05/15: gnu: Update scotch to 6.0.4.

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05/15: gnu: Update scotch to 6.0.4.

From:	Eric Bavier
Subject:	05/15: gnu: Update scotch to 6.0.4.
Date:	Tue, 30 Jun 2015 01:29:45 +0000

bavier pushed a commit to branch master
in repository guix.

commit 6c7985408f045e3e0cbf889f1656b27cab5fd890
Author: Eric Bavier <address@hidden>
Date:   Sat Jan 10 01:02:46 2015 -0600

    gnu: Update scotch to 6.0.4.
    
    * gnu/packages/maths.scm (scotch): Update to 6.0.4.
      [arguments]: Add -fPIC to CFLAGS.
    * gnu/packages/patches/scotch-test-threading.patch: Adjust patch for a
      new set of test fixes.
    * gnu/packages/patches/pt-scotch-build-parallelism.patch: New patch.
    * gnu-system.am (dist_patch_DATA): Add it.
---
 gnu-system.am                                      |    1 +
 gnu/packages/maths.scm                             |   16 ++--
 .../patches/pt-scotch-build-parallelism.patch      |   13 ++
 gnu/packages/patches/scotch-test-threading.patch   |  131 +------------------
 4 files changed, 29 insertions(+), 132 deletions(-)

diff --git a/gnu-system.am b/gnu-system.am
index 91e5e52..cbf9223 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -550,6 +550,7 @@ dist_patch_DATA =                                           
\
   gnu/packages/patches/polkit-drop-test.patch                  \
   gnu/packages/patches/portaudio-audacity-compat.patch         \
   gnu/packages/patches/procps-make-3.82.patch                  \
+  gnu/packages/patches/pt-scotch-build-parallelism.patch       \
   gnu/packages/patches/pulseaudio-fix-mult-test.patch          \
   gnu/packages/patches/pulseaudio-longer-test-timeout.patch    \
   gnu/packages/patches/pycairo-wscript.patch                   \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4e0b1ee..e4fe03b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <address@hidden>
 ;;; Copyright © 2013 Nikita Karetnikov <address@hidden>
 ;;; Copyright © 2014 John Darrington <address@hidden>
-;;; Copyright © 2014 Eric Bavier <address@hidden>
+;;; Copyright © 2014, 2015 Eric Bavier <address@hidden>
 ;;; Copyright © 2014 Federico Beffa <address@hidden>
 ;;; Copyright © 2014 Mathieu Lirzin <address@hidden>
 ;;; Copyright © 2015 Ricardo Wurmus <address@hidden>
@@ -785,15 +785,16 @@ implemented in ANSI C, and MPI for communications.")
 (define-public scotch
   (package
     (name "scotch")
-    (version "6.0.0")
+    (version "6.0.4")
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/";
+      (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/";
                           "scotch_" version ".tar.gz"))
       (sha256
-       (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5"))
-      (patches (list (search-patch "scotch-test-threading.patch")))))
+       (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
+      (patches (list (search-patch "scotch-test-threading.patch")
+                     (search-patch "pt-scotch-build-parallelism.patch")))))
     (build-system gnu-build-system)
     (inputs
      `(("zlib" ,zlib)
@@ -820,7 +821,7 @@ CCS = gcc
 CCP = mpicc
 CCD = gcc
 CPPFLAGS =~{ -D~a~}
-CFLAGS = -O2 -g $(CPPFLAGS)
+CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
 LDFLAGS = -lz -lm -lrt -lpthread
 CP = cp
 LEX = flex -Pscotchyy -olex.yy.c
@@ -833,8 +834,7 @@ YACC = bison -pscotchyy -y -b y
                        '("COMMON_FILE_COMPRESS_GZ"
                          "COMMON_PTHREAD"
                          "COMMON_RANDOM_FIXED_SEED"
-                         ;; TODO: Define once our MPI supports
-                         ;; MPI_THREAD_MULTIPLE
+                         ;; XXX: Causes invalid frees in superlu-dist tests
                          ;; "SCOTCH_PTHREAD"
                          ;; "SCOTCH_PTHREAD_NUMBER=2"
                          "restrict=__restrict")))))
diff --git a/gnu/packages/patches/pt-scotch-build-parallelism.patch 
b/gnu/packages/patches/pt-scotch-build-parallelism.patch
new file mode 100644
index 0000000..2ac5f27
--- /dev/null
+++ b/gnu/packages/patches/pt-scotch-build-parallelism.patch
@@ -0,0 +1,13 @@
+Building with -j may cause the esmumps_main target to fail with a "no rule for
+dependency libptesmumps.a" error.  Fix the dependency name.
+
+--- scotch_6.0.4/src/esmumps/Makefile  2012-12-01 08:29:29.000000000 -0600
++++ scotch_6.0.4/src/esmumps/Makefile  2015-06-15 17:29:23.279605734 -0500
+@@ -160,6 +160,6 @@
+                                       order.h                                 
\
+                                       symbol.h                                
\
+                                       esmumps.h                               
\
+-                                      lib$(ESMUMPSLIB)$(LIB)                  
\
++                                      libesmumps$(LIB)                        
\
+                                       $(libdir)/lib$(SCOTCHLIB)$(LIB)         
\
+                                       $(libdir)/lib$(SCOTCHLIB)errexit$(LIB)
diff --git a/gnu/packages/patches/scotch-test-threading.patch 
b/gnu/packages/patches/scotch-test-threading.patch
index 2527a6e..de8cc49 100644
--- a/gnu/packages/patches/scotch-test-threading.patch
+++ b/gnu/packages/patches/scotch-test-threading.patch
@@ -1,139 +1,22 @@
-* These tests assume threading support, even when the library is compiled
-  without it.  Protect these checks.
+Fix this test so that it succeeds when the library is not compiled with
+SCOTCH_PTHREAD.
 
-* Tests should not require keyboard interaction.
-
---- a/src/check/test_scotch_dgraph_band.c      2012-09-27 10:46:42.000000000 
-0500
-+++ b/src/check/test_scotch_dgraph_band.c      2014-05-13 14:36:07.479270243 
-0500
-@@ -99,10 +99,12 @@
-     errorPrint ("main: Cannot initialize (1)");
-     exit       (1);
-   }
-+#ifdef SCOTCH_PTHREAD
-   if (thrdlvlreqval > thrdlvlproval) {
-     errorPrint ("main: Cannot initialize (2)");
-     exit       (1);
-   }
-+#endif
- 
-   if (argc != 2) {
-     errorPrint ("main: invalid number of parameters");
-@@ -115,12 +117,14 @@
- 
-   fprintf (stderr, "Proc %2d of %2d, pid %d\n", proclocnum, procglbnbr, 
getpid ());
- 
-+#ifdef SCOTCH_DEBUG_CHECK2
-   if (proclocnum == 0) {                          /* Synchronize on keybord 
input */
-     char           c;
- 
-     printf ("Waiting for key press...\n");
-     scanf ("%c", &c);
-   }
-+#endif /* SCOTCH_DEBUG_CHECK2 */
- 
-   if (MPI_Barrier (proccomm) != MPI_SUCCESS) {    /* Synchronize for debug */
-     errorPrint ("main: cannot communicate");
---- a/src/check/test_scotch_dgraph_grow.c      2012-11-30 12:19:33.000000000 
-0600
-+++ b/src/check/test_scotch_dgraph_grow.c      2014-05-13 14:35:31.307269303 
-0500
-@@ -103,10 +103,12 @@
-     errorPrint ("main: Cannot initialize (1)");
-     exit       (1);
-   }
-+#ifdef SCOTCH_PTHREAD
-   if (thrdlvlreqval > thrdlvlproval) {
-     errorPrint ("main: Cannot initialize (2)");
-     exit       (1);
-   }
-+#endif
- 
-   if (argc != 2) {
-     errorPrint ("main: invalid number of parameters");
-@@ -119,12 +121,14 @@
- 
-   fprintf (stderr, "Proc %2d of %2d, pid %d\n", proclocnum, procglbnbr, 
getpid ());
- 
-+#ifdef SCOTCH_DEBUG_CHECK2
-   if (proclocnum == 0) {                          /* Synchronize on keybord 
input */
-     char           c;
- 
-     printf ("Waiting for key press...\n");
-     scanf ("%c", &c);
-   }
-+#endif /* SCOTCH_DEBUG_CHECK2 */
- 
-   if (MPI_Barrier (proccomm) != MPI_SUCCESS) {    /* Synchronize for debug */
-     errorPrint ("main: cannot communicate");
---- a/src/check/test_scotch_dgraph_redist.c    2012-09-26 11:42:27.000000000 
-0500
-+++ b/src/check/test_scotch_dgraph_redist.c    2014-05-13 14:34:30.323267722 
-0500
-@@ -98,10 +98,12 @@
-     errorPrint ("main: Cannot initialize (1)");
-     exit       (1);
-   }
-+#ifdef SCOTCH_PTHREAD
-   if (thrdlvlreqval > thrdlvlproval) {
-     errorPrint ("main: Cannot initialize (2)");
-     exit       (1);
-   }
-+#endif
- 
-   if (argc != 2) {
-     errorPrint ("main: invalid number of parameters");
-@@ -114,7 +116,6 @@
- 
-   fprintf (stderr, "Proc %2d of %2d, pid %d\n", proclocnum, procglbnbr, 
getpid ());
- 
--#define SCOTCH_DEBUG_CHECK2
- #ifdef SCOTCH_DEBUG_CHECK2
-   if (proclocnum == 0) {                          /* Synchronize on keybord 
input */
-     char           c;
---- 
/tmp/nix-build-scotch-6.0.0.drv-9/scotch_6.0.0/src/check/test_common_thread.c   
   2012-11-30 11:05:23.000000000 -0600
-+++ scotch_6.0.0/src/check/test_common_thread.c        2014-05-13 
17:26:27.159535244 -0500
-@@ -90,7 +90,7 @@
- /*                       */
- /*************************/
- 
--#if ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD))
-+#ifdef SCOTCH_PTHREAD
- 
- static
- void
-@@ -161,7 +161,7 @@
-   return (o);
- }
- 
--#endif /* ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD)) */
-+#endif /* 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))
-+#ifdef SCOTCH_PTHREAD
++#if ((defined COMMON_PTHREAD) && (defined SCOTCH_PTHREAD))
    TestThread * restrict thrdtab;
    int                   thrdnbr;
--#endif /* ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD)) */
-+#endif /* SCOTCH_PTHREAD */
+ #endif /* ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD)) */
  
    SCOTCH_errorProg (argv[0]);
  
 -#if ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD))
-+#ifdef SCOTCH_PTHREAD
++#if ((defined COMMON_PTHREAD) && (defined SCOTCH_PTHREAD))
    thrdnbr = SCOTCH_PTHREAD_NUMBER;
  
    groudat.redusum = COMPVAL (thrdnbr);
-@@ -197,9 +197,9 @@
-     errorPrint ("main: cannot launch or run threads");
-     return     (1);
-   }
--#else /* ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD)) */
--  printf ("Scotch not compiled with either COMMON_PTHREAD or 
SCOTCH_PTHREAD\n");
--#endif /* ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD)) */
-+#else /* not SCOTCH_PTHREAD */
-+  printf ("Scotch not compiled with SCOTCH_PTHREAD\n");
-+#endif /* not SCOTCH_PTHREAD */
- 
-   return (0);
- }

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branch master updated (e8df8f4 -> a17d456), Eric Bavier, 2015/06/29
- 01/15: gnu: python-mccabe: Fix license field., Eric Bavier, 2015/06/29
- 04/15: gnu: openmpi: Upgrade to 1.8.5., Eric Bavier, 2015/06/29
- 03/15: gnu: hwloc: Move numactl to inputs., Eric Bavier, 2015/06/29
- 06/15: gnu: scotch, pt-scotch: Use modify-phases., Eric Bavier, 2015/06/29
- 08/15: gnu: Add ScaLAPACK., Eric Bavier, 2015/06/29
- 07/15: gnu: scotch, pt-scotch: Build esmumps libraries., Eric Bavier, 2015/06/29
- 09/15: gnu: Add p4est., Eric Bavier, 2015/06/29
- 02/15: gnu: hwloc: Upgrade to 1.10.1., Eric Bavier, 2015/06/29
- 10/15: gnu: Add METIS., Eric Bavier, 2015/06/29
- 05/15: gnu: Update scotch to 6.0.4., Eric Bavier <=
- 11/15: gnu: Add MUMPS., Eric Bavier, 2015/06/29
- 13/15: gnu: Add arpack-ng-openmpi., Eric Bavier, 2015/06/29
- 12/15: gnu: petsc: Upgrade to 3.6.0., Eric Bavier, 2015/06/29
- 14/15: gnu: Add SLEPc., Eric Bavier, 2015/06/29
- 15/15: gnu: Add deal.II., Eric Bavier, 2015/06/29

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