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pkgs/by-name/sp/spooles/allocate.patch

@@ -0,0 +1,38 @@
+From cc153b180829c6b561765cbbb9b621d1142ff1cd Mon Sep 17 00:00:00 2001
+From: annalee <150648636+a-n-n-a-l-e-e@users.noreply.github.com>
+Date: Tue, 28 Nov 2023 13:13:44 +0000
+Subject: [PATCH] use proper format specifier for size_t
+
+---
+ Utilities/MM.h | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Utilities/MM.h b/Utilities/MM.h
+index 11e86c5..301c3ec 100644
+--- a/Utilities/MM.h
++++ b/Utilities/MM.h
+@@ -33,18 +33,18 @@ if ( (count) > 0 ) { \
+    if ( (ptr = (type *)malloc((unsigned long)((count)*sizeof(type)))) \
+         == NULL ) {\
+       fprintf(stderr, \
+-              "\n ALLOCATE failure : bytes %d, line %d, file %s", \
++              "\n ALLOCATE failure : bytes %zu, line %d, file %s", \
+               (count)*sizeof(type), __LINE__, __FILE__) ; \
+       exit(-1) ; } \
+    else if ( MEMORY_DEBUG > 0 ) { \
+       fprintf(stderr, \
+-              "\n ALLOCATE : address %p, bytes %d, line %d, file %s", \
++              "\n ALLOCATE : address %p, bytes %zu, line %d, file %s", \
+               ptr, (count)*sizeof(type), __LINE__, __FILE__) ; } } \
+ else if ( (count) == 0 ) { \
+    ptr = NULL ; } \
+ else { \
+    fprintf(stderr, \
+-           "\n ALLOCATE error : bytes %d, line %d, file %s", \
++           "\n ALLOCATE error : bytes %zu, line %d, file %s", \
+            (count)*sizeof(type), __LINE__, __FILE__) ; \
+    exit(-1) ; }
+ /*
+-- 
+2.42.0
+

pkgs/by-name/sp/spooles/package.nix

@@ -0,0 +1,61 @@
+{
+  lib,
+  stdenv,
+  fetchurl,
+  perl,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "spooles";
+  version = "2.2";
+
+  src = fetchurl {
+    url = "http://www.netlib.org/linalg/spooles/spooles.${version}.tgz";
+    sha256 = "1pf5z3vvwd8smbpibyabprdvcmax0grzvx2y0liy98c7x6h5jid8";
+  };
+
+  sourceRoot = ".";
+
+  patches = [
+    ./spooles.patch
+    # fix compiler error where NULL is used as a zero parameter
+    ./transform.patch
+    # use proper format specifier for size_t
+    ./allocate.patch
+  ];
+
+  postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
+    substituteInPlace makefile --replace "-Wl,-soname," "-Wl,-install_name,$out/lib/"
+  '';
+
+  buildPhase = ''
+    make lib
+  '';
+
+  installPhase = ''
+    mkdir -p $out/lib $out/include/spooles
+    cp libspooles.a libspooles.so.2.2 $out/lib/
+    ln -s libspooles.so.2.2 $out/lib/libspooles.so.2
+    ln -s libspooles.so.2 $out/lib/libspooles.so
+    for h in *.h; do
+      if [ $h != 'MPI.h' ]; then
+         cp $h $out/include/spooles
+         d=`basename $h .h`
+         if [ -d $d ]; then
+            mkdir $out/include/spooles/$d
+            cp $d/*.h $out/include/spooles/$d
+         fi
+      fi
+    done
+  '';
+
+  nativeBuildInputs = [ perl ];
+
+  meta = with lib; {
+    homepage = "http://www.netlib.org/linalg/spooles/";
+    description = "Library for solving sparse real and complex linear systems of equations";
+    license = licenses.publicDomain;
+    maintainers = [ ];
+    platforms = platforms.unix;
+  };
+}

pkgs/by-name/sp/spooles/spooles.patch

@@ -0,0 +1,188 @@
+diff --git a/I2Ohash/src/util.c b/I2Ohash/src/util.c
+index 72d082e..f32f667 100644
+--- a/I2Ohash/src/util.c
++++ b/I2Ohash/src/util.c
+@@ -39,9 +39,10 @@ fflush(stdout) ;
+ */
+ loc1 = (key1 + 1) % hashtable->nlist ;
+ loc2 = (key2 + 1) % hashtable->nlist ;
+-loc  = (loc1*loc2) % hashtable->nlist ;
++long int loc3  = (long int)loc1*(long int)loc2 % hashtable->nlist ;
++loc =(int) loc3;
+ #if MYDEBUG > 0
+-fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %d", loc1, loc2, loc) ;
++fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %ld, loc = %d", loc1, loc2, loc3, loc) ;
+ fflush(stdout) ;
+ #endif
+ /*
+@@ -158,9 +159,10 @@ fflush(stdout) ;
+ #endif
+ loc1 = (key1 + 1) % hashtable->nlist ;
+ loc2 = (key2 + 1) % hashtable->nlist ;
+-loc  = (loc1*loc2) % hashtable->nlist ;
++long int loc3  = (long int)loc1*(long int)loc2 % hashtable->nlist ;
++loc =(int) loc3;
+ #if MYDEBUG > 0
+-fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %d", loc1, loc2, loc) ;
++fprintf(stdout, "\n loc1 = %d, loc2 = %d, loc3 = %ld, loc = %d", loc1, loc2, loc3, loc) ;
+ fflush(stdout) ;
+ #endif
+ /*
+diff --git a/MPI/makefile b/MPI/makefile
+index 0c09f86..d25e70a 100644
+--- a/MPI/makefile
++++ b/MPI/makefile
+@@ -2,7 +2,7 @@ all_drivers :
+ 	cd drivers ; make drivers
+ 
+ lib :
+-	cd src ; make spoolesMPI.a
++	cd src ; make makeLib
+ 
+ clean :
+ 	cd src ; make clean
+diff --git a/MPI/src/makefile b/MPI/src/makefile
+index f7650b7..71e4c49 100644
+--- a/MPI/src/makefile
++++ b/MPI/src/makefile
+@@ -42,3 +42,8 @@ $(OBJ).a : \
+ 
+ clean :
+ 	- rm -f *.a *.o
++
++makeLib :
++	perl ../../makeLib > makeG
++	make -f makeG
++	rm -f makeG
+diff --git a/MT/makefile b/MT/makefile
+index 9b86a32..d25e70a 100644
+--- a/MT/makefile
++++ b/MT/makefile
+@@ -2,7 +2,7 @@ all_drivers :
+ 	cd drivers ; make drivers
+ 
+ lib :
+-	cd src ; make spoolesMT.a
++	cd src ; make makeLib
+ 
+ clean :
+ 	cd src ; make clean
+diff --git a/Make.inc b/Make.inc
+index f99eb8f..2de8a25 100644
+--- a/Make.inc
++++ b/Make.inc
+@@ -12,7 +12,7 @@
+ # for solaris
+ #
+ # CC = gcc
+-  CC = /usr/lang-4.0/bin/cc
++#  CC = /usr/lang-4.0/bin/cc
+ #
+ # for sgi
+ #
+@@ -28,7 +28,7 @@
+ # 
+ # OPTLEVEL = 
+ # OPTLEVEL = -g -v
+-  OPTLEVEL = -O
++  OPTLEVEL = -O3
+ # OPTLEVEL = -xO5 -v
+ # OPTLEVEL = -O3
+ # OPTLEVEL = -O4
+@@ -43,7 +43,7 @@
+ #  set any load flags
+ #
+ #  LDFLAGS = -Wl,+parallel -Wl,+tm,spp2000 # for hp exemplar
+-   LDFLAGS =
++#   LDFLAGS =
+ #
+ #---------------------------------------------------------------------
+ #
+@@ -103,7 +103,7 @@
+ #  MPI install library
+ #
+ # MPI_INSTALL_DIR = 
+-  MPI_INSTALL_DIR = /usr/local/mpich-1.0.13
++#  MPI_INSTALL_DIR = /usr/lib/openmpi
+ #
+ #---------------------------------------------------------------------
+ #
+@@ -142,6 +142,6 @@
+ #  MPI include path
+ #
+ # MPI_INCLUDE_DIR = 
+-  MPI_INCLUDE_DIR = -I$(MPI_INSTALL_DIR)/include
++#  MPI_INCLUDE_DIR = -I/usr/include/mpi
+ #
+ #---------------------------------------------------------------------
+diff --git a/Utilities/src/iohb.c b/Utilities/src/iohb.c
+index ac38f7b..ac34034 100644
+--- a/Utilities/src/iohb.c
++++ b/Utilities/src/iohb.c
+@@ -1725,7 +1725,7 @@ static void upcase(char* S)
+ 
+ static void IOHBTerminate(char* message) 
+ {
+-   fprintf(stderr,message);
++   fputs(message, stderr);
+    exit(1);
+ }
+ 
+diff --git a/makeLib b/makeLib
+index 1780f39..7697b06 100755
+--- a/makeLib
++++ b/makeLib
+@@ -64,14 +64,19 @@ foreach $src ( @srcnames ) {
+    $srcname = " \\\n     " . $src ;
+    print $srcname ;
+ }
++print "\n\n.SUFFIXES: .c .o .lo .a .so" ;
+ print "\n\nOBJ_FILES = \$\{SRC:.c=.o\}" ;
++print "\n\nLOBJ_FILES = \$\{SRC:.c=.lo\}" ;
+ print "\n\n" ;
+ print <<'EOF' ;
+ .c.o :
+-	$(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o
++	$(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o $(MPI_INCLUDE_DIR)
+ 
+-../../spooles.a : ${OBJ_FILES}
+-	$(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o
++.c.lo :
++	$(PURIFY) $(CC) -c $(CFLAGS) $*.c -fPIC -DPIC -o $(OBJ)_$*.lo $(MPI_INCLUDE_DIR)
++
++../../libspooles.a : ${OBJ_FILES} ${LOBJ_FILES}
++	$(AR) $(ARFLAGS) ../../libspooles.a $(OBJ)_*.o
+ 	rm -f $(OBJ)_*.o
+-	$(RANLIB) ../../spooles.a
++	$(RANLIB) ../../libspooles.a
+ EOF
+diff --git a/makefile b/makefile
+index f014c7d..7c8042a 100755
+--- a/makefile
++++ b/makefile
+@@ -124,7 +124,9 @@ lib :
+ 	cd ZV               ; make lib
+ 	cd misc             ; make lib
+ #cd MPI              ; make lib
+-#cd MT               ; make lib
++	cd MT               ; make lib
++	$(CC) -shared */*/*.lo -Wl,-soname,libspooles.so.2.2 -o libspooles.so.2.2 -lpthread -lm
++	ln -s libspooles.so.2.2 libspooles.so
+ 
+ global :
+ 	cd A2/src             ; make -f makeGlobalLib
+diff --git a/timings.h b/timings.h
+index 23df189..685800b 100644
+--- a/timings.h
++++ b/timings.h
+@@ -2,9 +2,8 @@
+ #define _TIMINGS_
+ #include <sys/time.h>
+ static struct timeval  TV ;
+-static struct timezone TZ ;
+ #define MARKTIME(t) \
+-   gettimeofday(&TV, &TZ) ; \
++   gettimeofday(&TV, NULL) ; \
+    t = (TV.tv_sec + 0.000001*TV.tv_usec)
+ #endif
+ 

pkgs/by-name/sp/spooles/transform.patch

@@ -0,0 +1,43 @@
+From c5d0574182d76af3bf286dce0bb147ae3f098916 Mon Sep 17 00:00:00 2001
+From: annalee <150648636+a-n-n-a-l-e-e@users.noreply.github.com>
+Date: Tue, 28 Nov 2023 12:57:18 +0000
+Subject: [PATCH] fix compiler error: use zero, not NULL, in calls to IVinit
+
+---
+ ETree/src/transform.c | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/ETree/src/transform.c b/ETree/src/transform.c
+index 1e36981..dbdfc70 100644
+--- a/ETree/src/transform.c
++++ b/ETree/src/transform.c
+@@ -291,7 +291,7 @@ etree2 = ETree_compress(etree, mapIV) ;
+    remap the nzeros[] vector
+    -------------------------
+ */
+-temp = IVinit(nfront, NULL) ;
++temp = IVinit(nfront, 0) ;
+ IVcopy(nfront, temp, nzeros) ;
+ IV_setSize(nzerosIV, nnew) ;
+ nzeros = IV_entries(nzerosIV) ;
+@@ -453,7 +453,7 @@ etree2 = ETree_compress(etree, mapIV) ;
+    remap the nzeros[] vector
+    -------------------------
+ */
+-temp = IVinit(nfront, NULL) ;
++temp = IVinit(nfront, 0) ;
+ IVcopy(nfront, temp, nzeros) ;
+ IV_setSize(nzerosIV, nnew) ;
+ nzeros = IV_entries(nzerosIV) ;
+@@ -614,7 +614,7 @@ etree2 = ETree_compress(etree, mapIV) ;
+    remap the nzeros[] vector
+    -------------------------
+ */
+-temp = IVinit(nfront, NULL) ;
++temp = IVinit(nfront, 0) ;
+ IVcopy(nfront, temp, nzeros) ;
+ IV_setSize(nzerosIV, nnew) ;
+ nzeros = IV_entries(nzerosIV) ;
+-- 
+2.42.0
+