Subject: [bug#56831] [PATCH v2] gnu: mumps: Update to 5.5.1

From: FELŠÖCI Marek <[email-masked]>
Date: Thu, 4 Aug 2022 19:08:39 +0200

* gnu/packages/maths.scm (mumps): Update to 5.5.1. Stop applying patches as the build configuration has been updated upstream. Allow for further optimized BLR compression by specifying the -DBLR_MT build option.
* gnu/packages/patches/mumps-build-parallelism.patch: File removed.
* gnu/packages/patches/mumps-shared-libseq.patch: File removed.
* gnu/packages/patches/mumps-shared-mumps.patch: File removed.
* gnu/packages/patches/mumps-shared-pord.patch: File removed.
---
 gnu/local.mk                                  |   4 -
 gnu/packages/maths.scm                        | 131 ++++++++++--------
 .../patches/mumps-build-parallelism.patch     |  13 --
 .../patches/mumps-shared-libseq.patch         |  42 ------
 gnu/packages/patches/mumps-shared-mumps.patch |  63 ---------
 gnu/packages/patches/mumps-shared-pord.patch  |  77 ----------
 6 files changed, 72 insertions(+), 258 deletions(-)
 delete mode 100644 gnu/packages/patches/mumps-build-parallelism.patch
 delete mode 100644 gnu/packages/patches/mumps-shared-libseq.patch
 delete mode 100644 gnu/packages/patches/mumps-shared-mumps.patch
 delete mode 100644 gnu/packages/patches/mumps-shared-pord.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 0e8b7b0447..88100416d5 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1525,10 +1525,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/mosaicatcher-unbundle-htslib.patch	\
   %D%/packages/patches/mrrescue-support-love-11.patch		\
   %D%/packages/patches/mtools-mformat-uninitialized.patch	\
-  %D%/packages/patches/mumps-build-parallelism.patch		\
-  %D%/packages/patches/mumps-shared-libseq.patch		\
-  %D%/packages/patches/mumps-shared-mumps.patch			\
-  %D%/packages/patches/mumps-shared-pord.patch			\
   %D%/packages/patches/mupen64plus-ui-console-notice.patch	\
   %D%/packages/patches/mupen64plus-video-z64-glew-correct-path.patch    \
   %D%/packages/patches/musl-cross-locale.patch			\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 789de8f500..27103d876f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -53,6 +53,7 @@
 ;;; Copyright © 2022 Zhu Zihao <[email-masked]>
 ;;; Copyright © 2022 Sharlatan Hellseher <[email-masked]>
 ;;; Copyright © 2022 Philip McGrath <[email-masked]>
+;;; Copyright © 2022 Marek Felšöci <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3735,7 +3736,7 @@ language understood by many solvers.")
 (define-public mumps
   (package
     (name "mumps")
-    (version "5.2.1")
+    (version "5.5.1")
     (source
      (origin
        (method url-fetch)
@@ -3743,11 +3744,7 @@ language understood by many solvers.")
                            version ".tar.gz"))
        (sha256
         (base32
-         "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
-       (patches (search-patches "mumps-build-parallelism.patch"
-                                "mumps-shared-libseq.patch"
-                                "mumps-shared-mumps.patch"
-                                "mumps-shared-pord.patch"))))
+         "05gs2i8b76m9flm1826fxpyfnwibjjawbmfza3ylrvj7zaag5gqs"))))
     (build-system gnu-build-system)
     (inputs
      (list gfortran
@@ -3764,58 +3761,71 @@ language understood by many solvers.")
        #:phases
        (modify-phases %standard-phases
          (replace 'configure
-          (lambda* (#:key inputs #:allow-other-keys)
+          (lambda* (#:key inputs outputs #:allow-other-keys)
             (call-with-output-file "Makefile.inc"
               (lambda (port)
                 (format port "
-PLAT         =
-LIBEXT       = .a
-OUTC         = -o
-OUTF         = -o
-RM           = rm -f~:[
-CC           = gcc
-FC           = gfortran
-FL           = gfortran
-INCSEQ       = -I$(topdir)/libseq
-LIBSEQ       = $(topdir)/libseq/libmpiseq.a
-LIBSEQNEEDED = libseqneeded~;
-CC           = mpicc
-FC           = mpifort
-FL           = mpifort~]
-AR           = ar vr # rules require trailing space, ugh...
-RANLIB       = ranlib
-BLASDIR      = ~a
-LIBBLAS      = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
-SCALAPDIR    = ~a
-SCALAP       = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
-LIBOTHERS    = -pthread
-CDEFS        = -DAdd_
-PIC          = -fPIC
-OPTF         = -O2 -DALLOW_NON_INIT -fallow-argument-mismatch $(PIC)
-OPTL         = -O2 $(PIC)
-OPTC         = -O2 $(PIC)
-INCS         = $(INCSEQ)
-LIBS         = $(SCALAP) $(LIBSEQ)
-LPORDDIR     = $(topdir)/PORD/lib
-IPORD        = -I$(topdir)/PORD/include
-LPORD        = $(LPORDDIR)/libpord.a
-ORDERINGSF   = -Dpord~@[
-METISDIR     = ~a
-IMETIS       = -I$(METISDIR)/include
-LMETIS       = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
-ORDERINGSF  += -Dmetis~]~@[~:{
-SCOTCHDIR    = ~a
-ISCOTCH      = -I$(SCOTCHDIR)/include
-LSCOTCH      = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
-ORDERINGSF  += ~a~}~]
-ORDERINGSC   = $(ORDERINGSF)
-LORDERINGS   = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
-IORDERINGSF  = $(ISCOTCH)
-IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
-                        (->bool (which "mpicc"))  ;MPI support enabled?
-                        (dirname
-                         (dirname (search-input-file inputs "/include/cblas.h")))
+PLAT          =
+LIBEXT        = .a
+LIBEXT_SHARED = .so
+OUTC          = -o
+OUTF          = -o
+BLASDIR       = ~a
+LIBBLAS       = -Wl,-rpath=$(BLASDIR)/lib -Wl,-rpath='$$ORIGIN'
+LIBBLAS      += -L$(BLASDIR)/lib
+LIBBLAS      += -lopenblas~@[
+SCALAPDIR     = ~a
+SCALAP        = -Wl,-rpath=$(SCALAPDIR)/lib -Wl,-rpath='$$ORIGIN'
+SCALAP       += -L$(SCALAPDIR)/lib -lscalapack~]
+RM            = rm -f~:[
+CC            = gcc
+FC            = gfortran
+FL            = gfortran
+INCSEQ        = -I$(topdir)/libseq
+LIBSEQ        = $(LAPACK) -L$(topdir)/libseq -lmpiseq
+LIBSEQNEEDED  = libseqneeded
+INCS          = $(INCSEQ)
+LIBS          = $(LIBSEQ)~;
+CC            = mpicc
+FC            = mpifort
+FL            = mpifort
+INCPAR        =
+LIBPAR        = $(SCALAP) $(LAPACK)
+LIBSEQNEEDED  = 
+INCS          = $(INCPAR)
+LIBS          = $(LIBPAR)~]
+AR            = ar vr # rules require trailing space, ugh...
+RANLIB        = ranlib
+LIBOTHERS     = -pthread
+CDEFS         = -DAdd_
+PIC           = -fPIC
+FPIC_OPT      = $(PIC)
+RPATH_OPT     = -Wl,-rpath,~a/lib
+OPTF          = -O2 -fopenmp -DALLOW_NON_INIT -DBLR_MT
+OPTF         += -fallow-argument-mismatch $(PIC)
+OPTL          = -O2 -fopenmp $(PIC)
+OPTC          = -O2 -fopenmp $(PIC)
+LPORDDIR      = $(topdir)/PORD/lib
+IPORD         = -I$(topdir)/PORD/include
+LPORD         = $(LPORDDIR)/libpord.a
+ORDERINGSF    = -Dpord~@[
+METISDIR      = ~a
+IMETIS        = -I$(METISDIR)/include
+LMETIS        = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
+ORDERINGSF   += -Dmetis~]~@[~:{
+SCOTCHDIR     = ~a
+ISCOTCH       = -I$(SCOTCHDIR)/include
+LSCOTCH       = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a -lesmumps
+LSCOTCH      += -lscotch -lscotcherr
+ORDERINGSF   += ~a~}~]
+ORDERINGSC    = $(ORDERINGSF)
+LORDERINGS    = $(LPORD) $(LMETIS) $(LSCOTCH)
+IORDERINGSF   = $(ISCOTCH)
+IORDERINGSC   = $(IPORD) $(IMETIS) $(ISCOTCH)"
+                        (assoc-ref inputs "openblas")
                         (assoc-ref inputs "scalapack")
+                        (->bool (which "mpicc"))  ;; MPI support enabled?
+                        (assoc-ref outputs "out")
                         (assoc-ref inputs "metis")
                         (match (list (assoc-ref inputs "pt-scotch")
                                      (assoc-ref inputs "scotch"))
@@ -3828,11 +3838,14 @@ IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
                               "-lesmumps -lptscotch -lptscotcherr "
                               "-Dptscotch")))))))))
          (replace 'build
-          ;; By default only the d-precision library is built.  Make with "all"
-          ;; target so that all precision libraries and examples are built.
-          (lambda _
-            (invoke "make" "all"
-                    (format #f "-j~a" (parallel-job-count)))))
+           ;; By default only the d-precision library is built. Make with "all"
+           ;; target so that all precision libraries and examples are built.
+           ;; Then, "make allshared" builts equivalent shared libraries as well.
+           (lambda _
+             (invoke "make" "all"
+                     (format #f "-j~a" (parallel-job-count)))
+             (invoke "make" "allshared"
+                     (format #f "-j~a" (parallel-job-count)))))
          (replace 'check
           ;; Run the simple test drivers, which read test input from stdin:
           ;; from the "real" input for the single- and double-precision
diff --git a/gnu/packages/patches/mumps-build-parallelism.patch b/gnu/packages/patches/mumps-build-parallelism.patch
deleted file mode 100644
index 26dd330311..0000000000
--- a/gnu/packages/patches/mumps-build-parallelism.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Building sublibraries in parallel can lead to race conditions on the libseq
-and lipord targets.
-
---- MUMPS_5.0.0/Makefile.orig	2015-06-15 10:08:54.523146562 -0500
-+++ MUMPS_5.0.0/Makefile	2015-06-15 10:19:44.074367512 -0500
-@@ -11,6 +11,7 @@
- 	sexamples dexamples cexamples zexamples \
- 	mumps_lib requiredobj libseqneeded clean
- 
-+.NOTPARALLEL:
- alllib:		c z s d
- all:		cexamples zexamples sexamples dexamples
- 
diff --git a/gnu/packages/patches/mumps-shared-libseq.patch b/gnu/packages/patches/mumps-shared-libseq.patch
deleted file mode 100644
index eccf528f7a..0000000000
--- a/gnu/packages/patches/mumps-shared-libseq.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Create a shared version of the sequential library, MUST BE LAST IN SERIES
-
-Index: mumps/libseq/Makefile
-===================================================================
---- mumps.orig/libseq/Makefile
-+++ mumps/libseq/Makefile
-@@ -8,15 +8,17 @@ all: libmpiseq
- 
- include ../Makefile.inc
- 
--libmpiseq: libmpiseq$(PLAT)$(LIBEXT)
-+libmpiseq: libmpiseq$(PLAT).a libmpiseq$(PLAT).so
- 
--libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o
--	$(AR)$@ mpi.o mpic.o elapse.o
-+libmpiseq$(PLAT).a: mpi.o mpic.o elapse.o
-+	$(AR) $@ mpi.o mpic.o elapse.o
- 	$(RANLIB) $@
-+libmpiseq$(PLAT).so: mpi.o mpic.o elapse.o
-+	$(FC) -shared $^ -Wl,-soname,libmpiseq$(PLAT)-5.2.1.so -o libmpiseq$(PLAT)-5.2.1.so -Wl,-z,defs
- .f.o:
--	$(FC) $(OPTF)              -c $*.f $(OUTF)$*.o
-+	$(FC) $(OPTF)              -fPIC -c $*.f $(OUTF)$*.o
- .c.o:
--	$(CC) $(OPTC) $(CDEFS) -I. -c $*.c $(OUTC)$*.o
-+	$(CC) $(OPTC) $(CDEFS) -I. -fPIC -c $*.c $(OUTC)$*.o
- 
- clean:
--	$(RM) *.o *$(LIBEXT)
-+	$(RM) *.o *.a *.so
-Index: mumps/Makefile
-===================================================================
---- mumps.orig/Makefile
-+++ mumps/Makefile
-@@ -60,6 +60,7 @@ requiredobj: Makefile.inc $(LIBSEQNEEDED
- 
- libseqneeded:
- 	(cd libseq; $(MAKE))
-+	cp libseq/lib* $(libdir)
- 
- # Build the libpord.a library and copy it into $(topdir)/lib
- $(libdir)/libpord$(PLAT).a:
diff --git a/gnu/packages/patches/mumps-shared-mumps.patch b/gnu/packages/patches/mumps-shared-mumps.patch
deleted file mode 100644
index d94ccf6ce9..0000000000
--- a/gnu/packages/patches/mumps-shared-mumps.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-Create a shared version of the MUMPS library.
-
-Index: mumps/src/Makefile
-===================================================================
---- mumps.orig/src/Makefile
-+++ mumps/src/Makefile
-@@ -23,8 +23,10 @@ z:
- 
- include $(topdir)/Makefile.inc
- 
--mumps_lib:    $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \
--              $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT)
-+mumps_lib:    $(libdir)/libmumps_common$(PLAT).a \
-+              $(libdir)/libmumps_common$(PLAT).so \
-+              $(libdir)/lib$(ARITH)mumps$(PLAT).a \
-+              $(libdir)/lib$(ARITH)mumps$(PLAT).so
- 
- OBJS_COMMON_MOD = \
-         lr_common.o \
-@@ -167,14 +169,22 @@ OBJS_OTHER = \
-         $(ARITH)tools.o\
-         $(ARITH)type3_root.o
- 
--$(libdir)/libmumps_common$(PLAT)$(LIBEXT):      $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER)
--	$(AR)$@ $?
-+$(libdir)/libmumps_common$(PLAT).a:      $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER)
-+	$(AR) $@ $?
- 	$(RANLIB) $@
- 
--$(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT):    $(OBJS_MOD) $(OBJS_OTHER)
--	$(AR)$@ $?
-+$(libdir)/libmumps_common$(PLAT).so:      $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER)
-+	$(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-5.2.1.so -L$(libdir) $(LORDERINGS) -lpthread $(MPIFLIB) $(MPICLIB) $(LEXTRAS) -o $(libdir)/libmumps_common$(PLAT)-5.2.1.so -Wl,-z,defs
-+	ln -s libmumps_common$(PLAT)-5.2.1.so $@
-+
-+$(libdir)/lib$(ARITH)mumps$(PLAT).a:    $(OBJS_MOD) $(OBJS_OTHER)
-+	$(AR) $@ $?
- 	$(RANLIB) $@
- 
-+$(libdir)/lib$(ARITH)mumps$(PLAT).so:    $(OBJS_MOD) $(OBJS_OTHER)
-+	$(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-5.2.1.so -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(MPIFLIB) $(LEXTRAS) $(LIBBLAS) $(SCALAP) $(LAPACK) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-5.2.1.so -Wl,-z,defs
-+	ln -s lib$(ARITH)mumps$(PLAT)-5.2.1.so $@
-+
- # Dependencies between modules:
- $(ARITH)mumps_load.o:		$(ARITH)mumps_comm_buffer.o \
- 				$(ARITH)mumps_struc_def.o \
-@@ -290,13 +300,13 @@ $(OBJS_OTHER):$(OBJS_COMMON_MOD) $(OBJS_
- 
- .SUFFIXES: .c .F .o
- .F.o:
--	$(FC) $(OPTF) $(INCS) $(IORDERINGSF) $(ORDERINGSF) -I. -I../include -c $*.F $(OUTF)$*.o
-+	$(FC) $(OPTF) $(INCS) $(IORDERINGSF) $(ORDERINGSF) -I. -I../include -fPIC -c $*.F $(OUTF)$*.o
- .c.o:
--	$(CC) $(OPTC) $(INCS) -I../include $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o
-+	$(CC) $(OPTC) $(INCS) -I../include $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o
- 
- $(ARITH)mumps_c.o:	mumps_c.c
- 	$(CC) $(OPTC) $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \
--	      $(IORDERINGSC) $(ORDERINGSC) -I../include -c mumps_c.c $(OUTC)$@
-+	      $(IORDERINGSC) $(ORDERINGSC) -I../include -fPIC -c mumps_c.c $(OUTC)$@
- 
- 
- clean:
diff --git a/gnu/packages/patches/mumps-shared-pord.patch b/gnu/packages/patches/mumps-shared-pord.patch
deleted file mode 100644
index d3915b0ad9..0000000000
--- a/gnu/packages/patches/mumps-shared-pord.patch
+++ /dev/null
@@ -1,77 +0,0 @@
-Create static and shared versions of the PORD library.
-
-Index: mumps/PORD/lib/Makefile
-===================================================================
---- mumps.orig/PORD/lib/Makefile
-+++ mumps/PORD/lib/Makefile
-@@ -9,7 +9,7 @@
- 
- INCLUDES = -I../include
- 
--COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS)
-+COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -fPIC
- 
- OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \
-        multisector.o gelim.o bucket.o tree.o \
-@@ -24,12 +24,16 @@ OBJS = graph.o gbipart.o gbisect.o ddcre
- .c.o:
- 	$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
- 
--libpord$(LIBEXT):$(OBJS)
--	$(AR)$@ $(OBJS)
-+libpord$(PLAT).a:$(OBJS)
-+	$(AR) $@ $(OBJS)
- 	$(RANLIB) $@
- 
-+libpord$(PLAT).so: $(OBJS)
-+	$(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-5.2.1.so -o libpord$(PLAT)-5.2.1.so -Wl,-z,defs
-+	ln -s libpord$(PLAT)-5.2.1.so $@
-+
- clean:
- 	rm -f *.o
- 
- realclean:
--	rm -f *.o libpord.a
-+	rm -f *.o libpord*.a *.so
-Index: mumps/Makefile
-===================================================================
---- mumps.orig/Makefile
-+++ mumps/Makefile
-@@ -54,7 +54,7 @@ dexamples:	d
- multi_example:	s d c z
- 	(cd examples ; $(MAKE) multi)
- 
--requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT)
-+requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT).a $(libdir)/libpord$(PLAT).so
- 
- # dummy MPI library (sequential version)
- 
-@@ -62,19 +62,25 @@ libseqneeded:
- 	(cd libseq; $(MAKE))
- 
- # Build the libpord.a library and copy it into $(topdir)/lib
--$(libdir)/libpord$(PLAT)$(LIBEXT):
-+$(libdir)/libpord$(PLAT).a:
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); \
- 	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
- 	fi;
- 	if [ "$(LPORDDIR)" != "" ] ; then \
--	  cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
-+	  cp $(LPORDDIR)/libpord$(PLAT).a $@; \
- 	fi;
- 
-+$(libdir)/libpord$(PLAT).so:
-+	if [ "$(LPORDDIR)" != "" ] ; then \
-+	cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi;
-+	if [ "$(LPORDDIR)" != "" ] ; then \
-+	cp -a $(LPORDDIR)/libpord*.so lib/; fi;
-+
- clean:
- 	(cd src; $(MAKE) clean)
- 	(cd examples; $(MAKE) clean)
--	(cd $(libdir); $(RM) *$(PLAT)$(LIBEXT))
-+	(cd $(libdir); $(RM) *$(PLAT).a *$(PLAT).so)
- 	(cd libseq; $(MAKE) clean)
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); $(MAKE) realclean; \
-- 
2.20.1