'v321.tar.gz':
+                '015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb'},
+            {'LOP-3.2.1_standalone-scip-lop-build.patch':
+                'f996e56f1311fa4a613635b38969da731faf0ea9f10097799b1fa9a84598651e'},
+        ],
+        'start_dir': 'scip-%s/examples/%%(name)s' % _scip_nodots_version,
+        'buildopts': '%(namelower)s COMP=gnu OPT=opt LPS=spx2',
+        'files_to_copy': [(['bin/%(namelower)s'], 'bin')],
+    }),
+    (name, version, {
+        'source_urls': ['http://www.cs.york.ac.uk/aig/sw/gobnilp'],
+        'sources': ['%(namelower)s%(version)s.tar.gz'],
+        'patches': ['%(name)s-%(version)s_use-eb-build-env.patch'],
+        'checksums': [
+            {'gobnilp1.6.3.tar.gz':
+                'b31e5c87032f85f7404654beca47d472fd6c5dd7a5f82108bd5043ff0b8fa33c'},
+            {'GOBNILP-1.6.3_use-eb-build-env.patch':
+                '9235ec8b9d05d9915f9961d4b46c2220e0d3b75f555a226a5667dcc69d76dae9'},
+        ],
+        'start_dir': '%(namelower)s' + _nodots_version,
+        'files_to_copy': [(['bin/%(namelower)s'], 'bin')],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/gobnilp', 'bin/lop'],
+    'dirs': [],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch
@@ -0,0 +1,79 @@
+Use build environment and dependencies from EasyBuild
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- Makefile.orig	2023-03-31 18:33:07.943785000 +0200
++++ Makefile	2023-03-31 18:42:53.636293000 +0200
+@@ -5,15 +5,25 @@
+ # This file was created by editing the Makefile for the linear ordering
+ # example in SCIP
+
+-# Set the path the SCIP directory
+-SCIPDIR = scip
+-
+-# Include default project Makefile from SCIP
+-include $(SCIPDIR)/make/make.project
++# Set paths and flags to SCIP libraries
++SCIPDIR        = $(EBROOTSCIP)
++SCIPLIB        = scip
++OBJSCIPLIB     = objscip
++LPILIB         = lpispx2
++NLPILIB        = nlpi.cppad
++LPSLDFLAGS     = -lzimpl -lsoplex -lgmp -lreadline -lncurses -lz
++
++# Set paths to LOP
++LOPSRC			=	../scip-321/examples/LOP/src
++LOPOBJ			=	../scip-321/examples/LOP/obj/cons_linearordering.o
+
+ # This missing for scip < 3
+ VALGRIND = false
+
++SRCDIR = src
++OBJDIR = obj
++BINDIR = bin
++
+ # Declare the phony targets
+ .PHONY: all doxygen manual pedmanual gobnilp clean test
+
+@@ -46,7 +57,7 @@
+ MAINSRC			=	$(wildcard $(SRCDIR)/*.c)
+ MAINOBJ			=	$(notdir $(MAINSRC:.c=.o))
+
+-MAIN				=	$(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION)
++MAIN				=	$(MAINNAME)
+ MAINFILE			=	$(BINDIR)/$(MAIN)
+ ifeq ($(OSTYPE),mingw)
+ 	MAINSHORTLINK	=	$(BINDIR)/$(MAINNAME).exe
+@@ -63,7 +74,7 @@
+ LATEXCMD			=	@pdflatex -halt-on-error -interaction=errorstopmode
+
+ #Needs to appear first so that "make" makes gobnilp
+-gobnilp: $(SCIP) $(MAINFILE) $(MAINSHORTLINK)
++gobnilp: $(MAINFILE) $(MAINSHORTLINK)
+
+ #-----------------------------------------------------------------------
+ #----------------------------      All      ----------------------------
+@@ -161,19 +172,16 @@
+
+ $(MAINSHORTLINK): $(MAINFILE)
+ 		@rm -f $@
+-		@cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@)
+
+-$(MAINFILE): $(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES)
+-		@echo "-> linking $@"
+-		@$(LINKCXX) $(STATICFLAG) $(MAINOBJFILES) \
+-		$(LINKCXX_L)$(SCIPDIR)/lib $(LINKCXX_l)$(SCIPLIB)$(LINKLIBSUFFIX) \
+-                $(LINKCXX_l)$(OBJSCIPLIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(LPILIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(NLPILIB)$(LINKLIBSUFFIX) \
+-                $(OFLAGS) $(LPSLDFLAGS) \
+-		$(LDFLAGS) $(LINKCXX_o)$@
++$(MAINFILE): $(BINDIR) $(OBJDIR) $(MAINOBJFILES)
++		echo "-> linking $@"
++		$(CXX) -static $(MAINOBJFILES) $(LOPOBJ) \
++		-L$(SCIPDIR)/lib -l$(SCIPLIB) -l$(OBJSCIPLIB) -l$(LPILIB) -l$(NLPILIB) \
++		$(LDFLAGS) $(LPSLDFLAGS) -o $@
+
+ $(OBJDIR)/%.o: $(SRCDIR)/%.c
+ 		@echo "-> compiling $*.c"
+-		@$(CC) $(FLAGS) $(OFLAGS) $(BINOFLAGS) $(CFLAGS) -c -g $< $(CC_o)$@
++		@$(CC) $(CFLAGS) $(CPPFLAGS) -I$(LOPSRC) -c -g $< -o $@
+
+ $(OBJDIR):
+ 		@-mkdir -p $(OBJDIR)
diff --git a/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch b/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch
@@ -0,0 +1,41 @@
+Build LOP example standalone without triggering a full build of SCIP
+author: Alex Domingo (Vrije Universiteit Brussel)
+--- Makefile.orig	2023-03-31 18:52:55.793723000 +0200
++++ Makefile	2023-03-31 18:54:59.590029000 +0200
+@@ -29,6 +29,7 @@
+ #-----------------------------------------------------------------------------
+
+ include $(SCIPDIR)/make/make.project
++OBJDIR		=	obj
+
+ #-----------------------------------------------------------------------------
+ # Main Program
+@@ -39,9 +40,9 @@
+ MAINSRC		=	$(addprefix $(SRCDIR)/,$(MAINOBJ:.o=.c))
+ MAINDEP		=	$(SRCDIR)/depend.cmain.$(OPT)
+
+-MAIN		=	$(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION)
++MAIN		=	$(MAINNAME)
+ MAINFILE	=	$(BINDIR)/$(MAIN)
+-MAINSHORTLINK	=	$(BINDIR)/$(MAINNAME)
++MAINSHORTLINK	=	$(MAINNAME)
+ MAINOBJFILES	=	$(addprefix $(OBJDIR)/,$(MAINOBJ))
+
+ #-----------------------------------------------------------------------------
+@@ -79,7 +80,6 @@
+
+ $(MAINSHORTLINK):	$(MAINFILE)
+ 		@rm -f $@
+-		cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@)
+
+ $(OBJDIR):
+ 		@-mkdir -p $(OBJDIR)
+@@ -123,7 +123,7 @@
+
+
+ # main target
+-$(MAINFILE):	$(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES)
++$(MAINFILE):	$(BINDIR) $(OBJDIR) $(MAINOBJFILES)
+ 		@echo "-> linking $@"
+ ifeq ($(VERBOSE),true)
+ 		$(LINKCXX) $(MAINOBJFILES) \
diff --git a/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb
@@ -0,0 +1,58 @@
+easyblock = 'ConfigureMake'
+
+name = 'SCIP'
+version = '3.2.1'
+
+homepage = 'https://www.scipopt.org/'
+description = """SCIP is currently one of the fastest non-commercial solvers for mixed integer
+programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a
+framework for constraint integer programming and branch-cut-and-price. It
+allows for total control of the solution process and the access of detailed
+information down to the guts of the solver."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'scipopt'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%s.tar.gz' % version.replace('.', '')]
+checksums = ['015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb']
+
+dependencies = [
+    ('SoPlex', '2.2.1'),
+    ('ZIMPL', '3.3.4'),
+    ('GMP', '6.2.1'),
+    ('libreadline', '8.1'),
+    ('zlib', '1.2.12'),
+]
+
+skipsteps = ['configure']
+
+# prepare symlinks to installation files of dependencies
+prebuildopts = 'mkdir -p lib && '
+prebuildopts += 'ln -sf "$EBROOTSOPLEX/include" "lib/spxinc" && '
+prebuildopts += 'ln -sf "$EBROOTZIMPL/include" "lib/zimplinc" && '
+prebuildopts += 'for lib in "$EBROOTSOPLEX/lib/libsoplex*.a"; do ln -sf "$lib" "lib/"; done && '
+prebuildopts += 'for lib in "$EBROOTZIMPL/lib/libzimpl*.a"; do ln -sf "$lib" "lib/"; done && '
+
+# use SoPlex v2 as LP solver
+buildopts = 'LPS=spx2 '
+buildopts += 'MAKESOFTLINKS=false COMP=gnu OPT=opt '
+
+installopts = 'INSTALLDIR="%(installdir)s" '
+installopts += buildopts
+
+postinstallcmds = [
+    # add extra headers to installation directory
+    'cp "src/scip/misc.h" "%(installdir)s/include/scip/"',
+    # copy examples folder
+    'cp -r "examples" "%(installdir)s/"',
+]
+
+sanity_check_paths = {
+    'files': ['bin/scip', 'lib/liblpispx2.a', 'lib/libnlpi.cppad.a', 'lib/libobjscip.a', 'lib/libscip.a'],
+    'dirs': ['examples', 'include'],
+}
+
+sanity_check_commands = ["scip -h"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb
@@ -0,0 +1,38 @@
+easyblock = 'ConfigureMake'
+
+name = 'SoPlex'
+version = '2.2.1'
+
+homepage = 'https://soplex.zib.de/'
+description = """SoPlex is an optimization package for solving linear programming problems (LPs)
+based on an advanced implementation of the primal and dual revised simplex
+algorithm. It provides special support for the exact solution of LPs with
+rational input data. It can be used as a standalone solver reading MPS or LP
+format files via a command line interface as well as embedded into other
+programs via a C++ class library."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'scipopt'
+source_urls = [GITHUB_SOURCE]
+sources = ['release-%s.tar.gz' % version.replace('.', '')]
+checksums = ['6c2e89cd7c8910f8989f2a860fa0446641bd16d76eb87872f70974838486c9b1']
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('zlib', '1.2.12'),
+]
+
+skipsteps = ['configure']
+
+buildopts = "COMP=gnu OPT=opt"
+installopts = "INSTALLDIR=%(installdir)s"
+
+sanity_check_paths = {
+    'files': ['bin/soplex', 'lib/libsoplex.a'],
+    'dirs': ['include'],
+}
+
+sanity_check_commands = ["soplex | grep -q '%(name)s version %(version)s'"]
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb
@@ -0,0 +1,42 @@
+easyblock = 'MakeCp'
+
+name = 'ZIMPL'
+version = '3.3.4'
+
+homepage = 'https://zimpl.zib.de/'
+description = """ZIMPL is a little language to translate the mathematical model of a problem
+into a linear or nonlinear (mixed-) integer mathematical program expressed in
+.lp or .mps file format which can be read and (hopefully) solved by a LP or MIP
+solver."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'scipopt'
+source_urls = ['https://zimpl.zib.de/download/']
+sources = [SOURCELOWER_TGZ]
+checksums = ['3362fb21524df459723d23f6e0c122ebdd684153a9cc991a2c7f5b2752a83eb2']
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('GMP', '6.2.1'),
+    ('zlib', '1.2.12'),
+]
+
+files_to_copy = ['bin', 'lib', (['src/*.h'], 'include/zimpl')]
+
+postinstallcmds = [
+    "cd %(installdir)s/bin && ln -sf zimpl-%(version)s.* zimpl",
+    "cd %(installdir)s/lib && ln -sf libzimpl-%(version)s.*.a libzimpl.a",
+]
+
+sanity_check_paths = {
+    'files': ['bin/zimpl', 'lib/libzimpl.a'],
+    'dirs': ['include/zimpl'],
+}
+
+sanity_check_commands = ["zimpl -h"]
+
+moduleclass = 'math'