bool SplitMPI_Communicator::CreateCommunicator(MPI_Comm comm_world, int np, int nb_ddc)
{
int n_DDC;
bool splitcomm;
if ((nb_ddc > 0) && (nb_ddc < np))
{ // if the number of total cores is larger than the number of DDCs is the same, two new MPI groups will be
// generated will be generated
#ifdef OGS_FEM_IPQC
splitcomm = true;
n_DDC = nb_ddc; // number of ddc
int DDC_ranks[n_DDC];
for (int k = 0; k < n_DDC; k++)
{
DDC_ranks[k] = k;
}
MPI_Comm comm_IPQC;
MPI_Group group_base, group_DDC, group_IPQC;
// define MPI group and communicator for DDC related processes WH
MPI_Comm_group(comm_world, &group_base);
MPI_Group_incl(group_base, n_DDC, DDC_ranks, &group_DDC); // define group flow and mass transport
MPI_Comm_create(comm_world, group_DDC, &comm_DDC);
// define MPI group and communicator for IPQC WH
MPI_Group_difference(group_base, group_DDC, &group_IPQC);
MPI_Comm_create(comm_world, group_IPQC, &comm_IPQC);
int myrank_IPQC, mysize_IPQC;
MPI_Group_size(group_DDC, &mysize); // WH
MPI_Group_rank(group_DDC, &myrank); // WH
MPI_Group_rank(group_IPQC, &myrank_IPQC);
MPI_Group_size(group_IPQC, &mysize_IPQC);
if (myrank_IPQC != MPI_UNDEFINED) // WH
std::cout << "After MPI_Init myrank_IPQC = " << myrank_IPQC << '\n';
if (myrank != MPI_UNDEFINED) // WH
std::cout << "After MPI_Init myrank_DDC = " << myrank << '\n';
if (myrank_IPQC != MPI_UNDEFINED) // ranks of group_IPQC will call to IPhreeqc
Call_IPhreeqc();
#endif
}
else
{ // if no -ddc is specified or the number of ddc is incorrect, make ddc = np, no new MPI groups willnot be
// generated;
splitcomm = false;
n_DDC = np;
comm_DDC = comm_world;
MPI_Comm_size(comm_DDC, &mysize);
MPI_Comm_rank(comm_DDC, &myrank);
std::cout << "After MPI_Init myrank_DDC = " << myrank << '\n';
}
return splitcomm;
}
int main( int argc, char **argv )
{
int rank, size, i;
MPI_Group group1, group2, group3, groupall, groupunion, newgroup;
MPI_Comm newcomm;
int ranks1[100], ranks2[100], ranks3[100];
int nranks1=0, nranks2=0, nranks3=0;
MPI_Init( &argc, &argv );
MPI_Barrier( MPI_COMM_WORLD );
MPI_Comm_rank( MPI_COMM_WORLD, &rank );
MPI_Comm_size( MPI_COMM_WORLD, &size );
MPI_Comm_group( MPI_COMM_WORLD, &groupall );
/* Divide groups */
for (i=0; i<size; i++)
if ( (i%3)==0 )
ranks1[nranks1++] = i;
else if ( (i%3)==1 )
ranks2[nranks2++] = i;
else
ranks3[nranks3++] = i;
MPI_Group_incl ( groupall, nranks1, ranks1, &group1 );
MPI_Group_incl ( groupall, nranks2, ranks2, &group2 );
MPI_Group_incl ( groupall, nranks3, ranks3, &group3 );
MPI_Group_difference ( groupall, group2, &groupunion );
MPI_Comm_create ( MPI_COMM_WORLD, group3, &newcomm );
newgroup = MPI_GROUP_NULL;
if (newcomm != MPI_COMM_NULL)
{
/* If we don't belong to group3, this would fail */
MPI_Comm_group ( newcomm, &newgroup );
}
/* Free the groups */
MPI_Group_free( &groupall );
MPI_Group_free( &group1 );
MPI_Group_free( &group2 );
MPI_Group_free( &group3 );
MPI_Group_free( &groupunion );
if (newgroup != MPI_GROUP_NULL)
{
MPI_Group_free( &newgroup );
}
/* Free the communicator */
if (newcomm != MPI_COMM_NULL)
MPI_Comm_free( &newcomm );
Test_Waitforall( );
MPI_Finalize();
return 0;
}
JNIEXPORT jlong JNICALL Java_mpi_Group_difference(
JNIEnv *env, jclass jthis, jlong group1, jlong group2)
{
MPI_Group newGroup;
int rc = MPI_Group_difference(
(MPI_Group)group1, (MPI_Group)group2, &newGroup);
ompi_java_exceptionCheck(env, rc);
return (jlong)newGroup;
}
int main (int argc, char **argv)
{
int num, i, rank, localRank;
MPI_Group all, odd, even;
MPI_Comm oddComm, evenComm;
char mess[11];
MPI_Init (&argc, &argv);
// copy all the processes in group "all"
MPI_Comm_group (MPI_COMM_WORLD, &all);
MPI_Comm_size (MPI_COMM_WORLD, &num);
MPI_Comm_rank (MPI_COMM_WORLD, &rank);
int grN = 0;
int ranks[num / 2];
for (i = 0; i < num; i += 2)
ranks[grN++] = i;
// extract from "all" only the odd ones
MPI_Group_excl (all, grN, ranks, &odd);
// sutract odd group from all to get the even ones
MPI_Group_difference (all, odd, &even);
MPI_Comm_create (MPI_COMM_WORLD, odd, &oddComm);
MPI_Comm_create (MPI_COMM_WORLD, even, &evenComm);
// check group membership
MPI_Group_rank (odd, &localRank);
if (localRank != MPI_UNDEFINED)
{
if (localRank == 0) // local group root, sets-up message
strcpy (mess, "ODD GROUP");
MPI_Bcast (mess, 11, MPI_CHAR, 0, oddComm);
MPI_Comm_free (&oddComm); // free communicator in processes where it is valid
}
else
{
MPI_Comm_rank (evenComm, &localRank);
if (localRank == 0) // local group root, sets-up message
strcpy (mess, "EVEN GROUP");
MPI_Bcast (mess, 11, MPI_CHAR, 0, evenComm);
MPI_Comm_free (&evenComm);
}
printf ("Process %i with local rank %i received %s\n", rank, localRank, mess);
// free up memory
MPI_Group_free (&all);
MPI_Group_free (&odd);
MPI_Group_free (&even);
MPI_Finalize ();
return 0;
}
/*
* Class: mpi_Group
* Method: difference
* Signature: (Lmpi/Group;Lmpi/Group;)J
*/
JNIEXPORT jlong JNICALL Java_mpi_Group_difference(JNIEnv *env, jclass jthis,
jobject group1, jobject group2)
{
MPI_Group newgroup;
ompi_java_clearFreeList(env) ;
MPI_Group_difference((MPI_Group)((*env)->GetLongField(env,group1,ompi_java.GrouphandleID)),
(MPI_Group)((*env)->GetLongField(env,group2,ompi_java.GrouphandleID)),
&newgroup);
return (jlong)newgroup;
}
int main(int argc, char **argv)
{
int rank, size, i;
MPI_Group groupall, groupunion, newgroup, group[GROUPS];
MPI_Comm newcomm;
int ranks[GROUPS][100];
int nranks[GROUPS] = { 0, 0, 0 };
MPI_Init(&argc, &argv);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_group(MPI_COMM_WORLD, &groupall);
/* Divide groups */
for (i = 0; i < size; i++)
ranks[i % GROUPS][nranks[i % GROUPS]++] = i;
for (i = 0; i < GROUPS; i++)
MPI_Group_incl(groupall, nranks[i], ranks[i], &group[i]);
MPI_Group_difference(groupall, group[1], &groupunion);
MPI_Comm_create(MPI_COMM_WORLD, group[2], &newcomm);
newgroup = MPI_GROUP_NULL;
if (newcomm != MPI_COMM_NULL)
{
/* If we don't belong to group[2], this would fail */
MPI_Comm_group(newcomm, &newgroup);
}
/* Free the groups */
MPI_Group_free(&groupall);
for (i = 0; i < GROUPS; i++)
MPI_Group_free(&group[i]);
MPI_Group_free(&groupunion);
if (newgroup != MPI_GROUP_NULL)
{
MPI_Group_free(&newgroup);
}
/* Free the communicator */
if (newcomm != MPI_COMM_NULL)
MPI_Comm_free(&newcomm);
Test_Waitforall();
Test_Global_Summary();
MPI_Finalize();
return 0;
}
static VALUE group_difference(VALUE self, VALUE rgrp2)
{
int rv;
MPI_Group *grp1, *grp2, *newgrp;
Data_Get_Struct(self, MPI_Group, grp1);
Data_Get_Struct(grp2, MPI_Group, grp2);
newgrp = ALLOC(MPI_Group);
rv = MPI_Group_difference(*grp1, *grp2, newgrp);
mpi_exception(rv);
return group_new(newgrp);
}
void mpi_group_difference_f(MPI_Fint *group1, MPI_Fint *group2, MPI_Fint *newgroup, MPI_Fint *ierr)
{
ompi_group_t *c_group1, *c_group2, *c_newgroup;
/* Make the fortran to c representation conversion */
c_group1 = MPI_Group_f2c(*group1);
c_group2 = MPI_Group_f2c(*group2);
*ierr = OMPI_INT_2_FINT(MPI_Group_difference(c_group1, c_group2,
&c_newgroup));
/* translate the results from c to fortran */
if (MPI_SUCCESS == OMPI_FINT_2_INT(*ierr)) {
*newgroup = c_newgroup->grp_f_to_c_index;
}
}
int main (int argc, char **argv)
{
int num, i, rank;
MPI_Group all, odd, even;
MPI_Init (&argc, &argv);
// copy all the processes in group "all"
MPI_Comm_group (MPI_COMM_WORLD, &all);
MPI_Comm_size (MPI_COMM_WORLD, &num);
MPI_Comm_rank (MPI_COMM_WORLD, &rank);
int grN = 0;
int ranks[num / 2];
for (i = 0; i < num; i += 2)
ranks[grN++] = i;
// extract from "all" only the odd ones
MPI_Group_excl (all, grN, ranks, &odd);
// sutract odd group from all to get the even ones
MPI_Group_difference (all, odd, &even);
// print group sizes
if (rank == 0)
{
MPI_Group_size (odd, &i);
printf ("Odd group has %i processes\n", i);
MPI_Group_size (even, &i);
printf ("Even group has %i processes\n", i);
}
// check group membership
MPI_Group_rank (odd, &i);
if (i == MPI_UNDEFINED)
printf ("Process %i belongs to even group\n", rank);
else
printf ("Process %i belongs to odd group\n", rank);
// free up memory
MPI_Group_free (&all);
MPI_Group_free (&odd);
MPI_Group_free (&even);
MPI_Finalize ();
return 0;
}
dart_ret_t dart_group_delmember(
dart_group_t *g,
dart_unit_t unitid)
{
int array[1];
MPI_Group newgroup, group_all;
MPI_Comm_group(MPI_COMM_WORLD, &group_all);
array[0] = unitid;
MPI_Group_incl(
group_all,
1,
array,
&newgroup);
MPI_Group_difference(
g -> mpi_group,
newgroup,
&(g -> mpi_group));
return DART_OK;
}
value caml_mpi_group_difference(value group1, value group2)
{
MPI_Group group;
MPI_Group_difference(Group_val(group1), Group_val(group2), &group);
return caml_mpi_alloc_group(group);
}
int
main (int argc, char **argv)
{
int nprocs = -1;
int rank = -1;
int comm = MPI_COMM_WORLD;
char processor_name[128];
int namelen = 128;
int i;
int ranks[2], ranges[1][3];
MPI_Group newgroup[GROUP_CONSTRUCTOR_COUNT];
MPI_Group newgroup2[GROUP_CONSTRUCTOR_COUNT];
MPI_Comm temp;
MPI_Comm intercomm = MPI_COMM_NULL;
/* init */
MPI_Init (&argc, &argv);
MPI_Comm_size (comm, &nprocs);
MPI_Comm_rank (comm, &rank);
MPI_Get_processor_name (processor_name, &namelen);
printf ("(%d) is alive on %s\n", rank, processor_name);
fflush (stdout);
ranks[0] = 0;
ranks[1] = 1;
ranges[0][0] = 0;
ranges[0][1] = 2;
ranges[0][2] = 2;
MPI_Barrier (comm);
if (nprocs < 3) {
printf ("requires at least 3 tasks\n");
}
else {
/* create the groups */
if (GROUP_CONSTRUCTOR_COUNT > 0)
MPI_Comm_group (MPI_COMM_WORLD, &newgroup[0]);
if (GROUP_CONSTRUCTOR_COUNT > 1)
MPI_Group_incl (newgroup[0], 2, ranks, &newgroup[1]);
if (GROUP_CONSTRUCTOR_COUNT > 2)
MPI_Group_excl (newgroup[0], 2, ranks, &newgroup[2]);
if (GROUP_CONSTRUCTOR_COUNT > 3)
MPI_Group_range_incl (newgroup[0], 1, ranges, &newgroup[3]);
if (GROUP_CONSTRUCTOR_COUNT > 4)
MPI_Group_range_excl (newgroup[0], 1, ranges, &newgroup[4]);
if (GROUP_CONSTRUCTOR_COUNT > 5)
MPI_Group_union (newgroup[1], newgroup[3], &newgroup[5]);
if (GROUP_CONSTRUCTOR_COUNT > 6)
MPI_Group_intersection (newgroup[5], newgroup[2], &newgroup[6]);
if (GROUP_CONSTRUCTOR_COUNT > 7)
MPI_Group_difference (newgroup[5], newgroup[2], &newgroup[7]);
if (GROUP_CONSTRUCTOR_COUNT > 8) {
/* need lots of stuff for this constructor... */
MPI_Comm_split (MPI_COMM_WORLD, rank % 3, nprocs - rank, &temp);
if (rank % 3) {
MPI_Intercomm_create (temp, 0, MPI_COMM_WORLD,
(((nprocs % 3) == 2) && ((rank % 3) == 2)) ?
nprocs - 1 : nprocs - (rank % 3) - (nprocs % 3),
INTERCOMM_CREATE_TAG, &intercomm);
MPI_Comm_remote_group (intercomm, &newgroup[8]);
MPI_Comm_free (&intercomm);
}
else {
MPI_Comm_group (temp, &newgroup[8]);
}
MPI_Comm_free (&temp);
}
}
MPI_Barrier (comm);
printf ("(%d) Finished normally\n", rank);
MPI_Finalize ();
}
void repairComm(MPI_Comm * broken, MPI_Comm * repaired, int iteration, int * listFails, int * numFails,
int * numNodeFails, int sumPrevNumNodeFails, int argc, char ** argv, int verbosity) {
MPI_Comm tempShrink, unorderIntracomm, tempIntercomm;
int i, ret, result, procsNeeded = 0, oldRank, newRank, oldGroupSize, rankKey = 0, flag;
int * tempRanks, * failedRanks, * errCodes, rank, hostfileLineIndex;
MPI_Group oldGroup, failedGroup, shrinkGroup;
int hostfileLastLineIndex, tempLineIndex, * failedNodeList = NULL, * nodeList = NULL, totNodeFailed = 0;
double startTime = 0.0, endTime;
int nprocs, j, * shrinkMergeList;
char hostName[128];
gethostname(hostName, sizeof(hostName));
char ** appToLaunch;
char *** argvToLaunch;
int * procsNeededToLaunch;
MPI_Info * hostInfoToLaunch;
char ** hostNameToLaunch;
MPI_Comm_rank(*broken, &rank);
if(rank == 0)
startTime = MPI_Wtime();
#ifndef GLOBAL_DETECTION
MPI_Comm_size(*broken, &oldGroupSize);
MPI_Comm_group(*broken, &oldGroup);
MPI_Comm_rank(*broken, &oldRank);
OMPI_Comm_failure_ack(*broken);
OMPI_Comm_failure_get_acked(*broken, &failedGroup);
MPI_Group_size(failedGroup, &procsNeeded);
errCodes = (int *) malloc(sizeof(int) * procsNeeded);
// Figure out ranks of the processes which had failed
tempRanks = (int *) malloc(sizeof(int) * oldGroupSize);
failedRanks = (int *) malloc(sizeof(int) * oldGroupSize);
#pragma omp parallel for default(shared)
for(i = 0; i < oldGroupSize; i++)
tempRanks[i] = i;
MPI_Group_translate_ranks(failedGroup, procsNeeded, tempRanks, oldGroup, failedRanks);
#endif
double shrinkTime = MPI_Wtime();
// Shrink the broken communicator to remove failed procs
if(MPI_SUCCESS != (ret = OMPI_Comm_shrink(*broken, &tempShrink)))
printf("Iteration %d: OMPI_Comm_shrink (parent): ERROR!\n", iteration);
else {
if(verbosity > 1 )
printf("Iteration %d: OMPI_Comm_shrink (parent): SUCCESS\n", iteration);
}
if (verbosity > 0 && rank == 0)
printf("OMPI_Comm_shrink takes %0.6f Sec\n", MPI_Wtime() - shrinkTime);
#ifdef GLOBAL_DETECTION
MPI_Comm_group(*broken, &oldGroup);
MPI_Comm_group(tempShrink, &shrinkGroup);
MPI_Comm_size(*broken, &oldGroupSize);
MPI_Group_compare(oldGroup, shrinkGroup, &result);
if(result != MPI_IDENT)
MPI_Group_difference(oldGroup, shrinkGroup, &failedGroup);
MPI_Comm_rank(*broken, &oldRank);
MPI_Group_size(failedGroup, &procsNeeded);
errCodes = (int *) malloc(sizeof(int)*procsNeeded);
// Figure out ranks of the processes which had failed
tempRanks = (int*)malloc(sizeof(int)*oldGroupSize);
failedRanks = (int*)malloc(sizeof(int)*oldGroupSize);
#pragma omp parallel for default(shared)
for(i = 0; i < oldGroupSize; i++)
tempRanks[i] = i;
MPI_Group_translate_ranks(failedGroup, procsNeeded, tempRanks, oldGroup, failedRanks);
MPI_Group_free(&shrinkGroup);
#endif
// Assign number of failed processes
*numFails = procsNeeded;
hostNameToLaunch = (char **) malloc(procsNeeded * sizeof(char *));
if(verbosity > 0 && rank == 0)
printf("*** Iteration %d: Application: Number of process(es) failed in the corresponding "
"communicator is %d ***\n", iteration, procsNeeded);
if(rank == 0) {
endTime = MPI_Wtime();
printf("[%d]----- Creating failed process list takes %0.6f Sec (MPI_Wtime) -----\n", rank, endTime - startTime);
}
#ifdef RECOV_ON_SPARE_NODES
// Determining total number of node failed, and a list of them
hostfileLastLineIndex = getHostfileLastLineIndex(); //started from 0
nodeList = (int *) malloc((hostfileLastLineIndex+1) * sizeof(int));
memset(nodeList, 0, (hostfileLastLineIndex+1)*sizeof(int)); // initialize nodeList with 0's
for(int i = 0; i < procsNeeded; ++i) {
tempLineIndex = failedRanks[i]/SLOTS; //started from 0
nodeList[tempLineIndex] = 1;
}
for(int nodeCounter = 0; nodeCounter < (hostfileLastLineIndex+1); ++nodeCounter)
totNodeFailed += nodeList[nodeCounter];
*numNodeFails = totNodeFailed;
// Check if there is sufficient spare node available for recovery
if((hostfileLastLineIndex - totNodeFailed -sumPrevNumNodeFails) < (oldGroupSize-1)/SLOTS) {
if(rank == 0)
printf("[%d] There is no sufficient spare node available for recovery.\n", rank);
exit(0);
}
failedNodeList = (int *) malloc(totNodeFailed * sizeof(int));
memset(failedNodeList, 0, totNodeFailed * sizeof(int)); // initialize failedNodeList with 0's
int failedNodeCounter = 0;
for(int nodeCounter = 0; nodeCounter < (hostfileLastLineIndex+1); ++nodeCounter) {
if(nodeList[nodeCounter] == 1)
failedNodeList[failedNodeCounter++] = nodeCounter;
}
#endif
char * hostNameFailed = NULL;
#pragma omp parallel for default(shared)
for(i = 0; i < procsNeeded; ++i) {
// Assign list of processes failed
listFails[i] = failedRanks[i];
#ifdef RUN_ON_COMPUTE_NODES
tempLineIndex = failedRanks[i]/SLOTS; //started from 0
#ifdef RECOV_ON_SPARE_NODES
for(int j = 0; j < totNodeFailed; ++j) {
if(failedNodeList[j] == tempLineIndex)
hostfileLineIndex = hostfileLastLineIndex - j - sumPrevNumNodeFails;
}
#else // Recovery on the same node (no node failure, only process failure)
hostfileLineIndex = tempLineIndex;
#endif
hostNameToLaunch[i] = getHostToLaunch(hostfileLineIndex);
hostNameFailed = getHostToLaunch(tempLineIndex);
#else // Run on head node or personal machine
hostNameToLaunch[i] = (char *)hostName;
hostNameFailed = (char *)hostName;
#endif
if(verbosity > 0 && rank == 0)
printf("--- Iteration %d: Application: Process %d on node %s is failed! ---\n", iteration, failedRanks[i], hostNameFailed);
}
// Release memory of hostNameFailed
free(hostNameFailed);
appToLaunch = (char **) malloc(procsNeeded * sizeof(char *));
argvToLaunch = (char ***) malloc(procsNeeded * sizeof(char **));
procsNeededToLaunch = (int *) malloc(procsNeeded * sizeof(int));
hostInfoToLaunch = (MPI_Info *) malloc(procsNeeded * sizeof(MPI_Info));
argv[argc] = NULL;
#pragma omp parallel for default(shared)
for(i = 0; i < procsNeeded; i++) {
appToLaunch[i] = (char *)argv[0];
argvToLaunch[i] = (char **)argv;
procsNeededToLaunch[i] = 1;
// Host information where to spawn the processes
MPI_Info_create(&hostInfoToLaunch[i]);
MPI_Info_set(hostInfoToLaunch[i], (char *)"host", hostNameToLaunch[i]);
//MPI_Info_set(hostInfoToLaunch[i], "hostfile", "hostfile");
}
double spawnTime = MPI_Wtime();
#ifdef HANG_ON_REMOVE
OMPI_Comm_agree(tempShrink, &flag);
#endif
// Spawn the new process(es)
if(MPI_SUCCESS != (ret = MPI_Comm_spawn_multiple(procsNeeded, appToLaunch, argvToLaunch, procsNeededToLaunch,
hostInfoToLaunch, 0, tempShrink, &tempIntercomm, MPI_ERRCODES_IGNORE))) {
free(tempRanks);
free(failedRanks);
free(errCodes);
if(MPI_ERR_COMM == ret)
printf("Iteration %d: MPI_Comm_spawn_multiple: Invalid communicator (parent)\n", iteration);
if(MPI_ERR_ARG == ret)
printf("Iteration %d: MPI_Comm_spawn_multiple: Invalid argument (parent)\n", iteration);
if(MPI_ERR_INFO == ret)
printf("Iteration %d: MPI_Comm_spawn_multiple: Invalid info (parent)\n", iteration);
if((MPI_ERR_PROC_FAILED == ret) || (MPI_ERR_REVOKED == ret)) {
OMPI_Comm_revoke(tempShrink);
return repairComm(broken, repaired, iteration, listFails, numFails, numNodeFails,
sumPrevNumNodeFails, argc, argv, verbosity);
}
else {
fprintf(stderr, "Iteration %d: Unknown error with MPI_Comm_spawn_multiple (parent): %d\n", iteration, ret);
exit(1);
}
}
else {
if(verbosity > 0 && rank == 0) {
for(i = 0; i < procsNeeded; i++)
printf("Iteration %d: MPI_Comm_spawn_multiple (parent) [spawning failed process %d on "
"node %s]: SUCCESS\n", iteration, failedRanks[i], hostNameToLaunch[i]);
}
// Memory release. Moving the last two to the end of the function causes segmentation faults for 4 processes failure
}
if (verbosity > 0 && rank == 0)
printf("MPI_Comm_spawn_multiple takes %0.6f Sec\n", MPI_Wtime() - spawnTime);
double mergeTime = MPI_Wtime();
// Merge the new processes into a new communicator
if(MPI_SUCCESS != (ret = MPI_Intercomm_merge(tempIntercomm, false, &unorderIntracomm))) {
free(tempRanks);
free(failedRanks);
if((MPI_ERR_PROC_FAILED == ret) || (MPI_ERR_REVOKED == ret)) {
// Start the recovery over again if there is a failure
OMPI_Comm_revoke(tempIntercomm);
return repairComm(broken, repaired, iteration, listFails, numFails,
numNodeFails, sumPrevNumNodeFails, argc, argv, verbosity);
}
else if(MPI_ERR_COMM == ret) {
fprintf(stderr, "Iteration %d: Invalid communicator in MPI_Intercomm_merge (parent) %d\n", iteration, ret);
exit(1);
}
else if(MPI_ERR_INTERN == ret) {
fprintf(stderr, "Iteration %d: Acquaring memory error in MPI_Intercomm_merge ()%d\n", iteration, ret);
exit(1);
}
else {
fprintf(stderr, "Iteration %d: Unknown error with MPI_Intercomm_merge: %d\n", iteration, ret);
exit(1);
}
}
else {
if(verbosity > 1 )
printf("Iteration %d: MPI_Intercomm_merge (parent): SUCCESS\n", iteration);
}
if (verbosity > 0 && rank == 0)
printf("MPI_Intercomm_merge takes %0.6f Sec\n", MPI_Wtime() - mergeTime);
double agreeTime = MPI_Wtime();
// Synchronize. sometimes hangs in without this
// position of code and intercommunicator (not intra) is important
#ifdef HANG_ON_REMOVE
//MPI_Barrier(tempIntercomm);
OMPI_Comm_agree(tempIntercomm, &flag);// since some of the times MPI_Barrier hangs
#endif
if (verbosity > 0 && rank == 0)
printf("OMPI_Comm_agree takes %0.6f Sec\n", MPI_Wtime() - agreeTime);
// Sending failed ranks and number of processes failed to the the newly created ranks.
// oldGroupSize is the size of communicator before failure.
// procsNeeded is the number of processes that are failed
int * child = (int *) malloc(procsNeeded*sizeof(int));
#pragma omp parallel for default(shared)
for(i = 0; i < procsNeeded; i++)
child[i] = oldGroupSize - procsNeeded + i;
MPI_Comm_rank(unorderIntracomm, &newRank);
if(newRank == 0) {
int send_val[2];
for(i = 0; i < procsNeeded; i++) {
send_val[0] = failedRanks[i];
send_val[1] = procsNeeded;
if(MPI_SUCCESS != (ret = MPI_Send(&send_val, 2, MPI_INT, child[i], MERGE_TAG, unorderIntracomm))) {
free(tempRanks);
free(failedRanks);
if((MPI_ERR_PROC_FAILED == ret) || (MPI_ERR_REVOKED == ret)) {
// Start the recovery over again if there is a failure
OMPI_Comm_revoke(unorderIntracomm);
return repairComm(broken, repaired, iteration, listFails, numFails,
numNodeFails, sumPrevNumNodeFails, argc, argv, verbosity);
}
else {
fprintf(stderr, "Iteration %d: Unknown error with MPI_Send1 (parent): %d\n", iteration, ret);
exit(1);
}
}
else {
if(verbosity > 1 )
printf("Iteration %d: MPI_Send1 (parent): SUCCESS\n", iteration);
}
}
}
// Split the current world (splitted from original) to order the ranks.
MPI_Comm_rank(unorderIntracomm, &newRank);
MPI_Comm_size(unorderIntracomm, &nprocs);
// For one or more process failure (ordering)
shrinkMergeList = (int *) malloc(nprocs*sizeof(int));
j = 0;
for(i = 0; i < nprocs; i++) {
if(rankIsNotOnFailedList(i, failedRanks, procsNeeded))
shrinkMergeList[j++] = i;
}
for(i = j; i < nprocs; i++)
shrinkMergeList[i] = failedRanks[i-j];
for(i = 0; i < (nprocs - procsNeeded); i++) {
if(newRank == i)
rankKey = shrinkMergeList[i];
}
if(MPI_SUCCESS != (MPI_Comm_split(unorderIntracomm, 0, rankKey, repaired))) {
if((MPI_ERR_PROC_FAILED == ret) || (MPI_ERR_REVOKED == ret)) {
// Start the recovery over again if there is a failure
OMPI_Comm_revoke(unorderIntracomm);
return repairComm(broken, repaired, iteration, listFails, numFails,
numNodeFails, sumPrevNumNodeFails, argc, argv, verbosity);
}
else {
fprintf(stderr, "Iteration %d: Unknown error with MPI_Comm_split (parent): %d\n", iteration, ret);
exit(1);
}
}
else {
if(verbosity > 1 )
printf("Iteration %d: MPI_Comm_split (parent): SUCCESS\n", iteration);
}
// Release memory
free(appToLaunch);
free(argvToLaunch);
free(procsNeededToLaunch);
free(hostInfoToLaunch);
free(hostNameToLaunch);
free(shrinkMergeList);
free(errCodes);
MPI_Comm_free(&tempShrink);
free(tempRanks);
free(failedRanks);
free(child);
MPI_Group_free(&failedGroup);
MPI_Group_free(&oldGroup);
MPI_Comm_free(&tempIntercomm);
MPI_Comm_free(&unorderIntracomm);
#ifdef RECOV_ON_SPARE_NODES
if(failedNodeList != NULL)
free(failedNodeList);
if(nodeList != NULL)
free(nodeList);
#endif
}//repairComm()
void declareBindings (void)
{
/* === Point-to-point === */
void* buf;
int count;
MPI_Datatype datatype;
int dest;
int tag;
MPI_Comm comm;
MPI_Send (buf, count, datatype, dest, tag, comm); // L12
int source;
MPI_Status status;
MPI_Recv (buf, count, datatype, source, tag, comm, &status); // L15
MPI_Get_count (&status, datatype, &count);
MPI_Bsend (buf, count, datatype, dest, tag, comm);
MPI_Ssend (buf, count, datatype, dest, tag, comm);
MPI_Rsend (buf, count, datatype, dest, tag, comm);
void* buffer;
int size;
MPI_Buffer_attach (buffer, size); // L22
MPI_Buffer_detach (buffer, &size);
MPI_Request request;
MPI_Isend (buf, count, datatype, dest, tag, comm, &request); // L25
MPI_Ibsend (buf, count, datatype, dest, tag, comm, &request);
MPI_Issend (buf, count, datatype, dest, tag, comm, &request);
MPI_Irsend (buf, count, datatype, dest, tag, comm, &request);
MPI_Irecv (buf, count, datatype, source, tag, comm, &request);
MPI_Wait (&request, &status);
int flag;
MPI_Test (&request, &flag, &status); // L32
MPI_Request_free (&request);
MPI_Request* array_of_requests;
int index;
MPI_Waitany (count, array_of_requests, &index, &status); // L36
MPI_Testany (count, array_of_requests, &index, &flag, &status);
MPI_Status* array_of_statuses;
MPI_Waitall (count, array_of_requests, array_of_statuses); // L39
MPI_Testall (count, array_of_requests, &flag, array_of_statuses);
int incount;
int outcount;
int* array_of_indices;
MPI_Waitsome (incount, array_of_requests, &outcount, array_of_indices,
array_of_statuses); // L44--45
MPI_Testsome (incount, array_of_requests, &outcount, array_of_indices,
array_of_statuses); // L46--47
MPI_Iprobe (source, tag, comm, &flag, &status); // L48
MPI_Probe (source, tag, comm, &status);
MPI_Cancel (&request);
MPI_Test_cancelled (&status, &flag);
MPI_Send_init (buf, count, datatype, dest, tag, comm, &request);
MPI_Bsend_init (buf, count, datatype, dest, tag, comm, &request);
MPI_Ssend_init (buf, count, datatype, dest, tag, comm, &request);
MPI_Rsend_init (buf, count, datatype, dest, tag, comm, &request);
MPI_Recv_init (buf, count, datatype, source, tag, comm, &request);
MPI_Start (&request);
MPI_Startall (count, array_of_requests);
void* sendbuf;
int sendcount;
MPI_Datatype sendtype;
int sendtag;
void* recvbuf;
int recvcount;
MPI_Datatype recvtype;
MPI_Datatype recvtag;
MPI_Sendrecv (sendbuf, sendcount, sendtype, dest, sendtag,
recvbuf, recvcount, recvtype, source, recvtag,
comm, &status); // L67--69
MPI_Sendrecv_replace (buf, count, datatype, dest, sendtag, source, recvtag,
comm, &status); // L70--71
MPI_Datatype oldtype;
MPI_Datatype newtype;
MPI_Type_contiguous (count, oldtype, &newtype); // L74
int blocklength;
{
int stride;
MPI_Type_vector (count, blocklength, stride, oldtype, &newtype); // L78
}
{
MPI_Aint stride;
MPI_Type_hvector (count, blocklength, stride, oldtype, &newtype); // L82
}
int* array_of_blocklengths;
{
int* array_of_displacements;
MPI_Type_indexed (count, array_of_blocklengths, array_of_displacements,
oldtype, &newtype); // L87--88
}
{
MPI_Aint* array_of_displacements;
MPI_Type_hindexed (count, array_of_blocklengths, array_of_displacements,
oldtype, &newtype); // L92--93
MPI_Datatype* array_of_types;
MPI_Type_struct (count, array_of_blocklengths, array_of_displacements,
array_of_types, &newtype); // L95--96
}
void* location;
MPI_Aint address;
MPI_Address (location, &address); // L100
MPI_Aint extent;
MPI_Type_extent (datatype, &extent); // L102
MPI_Type_size (datatype, &size);
MPI_Aint displacement;
MPI_Type_lb (datatype, &displacement); // L105
MPI_Type_ub (datatype, &displacement);
MPI_Type_commit (&datatype);
MPI_Type_free (&datatype);
MPI_Get_elements (&status, datatype, &count);
void* inbuf;
void* outbuf;
int outsize;
int position;
MPI_Pack (inbuf, incount, datatype, outbuf, outsize, &position, comm); // L114
int insize;
MPI_Unpack (inbuf, insize, &position, outbuf, outcount, datatype,
comm); // L116--117
MPI_Pack_size (incount, datatype, comm, &size);
/* === Collectives === */
MPI_Barrier (comm); // L121
int root;
MPI_Bcast (buffer, count, datatype, root, comm); // L123
MPI_Gather (sendbuf, sendcount, sendtype, recvbuf, recvcount, recvtype,
root, comm); // L124--125
int* recvcounts;
int* displs;
MPI_Gatherv (sendbuf, sendcount, sendtype,
recvbuf, recvcounts, displs, recvtype,
root, comm); // L128--130
MPI_Scatter (sendbuf, sendcount, sendtype, recvbuf, recvcount, recvtype,
root, comm); // L131--132
int* sendcounts;
MPI_Scatterv (sendbuf, sendcounts, displs, sendtype,
recvbuf, recvcount, recvtype, root, comm); // L134--135
MPI_Allgather (sendbuf, sendcount, sendtype, recvbuf, recvcount, recvtype,
comm); // L136--137
MPI_Allgatherv (sendbuf, sendcount, sendtype,
recvbuf, recvcounts, displs, recvtype,
comm); // L138--140
MPI_Alltoall (sendbuf, sendcount, sendtype, recvbuf, recvcount, recvtype,
comm); // L141--142
int* sdispls;
int* rdispls;
MPI_Alltoallv (sendbuf, sendcounts, sdispls, sendtype,
recvbuf, recvcounts, rdispls, recvtype,
comm); // L145--147
MPI_Op op;
MPI_Reduce (sendbuf, recvbuf, count, datatype, op, root, comm); // L149
#if 0
MPI_User_function function;
int commute;
MPI_Op_create (function, commute, &op); // L153
#endif
MPI_Op_free (&op); // L155
MPI_Allreduce (sendbuf, recvbuf, count, datatype, op, comm);
MPI_Reduce_scatter (sendbuf, recvbuf, recvcounts, datatype, op, comm);
MPI_Scan (sendbuf, recvbuf, count, datatype, op, comm);
/* === Groups, contexts, and communicators === */
MPI_Group group;
MPI_Group_size (group, &size); // L162
int rank;
MPI_Group_rank (group, &rank); // L164
MPI_Group group1;
int n;
int* ranks1;
MPI_Group group2;
int* ranks2;
MPI_Group_translate_ranks (group1, n, ranks1, group2, ranks2); // L170
int result;
MPI_Group_compare (group1, group2, &result); // L172
MPI_Group newgroup;
MPI_Group_union (group1, group2, &newgroup); // L174
MPI_Group_intersection (group1, group2, &newgroup);
MPI_Group_difference (group1, group2, &newgroup);
int* ranks;
MPI_Group_incl (group, n, ranks, &newgroup); // L178
MPI_Group_excl (group, n, ranks, &newgroup);
extern int ranges[][3];
MPI_Group_range_incl (group, n, ranges, &newgroup); // L181
MPI_Group_range_excl (group, n, ranges, &newgroup);
MPI_Group_free (&group);
MPI_Comm_size (comm, &size);
MPI_Comm_rank (comm, &rank);
MPI_Comm comm1;
MPI_Comm comm2;
MPI_Comm_compare (comm1, comm2, &result);
MPI_Comm newcomm;
MPI_Comm_dup (comm, &newcomm);
MPI_Comm_create (comm, group, &newcomm);
int color;
int key;
MPI_Comm_split (comm, color, key, &newcomm); // L194
MPI_Comm_free (&comm);
MPI_Comm_test_inter (comm, &flag);
MPI_Comm_remote_size (comm, &size);
MPI_Comm_remote_group (comm, &group);
MPI_Comm local_comm;
int local_leader;
MPI_Comm peer_comm;
int remote_leader;
MPI_Comm newintercomm;
MPI_Intercomm_create (local_comm, local_leader, peer_comm, remote_leader, tag,
&newintercomm); // L204--205
MPI_Comm intercomm;
MPI_Comm newintracomm;
int high;
MPI_Intercomm_merge (intercomm, high, &newintracomm); // L209
int keyval;
#if 0
MPI_Copy_function copy_fn;
MPI_Delete_function delete_fn;
void* extra_state;
MPI_Keyval_create (copy_fn, delete_fn, &keyval, extra_state); // L215
#endif
MPI_Keyval_free (&keyval); // L217
void* attribute_val;
MPI_Attr_put (comm, keyval, attribute_val); // L219
MPI_Attr_get (comm, keyval, attribute_val, &flag);
MPI_Attr_delete (comm, keyval);
/* === Environmental inquiry === */
char* name;
int resultlen;
MPI_Get_processor_name (name, &resultlen); // L226
MPI_Errhandler errhandler;
#if 0
MPI_Handler_function function;
MPI_Errhandler_create (function, &errhandler); // L230
#endif
MPI_Errhandler_set (comm, errhandler); // L232
MPI_Errhandler_get (comm, &errhandler);
MPI_Errhandler_free (&errhandler);
int errorcode;
char* string;
MPI_Error_string (errorcode, string, &resultlen); // L237
int errorclass;
MPI_Error_class (errorcode, &errorclass); // L239
MPI_Wtime ();
MPI_Wtick ();
int argc;
char** argv;
MPI_Init (&argc, &argv); // L244
MPI_Finalize ();
MPI_Initialized (&flag);
MPI_Abort (comm, errorcode);
}
FC_FUNC( mpi_group_difference, MPI_GROUP_DIFFERENCE )
(int *group1, int *group2, int *newgroup, int *ierror)
{
*ierror= MPI_Group_difference(*group1,*group2,newgroup);
}