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[PATCH 2/4] gnu: Add scotch package.
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From: |
Eric Bavier |
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Subject: |
[PATCH 2/4] gnu: Add scotch package. |
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Date: |
Sat, 17 May 2014 00:56:13 -0500 |
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User-agent: |
mu4e 0.9.9.5; emacs 23.3.1 |
>From 1fad4e1e207870c3e5aab2dc6c17fdfa6e0cb404 Mon Sep 17 00:00:00 2001
From: Eric Bavier <address@hidden>
Date: Sat, 17 May 2014 00:30:13 -0500
Subject: [PATCH 2/4] gnu: Add scotch package.
* gnu/packages/maths.scm (scotch): New variable.
* gnu/packages/patches/scotch-test-threading.patch: New patch.
* gnu-system.am (dist_patch_DATA): Add it.
---
gnu-system.am | 1 +
gnu/packages/maths.scm | 74 ++++++++++++
gnu/packages/patches/scotch-test-threading.patch | 139 ++++++++++++++++++++++
3 files changed, 214 insertions(+)
create mode 100644 gnu/packages/patches/scotch-test-threading.patch
diff --git a/gnu-system.am b/gnu-system.am
index b54aba1..829c997 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -339,6 +339,7 @@ dist_patch_DATA =
\
gnu/packages/patches/readline-link-ncurses.patch \
gnu/packages/patches/ripperx-libm.patch \
gnu/packages/patches/scheme48-tests.patch \
+ gnu/packages/patches/scotch-test-threading.patch \
gnu/packages/patches/slim-session.patch \
gnu/packages/patches/slim-config.patch \
gnu/packages/patches/slim-sigusr1.patch \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 49fdace..0366385 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -589,3 +589,77 @@ library routines perform an LU decomposition with partial
pivoting and
triangular system solves through forward and back substitution. The library
also provides threshold-based ILU factorization preconditioners.")
(license license:bsd-3)))
+(define-public scotch
+ (package
+ (name "scotch")
+ (version "6.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/";
+ "scotch_" version ".tar.gz"))
+ (sha256
+ (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5"))
+ (patches (list (search-patch "scotch-test-threading.patch")))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)
+ ("flex" ,flex)
+ ("bison" ,bison)))
+ (arguments
+ `(#:phases
+ (alist-cons-after
+ 'unpack 'chdir-to-src
+ (lambda _ (chdir "src"))
+ (alist-replace
+ 'configure
+ (lambda _
+ (call-with-output-file "Makefile.inc"
+ (lambda (port)
+ (format port "
+EXE =
+LIB = .a
+OBJ = .o
+MAKE = make
+AR = ar
+ARFLAGS = -ruv
+CCS = gcc
+CCP = gcc
+CCD = gcc
+CPPFLAGS =~{ -D~a~}
+CFLAGS = -O2 -g $(CPPFLAGS)
+LDFLAGS = -lz -lm -lrt -lpthread
+CP = cp
+LEX = flex -Pscotchyy -olex.yy.c
+LN = ln
+MKDIR = mkdir
+MV = mv
+RANLIB = ranlib
+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
+ ;; "SCOTCH_PTHREAD"
+ ;; "SCOTCH_PTHREAD_NUMBER=2"
+ "restrict=__restrict")))))
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (mkdir out)
+ (zero? (system* "make"
+ (string-append "prefix=" out)
+ "install"))))
+ %standard-phases)))))
+ (home-page "http://www.labri.fr/perso/pelegrin/scotch/";)
+ (synopsis "Programs and libraries for graph algorithms")
+ (description "SCOTCH is a set of programs and libraries which implement
+the static mapping and sparse matrix reordering algorithms developed within
+the SCOTCH project. Its purpose is to apply graph theory, with a divide and
+conquer approach, to scientific computing problems such as graph and mesh
+partitioning, static mapping, and sparse matrix ordering, in application
+domains ranging from structural mechanics to operating systems or
+bio-chemistry.")
+ (license (license:fsf-free "file://LICENSE_en.txt"))))
diff --git a/gnu/packages/patches/scotch-test-threading.patch
b/gnu/packages/patches/scotch-test-threading.patch
new file mode 100644
index 0000000..2527a6e
--- /dev/null
+++ b/gnu/packages/patches/scotch-test-threading.patch
@@ -0,0 +1,139 @@
+* These tests assume threading support, even when the library is compiled
+ without it. Protect these checks.
+
+* 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 */
+
+ /*********************/
+ /* */
+@@ -175,14 +175,14 @@
+ char * argv[])
+ {
+ TestThreadGroup groudat;
+-#if ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD))
++#ifdef SCOTCH_PTHREAD
+ TestThread * restrict thrdtab;
+ int thrdnbr;
+-#endif /* ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD)) */
++#endif /* SCOTCH_PTHREAD */
+
+ SCOTCH_errorProg (argv[0]);
+
+-#if ((defined COMMON_PTHREAD) || (defined SCOTCH_PTHREAD))
++#ifdef 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);
+ }
--
1.7.9.5
--
Eric Bavier
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
- [PATCH 2/4] gnu: Add scotch package.,
Eric Bavier <=