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parmetis: Use petsc bitbucket source instead of glaros
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This is needed as the upstream source is quite unreliable, timing out in
many cases. petsc has an adjusted version of the source.
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@cheriimoya
cheriimoya committed Jul 24, 2024
1 parent db2396c commit fbff98c
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36 changes: 19 additions & 17 deletions pkgs/by-name/pa/parmetis/package.nix
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Original file line number Diff line number Diff line change
@@ -1,28 +1,30 @@
{ lib, stdenv
, fetchurl
, cmake
, mpi
{
lib,
stdenv,
fetchFromBitbucket,
cmake,
metis,
mpi,
}:

stdenv.mkDerivation rec {
pname = "parmetis";
version = "4.0.3";
version = "4.0.3-p9";

src = fetchurl {
url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-${version}.tar.gz";
sha256 = "0pvfpvb36djvqlcc3lq7si0c5xpb2cqndjg8wvzg35ygnwqs5ngj";
src = fetchFromBitbucket {
owner = "petsc";
repo = "pkg-parmetis";
rev = "v${version}";
hash = "sha256-r38msBghAn1MXtvkclxv+VOua5aTT/iAxIN/2EnHTeU=";
};

patches = [ ./use-local-gklib.patch ];
nativeBuildInputs = [ cmake ];
buildInputs = [ mpi ];

# metis and GKlib are packaged with distribution
# AUR https://aur.archlinux.org/packages/parmetis/ has reported that
# it easier to build with the included packages as opposed to using the metis
# package. Compilation time is short.
configurePhase = ''
make config metis_path=$PWD/metis gklib_path=$PWD/metis/GKlib prefix=$out
'';
enableParallelBuilding = true;
buildInputs = [
mpi
metis
];

meta = with lib; {
description = "MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices";
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260 changes: 260 additions & 0 deletions pkgs/by-name/pa/parmetis/use-local-gklib.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,260 @@
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 911a32d..c55ff11 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,8 +1,8 @@
cmake_minimum_required(VERSION 2.8)
project(ParMETIS C)

-set(GKLIB_PATH ${CMAKE_CURRENT_SOURCE_DIR}/metis/GKlib CACHE PATH "path to GKlib")
-set(METIS_PATH ${CMAKE_CURRENT_SOURCE_DIR}/metis CACHE PATH "path to METIS")
+set(GKLIB_PATH ${CMAKE_CURRENT_SOURCE_DIR}/headers CACHE PATH "path to GKlib")
+set(METIS_PATH ${CMAKE_CURRENT_SOURCE_DIR}/headers CACHE PATH "path to METIS")

# Search for MPI.
# GK commented this out as it seems to be creating problems
diff --git a/headers/gk_externs.h b/headers/gk_externs.h
index e63f2ab..c31b3a7 100644
--- a/headers/gk_externs.h
+++ b/headers/gk_externs.h
@@ -14,16 +14,11 @@
/*************************************************************************
* Extern variable definition. Hopefully, the __thread makes them thread-safe.
**************************************************************************/
-
-/* include the definition of metis__thread; it is assumed that
- gklib_tls.h will be installed 'globally' i.e. into $PREFIX */
-#include <gklib_tls.h>
-
#ifndef _GK_ERROR_C_
/* declared in error.c */
-extern metis__thread int gk_cur_jbufs;
-extern metis__thread jmp_buf gk_jbufs[];
-extern metis__thread jmp_buf gk_jbuf;
+extern __thread int gk_cur_jbufs;
+extern __thread jmp_buf gk_jbufs[];
+extern __thread jmp_buf gk_jbuf;

#endif

diff --git a/headers/gklib_defs.h b/headers/gklib_defs.h
new file mode 100644
index 0000000..dfac5ca
--- /dev/null
+++ b/headers/gklib_defs.h
@@ -0,0 +1,53 @@
+/*!
+\file
+\brief Data structures and prototypes for GKlib integration
+
+\date Started 12/23/2008
+\author George
+\version\verbatim $Id: gklib_defs.h 10395 2011-06-23 23:28:06Z karypis $ \endverbatim
+*/
+
+#ifndef _LIBMETIS_GKLIB_H_
+#define _LIBMETIS_GKLIB_H_
+
+#include "gklib_rename.h"
+
+/*************************************************************************/
+/*! Stores a weighted edge */
+/*************************************************************************/
+typedef struct {
+ idx_t u, v, w; /*!< Edge (u,v) with weight w */
+} uvw_t;
+
+/*************************************************************************
+* Define various data structure using GKlib's templates.
+**************************************************************************/
+GK_MKKEYVALUE_T(ikv_t, idx_t, idx_t)
+GK_MKKEYVALUE_T(rkv_t, real_t, idx_t)
+GK_MKPQUEUE_T(ipq_t, ikv_t)
+GK_MKPQUEUE_T(rpq_t, rkv_t)
+
+
+/* gklib.c */
+GK_MKBLAS_PROTO(i, idx_t, idx_t)
+GK_MKBLAS_PROTO(r, real_t, real_t)
+GK_MKALLOC_PROTO(i, idx_t)
+GK_MKALLOC_PROTO(r, real_t)
+GK_MKALLOC_PROTO(ikv, ikv_t)
+GK_MKALLOC_PROTO(rkv, rkv_t)
+GK_MKPQUEUE_PROTO(ipq, ipq_t, idx_t, idx_t)
+GK_MKPQUEUE_PROTO(rpq, rpq_t, real_t, idx_t)
+GK_MKRANDOM_PROTO(i, idx_t, idx_t)
+GK_MKARRAY2CSR_PROTO(i, idx_t)
+void isorti(size_t n, idx_t *base);
+void isortd(size_t n, idx_t *base);
+void rsorti(size_t n, real_t *base);
+void rsortd(size_t n, real_t *base);
+void ikvsorti(size_t n, ikv_t *base);
+void ikvsortii(size_t n, ikv_t *base);
+void ikvsortd(size_t n, ikv_t *base);
+void rkvsorti(size_t n, rkv_t *base);
+void rkvsortd(size_t n, rkv_t *base);
+void uvwsorti(size_t n, uvw_t *base);
+
+#endif
diff --git a/headers/gklib_rename.h b/headers/gklib_rename.h
new file mode 100644
index 0000000..78dc8b3
--- /dev/null
+++ b/headers/gklib_rename.h
@@ -0,0 +1,122 @@
+/*!
+\file
+
+ * Copyright 1997, Regents of the University of Minnesota
+ *
+ * This file contains header files
+ *
+ * Started 10/2/97
+ * George
+ *
+ * $Id: gklib_rename.h 10395 2011-06-23 23:28:06Z karypis $
+ *
+ */
+
+
+#ifndef _LIBMETIS_GKLIB_RENAME_H_
+#define _LIBMETIS_GKLIB_RENAME_H_
+
+/* gklib.c - generated from the .o files using the ./utils/listundescapedsumbols.csh */
+#define iAllocMatrix libmetis__iAllocMatrix
+#define iFreeMatrix libmetis__iFreeMatrix
+#define iSetMatrix libmetis__iSetMatrix
+#define iargmax libmetis__iargmax
+#define iargmax_n libmetis__iargmax_n
+#define iargmin libmetis__iargmin
+#define iarray2csr libmetis__iarray2csr
+#define iaxpy libmetis__iaxpy
+#define icopy libmetis__icopy
+#define idot libmetis__idot
+#define iincset libmetis__iincset
+#define ikvAllocMatrix libmetis__ikvAllocMatrix
+#define ikvFreeMatrix libmetis__ikvFreeMatrix
+#define ikvSetMatrix libmetis__ikvSetMatrix
+#define ikvcopy libmetis__ikvcopy
+#define ikvmalloc libmetis__ikvmalloc
+#define ikvrealloc libmetis__ikvrealloc
+#define ikvset libmetis__ikvset
+#define ikvsmalloc libmetis__ikvsmalloc
+#define ikvsortd libmetis__ikvsortd
+#define ikvsorti libmetis__ikvsorti
+#define ikvsortii libmetis__ikvsortii
+#define imalloc libmetis__imalloc
+#define imax libmetis__imax
+#define imin libmetis__imin
+#define inorm2 libmetis__inorm2
+#define ipqCheckHeap libmetis__ipqCheckHeap
+#define ipqCreate libmetis__ipqCreate
+#define ipqDelete libmetis__ipqDelete
+#define ipqDestroy libmetis__ipqDestroy
+#define ipqFree libmetis__ipqFree
+#define ipqGetTop libmetis__ipqGetTop
+#define ipqInit libmetis__ipqInit
+#define ipqInsert libmetis__ipqInsert
+#define ipqLength libmetis__ipqLength
+#define ipqReset libmetis__ipqReset
+#define ipqSeeKey libmetis__ipqSeeKey
+#define ipqSeeTopKey libmetis__ipqSeeTopKey
+#define ipqSeeTopVal libmetis__ipqSeeTopVal
+#define ipqUpdate libmetis__ipqUpdate
+#define isrand libmetis__isrand
+#define irand libmetis__irand
+#define irandArrayPermute libmetis__irandArrayPermute
+#define irandArrayPermuteFine libmetis__irandArrayPermuteFine
+#define irandInRange libmetis__irandInRange
+#define irealloc libmetis__irealloc
+#define iscale libmetis__iscale
+#define iset libmetis__iset
+#define ismalloc libmetis__ismalloc
+#define isortd libmetis__isortd
+#define isorti libmetis__isorti
+#define isrand libmetis__isrand
+#define isum libmetis__isum
+#define rAllocMatrix libmetis__rAllocMatrix
+#define rFreeMatrix libmetis__rFreeMatrix
+#define rSetMatrix libmetis__rSetMatrix
+#define rargmax libmetis__rargmax
+#define rargmax_n libmetis__rargmax_n
+#define rargmin libmetis__rargmin
+#define raxpy libmetis__raxpy
+#define rcopy libmetis__rcopy
+#define rdot libmetis__rdot
+#define rincset libmetis__rincset
+#define rkvAllocMatrix libmetis__rkvAllocMatrix
+#define rkvFreeMatrix libmetis__rkvFreeMatrix
+#define rkvSetMatrix libmetis__rkvSetMatrix
+#define rkvcopy libmetis__rkvcopy
+#define rkvmalloc libmetis__rkvmalloc
+#define rkvrealloc libmetis__rkvrealloc
+#define rkvset libmetis__rkvset
+#define rkvsmalloc libmetis__rkvsmalloc
+#define rkvsortd libmetis__rkvsortd
+#define rkvsorti libmetis__rkvsorti
+#define rmalloc libmetis__rmalloc
+#define rmax libmetis__rmax
+#define rmin libmetis__rmin
+#define rnorm2 libmetis__rnorm2
+#define rpqCheckHeap libmetis__rpqCheckHeap
+#define rpqCreate libmetis__rpqCreate
+#define rpqDelete libmetis__rpqDelete
+#define rpqDestroy libmetis__rpqDestroy
+#define rpqFree libmetis__rpqFree
+#define rpqGetTop libmetis__rpqGetTop
+#define rpqInit libmetis__rpqInit
+#define rpqInsert libmetis__rpqInsert
+#define rpqLength libmetis__rpqLength
+#define rpqReset libmetis__rpqReset
+#define rpqSeeKey libmetis__rpqSeeKey
+#define rpqSeeTopKey libmetis__rpqSeeTopKey
+#define rpqSeeTopVal libmetis__rpqSeeTopVal
+#define rpqUpdate libmetis__rpqUpdate
+#define rrealloc libmetis__rrealloc
+#define rscale libmetis__rscale
+#define rset libmetis__rset
+#define rsmalloc libmetis__rsmalloc
+#define rsortd libmetis__rsortd
+#define rsorti libmetis__rsorti
+#define rsum libmetis__rsum
+#define uvwsorti libmetis__uvwsorti
+
+#endif
+
+
diff --git a/libparmetis/parmetislib.h b/libparmetis/parmetislib.h
index 0f2ed89..993f108 100644
--- a/libparmetis/parmetislib.h
+++ b/libparmetis/parmetislib.h
@@ -16,11 +16,11 @@
#define DMALLOC 1
*/

-#include <GKlib.h>
+#include "GKlib.h"

#include <parmetis.h>

-#include <gklib_defs.h>
+#include "gklib_defs.h"

#include <mpi.h>

diff --git a/programs/parmetisbin.h b/programs/parmetisbin.h
index 6590087..80eec81 100644
--- a/programs/parmetisbin.h
+++ b/programs/parmetisbin.h
@@ -16,9 +16,9 @@
#define DMALLOC 1
*/

-#include <GKlib.h>
+#include "GKlib.h"
#include <parmetis.h>
-#include <gklib_defs.h>
+#include "gklib_defs.h"

#include "../libparmetis/rename.h"
#include "../libparmetis/defs.h"

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