added rendezvous via all2all
This commit is contained in:
Steve Plimpton
committed by
Axel Kohlmeyer
Axel Kohlmeyer
parent
981f12ebeb
commit
fc002e30d3
318
src/comm.cpp
318
src/comm.cpp
@ -729,34 +729,78 @@ void Comm::ring(int n, int nper, void *inbuf, int messtag,
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/* ----------------------------------------------------------------------
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rendezvous communication operation
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three stages:
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first Irregular converts inbuf from caller decomp to rvous decomp
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first comm sends inbuf from caller decomp to rvous decomp
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callback operates on data in rendevous decomp
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last Irregular converts outbuf from rvous decomp back to caller decomp
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second comm sends outbuf from rvous decomp back to caller decomp
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inputs:
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n = # of input datums
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proclist = proc that owns each input datum in rendezvous decomposition
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inbuf = list of input datums
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insize = size in bytes of each input datum
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which = perform (0) irregular or (1) MPI_All2allv communication
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n = # of datums in inbuf
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inbuf = vector of input datums
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insize = byte size of each input datum
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inorder = 0 for inbuf in random proc order, 1 for datums ordered by proc
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procs: inorder 0 = proc to send each datum to, 1 = # of datums/proc,
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callback = caller function to invoke in rendezvous decomposition
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takes input datums, returns output datums
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outorder = same as inorder, but for datums returned by callback()
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ptr = pointer to caller class, passed to callback()
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outputs:
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nout = # of output datums (function return)
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outbuf = list of output datums
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outsize = size in bytes of each output datum
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outbuf = vector of output datums
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outsize = byte size of each output datum
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callback inputs:
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nrvous = # of rvous decomp datums in inbuf_rvous
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inbuf_rvous = vector of rvous decomp input datums
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ptr = pointer to caller class
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callback outputs:
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nrvous_out = # of rvous decomp output datums (function return)
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flag = 0 for no second comm, 1 for outbuf_rvous = inbuf_rvous,
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2 for second comm with new outbuf_rvous
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procs_rvous = outorder 0 = proc to send each datum to, 1 = # of datums/proc
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allocated
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outbuf_rvous = vector of rvous decomp output datums
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NOTE: could use MPI_INT or MPI_DOUBLE insead of MPI_CHAR
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to avoid checked-for overflow in MPI_Alltoallv?
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------------------------------------------------------------------------- */
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int Comm::rendezvous(int n, int *proclist, char *inbuf, int insize,
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int (*callback)(int, char *, int &, int *&, char *&, void *),
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char *&outbuf, int outsize, void *ptr)
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int Comm::
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rendezvous(int which, int n, char *inbuf, int insize,
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int inorder, int *procs,
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int (*callback)(int, char *, int &, int *&, char *&, void *),
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int outorder, char *&outbuf, int outsize, void *ptr)
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{
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// comm inbuf from caller decomposition to rendezvous decomposition
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int nout;
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if (which == 0)
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nout = rendezvous_irregular(n,inbuf,insize,inorder,procs,callback,
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outorder,outbuf,outsize,ptr);
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else
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nout = rendezvous_all2all(n,inbuf,insize,inorder,procs,callback,
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outorder,outbuf,outsize,ptr);
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return nout;
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}
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/* ---------------------------------------------------------------------- */
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int Comm::
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rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
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int (*callback)(int, char *, int &, int *&, char *&, void *),
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int outorder, char *&outbuf,
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int outsize, void *ptr)
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{
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// irregular comm of inbuf from caller decomp to rendezvous decomp
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Irregular *irregular = new Irregular(lmp);
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int n_rvous = irregular->create_data(n,proclist); // add sort
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char *inbuf_rvous = (char *) memory->smalloc((bigint) n_rvous*insize,
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"rendezvous:inbuf_rvous");
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int nrvous;
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if (inorder) nrvous = irregular->create_data_grouped(n,procs);
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else nrvous = irregular->create_data(n,procs);
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char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize,
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"rendezvous:inbuf");
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irregular->exchange_data(inbuf,insize,inbuf_rvous);
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bigint irregular1_bytes = 0; //irregular->irregular_bytes;
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irregular->destroy_data();
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delete irregular;
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@ -764,29 +808,253 @@ int Comm::rendezvous(int n, int *proclist, char *inbuf, int insize,
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// callback() allocates/populates proclist_rvous and outbuf_rvous
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int flag;
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int *proclist_rvous;
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int *procs_rvous;
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char *outbuf_rvous;
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int nout_rvous =
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callback(n_rvous,inbuf_rvous,flag,proclist_rvous,outbuf_rvous,ptr);
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int nrvous_out = callback(nrvous,inbuf_rvous,flag,
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procs_rvous,outbuf_rvous,ptr);
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if (flag != 1) memory->sfree(inbuf_rvous); // outbuf_rvous = inbuf_vous
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if (flag == 0) return 0; // all nout_rvous are 0, no 2nd irregular
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if (flag == 0) return 0; // all nout_rvous are 0, no 2nd comm stage
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// comm outbuf from rendezvous decomposition back to caller
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// irregular comm of outbuf from rendezvous decomp back to caller decomp
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// caller will free outbuf
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irregular = new Irregular(lmp);
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int nout = irregular->create_data(nout_rvous,proclist_rvous);
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outbuf = (char *) memory->smalloc((bigint) nout*outsize,"rendezvous:outbuf");
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int nout;
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if (outorder)
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nout = irregular->create_data_grouped(nrvous_out,procs_rvous);
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else nout = irregular->create_data(nrvous_out,procs_rvous);
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outbuf = (char *) memory->smalloc((bigint) nout*outsize,
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"rendezvous:outbuf");
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irregular->exchange_data(outbuf_rvous,outsize,outbuf);
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bigint irregular2_bytes = 0; //irregular->irregular_bytes;
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irregular->destroy_data();
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delete irregular;
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memory->destroy(proclist_rvous);
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memory->destroy(procs_rvous);
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memory->sfree(outbuf_rvous);
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// approximate memory tally
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bigint rvous_bytes = 0;
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rvous_bytes += n*insize; // inbuf
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rvous_bytes += nout*outsize; // outbuf
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rvous_bytes += nrvous*insize; // inbuf_rvous
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rvous_bytes += nrvous_out*outsize; // outbuf_rvous
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rvous_bytes += nrvous_out*sizeof(int); // procs_rvous
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rvous_bytes += MAX(irregular1_bytes,irregular2_bytes); // max of 2 comms
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// return number of output datums
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return nout;
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}
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/* ---------------------------------------------------------------------- */
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int Comm::
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rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
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int (*callback)(int, char *, int &, int *&, char *&, void *),
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int outorder, char *&outbuf, int outsize, void *ptr)
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{
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int iproc;
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bigint all2all1_bytes,all2all2_bytes;
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int *sendcount,*sdispls,*recvcount,*rdispls;
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int *procs_a2a;
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bigint *offsets;
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char *inbuf_a2a,*outbuf_a2a;
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// create procs and inbuf for All2all if necesary
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if (!inorder) {
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memory->create(procs_a2a,nprocs,"rendezvous:procs");
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inbuf_a2a = (char *) memory->smalloc((bigint) n*insize,
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"rendezvous:inbuf");
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memory->create(offsets,nprocs,"rendezvous:offsets");
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for (int i = 0; i < nprocs; i++) procs_a2a[i] = 0;
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for (int i = 0; i < n; i++) procs_a2a[procs[i]]++;
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offsets[0] = 0;
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for (int i = 1; i < nprocs; i++)
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offsets[i] = offsets[i-1] + insize*procs_a2a[i-1];
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bigint offset = 0;
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for (int i = 0; i < n; i++) {
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iproc = procs[i];
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memcpy(&inbuf_a2a[offsets[iproc]],&inbuf[offset],insize);
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offsets[iproc] += insize;
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offset += insize;
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}
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all2all1_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) + n*insize;
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} else {
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procs_a2a = procs;
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inbuf_a2a = inbuf;
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all2all1_bytes = 0;
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}
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// create args for MPI_Alltoallv() on input data
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memory->create(sendcount,nprocs,"rendezvous:sendcount");
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memcpy(sendcount,procs_a2a,nprocs*sizeof(int));
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memory->create(recvcount,nprocs,"rendezvous:recvcount");
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MPI_Alltoall(sendcount,1,MPI_INT,recvcount,1,MPI_INT,world);
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memory->create(sdispls,nprocs,"rendezvous:sdispls");
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memory->create(rdispls,nprocs,"rendezvous:rdispls");
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sdispls[0] = rdispls[0] = 0;
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for (int i = 1; i < nprocs; i++) {
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sdispls[i] = sdispls[i-1] + sendcount[i-1];
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rdispls[i] = rdispls[i-1] + recvcount[i-1];
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}
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int nrvous = rdispls[nprocs-1] + recvcount[nprocs-1];
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// test for overflow of input data due to imbalance or insize
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// means that individual sdispls or rdispls values overflow
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int overflow = 0;
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if ((bigint) n*insize > MAXSMALLINT) overflow = 1;
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if ((bigint) nrvous*insize > MAXSMALLINT) overflow = 1;
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int overflowall;
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MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_MAX,world);
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if (overflowall) error->all(FLERR,"Overflow input size in rendezvous_a2a");
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for (int i = 0; i < nprocs; i++) {
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sendcount[i] *= insize;
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sdispls[i] *= insize;
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recvcount[i] *= insize;
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rdispls[i] *= insize;
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}
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// all2all comm of inbuf from caller decomp to rendezvous decomp
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char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize,
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"rendezvous:inbuf");
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MPI_Alltoallv(inbuf_a2a,sendcount,sdispls,MPI_CHAR,
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inbuf_rvous,recvcount,rdispls,MPI_CHAR,world);
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if (!inorder) {
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memory->destroy(procs_a2a);
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memory->sfree(inbuf_a2a);
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memory->destroy(offsets);
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}
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// peform rendezvous computation via callback()
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// callback() allocates/populates proclist_rvous and outbuf_rvous
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int flag;
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int *procs_rvous;
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char *outbuf_rvous;
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int nrvous_out = callback(nrvous,inbuf_rvous,flag,
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procs_rvous,outbuf_rvous,ptr);
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if (flag != 1) memory->sfree(inbuf_rvous); // outbuf_rvous = inbuf_vous
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if (flag == 0) return 0; // all nout_rvous are 0, no 2nd irregular
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// create procs and outbuf for All2all if necesary
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if (!outorder) {
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memory->create(procs_a2a,nprocs,"rendezvous_a2a:procs");
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outbuf_a2a = (char *) memory->smalloc((bigint) nrvous_out*outsize,
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"rendezvous:outbuf");
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memory->create(offsets,nprocs,"rendezvous:offsets");
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for (int i = 0; i < nprocs; i++) procs_a2a[i] = 0;
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for (int i = 0; i < nrvous_out; i++) procs_a2a[procs_rvous[i]]++;
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offsets[0] = 0;
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for (int i = 1; i < nprocs; i++)
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offsets[i] = offsets[i-1] + outsize*procs_a2a[i-1];
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bigint offset = 0;
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for (int i = 0; i < nrvous_out; i++) {
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iproc = procs_rvous[i];
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memcpy(&outbuf_a2a[offsets[iproc]],&outbuf_rvous[offset],outsize);
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offsets[iproc] += outsize;
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offset += outsize;
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}
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all2all2_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) +
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nrvous_out*outsize;
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} else {
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procs_a2a = procs_rvous;
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outbuf_a2a = outbuf_rvous;
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all2all2_bytes = 0;
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}
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// comm outbuf from rendezvous decomposition back to caller
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memcpy(sendcount,procs_a2a,nprocs*sizeof(int));
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MPI_Alltoall(sendcount,1,MPI_INT,recvcount,1,MPI_INT,world);
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sdispls[0] = rdispls[0] = 0;
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for (int i = 1; i < nprocs; i++) {
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sdispls[i] = sdispls[i-1] + sendcount[i-1];
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rdispls[i] = rdispls[i-1] + recvcount[i-1];
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}
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int nout = rdispls[nprocs-1] + recvcount[nprocs-1];
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// test for overflow of outbuf due to imbalance or outsize
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// means that individual sdispls or rdispls values overflow
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overflow = 0;
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if ((bigint) nrvous*outsize > MAXSMALLINT) overflow = 1;
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if ((bigint) nout*outsize > MAXSMALLINT) overflow = 1;
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MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_MAX,world);
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if (overflowall) error->all(FLERR,"Overflow output in rendezvous_a2a");
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for (int i = 0; i < nprocs; i++) {
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sendcount[i] *= outsize;
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sdispls[i] *= outsize;
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recvcount[i] *= outsize;
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rdispls[i] *= outsize;
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}
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// all2all comm of outbuf from rendezvous decomp back to caller decomp
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// caller will free outbuf
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outbuf = (char *) memory->smalloc((bigint) nout*outsize,"rendezvous:outbuf");
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MPI_Alltoallv(outbuf_a2a,sendcount,sdispls,MPI_CHAR,
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outbuf,recvcount,rdispls,MPI_CHAR,world);
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memory->destroy(procs_rvous);
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memory->sfree(outbuf_rvous);
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if (!outorder) {
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memory->destroy(procs_a2a);
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memory->sfree(outbuf_a2a);
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memory->destroy(offsets);
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}
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// clean up
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memory->destroy(sendcount);
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memory->destroy(recvcount);
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memory->destroy(sdispls);
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memory->destroy(rdispls);
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// approximate memory tally
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bigint rvous_bytes = 0;
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rvous_bytes += n*insize; // inbuf
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rvous_bytes += nout*outsize; // outbuf
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rvous_bytes += nrvous*insize; // inbuf_rvous
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rvous_bytes += nrvous_out*outsize; // outbuf_rvous
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rvous_bytes += nrvous_out*sizeof(int); // procs_rvous
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rvous_bytes += 4*nprocs*sizeof(int); // all2all vectors
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rvous_bytes += MAX(all2all1_bytes,all2all2_bytes); // reorder ops
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// return number of datums
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return nout;
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