Actual source code: mal.c

  1: /*
  2:     Code that allows a user to dictate what malloc() PETSc uses.
  3: */
  4: #define PETSC_DESIRE_FEATURE_TEST_MACROS /* for posix_memalign() */
  5: #include <petscsys.h>
  6: #include <stdarg.h>
  7: #if defined(PETSC_HAVE_MALLOC_H)
  8:   #include <malloc.h>
  9: #endif
 10: #if defined(PETSC_HAVE_MEMKIND)
 11:   #include <errno.h>
 12:   #include <memkind.h>
 13: typedef enum {
 14:   PETSC_MK_DEFAULT       = 0,
 15:   PETSC_MK_HBW_PREFERRED = 1
 16: } PetscMemkindType;
 17: PetscMemkindType currentmktype  = PETSC_MK_HBW_PREFERRED;
 18: PetscMemkindType previousmktype = PETSC_MK_HBW_PREFERRED;
 19: #endif
 20: /*
 21:         We want to make sure that all mallocs of double or complex numbers are complex aligned.
 22:     1) on systems with memalign() we call that routine to get an aligned memory location
 23:     2) on systems without memalign() we
 24:        - allocate one sizeof(PetscScalar) extra space
 25:        - we shift the pointer up slightly if needed to get PetscScalar aligned
 26:        - if shifted we store at ptr[-1] the amount of shift (plus a classid)
 27: */
 28: #define SHIFT_CLASSID 456123

 30: PETSC_EXTERN PetscErrorCode PetscMallocAlign(size_t mem, PetscBool clear, int line, const char func[], const char file[], void **result)
 31: {
 32:   if (!mem) {
 33:     *result = NULL;
 34:     return PETSC_SUCCESS;
 35:   }
 36: #if PetscDefined(HAVE_MEMKIND)
 37:   {
 38:     int err = memkind_posix_memalign(currentmktype ? MEMKIND_HBW_PREFERRED : MEMKIND_DEFAULT, result, PETSC_MEMALIGN, mem);
 39:     PetscCheck(err != EINVAL, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memkind: invalid 3rd or 4th argument of memkind_posix_memalign()");
 40:     if (err == ENOMEM) PetscInfo(NULL, "Memkind: fail to request HBW memory %.0f, falling back to normal memory\n", (PetscLogDouble)mem);
 41:     PetscCheck(*result, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memory requested %.0f", (PetscLogDouble)mem);
 42:     if (clear) PetscCall(PetscMemzero(*result, mem));
 43:   }
 44: #else /* PetscDefined(HAVE_MEMKIND) */
 45:   #if PetscDefined(HAVE_DOUBLE_ALIGN_MALLOC) && (PETSC_MEMALIGN == 8)
 46:   if (clear) *result = calloc(1 + mem / sizeof(int), sizeof(int));
 47:   else *result = malloc(mem);

 49:   PetscCheck(*result, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memory requested %.0f", (PetscLogDouble)mem);
 50:   if (PetscLogMemory) PetscCall(PetscMemzero(*result, mem));
 51:   #elif PetscDefined(HAVE_POSIX_MEMALIGN)
 52:   int ret = posix_memalign(result, PETSC_MEMALIGN, mem);
 53:   PetscCheck(ret == 0, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memory requested %.0f", (PetscLogDouble)mem);
 54:   if (clear || PetscLogMemory) PetscCall(PetscMemzero(*result, mem));
 55:   #else  /* PetscDefined(HAVE_DOUBLE_ALIGN_MALLOC) || PetscDefined(HAVE_POSIX_MEMALIGN) */
 56:   {
 57:     int *ptr, shift;
 58:     /*
 59:       malloc space for two extra chunks and shift ptr 1 + enough to get it PetscScalar aligned
 60:     */
 61:     if (clear) {
 62:       ptr = (int *)calloc(1 + (mem + 2 * PETSC_MEMALIGN) / sizeof(int), sizeof(int));
 63:     } else {
 64:       ptr = (int *)malloc(mem + 2 * PETSC_MEMALIGN);
 65:     }
 66:     PetscCheck(ptr, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memory requested %.0f", (PetscLogDouble)mem);
 67:     shift          = (int)(((PETSC_UINTPTR_T)ptr) % PETSC_MEMALIGN);
 68:     shift          = (2 * PETSC_MEMALIGN - shift) / sizeof(int);
 69:     ptr[shift - 1] = shift + SHIFT_CLASSID;
 70:     ptr += shift;
 71:     *result = (void *)ptr;
 72:     if (PetscLogMemory) PetscCall(PetscMemzero(*result, mem));
 73:   }
 74:   #endif /* PetscDefined(HAVE_DOUBLE_ALIGN_MALLOC) || PetscDefined(HAVE_POSIX_MEMALIGN) */
 75: #endif   /* PetscDefined(HAVE_MEMKIND) */
 76:   return PETSC_SUCCESS;
 77: }

 79: PETSC_EXTERN PetscErrorCode PetscFreeAlign(void *ptr, int line, const char func[], const char file[])
 80: {
 81:   if (!ptr) return PETSC_SUCCESS;
 82: #if PetscDefined(HAVE_MEMKIND)
 83:   memkind_free(0, ptr); /* specify the kind to 0 so that memkind will look up for the right type */
 84: #else                   /* PetscDefined(HAVE_MEMKIND) */
 85:   #if (!(PetscDefined(HAVE_DOUBLE_ALIGN_MALLOC) && (PETSC_MEMALIGN == 8)) && !PetscDefined(HAVE_POSIX_MEMALIGN))
 86:   {
 87:     /*
 88:       Previous int tells us how many ints the pointer has been shifted from
 89:       the original address provided by the system malloc().
 90:     */
 91:     const int shift = *((int *)ptr - 1) - SHIFT_CLASSID;

 93:     PetscCheck(shift <= PETSC_MEMALIGN - 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Likely memory corruption in heap");
 94:     PetscCheck(shift >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Likely memory corruption in heap");
 95:     ptr = (void *)((int *)ptr - shift);
 96:   }
 97:   #endif

 99:   #if PetscDefined(HAVE_FREE_RETURN_INT)
100:   int err = free(ptr);
101:   PetscCheck(!err, PETSC_COMM_SELF, PETSC_ERR_PLIB, "System free returned error %d", err);
102:   #else
103:   free(ptr);
104:   #endif
105: #endif
106:   return PETSC_SUCCESS;
107: }

109: PETSC_EXTERN PetscErrorCode PetscReallocAlign(size_t mem, int line, const char func[], const char file[], void **result)
110: {
111:   if (!mem) {
112:     PetscCall(PetscFreeAlign(*result, line, func, file));
113:     *result = NULL;
114:     return PETSC_SUCCESS;
115:   }
116: #if PetscDefined(HAVE_MEMKIND)
117:   *result = memkind_realloc(currentmktype ? MEMKIND_HBW_PREFERRED : MEMKIND_DEFAULT, *result, mem);
118: #else
119:   #if (!(PetscDefined(HAVE_DOUBLE_ALIGN_MALLOC) && (PETSC_MEMALIGN == 8)) && !PetscDefined(HAVE_POSIX_MEMALIGN))
120:   {
121:     /*
122:       Previous int tells us how many ints the pointer has been shifted from
123:       the original address provided by the system malloc().
124:     */
125:     int shift = *(((int *)*result) - 1) - SHIFT_CLASSID;
126:     PetscCheck(shift <= PETSC_MEMALIGN - 1, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Likely memory corruption in heap");
127:     PetscCheck(shift >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Likely memory corruption in heap");
128:     *result = (void *)(((int *)*result) - shift);
129:   }
130:   #endif

132:   #if (PetscDefined(HAVE_DOUBLE_ALIGN_MALLOC) && (PETSC_MEMALIGN == 8)) || PetscDefined(HAVE_POSIX_MEMALIGN)
133:   *result = realloc(*result, mem);
134:   #else
135:   {
136:     /*
137:       malloc space for two extra chunks and shift ptr 1 + enough to get it PetscScalar aligned
138:     */
139:     int *ptr = (int *)realloc(*result, mem + 2 * PETSC_MEMALIGN);
140:     if (ptr) {
141:       int shift      = (int)(((PETSC_UINTPTR_T)ptr) % PETSC_MEMALIGN);
142:       shift          = (2 * PETSC_MEMALIGN - shift) / sizeof(int);
143:       ptr[shift - 1] = shift + SHIFT_CLASSID;
144:       ptr += shift;
145:       *result = (void *)ptr;
146:     } else {
147:       *result = NULL;
148:     }
149:   }
150:   #endif
151: #endif
152:   PetscCheck(*result, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memory requested %.0f", (PetscLogDouble)mem);
153: #if PetscDefined(HAVE_POSIX_MEMALIGN)
154:   /* There are no standard guarantees that realloc() maintains the alignment of memalign(), so I think we have to
155:    * realloc and, if the alignment is wrong, malloc/copy/free. */
156:   if (((size_t)*result) % PETSC_MEMALIGN) {
157:     void *newResult;
158:   #if PetscDefined(HAVE_MEMKIND)
159:     {
160:       int err = memkind_posix_memalign(currentmktype ? MEMKIND_HBW_PREFERRED : MEMKIND_DEFAULT, &newResult, PETSC_MEMALIGN, mem);
161:       PetscCheck(err != EINVAL, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memkind: invalid 3rd or 4th argument of memkind_posix_memalign()");
162:       if (err == ENOMEM) PetscInfo(NULL, "Memkind: fail to request HBW memory %.0f, falling back to normal memory\n", (PetscLogDouble)mem);
163:     }
164:     PetscCheck(newResult, PETSC_COMM_SELF, PETSC_ERR_MEM, "Memory requested %.0f", (PetscLogDouble)mem);
165:   #else
166:     int ret = posix_memalign(&newResult, PETSC_MEMALIGN, mem);
167:     PetscCheck(ret == 0, PETSC_COMM_SELF, PETSC_ERR_LIB, "posix_memalign() failed with error code %d, memory requested %.0f", ret, (PetscLogDouble)mem);
168:   #endif
169:     PetscCall(PetscMemcpy(newResult, *result, mem));
170:   #if PetscDefined(HAVE_FREE_RETURN_INT)
171:     {
172:       int err = free(*result);
173:       PetscCheck(!err, PETSC_COMM_SELF, PETSC_ERR_PLIB, "System free returned error %d", err);
174:     }
175:   #else
176:     #if defined(PETSC_HAVE_MEMKIND)
177:     memkind_free(0, *result);
178:     #else
179:     free(*result);
180:     #endif
181:   #endif
182:     *result = newResult;
183:   }
184: #endif
185:   return PETSC_SUCCESS;
186: }

188: PetscErrorCode (*PetscTrMalloc)(size_t, PetscBool, int, const char[], const char[], void **) = PetscMallocAlign;
189: PetscErrorCode (*PetscTrFree)(void *, int, const char[], const char[])                       = PetscFreeAlign;
190: PetscErrorCode (*PetscTrRealloc)(size_t, int, const char[], const char[], void **)           = PetscReallocAlign;

192: PETSC_INTERN PetscBool petscsetmallocvisited;
193: PetscBool              petscsetmallocvisited = PETSC_FALSE;

195: /*@C
196:   PetscMallocSet - Sets the underlying allocation routines used by `PetscMalloc()` and `PetscFree()`

198:   Not Collective, No Fortran Support

200:   Input Parameters:
201: + imalloc - the routine that provides the `malloc()` implementation (also provides `calloc()`, which is used depending on the second argument)
202: . ifree   - the routine that provides the `free()` implementation
203: - iralloc - the routine that provides the `realloc()` implementation

205:   Level: developer

207:   Note:
208:   This routine MUST be called before `PetscInitialize()` and may be
209:   called only once.

211: .seealso: `PetscMallocClear()`, `PetscInitialize()`, `PetscMalloc()`, `PetscFree()`
212: @*/
213: PetscErrorCode PetscMallocSet(PetscErrorCode (*imalloc)(size_t, PetscBool, int, const char[], const char[], void **), PetscErrorCode (*ifree)(void *, int, const char[], const char[]), PetscErrorCode (*iralloc)(size_t, int, const char[], const char[], void **))
214: {
215:   PetscFunctionBegin;
216:   PetscCheck(!petscsetmallocvisited || !(imalloc != PetscTrMalloc || ifree != PetscTrFree), PETSC_COMM_SELF, PETSC_ERR_SUP, "cannot call multiple times");
217:   PetscTrMalloc         = imalloc;
218:   PetscTrFree           = ifree;
219:   PetscTrRealloc        = iralloc;
220:   petscsetmallocvisited = PETSC_TRUE;
221:   PetscFunctionReturn(PETSC_SUCCESS);
222: }

224: /*@
225:   PetscMallocClear - Resets the routines used by `PetscMalloc()` and `PetscFree()`

227:   Not Collective

229:   Level: developer

231:   Notes:
232:   In general one should never run a PETSc program with different `malloc()` and
233:   `free()` settings for different parts; this is because one NEVER wants to
234:   `free()` an address that was malloced by a different memory management system

236:   Called in `PetscFinalize()` so that if `PetscInitialize()` is called again it starts with a fresh slate of allocation information

238: .seealso: `PetscMallocSet()`, `PetscMalloc()`, `PetscFree()`
239: @*/
240: PetscErrorCode PetscMallocClear(void)
241: {
242:   PetscFunctionBegin;
243:   PetscTrMalloc         = PetscMallocAlign;
244:   PetscTrFree           = PetscFreeAlign;
245:   PetscTrRealloc        = PetscReallocAlign;
246:   petscsetmallocvisited = PETSC_FALSE;
247:   PetscFunctionReturn(PETSC_SUCCESS);
248: }

250: PetscErrorCode PetscMemoryTrace(const char label[])
251: {
252:   PetscLogDouble        mem, mal;
253:   static PetscLogDouble oldmem = 0, oldmal = 0;

255:   PetscFunctionBegin;
256:   PetscCall(PetscMemoryGetCurrentUsage(&mem));
257:   PetscCall(PetscMallocGetCurrentUsage(&mal));

259:   PetscCall(PetscPrintf(PETSC_COMM_WORLD, "%s High water  %8.3f MB increase %8.3f MB Current %8.3f MB increase %8.3f MB\n", label, mem * 1e-6, (mem - oldmem) * 1e-6, mal * 1e-6, (mal - oldmal) * 1e-6));
260:   oldmem = mem;
261:   oldmal = mal;
262:   PetscFunctionReturn(PETSC_SUCCESS);
263: }

265: static PetscErrorCode (*PetscTrMallocOld)(size_t, PetscBool, int, const char[], const char[], void **) = PetscMallocAlign;
266: static PetscErrorCode (*PetscTrReallocOld)(size_t, int, const char[], const char[], void **)           = PetscReallocAlign;
267: static PetscErrorCode (*PetscTrFreeOld)(void *, int, const char[], const char[])                       = PetscFreeAlign;

269: /*@
270:   PetscMallocSetDRAM - Set `PetscMalloc()` to use DRAM.
271:   If memkind is available, change the memkind type. Otherwise, switch the
272:   current malloc and free routines to the `PetscMallocAlign()` and
273:   `PetscFreeAlign()` (PETSc default).

275:   Not Collective

277:   Level: developer

279:   Note:
280:   This provides a way to do the allocation on DRAM temporarily. One
281:   can switch back to the previous choice by calling `PetscMallocReset()`.

283: .seealso: `PetscMallocReset()`, `PetscMalloc()`, `PetscFree()`
284: @*/
285: PetscErrorCode PetscMallocSetDRAM(void)
286: {
287:   PetscFunctionBegin;
288:   if (PetscTrMalloc == PetscMallocAlign) {
289: #if defined(PETSC_HAVE_MEMKIND)
290:     previousmktype = currentmktype;
291:     currentmktype  = PETSC_MK_DEFAULT;
292: #endif
293:   } else {
294:     /* Save the previous choice */
295:     PetscTrMallocOld  = PetscTrMalloc;
296:     PetscTrReallocOld = PetscTrRealloc;
297:     PetscTrFreeOld    = PetscTrFree;
298:     PetscTrMalloc     = PetscMallocAlign;
299:     PetscTrFree       = PetscFreeAlign;
300:     PetscTrRealloc    = PetscReallocAlign;
301:   }
302:   PetscFunctionReturn(PETSC_SUCCESS);
303: }

305: /*@
306:   PetscMallocResetDRAM - Reset the changes made by `PetscMallocSetDRAM()`

308:   Not Collective

310:   Level: developer

312: .seealso: `PetscMallocSetDRAM()`
313: @*/
314: PetscErrorCode PetscMallocResetDRAM(void)
315: {
316:   PetscFunctionBegin;
317:   if (PetscTrMalloc == PetscMallocAlign) {
318: #if defined(PETSC_HAVE_MEMKIND)
319:     currentmktype = previousmktype;
320: #endif
321:   } else {
322:     /* Reset to the previous choice */
323:     PetscTrMalloc  = PetscTrMallocOld;
324:     PetscTrRealloc = PetscTrReallocOld;
325:     PetscTrFree    = PetscTrFreeOld;
326:   }
327:   PetscFunctionReturn(PETSC_SUCCESS);
328: }

330: static PetscBool petscmalloccoalesce =
331: #if defined(PETSC_USE_MALLOC_COALESCED)
332:   PETSC_TRUE;
333: #else
334:   PETSC_FALSE;
335: #endif

337: /*@
338:   PetscMallocSetCoalesce - Use coalesced `PetscMalloc()` when allocating groups of objects, that is when using `PetscMallocN()`

340:   Not Collective

342:   Input Parameter:
343: . coalesce - `PETSC_TRUE` to use coalesced malloc for multi-memory allocation.

345:   Options Database Key:
346: . -malloc_coalesce - turn coalesced `PetscMallocN()` on or off

348:   Level: developer

350:   Notes:
351:   PETSc uses coalesced `PetscMallocN()` by default for optimized builds and not for debugging builds.

353:   This default can be changed via the command-line option `-malloc_coalesce` or by calling this function.

355:   This function can only be called immediately after `PetscInitialize()`

357: .seealso: `PetscMallocA()`, `PetscMalloc()`, `PetscFree()`
358: @*/
359: PetscErrorCode PetscMallocSetCoalesce(PetscBool coalesce)
360: {
361:   PetscFunctionBegin;
362:   petscmalloccoalesce = coalesce;
363:   PetscFunctionReturn(PETSC_SUCCESS);
364: }

366: /*@C
367:   PetscMallocA - Allocate and optionally clear one or more memory locations, possibly using coalesced malloc

369:   Not Collective, No Fortran Support

371:   Input Parameters:
372: + n        - number of objects to allocate (at least 1)
373: . clear    - use `calloc()` to allocate space initialized to zero
374: . lineno   - line number to attribute allocation (typically `__LINE__`)
375: . function - function to attribute allocation (typically `PETSC_FUNCTION_NAME`)
376: . filename - file name to attribute allocation (typically `__FILE__`)
377: - bytes0   - first of `n` object sizes

379:   Output Parameter:
380: . ptr0 - first of `n` pointers to allocate

382:   Level: developer

384:   Note:
385:   This function is not normally called directly by users, but rather via the macros `PetscMalloc1()`, `PetscMalloc2()`, or `PetscCalloc1()`, etc.

387: .seealso: `PetscMallocAlign()`, `PetscMallocSet()`, `PetscMalloc1()`, `PetscMalloc2()`, `PetscMalloc3()`, `PetscMalloc4()`, `PetscMalloc5()`, `PetscMalloc6()`, `PetscMalloc7()`,
388:           `PetscCalloc1()`, `PetscCalloc2()`, `PetscCalloc3()`, `PetscCalloc4()`, `PetscCalloc5()`, `PetscCalloc6()`, `PetscCalloc7()`, `PetscFreeA()`
389: @*/
390: PetscErrorCode PetscMallocA(int n, PetscBool clear, int lineno, const char *function, const char *filename, size_t bytes0, void *ptr0, ...)
391: {
392:   va_list Argp;
393:   size_t  bytes[8], sumbytes;
394:   void  **ptr[8];
395:   int     i;

397:   PetscFunctionBegin;
398:   PetscCheck(n <= 8, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Attempt to allocate %d objects but only 8 supported", n);
399:   bytes[0] = bytes0;
400:   ptr[0]   = (void **)ptr0;
401:   sumbytes = (bytes0 + PETSC_MEMALIGN - 1) & ~(PETSC_MEMALIGN - 1);
402:   va_start(Argp, ptr0);
403:   for (i = 1; i < n; i++) {
404:     bytes[i] = va_arg(Argp, size_t);
405:     ptr[i]   = va_arg(Argp, void **);
406:     sumbytes += (bytes[i] + PETSC_MEMALIGN - 1) & ~(PETSC_MEMALIGN - 1);
407:   }
408:   va_end(Argp);
409:   if (petscmalloccoalesce) {
410:     char *p;
411:     PetscCall((*PetscTrMalloc)(sumbytes, clear, lineno, function, filename, (void **)&p));
412:     if (p == NULL) {
413:       for (i = 0; i < n; i++) *ptr[i] = NULL;
414:     } else {
415:       for (i = 0; i < n; i++) {
416:         *ptr[i] = bytes[i] ? p : NULL;
417:         p       = (char *)PetscAddrAlign(p + bytes[i]);
418:       }
419:     }
420:   } else {
421:     for (i = 0; i < n; i++) PetscCall((*PetscTrMalloc)(bytes[i], clear, lineno, function, filename, ptr[i]));
422:   }
423:   PetscFunctionReturn(PETSC_SUCCESS);
424: }

426: /*@C
427:   PetscFreeA - Free one or more memory locations, possibly allocated using coalesced `PetscMallocN()`

429:   Not Collective, No Fortran Support

431:   Input Parameters:
432: + n        - number of objects to free (at least 1)
433: . lineno   - line number to attribute deallocation (typically `__LINE__`)
434: . function - function to attribute deallocation (typically `PETSC_FUNCTION_NAME`)
435: . filename - file name to attribute deallocation (typically `__FILE__`)
436: - ptr0     - first of `n` pointers to free

438:   Level: developer

440:   Notes:
441:   This function is not normally called directly by users, but rather via the macros `PetscFree()`, `PetscFree2()`, etc.

443:   The pointers are zeroed to prevent users from accidentally reusing space that has been freed.

445:   If the arguments were obtained via `PetscMallocA()`, `PetscMalloc2()`, `PetscMalloc3()`, etc., then the arguments must be passed in the same order to the corresponding `PetscFreeA()`, `PetscFree2()`, `PetscFree3()`, respectively.

447: .seealso: `PetscMallocAlign()`, `PetscMallocSet()`, `PetscMallocA()`, `PetscFree1()`, `PetscFree2()`, `PetscFree3()`, `PetscFree4()`, `PetscFree5()`, `PetscFree6()`, `PetscFree7()`
448: @*/
449: PetscErrorCode PetscFreeA(int n, int lineno, const char *function, const char *filename, void *ptr0, ...)
450: {
451:   va_list Argp;
452:   void  **ptr[8];
453:   int     i;

455:   PetscFunctionBegin;
456:   PetscCheck((n >= 1) && (n <= 8), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Attempt to allocate %d objects but only up to 8 supported", n);
457:   ptr[0] = (void **)ptr0;
458:   va_start(Argp, ptr0);
459:   for (i = 1; i < n; i++) ptr[i] = va_arg(Argp, void **);
460:   va_end(Argp);
461:   if (petscmalloccoalesce) {
462:     for (i = 0; i < n; i++) { /* Find first nonempty allocation */
463:       if (*ptr[i]) break;
464:     }
465:     while (--n > i) *ptr[n] = NULL;
466:     PetscCall((*PetscTrFree)(*ptr[n], lineno, function, filename));
467:     *ptr[n] = NULL;
468:   } else {
469:     while (--n >= 0) {
470:       PetscCall((*PetscTrFree)(*ptr[n], lineno, function, filename));
471:       *ptr[n] = NULL;
472:     }
473:   }
474:   PetscFunctionReturn(PETSC_SUCCESS);
475: }