scotch: Upgrade to 6.0.6.

* gnu/packages/maths.scm (scotch): Upgrade to 6.0.6.
[source]: Remove patches that have been fixed upstream.
[arguments]: Add 'install-metis' phase.
[outputs]: New field.
(pt-scotch, pt-scotch32)[arguments]: Add 'mpi-setup' phase.  Use 'invoke'.
* gnu/packages/patches/scotch-graph-diam-64.patch,
gnu/packages/patches/scotch-graph-induce-type-64.patch,
gnu/packages/patches/scotch-test-threading.patch: Delete files.
* gnu/packages/patches/scotch-integer-declarations.patch: New file.
* gnu/local.mk (dist_patch_DATA): Adjust as necessary.

gnu/local.mk

@@ -1219,10 +1219,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/rust-reproducible-builds.patch		 \
   %D%/packages/patches/rxvt-unicode-escape-sequences.patch	\
   %D%/packages/patches/scheme48-tests.patch			\
-  %D%/packages/patches/scotch-test-threading.patch		\
   %D%/packages/patches/scotch-build-parallelism.patch		\
-  %D%/packages/patches/scotch-graph-diam-64.patch		\
+  %D%/packages/patches/scotch-integer-declarations.patch	\
-  %D%/packages/patches/scotch-graph-induce-type-64.patch	\
   %D%/packages/patches/scribus-poppler.patch			\
   %D%/packages/patches/sdl-libx11-1.6.patch			\
   %D%/packages/patches/seq24-rename-mutex.patch			\

gnu/packages/maths.scm

@@ -2424,25 +2424,25 @@ (define-public superlu-dist
 (define-public scotch
   (package
     (name "scotch")
-    (version "6.0.5a")
+    (version "6.0.6")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "https://gforge.inria.fr/frs/download.php/"
                           "latestfile/298/scotch_" version ".tar.gz"))
       (sha256
-       (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
+       (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
-      (patches (search-patches "scotch-test-threading.patch"
+      (patches (search-patches "scotch-build-parallelism.patch"
-                               "scotch-build-parallelism.patch"
+                               "scotch-integer-declarations.patch"))))
-                               "scotch-graph-induce-type-64.patch"
-                               "scotch-graph-diam-64.patch"))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)
        ("flex" ,flex)
        ("bison" ,bison)))
+    (outputs '("out" "metis"))
     (arguments
-     `(#:phases
+     `(#:make-flags (list (string-append "prefix=" %output))
+       #:phases
        (modify-phases %standard-phases
          (add-after
           'unpack 'chdir-to-src
@@ -2477,7 +2477,7 @@ (define-public scotch
                         '("COMMON_FILE_COMPRESS_GZ"
                           "COMMON_PTHREAD"
                           "COMMON_RANDOM_FIXED_SEED"
-                          "INTSIZE64"             ;use 'long' instead of 'int'
+                          "INTSIZE64"             ;use 'int64_t'
                           ;; Prevents symbolc clashes with libesmumps
                           "SCOTCH_RENAME"
                           ;; XXX: Causes invalid frees in superlu-dist tests
@@ -2490,21 +2490,20 @@ (define-public scotch
             (invoke "make"
                     (format #f "-j~a" (parallel-job-count))
                     "esmumps")))
-         (replace
+         (add-before 'install 'make-install-dirs
-          'install
            (lambda* (#:key outputs #:allow-other-keys)
-            (let ((out (assoc-ref outputs "out")))
+             (mkdir (assoc-ref outputs "out"))))
+         (add-after 'install 'install-metis
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "metis")))
                (mkdir out)
-              (invoke "make"
+               ;; metis files are not installed with 'make install'
-                      (string-append "prefix=" out)
-                      "install")
-              ;; esmumps files are not installed with the above
                (for-each (lambda (f)
-                          (copy-file f (string-append out "/include/" f)))
+                           (install-file f (string-append out "/include")))
-                        (find-files "../include" ".*esmumps.h$"))
+                         (find-files "../include/" ".*metis\\.h"))
                (for-each (lambda (f)
-                          (copy-file f (string-append out "/lib/" f)))
+                           (install-file f (string-append out "/lib")))
-                        (find-files "../lib" "^lib.*esmumps.*"))
+                         (find-files "../lib/" ".*metis\\..*"))
                #t))))))
     (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
     (synopsis "Programs and libraries for graph algorithms")

gnu/packages/patches/scotch-graph-diam-64.patch

@@ -1,27 +0,0 @@
-Fixes test_scotch_graph_diam test with -DINTSIZE64.
-
-Reported upstream at
-https://gforge.inria.fr/tracker/index.php?func=detail&aid=21650&group_id=248&atid=1081
-
---- scotch-6.0.5a/src/libscotch/library.h
-+++ scotch-6.0.5a/src/libscotch/library.h
-@@ -187,6 +187,7 @@ SCOTCH_Num                  SCOTCH_graphBase    (SCOTCH_Graph * const, const SCO
- int                         SCOTCH_graphCheck   (const SCOTCH_Graph * const);
- void                        SCOTCH_graphSize    (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const);
- void                        SCOTCH_graphData    (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num ** const, SCOTCH_Num * const, SCOTCH_Num ** const, SCOTCH_Num ** const);
-+SCOTCH_Num                  SCOTCH_graphDiamPV  (SCOTCH_Graph * const);
- void                        SCOTCH_graphStat    (const SCOTCH_Graph * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, double * const, double * const);
- int                         SCOTCH_graphCoarsen (const SCOTCH_Graph * const, const SCOTCH_Num, const double, const SCOTCH_Num, SCOTCH_Graph * const, SCOTCH_Num * const);
- int                         SCOTCH_graphCoarsenMatch (const SCOTCH_Graph * const, SCOTCH_Num * const, const double, const SCOTCH_Num, SCOTCH_Num * const);
---- scotch-6.0.5a/src/libscotch/library_graph_diam.c
-+++ scotch-6.0.5a/src/libscotch/library_graph_diam.c
-@@ -72,8 +72,7 @@
- 
- SCOTCH_Num
- SCOTCH_graphDiamPV (
--SCOTCH_Graph * const        grafptr,
--const SCOTCH_Num            baseval)
-+SCOTCH_Graph * const        grafptr)
- {
-   return ((SCOTCH_Num) graphDiamPV ((Graph * const) grafptr));
- }

gnu/packages/patches/scotch-graph-induce-type-64.patch

@@ -1,19 +0,0 @@
-Fixes return type of SCOTCH_graphInduceList and SCOTCH_graphInducePart
-so that the definition matches with -DINTSIZE64.
-
-Reported upstream at
-https://gforge.inria.fr/tracker/index.php?func=detail&aid=21608&group_id=248&atid=1081
-
---- scotch_6.0.5a/src/libscotch/library.h.orig	2018-02-11 10:52:38.000000000 -0600
-+++ scotch_6.0.5a/src/libscotch/library.h	2018-02-23 16:56:41.000000000 -0600
-@@ -199,8 +199,8 @@
- int                         SCOTCH_graphGeomSaveChac (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const);
- int                         SCOTCH_graphGeomSaveMmkt (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const);
- int                         SCOTCH_graphGeomSaveScot (const SCOTCH_Graph * const, const SCOTCH_Geom * const, FILE * const, FILE * const, const char * const);
--int                         SCOTCH_graphInduceList (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, SCOTCH_Graph * const);
--int                         SCOTCH_graphInducePart (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_GraphPart2 * const, const SCOTCH_GraphPart2, SCOTCH_Graph * const);
-+SCOTCH_Num                  SCOTCH_graphInduceList (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_Num * const, SCOTCH_Graph * const);
-+SCOTCH_Num                  SCOTCH_graphInducePart (const SCOTCH_Graph * const, const SCOTCH_Num, const SCOTCH_GraphPart2 * const, const SCOTCH_GraphPart2, SCOTCH_Graph * const);
- 
- int                         SCOTCH_graphMapInit (const SCOTCH_Graph * const, SCOTCH_Mapping * const, const SCOTCH_Arch * const, SCOTCH_Num * const);
- void                        SCOTCH_graphMapExit (const SCOTCH_Graph * const, SCOTCH_Mapping * const);

gnu/packages/patches/scotch-integer-declarations.patch

@@ -0,0 +1,37 @@
+diff --git a/src/libscotch/library.h b/src/libscotch/library.h
+index 1891c19..ecc0533 100644
+--- a/src/libscotch/library.h
++++ b/src/libscotch/library.h
+@@ -67,6 +67,8 @@
+ 
+ /*+ Integer type. +*/
+ 
++#include <stdint.h>
++
+ typedef DUMMYIDX SCOTCH_Idx;
+ 
+ typedef DUMMYINT SCOTCH_Num;
+diff --git a/src/libscotchmetis/library_metis.h b/src/libscotchmetis/library_metis.h
+index e6767e1..04e71c3 100644
+--- a/src/libscotchmetis/library_metis.h
++++ b/src/libscotchmetis/library_metis.h
+@@ -99,6 +99,7 @@ typedef enum {
+ */
+ 
+ #ifndef SCOTCH_H                                  /* In case "scotch.h" not included before */
++#include <stdint.h>
+ typedef DUMMYINT SCOTCH_Num;
+ #endif /* SCOTCH_H */
+ 
+diff --git a/src/libscotchmetis/library_parmetis.h b/src/libscotchmetis/library_parmetis.h
+index 6d2f0b0..3c803fc 100644
+--- a/src/libscotchmetis/library_parmetis.h
++++ b/src/libscotchmetis/library_parmetis.h
+@@ -106,6 +106,7 @@ typedef enum {
+ */
+ 
+ #ifndef SCOTCH_H                                  /* In case "scotch.h" not included before */
++#include <stdint.h>
+ typedef DUMMYINT SCOTCH_Num;
+ #endif /* SCOTCH_H */
+ 

gnu/packages/patches/scotch-test-threading.patch

@@ -1,22 +0,0 @@
-Fix this test so that it succeeds when the library is not compiled with
-SCOTCH_PTHREAD.
-
---- scotch_6.0.4/src/check/test_common_thread.c	2014-09-28 11:39:59.000000000 -0500
-+++ scotch_6.0.4/src/check/test_common_thread.c	2015-01-10 00:52:00.076229542 -0600
-@@ -175,14 +175,14 @@
- char *              argv[])
- {
-   TestThreadGroup       groudat;
--#if ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD))
-+#if ((defined COMMON_PTHREAD) && (defined SCOTCH_PTHREAD))
-   TestThread * restrict thrdtab;
-   int                   thrdnbr;
- #endif /* ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD)) */
- 
-   SCOTCH_errorProg (argv[0]);
- 
--#if ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD))
-+#if ((defined COMMON_PTHREAD) && (defined SCOTCH_PTHREAD))
-   thrdnbr = SCOTCH_PTHREAD_NUMBER;
- 
-   groudat.redusum = COMPVAL (thrdnbr);