File: mem_alloc.patch

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--- ./src/sia/sip_shared/mem_alloc.c	2014-10-14 12:40:26.000000000 +0200
+++ /dev/null	2014-10-10 00:17:42.528636087 +0200
@@ -1,210 +0,0 @@
-//TODO unit tests
-
-#include "mem_alloc.h"
-
-#include <assert.h>
-#include <stdlib.h>
-#include <stddef.h>
-#include <stdio.h>
-#include <limits.h>
-#include "f77_name.h"
-#include "f_types.h"
-
-#define BYTES_PER_MB 1048576
-#define ALIGN 8
-
-char * base_ptr = NULL;      //start of allocated memory
-char * nxt_ptr = NULL;       //address of next free memory
-long long top_int = 0LL;     //highest address (as long long int) of allocated memory + 1
-long long total_bytes = 0LL; //total number of bytes allocated
-
-
-/** 
-  *  initializes dynamic memory system by obtaining requested memory via malloc
-  *
-  *  @param[in] megabytes amount of memory to be allocate and managed
-  *  @param[in] sheap_flag  not currently implemented
-  *  @param[out] ierr 0 if successful, -1 if not successful
-  *
-  *  If successful, this routine makes the memory management system active.
-  *  If this subroutine is called again while the memory system is active, it will simply return.
-*/
-void F77_NAME(mem_alloc_init,MEM_ALLOC_INIT)(f_int *megabytes, f_int *sheap_flag, f_int *ierr){
-#ifdef ALTIX
-	assert (false); //altix memory management not implemented
-#endif
-//         printf("mem_alloc_init called  with %d megabytes\n", *megabytes);
-	 assert( sizeof(long long) == sizeof(char *));  //verify assumption about size of pointers
-	 *ierr = 0;
-	 if (total_bytes == 0){  //only do this once unless free has been called to reset.
-		total_bytes = (long long)(*megabytes) * BYTES_PER_MB;
-		// total_bytes = (*megabytes) * BYTES_PER_MB;
-		base_ptr = (char *)malloc(total_bytes);
-		if (base_ptr == 0)
-		{
-			printf("malloc failed: %d megabytes",*megabytes);
-			total_bytes = 0;
-			*ierr = -1;
-			return;
-		}
-		nxt_ptr = base_ptr;
-		top_int = (long long)base_ptr + total_bytes;
-		assert (top_int > 0); //check that using signed type (long long) for addresses OK
-		return;
-	 }
-	return;
-}
-
-/** 
- * Allocates nwords elements of size element_size from managed array.  It is assumed that this subroutine
- * will be invoked from Fortran, so the parameters are described from the point of view of the Fortran code.
- * After return, the allocated memory is in base(ixmem):base(ixmem+nwords-1)
- *
- *  @param[in] base  the first element of a 1-element array declared and allocated in fortran
- *  @param[in] element_size the size of the elements in the array
- *  @param[out] ixmem integer*8 index into array indicating start of allocated memory.
- *  @param[in] heap  not currently implemented
- *  @param[out] ierr  value is 0 if successful
- */
-void F77_NAME(mem_alloc,MEM_ALLOC)
-      (char *base, f_int *nwords, f_int *element_size, long long *ixmem, f_int *heap, f_int *ierr){
-	assert (total_bytes != 0);
-	*ierr = 0;
-    f_int esize = *element_size;
-	long long nbytes = (long long)(*nwords) * esize;
-	long long fiddle = ALIGN-1;
-	long long nxt_int = (long long)nxt_ptr;
-//        printf("mem_alloc called with nwords %d and esize %d, previous nxt_int is %lld.\n",*nwords,esize,nxt_int);
-	long long alloc_int = (nxt_int + fiddle) & ~(fiddle); //align on ALIGN byte boundary
-	nxt_int = alloc_int + nbytes;
-//        printf("mem_alloc calculated nxt_int is %lld.\n",nxt_int);
-	if (nxt_int > top_int){
-		printf("Error base_ptr=%lld, nxt_int= %lld, top_int = %lld",base_ptr, nxt_int,top_int);
-		*ierr = -1;
-		return;
-	}
-	nxt_ptr = (char *)nxt_int;
-	long long base_int = (long long)base;
- //       printf("mem_alloc done with nwords %d.base_ptr is %lld and nxt_ptr is %lld\n",*nwords, base_ptr, nxt_ptr);
- //       printf("size of f_int is %d\n.",sizeof(f_int));
- //      printf ("result of adding 1 to esize is %d\n", 1+esize);fflush(stdout); 
-	*ixmem = (long long)((alloc_int - base_int)/esize + 1);
-}
-
-
-/** allocates nbytes bytes from the managed array.  It is assumed that this subroutine
- * will be invoked from C and has an interface similar to malloc
- *
- *  @param nbytes[n] number of bytes
- *  @return  address of allocated memory, or 0 if not successful
- */
-char * mem_alloc_c(size_t nbytes){
-	assert (total_bytes != 0);
-	long long fiddle = ALIGN-1;
-	long long nxt_int = (long long)nxt_ptr;
-	long long alloc_int = (nxt_int + fiddle) & ~(fiddle); //align on ALIGN byte boundary
-	nxt_int = alloc_int + nbytes;
-        printf("mem_alloc_c called with %d bytes\n",nbytes);
-	if (nxt_int >= top_int || nxt_int <= 0 ){  //check that enough memory available
-		printf("nxt_int= %lld, top_int = %lld\n",nxt_int,top_int);
-		alloc_int = 0;
-		return NULL;
-	}
-	nxt_ptr = (char *)nxt_int;
-	return (char *)alloc_int;
-}
-
-
-/** 
- *  frees all memory above addr so that it can be reallocated.
- *
- *  @param addr[in] starting address of memory to be free. Must be in allocated memory
- *  @param ierr[out] return code
- *
- *  Note:  mem_alloc_free will fail if called with invalid input.  There is no scenario where there is a normal
- *  return and ierr != 0.  We may want to change this interface.
-*/
-void F77_NAME(mem_alloc_free,MEM_ALLOC_FREE)(char *addr, f_int *ierr){
-	*ierr = 0;
-	assert(base_ptr <= addr && (long long) addr <= top_int); //given address must be in allocated memory
-	nxt_ptr = addr;
-}
-
-/**  
-*  mem_alloc_free_all returns all managed memory to OS and makes memory management inactive.
-*  After calling this subroutine, the mem_alloc_init may be called to reinitialize the memory
-*  management system.
-*/
-void F77_NAME(mem_alloc_free_all,MEM_ALLOC_FREE_ALL)(){
-	if (base_ptr != 0) free(base_ptr);
-	base_ptr = NULL;
-	nxt_ptr = NULL;
-	total_bytes = 0;
-}
-
-
-/**  
- *  Frees all memory allocated by mem_alloc so that it can be reallocated.  The
- *  memory system remains active.  Freed memory is not reinitialized to 0.
-*/
-void F77_NAME(mem_alloc_reset,MEM_ALLOC_RESET)(){
-	nxt_ptr = base_ptr;
-}
-
-
-/** 
- *  returns the amount of memory allocated
- *
- *     *param nbused[out] amount of memory already allocated by mem_alloc
- */
-void F77_NAME(mem_alloc_query, MEM_ALLOC_QUERY)(long long *nbused){
-	*nbused = (long long)nxt_ptr - (long long)base_ptr;
-}
-
-
-/** 
- *  returns the number of objects of a particular size that can be allocated.
- *
- *     *param size[in] size of the object 
- *     *param number[out] number of objects that can be allocated
- */
-void F77_NAME(mem_query_free, MEM_QUERY_FREE)(f_int* size,f_int *number){
-        *number = (f_int) (total_bytes)/(*size);
-}
-
-
-/** 
- * returns the base address of the managed memory
- */
-long long F77_NAME(get_mem_base_addr,GET_MEM_BASE_ADDR)(){
-	return (long long)base_ptr;
-}
-
-/** returns address of base(ix) where base is an array with 'size'-byte elements
- *
- *   @param[in] base first element of array
- *   @param[in] ix   index of element whose address is to be returned
- *   @param[in] size size of elements of array
- *
- *   @returns address of base(ix)
- */
-long long F77_NAME(c_loc64, C_LOC64)(char *base, long long *ix, f_int *size)
-{
-   long long addr;
-   addr = (long long) base + (*ix-1)*(*size);
-   return addr;
-}
-
-long long F77_NAME(get_max_heap_usage,GET_MAX_HEAP_USAGE) () 
-{
-   return total_bytes;
-
-}
-
-/*for debugging*/
-void print_mem_values(){
-	printf("base_ptr = %p\n",  (void *)base_ptr);
-	printf("nxt_ptr =  %p\n",  (void *) nxt_ptr);
-	printf("top_int = %lld\n", top_int);
-	printf("total_bytes = %lld\n", total_bytes);
-}
--- /dev/null	2014-10-10 00:17:42.528636087 +0200
+++ ./src/sia/sip_shared/mem_alloc.F	2014-10-14 12:40:36.000652136 +0200
@@ -0,0 +1,272 @@
+C  Copyright (c) 2003-2010 University of Florida
+C
+C  This program is free software; you can redistribute it and/or modify
+C  it under the terms of the GNU General Public License as published by
+C  the Free Software Foundation; either version 2 of the License, or
+C  (at your option) any later version.
+
+C  This program is distributed in the hope that it will be useful,
+C  but WITHOUT ANY WARRANTY; without even the implied warranty of
+C  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+C  GNU General Public License for more details.
+
+C  The GNU General Public License is included in this distribution
+C  in the file COPYRIGHT.
+      subroutine mem_alloc(base, nwords, element_size, ixmem, 
+     *                     heap, ierr)
+c--------------------------------------------------------------------------
+c   Allocates "nwords*element_size" bytes of memory using MPI_ALLOC_MEM,
+c   and returns an index "ixmem" relative to the base address.  Upon 
+c   return, the memory may be referenced by Fortran code as base(ixmem+i-1),
+c   i = 1, 2, 3, ...,nwords.
+c
+c   Arguments:
+c	base		Base array to reference the returned index.
+c	nwords		Number of words of memory to allocate.
+c	element_size	Number of bytes per element.
+c 	ixmem		Returned index used in conjunction with "base" to
+c			reference the allocated memory. This argument 
+c			should also be declared integer*8.
+c       heap            Logical variable.  heap = .true. requests heap  
+c                       allocation, .false. requests allocation on 
+c                       shared heap. 
+c	ierr		Return code.  0 = Successful allocation, otherwise
+c			the subroutine was unable to obtain the required
+c			amount of memory.
+c	
+c--------------------------------------------------------------------------
+
+      implicit none
+      include 'machine_types.h'
+      include 'mem_alloc_data.h'
+      include 'parallel_info.h'
+#ifdef ALTIX
+      include 'sheap.h'
+#endif
+
+      integer base(*)
+      integer nwords, element_size, ierr
+      integer*8 ixmem
+      integer*8 addr1, addr2
+      integer*8 get_index_from_base
+      integer*8 size
+      integer type
+      integer sheap_flag 
+
+      integer*8 ixx, c_loc64
+
+      logical heap
+
+      ierr = 0
+
+      if (nwords .lt. 0) then
+         print *,'Error: mem_alloc was called with nwords = ',nwords
+         call abort_job()
+      endif
+
+      if (element_size .eq. 8) then
+
+c-------------------------------------------------------------------------
+c   Force alignment on a 8-byte boundary.
+c-------------------------------------------------------------------------
+
+         if (memnxt/8*8 .ne. memnxt) then
+            memnxt = (memnxt+7)/8*8 
+         endif
+      endif
+
+      size = nwords
+      size = size * element_size
+
+c      print *,'Task ',me,' MEM_ALLOC: nwords, element_size, size ',
+c     *   nwords, element_size, size,' memnxt ',memnxt,
+c     *   ' mem_malloced ',mem_malloced
+      if (memnxt + size .gt. mem_malloced) then
+         print *,'Memory exhausted.'
+         print *,'mem_malloced: ',mem_malloced,' memnxt ',memnxt,
+     *        ' size requested ',element_size,'*',nwords
+         ierr = 1
+         return
+      endif
+
+c      print *,'Task ',me,' memix, intsize = ',memix,intsize
+#ifdef ALTIX
+      addr1 = %loc(ishared_heap)
+#else
+      addr1 = c_loc64(membase, memix, intsize)
+#endif
+      addr2 = addr1 + memnxt
+      if (element_size .eq. 4) then
+         type = 1
+      else if (element_size .eq. 8) then
+         type = 2
+      else
+         print *,'MEM_ALLOC: invalid element size ',element_size
+      endif
+
+c      print *,'Task ',me,' ADDR1, ADDR2 ',ADDR1,ADDR2
+#ifdef ALTIX
+      ixmem = get_index_from_base(addr2, ishared_heap, type)
+#else
+      ixmem = get_index_from_base(addr2, base, type) 
+#endif
+c      print *,'Task ',me,' IXMEM RETURNED FROM MEM_ALLOC: ',
+c     *       ixmem,' @base(ixmem) ',
+#ifdef ALTIX
+c     *   %loc(ishared_heap(ixmem)), %loc(dshared_heap(ixmem))
+#else
+c     *   c_loc64(base, ixmem, element_size)
+#endif
+      memnxt = memnxt + size
+c      print *,'Task ',me,' New value of memnxt = ',memnxt
+
+      return
+      end
+
+      subroutine mem_alloc_init(mem_needed, sheap_flag, ierr)
+c------------------------------------------------------------------
+c   Performs an actual malloc of the amount of memory needed.  This
+c   will only be done one time in the life of an execution, even
+c   if we are called multiple times.
+c------------------------------------------------------------------
+      implicit none
+      include 'mem_alloc_data.h'
+      include 'machine_types.h'
+      include 'parallel_info.h'
+c      include 'nothreads.h'
+#ifdef ALTIX
+      include 'sheap.h'
+#endif
+      
+      integer mem_needed
+      integer nwords, ierr
+      integer*8 c_loc64
+      integer sheap_flag
+      integer*8 temp
+
+      logical first
+      save first
+
+      data first/.true./
+
+      ierr = 0
+
+      if (first) then
+         first = .false.
+
+         call init_machine_types()   ! must be initialized.
+         temp = mem_needed * 1024
+         mem_malloced = temp * 1024
+
+         nwords = mem_malloced / intsize
+#ifdef ALTIX
+         call fallocate_it(sheap_flag, nwords, ierr )
+#else
+
+c--------------------------------------------------------------------------
+c   "Normal" memory allocation via malloc.
+c-------------------------------------------------------------------------
+
+         call malloc_wrapper(nwords, intsize, sheap_flag,
+     *                    membase, memix, ierr)
+#endif
+
+         memnxt = 0
+c         print *,'MEM_ALLOC_INIT: mem_needed ',mem_needed,
+c     *          ' mem_malloced ',mem_malloced
+c         print *,'Task ',me,' MEM BASE ADDR :',
+#ifdef ALTIX
+c     *      ishptr
+#else
+c     *      c_loc64(membase,memix,intsize)
+#endif
+c         print *,'Task ',me,
+c     *     ' memix at end of mem_alloc_init= ',memix
+      endif
+
+      return
+      end
+      
+      subroutine mem_alloc_reset()
+c-----------------------------------------------------------------------
+c   Resets the "next" pointer for the mem_alloc block.
+c----------------------------------------------------------------------
+      implicit none
+      include 'mem_alloc_data.h'
+      
+      memnxt = 0
+      return
+      end
+
+      subroutine mem_alloc_query(nbused)
+c--------------------------------------------------------------------------
+c   Returns the total bytes used so far.
+c--------------------------------------------------------------------------
+      implicit none
+      include 'mem_alloc_data.h'
+
+      integer*8 nbused
+      nbused = memnxt
+      return
+      end 
+
+      integer*8 function get_mem_base_addr()
+      implicit none
+c--------------------------------------------------------------------------
+c   Returns the address of the processor's heap memory.
+c--------------------------------------------------------------------------
+
+      include 'mem_alloc_data.h'
+      include 'machine_types.h'
+      integer*8 c_loc64
+
+#ifdef ALTIX
+      include 'sheap.h'
+
+      get_mem_base_addr = ishptr
+#else
+      get_mem_base_addr = c_loc64(membase, memix, intsize)
+#endif
+      return
+      end 
+
+      subroutine mem_alloc_free(addr, ierr)
+c--------------------------------------------------------------------------
+c   Reclaims all memory allocated beyond "addr" in mem_alloc_init.
+c   This memory can then be claimed again via mem_alloc.
+c--------------------------------------------------------------------------
+      include 'mem_alloc_data.h' 
+      include 'machine_types.h'
+#ifdef ALTIX
+      include 'sheap.h'
+#endif
+      integer*8 addr
+      integer ierr
+
+      integer*8 c_loc64, base
+       
+      ierr = 0 
+#ifdef ALTIX
+      base = %loc(ishared_heap)
+#else
+      base = c_loc64(membase, memix, intsize)
+#endif
+      if (addr .lt. base) then
+         print *,'Error in mem_alloc_free: called with addr ',
+     *       addr,' but the base address is ',base
+         ierr = 1
+      endif
+      memnxt = addr - base
+      return
+      end
+
+      integer*8 function get_max_heap_usage()
+c--------------------------------------------------------------------------
+c   Returns the number of bytes malloced for heap memory.
+c--------------------------------------------------------------------------
+      implicit none
+      include 'mem_alloc_data.h'
+
+      get_max_heap_usage = mem_malloced
+      return
+      end
--- /dev/null	2014-10-10 00:17:42.528636087 +0200
+++ ./src/sia/include/mem_alloc_data.h	2014-10-14 13:06:57.735842888 +0200
@@ -0,0 +1,4 @@
+      common /mem_alloc_data/memnxt, memix, mem_malloced, membase
+      integer*8 memnxt
+      integer*8 memix, mem_malloced
+      integer membase(1)
--- /dev/null	2014-10-10 00:17:42.528636087 +0200
+++ ./src/sia/sip_shared/malloc_wrapper.c	2014-10-14 13:21:03.656435546 +0200
@@ -0,0 +1,136 @@
+/*
+*  Copyright (c) 2003-2010 University of Florida
+*
+*  This program is free software; you can redistribute it and/or modify
+*  it under the terms of the GNU General Public License as published by
+*  the Free Software Foundation; either version 2 of the License, or
+*  (at your option) any later version.
+*
+*  This program is distributed in the hope that it will be useful,
+*  but WITHOUT ANY WARRANTY; without even the implied warranty of
+*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*  GNU General Public License for more details.
+*
+*  The GNU General Public License is included in this distribution
+*  in the file COPYRIGHT.
+*/ 
+#include <stdio.h>
+#include <stdlib.h>      
+#include "f77_name.h"
+#include "f_types.h"
+#ifdef HP
+#include <stddef.h>
+#endif
+
+#ifdef ALTIX
+#include <mpp/shmem.h>
+#endif
+
+#define MAX_MEM_ALLOC_PTRS 1000
+f_int *malloced_pointers[MAX_MEM_ALLOC_PTRS];
+int malloced_len[MAX_MEM_ALLOC_PTRS];
+int n_malloced_pointers = 0;
+
+void F77_NAME(malloc_wrapper, MALLOC_WRAPPER)(f_int *nwords,
+                f_int *element_size, f_int *sheap_flag,
+                void *x, long long *ixmem, 
+                f_int *ierr)
+{
+   size_t nbytes = (*nwords) * (*element_size);
+   size_t nb_shmalloc;
+   f_int *fp, *fp2;
+   long long llvar;
+#ifdef HP
+   ptrdiff_t offset;
+#else
+   long long  offset;
+#endif
+
+   if (*sheap_flag) 
+   {
+#ifdef USE_SHMEM
+      nb_shmalloc = (size_t) nbytes;
+      printf("Call shmalloc with %ld\n", nb_shmalloc);
+      fp = (f_int *) shmalloc(nb_shmalloc);
+      printf("Pointer from shmalloc: %x\n", fp);
+#else
+      printf("Error: shmalloc not implemented for this machine.\n");
+      *ierr = -1; 
+      return;
+#endif
+   }
+   else
+   {
+      nbytes = (*nwords);
+      nbytes *= (*element_size);
+      nbytes += 8;
+
+      fp = (f_int *) malloc(nbytes);
+   }
+
+   if (!fp)
+   {
+      printf("(SH)MALLOC ERROR: nwords %d, element size %d\n",*nwords,
+              *element_size);
+      *ierr = -1;
+      return;
+   }
+  
+   llvar = (long long) fp;
+   if (llvar/8*8 == llvar) 
+      fp2 = fp;
+   else
+      fp2 = fp + 1;
+   
+   /* Enter the memory pointer into the set of malloc'd pointers. */
+   if (n_malloced_pointers >= MAX_MEM_ALLOC_PTRS)
+   {
+      printf("Error: Limit of %d mem_alloc pointers has been exceeded.\n",
+             MAX_MEM_ALLOC_PTRS);
+      *ierr = -1;
+      return;
+   }
+
+   malloced_pointers[n_malloced_pointers] = fp;
+   malloced_len[n_malloced_pointers] = nbytes;
+   n_malloced_pointers++; 
+ 
+    offset = ( fp2 - (f_int *) x);
+   *ixmem = (long long) (( fp2 - (f_int *) x) / (*element_size/sizeof(f_int)) + 1);
+    /* printf("malloc_wrapper: fp = %x %ld, address of x = %x %ld, ixmem = %ld\n",fp,fp,x,x,*ixmem);  */ 
+
+   *ierr = 0;
+}
+
+void F77_NAME(free_mem_alloc, FREE_MEM_ALLOC) ()
+{
+   /* Frees all memory allocated by calls to mem_alloc */
+   int i;
+
+   for (i = 0; i < n_malloced_pointers; i++)
+   {
+      free( malloced_pointers[i] );
+   }
+
+   n_malloced_pointers = 0;
+}
+
+long long F77_NAME(c_loc64, C_LOC64)(char *base, long long *ix, f_int *size)
+{
+   long long addr;
+
+   addr = (long long) base + (*ix-1)*(*size);
+   /* printf("C_LOC64: base address %x %ld, ix %ld, size %d, addr %x %ld\n",
+        base,base,*ix,*size,addr,addr); */
+   return addr;
+}
+
+long long F77_NAME(c_loc64p, C_LOC64P)(char *base, long long *ix, f_int *size)
+{
+   long long addr;
+
+   addr = (long long) base + (*ix-1)*(*size);
+   return addr;
+}
+
+