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raafatfekiraafatfeki
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Merge pull request #8433 from raafatfeki/topic/fcoll_readall
mca/fcoll: read_all Receive data without temp buff by using MPI datatypes
2 parents 651e2ed + b8dd71d commit e894138

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6 files changed

+232
-232
lines changed

6 files changed

+232
-232
lines changed

‎ompi/mca/fcoll/dynamic_gen2/fcoll_dynamic_gen2.h

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
* University of Stuttgart. All rights reserved.
1010
* Copyright (c) 2004-2005 The Regents of the University of California.
1111
* All rights reserved.
12-
* Copyright (c) 2008-2020 University of Houston. All rights reserved.
12+
* Copyright (c) 2008-2021 University of Houston. All rights reserved.
1313
* Copyright (c) 2015-2018 Research Organization for Information Science
1414
* and Technology (RIST). All rights reserved.
1515
* $COPYRIGHT$
@@ -30,6 +30,9 @@
3030
#include "ompi/mca/fcoll/base/base.h"
3131
#include "ompi/mca/common/ompio/common_ompio.h"
3232

33+
#define FCOLL_DYNAMIC_GEN2_SHUFFLE_TAG 123
34+
#define INIT_LEN 10
35+
3336
BEGIN_C_DECLS
3437

3538
/* Globally exported variables */

‎ompi/mca/fcoll/dynamic_gen2/fcoll_dynamic_gen2_file_read_all.c

Lines changed: 111 additions & 112 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
* University of Stuttgart. All rights reserved.
1010
* Copyright (c) 2004-2005 The Regents of the University of California.
1111
* All rights reserved.
12-
* Copyright (c) 2008-2015 University of Houston. All rights reserved.
12+
* Copyright (c) 2008-2021 University of Houston. All rights reserved.
1313
* Copyright (c) 2017-2018 Research Organization for Information Science
1414
* and Technology (RIST). All rights reserved.
1515
* Copyright (c) 2017 IBM Corporation. All rights reserved.
@@ -56,7 +56,6 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
5656
struct ompi_datatype_t *datatype,
5757
ompi_status_public_t *status)
5858
{
59-
MPI_Aint position = 0;
6059
MPI_Aint total_bytes = 0; /* total bytes to be read */
6160
MPI_Aint bytes_to_read_in_cycle = 0; /* left to be read in a cycle*/
6261
MPI_Aint bytes_per_cycle = 0; /* total read in each cycle by each process*/
@@ -75,7 +74,6 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
7574
int iov_index = 0;
7675
size_t current_position = 0;
7776
struct iovec *local_iov_array=NULL, *global_iov_array=NULL;
78-
char *receive_buf = NULL;
7977
MPI_Aint *memory_displacements=NULL;
8078
/* global iovec at the readers that contain the iovecs created from
8179
file_set_view */
@@ -96,12 +94,12 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
9694
size_t max_data = 0;
9795
MPI_Aint *total_bytes_per_process = NULL;
9896
ompi_datatype_t **sendtype = NULL;
99-
MPI_Request *send_req=NULL, recv_req=NULL;
97+
MPI_Request *send_req = NULL;
98+
MPI_Request recv_req = MPI_REQUEST_NULL;
10099
int my_aggregator =-1;
101-
bool recvbuf_is_contiguous=false;
102-
size_t ftype_size;
103-
ptrdiff_t ftype_extent, lb;
104100

101+
int* blocklength_proc = NULL;
102+
ptrdiff_t* displs_proc = NULL;
105103

106104
#if OMPIO_FCOLL_WANT_TIME_BREAKDOWN
107105
double read_time = 0.0, start_read_time = 0.0, end_read_time = 0.0;
@@ -113,32 +111,16 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
113111
/**************************************************************************
114112
** 1. In case the data is not contigous in memory, decode it into an iovec
115113
**************************************************************************/
116-
117-
opal_datatype_type_size ( &datatype->super, &ftype_size );
118-
opal_datatype_get_extent ( &datatype->super, &lb, &ftype_extent );
119-
120-
if ( (ftype_extent == (ptrdiff_t) ftype_size) &&
121-
opal_datatype_is_contiguous_memory_layout(&datatype->super,1) &&
122-
0 == lb ) {
123-
recvbuf_is_contiguous = true;
124-
}
125-
126-
127-
if (! recvbuf_is_contiguous ) {
128-
ret = mca_common_ompio_decode_datatype ((struct ompio_file_t *)fh,
129-
datatype,
130-
count,
131-
buf,
132-
&max_data,
133-
fh->f_mem_convertor,
134-
&decoded_iov,
135-
&iov_count);
136-
if (OMPI_SUCCESS != ret){
137-
goto exit;
138-
}
139-
}
140-
else {
141-
max_data = count * datatype->super.size;
114+
ret = mca_common_ompio_decode_datatype ((struct ompio_file_t *)fh,
115+
datatype,
116+
count,
117+
buf,
118+
&max_data,
119+
fh->f_mem_convertor,
120+
&decoded_iov,
121+
&iov_count);
122+
if (OMPI_SUCCESS != ret){
123+
goto exit;
142124
}
143125

144126
if ( MPI_STATUS_IGNORE != status ) {
@@ -743,6 +725,7 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
743725
start_rcomm_time = MPI_Wtime();
744726
#endif
745727
for (i=0;i<fh->f_procs_per_group;i++){
728+
size_t datatype_size;
746729
send_req[i] = MPI_REQUEST_NULL;
747730
if ( 0 < disp_index[i] ) {
748731
ompi_datatype_create_hindexed(disp_index[i],
@@ -751,16 +734,20 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
751734
MPI_BYTE,
752735
&sendtype[i]);
753736
ompi_datatype_commit(&sendtype[i]);
754-
ret = MCA_PML_CALL (isend(global_buf,
755-
1,
756-
sendtype[i],
757-
fh->f_procs_in_group[i],
758-
123,
759-
MCA_PML_BASE_SEND_STANDARD,
760-
fh->f_comm,
761-
&send_req[i]));
762-
if(OMPI_SUCCESS != ret){
763-
goto exit;
737+
opal_datatype_type_size(&sendtype[i]->super, &datatype_size);
738+
739+
if(datatype_size) {
740+
ret = MCA_PML_CALL (isend(global_buf,
741+
1,
742+
sendtype[i],
743+
fh->f_procs_in_group[i],
744+
FCOLL_DYNAMIC_GEN2_SHUFFLE_TAG,
745+
MCA_PML_BASE_SEND_STANDARD,
746+
fh->f_comm,
747+
&send_req[i]));
748+
if(OMPI_SUCCESS != ret){
749+
goto exit;
750+
}
764751
}
765752
}
766753
}
@@ -773,35 +760,80 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
773760
/**********************************************************
774761
*** 7f. Scatter the Data from the readers
775762
*********************************************************/
776-
if ( recvbuf_is_contiguous ) {
777-
receive_buf = &((char*)buf)[position];
778-
}
779-
else if (bytes_received) {
780-
/* allocate a receive buffer and copy the data that needs
781-
to be received into it in case the data is non-contigous
782-
in memory */
783-
receive_buf = malloc (bytes_received);
784-
if (NULL == receive_buf) {
763+
if(bytes_received) {
764+
size_t remaining = bytes_received;
765+
int block_index = -1;
766+
int blocklength_size = INIT_LEN;
767+
768+
ptrdiff_t recv_mem_address = 0;
769+
ompi_datatype_t *newType = MPI_DATATYPE_NULL;
770+
771+
blocklength_proc = (int *) calloc (blocklength_size, sizeof (int));
772+
displs_proc = (ptrdiff_t *) calloc (blocklength_size, sizeof (ptrdiff_t));
773+
774+
if (NULL == blocklength_proc || NULL == displs_proc ) {
785775
opal_output (1, "OUT OF MEMORY\n");
786776
ret = OMPI_ERR_OUT_OF_RESOURCE;
787777
goto exit;
788778
}
789-
}
779+
780+
while (remaining) {
781+
block_index++;
782+
783+
if(0 == block_index) {
784+
recv_mem_address = (ptrdiff_t) (decoded_iov[iov_index].iov_base) + current_position;
785+
}
786+
else {
787+
// Reallocate more memory if blocklength_size is not enough
788+
if(0 == block_index % INIT_LEN) {
789+
blocklength_size += INIT_LEN;
790+
blocklength_proc = (int *) realloc(blocklength_proc, blocklength_size * sizeof(int));
791+
displs_proc = (ptrdiff_t *) realloc(displs_proc, blocklength_size * sizeof(ptrdiff_t));
792+
}
793+
displs_proc[block_index] = (ptrdiff_t) (decoded_iov[iov_index].iov_base) +
794+
current_position - recv_mem_address;
795+
}
796+
797+
if (remaining >= (decoded_iov[iov_index].iov_len - current_position)) {
798+
blocklength_proc[block_index] = decoded_iov[iov_index].iov_len - current_position;
799+
800+
remaining = remaining - blocklength_proc[block_index];
801+
iov_index = iov_index + 1;
802+
current_position = 0;
803+
}
804+
else {
805+
blocklength_proc[block_index] = remaining;
806+
current_position += remaining;
807+
remaining = 0;
808+
}
809+
}
810+
811+
ompi_datatype_create_hindexed(block_index+1,
812+
blocklength_proc,
813+
displs_proc,
814+
MPI_BYTE,
815+
&newType);
816+
ompi_datatype_commit(&newType);
790817

791818
#if OMPIO_FCOLL_WANT_TIME_BREAKDOWN
792-
start_rcomm_time = MPI_Wtime();
819+
start_rcomm_time = MPI_Wtime();
793820
#endif
794-
ret = MCA_PML_CALL(irecv(receive_buf,
795-
bytes_received,
796-
MPI_BYTE,
797-
my_aggregator,
798-
123,
799-
fh->f_comm,
800-
&recv_req));
801-
if (OMPI_SUCCESS != ret){
802-
goto exit;
803-
}
821+
ret = MCA_PML_CALL(irecv((char *)recv_mem_address,
822+
1,
823+
newType,
824+
my_aggregator,
825+
FCOLL_DYNAMIC_GEN2_SHUFFLE_TAG,
826+
fh->f_comm,
827+
&recv_req));
828+
829+
if ( MPI_DATATYPE_NULL != newType ) {
830+
ompi_datatype_destroy(&newType);
831+
}
804832

833+
if (OMPI_SUCCESS != ret){
834+
goto exit;
835+
}
836+
}
805837

806838
if (my_aggregator == fh->f_rank){
807839
ret = ompi_request_wait_all (fh->f_procs_per_group,
@@ -816,50 +848,12 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
816848
if (OMPI_SUCCESS != ret){
817849
goto exit;
818850
}
819-
position += bytes_received;
820-
821-
/* If data is not contigous in memory, copy the data from the
822-
receive buffer into the buffer passed in */
823-
if (!recvbuf_is_contiguous ) {
824-
ptrdiff_t mem_address;
825-
size_t remaining = 0;
826-
size_t temp_position = 0;
827851

828-
remaining = bytes_received;
829-
830-
while (remaining) {
831-
mem_address = (ptrdiff_t)
832-
(decoded_iov[iov_index].iov_base) + current_position;
833-
834-
if (remaining >=
835-
(decoded_iov[iov_index].iov_len - current_position)) {
836-
memcpy ((IOVBASE_TYPE *) mem_address,
837-
receive_buf+temp_position,
838-
decoded_iov[iov_index].iov_len - current_position);
839-
remaining = remaining -
840-
(decoded_iov[iov_index].iov_len - current_position);
841-
temp_position = temp_position +
842-
(decoded_iov[iov_index].iov_len - current_position);
843-
iov_index = iov_index + 1;
844-
current_position = 0;
845-
}
846-
else {
847-
memcpy ((IOVBASE_TYPE *) mem_address,
848-
receive_buf+temp_position,
849-
remaining);
850-
current_position = current_position + remaining;
851-
remaining = 0;
852-
}
853-
}
854-
855-
if (NULL != receive_buf) {
856-
free (receive_buf);
857-
receive_buf = NULL;
858-
}
859-
}
860852
#if OMPIO_FCOLL_WANT_TIME_BREAKDOWN
861-
end_rcomm_time = MPI_Wtime();
862-
rcomm_time += end_rcomm_time - start_rcomm_time;
853+
if(bytes_received) {
854+
end_rcomm_time = MPI_Wtime();
855+
rcomm_time += end_rcomm_time - start_rcomm_time;
856+
}
863857
#endif
864858
} /* end for (index=0; index < cycles; index ++) */
865859

@@ -881,12 +875,6 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
881875
#endif
882876

883877
exit:
884-
if (!recvbuf_is_contiguous) {
885-
if (NULL != receive_buf) {
886-
free (receive_buf);
887-
receive_buf = NULL;
888-
}
889-
}
890878
if (NULL != global_buf) {
891879
free (global_buf);
892880
global_buf = NULL;
@@ -916,6 +904,17 @@ mca_fcoll_dynamic_gen2_file_read_all (ompio_file_t *fh,
916904
free (displs);
917905
displs = NULL;
918906
}
907+
908+
if (NULL != blocklength_proc) {
909+
free (blocklength_proc);
910+
blocklength_proc = NULL;
911+
}
912+
913+
if (NULL != displs_proc) {
914+
free (displs_proc);
915+
displs_proc = NULL;
916+
}
917+
919918
if (my_aggregator == fh->f_rank) {
920919

921920
if (NULL != sorted_file_offsets){

‎ompi/mca/fcoll/dynamic_gen2/fcoll_dynamic_gen2_file_write_all.c

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
* University of Stuttgart. All rights reserved.
1010
* Copyright (c) 2004-2005 The Regents of the University of California.
1111
* All rights reserved.
12-
* Copyright (c) 2008-2020 University of Houston. All rights reserved.
12+
* Copyright (c) 2008-2021 University of Houston. All rights reserved.
1313
* Copyright (c) 2015-2018 Research Organization for Information Science
1414
* and Technology (RIST). All rights reserved.
1515
* Copyright (c) 2017 IBM Corporation. All rights reserved.
@@ -36,8 +36,6 @@
3636

3737

3838
#define DEBUG_ON 0
39-
#define FCOLL_DYNAMIC_GEN2_SHUFFLE_TAG 123
40-
#define INIT_LEN 10
4139

4240
/*Used for loading file-offsets per aggregator*/
4341
typedef struct mca_io_ompio_local_io_array{

‎ompi/mca/fcoll/vulcan/fcoll_vulcan.h

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
* University of Stuttgart. All rights reserved.
1010
* Copyright (c) 2004-2005 The Regents of the University of California.
1111
* All rights reserved.
12-
* Copyright (c) 2008-2017 University of Houston. All rights reserved.
12+
* Copyright (c) 2008-2021 University of Houston. All rights reserved.
1313
* Copyright (c) 2015-2018 Research Organization for Information Science
1414
* and Technology (RIST). All rights reserved.
1515
* $COPYRIGHT$
@@ -30,6 +30,9 @@
3030
#include "ompi/mca/fcoll/base/base.h"
3131
#include "ompi/mca/common/ompio/common_ompio.h"
3232

33+
#define FCOLL_VULCAN_SHUFFLE_TAG 123
34+
#define INIT_LEN 10
35+
3336
BEGIN_C_DECLS
3437

3538
/* Globally exported variables */

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