[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[PATCH 04/14] gnu: Update scotch to 6.0.4.
From: |
ericbavier |
Subject: |
[PATCH 04/14] gnu: Update scotch to 6.0.4. |
Date: |
Sat, 27 Jun 2015 22:45:41 -0500 |
From: Eric Bavier <address@hidden>
* 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(-)
create mode 100644 gnu/packages/patches/pt-scotch-build-parallelism.patch
diff --git a/gnu-system.am b/gnu-system.am
index 2d45e40..0c9a2eb 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -549,6 +549,7 @@ 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);
- }
--
2.2.1
- [PATCH 00/14] Add deal.II and some dependencies., ericbavier, 2015/06/27
- [PATCH 01/14] gnu: hwloc: Upgrade to 1.10.1., ericbavier, 2015/06/27
- [PATCH 02/14] gnu: hwloc: Move numactl to inputs., ericbavier, 2015/06/27
- [PATCH 03/14] gnu: openmpi: Upgrade to 1.8.5., ericbavier, 2015/06/27
- [PATCH 04/14] gnu: Update scotch to 6.0.4.,
ericbavier <=
- [PATCH 07/14] gnu: Add ScaLAPACK., ericbavier, 2015/06/27
- [PATCH 05/14] gnu: scotch, pt-scotch: Use modify-phases., ericbavier, 2015/06/27
- [PATCH 06/14] gnu: scotch, pt-scotch: Build esmumps libraries., ericbavier, 2015/06/27
- [PATCH 08/14] gnu: Add p4est., ericbavier, 2015/06/27
- [PATCH 13/14] gnu: Add SLEPc., ericbavier, 2015/06/27