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avoid overflows when computing memory offsets and allocating memory

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This commit is contained in:
Axel Kohlmeyer
2021-02-06 18:12:47 -05:00
parent 1380b7b142
commit 77402bdbc8
13 changed files with 28 additions and 27 deletions
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2
src/KSPACE/remap.cpp
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@ -597,7 +597,7 @@ struct remap_plan_3d *remap_3d_create_plan(
if (memory == 1) {
if (nrecv > 0) {
plan->scratch =
(FFT_SCALAR *) malloc(nqty*out.isize*out.jsize*out.ksize *
(FFT_SCALAR *) malloc((size_t)nqty*out.isize*out.jsize*out.ksize *
sizeof(FFT_SCALAR));
if (plan->scratch == nullptr) return nullptr;
}

4
src/OPT/pair_eam_opt.cpp
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@ -112,7 +112,7 @@ void PairEAMOpt::eval()
int ntypes2 = ntypes*ntypes;
fast_alpha_t* _noalias fast_alpha =
(fast_alpha_t*) malloc(ntypes2*(nr+1)*sizeof(fast_alpha_t));
(fast_alpha_t*) malloc((size_t)ntypes2*(nr+1)*sizeof(fast_alpha_t));
for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {
fast_alpha_t* _noalias tab = &fast_alpha[i*ntypes*nr+j*nr];
if (type2rhor[i+1][j+1] >= 0) {
@ -135,7 +135,7 @@ void PairEAMOpt::eval()
fast_alpha_t* _noalias tabeight = fast_alpha;
fast_gamma_t* _noalias fast_gamma =
(fast_gamma_t*) malloc(ntypes2*(nr+1)*sizeof(fast_gamma_t));
(fast_gamma_t*) malloc((size_t)ntypes2*(nr+1)*sizeof(fast_gamma_t));
for (i = 0; i < ntypes; i++) for (j = 0; j < ntypes; j++) {
fast_gamma_t* _noalias tab = &fast_gamma[i*ntypes*nr+j*nr];
if (type2rhor[i+1][j+1] >= 0) {

6
src/USER-DPD/pair_multi_lucy.cpp
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@ -221,9 +221,9 @@ void PairMultiLucy::allocate()
memory->create(cutsq,nt,nt,"pair:cutsq");
memory->create(tabindex,nt,nt,"pair:tabindex");
memset(&setflag[0][0],0,nt*nt*sizeof(int));
memset(&cutsq[0][0],0,nt*nt*sizeof(double));
memset(&tabindex[0][0],0,nt*nt*sizeof(int));
memset(&setflag[0][0],0,sizeof(int)*nt*nt);
memset(&cutsq[0][0],0,sizeof(double)*nt*nt);
memset(&tabindex[0][0],0,sizeof(int)*nt*nt);
}
/* ----------------------------------------------------------------------

6
src/USER-DPD/pair_multi_lucy_rx.cpp
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@ -310,9 +310,9 @@ void PairMultiLucyRX::allocate()
memory->create(cutsq,nt,nt,"pair:cutsq");
memory->create(tabindex,nt,nt,"pair:tabindex");
memset(&setflag[0][0],0,nt*nt*sizeof(int));
memset(&cutsq[0][0],0,nt*nt*sizeof(double));
memset(&tabindex[0][0],0,nt*nt*sizeof(int));
memset(&setflag[0][0],0,sizeof(int)*nt*nt);
memset(&cutsq[0][0],0,sizeof(double)*nt*nt);
memset(&tabindex[0][0],0,sizeof(int)*nt*nt);
}
/* ----------------------------------------------------------------------

4
src/USER-MISC/fix_imd.cpp
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@ -919,7 +919,7 @@ void FixIMD::post_force(int /*vflag*/)
if (imd_forces < length) { /* grow holding space for forces, if needed. */
memory->destroy(force_buf);
force_buf = (void *) memory->smalloc(length*size_one,
force_buf = (void *) memory->smalloc((bigint)length*size_one,
"imd:force_buf");
}
imd_forces = length;
@ -960,7 +960,7 @@ void FixIMD::post_force(int /*vflag*/)
if (old_imd_forces < imd_forces) { /* grow holding space for forces, if needed. */
if (force_buf != nullptr)
memory->sfree(force_buf);
force_buf = memory->smalloc(imd_forces*size_one, "imd:force_buf");
force_buf = memory->smalloc((bigint)imd_forces*size_one, "imd:force_buf");
}
}
MPI_Bcast(force_buf, imd_forces*size_one, MPI_BYTE, 0, world);

2
src/USER-MISC/fix_ttm_mod.cpp
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@ -136,7 +136,7 @@ FixTTMMod::FixTTMMod(LAMMPS *lmp, int narg, char **arg) :
gfactor1 = new double[atom->ntypes+1];
gfactor2 = new double[atom->ntypes+1];
// allocate 3d grid variables
total_nnodes = nxnodes*nynodes*nznodes;
total_nnodes = (bigint)nxnodes*nynodes*nznodes;
memory->create(nsum,nxnodes,nynodes,nznodes,"ttm/mod:nsum");
memory->create(nsum_all,nxnodes,nynodes,nznodes,"ttm/mod:nsum_all");
memory->create(sum_vsq,nxnodes,nynodes,nznodes,"ttm/mod:sum_vsq");

2
src/USER-PHONON/fix_phonon.cpp
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@ -723,7 +723,7 @@ void FixPhonon::postprocess( )
fwrite(&nucell, sizeof(int), 1, fp_bin);
fwrite(&boltz, sizeof(double), 1, fp_bin);
fwrite(Phi_all[0],sizeof(double),ntotal*fft_dim2*2,fp_bin);
fwrite(Phi_all[0],sizeof(double),(bigint)ntotal*fft_dim2*2,fp_bin);
fwrite(&TempAve, sizeof(double),1, fp_bin);
fwrite(&basevec[0], sizeof(double),9, fp_bin);

4
src/USER-REAXC/reaxc_allocate.cpp
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@ -302,10 +302,10 @@ int Allocate_Workspace( reax_system * /*system*/, control_params * control,
// storage for reductions with multiple threads
#ifdef LMP_USER_OMP
workspace->CdDeltaReduction = (double *) scalloc(control->error_ptr, sizeof(double), total_cap*control->nthreads,
workspace->CdDeltaReduction = (double *) scalloc(control->error_ptr, sizeof(double), (rc_bigint)total_cap*control->nthreads,
"cddelta_reduce");
workspace->forceReduction = (rvec *) scalloc(control->error_ptr, sizeof(rvec), total_cap*control->nthreads,
workspace->forceReduction = (rvec *) scalloc(control->error_ptr, sizeof(rvec), (rc_bigint)total_cap*control->nthreads,
"forceReduction");
workspace->valence_angle_atom_myoffset = (int *) scalloc(control->error_ptr, sizeof(int), total_cap, "valence_angle_atom_myoffset");

2
src/angle_hybrid.cpp
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@ -113,7 +113,7 @@ void AngleHybrid::compute(int eflag, int vflag)
const int nthreads = comm->nthreads;
if (comm->nthreads > 1) {
const int nall = atom->nlocal + atom->nghost;
const bigint nall = atom->nlocal + atom->nghost;
if (eflag_atom)
memset(&eatom[0],0,nall*nthreads*sizeof(double));
if (vflag_atom)

2
src/bond_hybrid.cpp
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@ -113,7 +113,7 @@ void BondHybrid::compute(int eflag, int vflag)
const int nthreads = comm->nthreads;
if (nthreads > 1) {
const int nall = atom->nlocal + atom->nghost;
const bigint nall = atom->nlocal + atom->nghost;
if (eflag_atom)
memset(&eatom[0],0,nall*nthreads*sizeof(double));
if (vflag_atom)

9
src/comm.cpp
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@ -979,7 +979,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
offsets[0] = 0;
for (int i = 1; i < nprocs; i++)
offsets[i] = offsets[i-1] + insize*procs_a2a[i-1];
offsets[i] = offsets[i-1] + (bigint)insize*procs_a2a[i-1];
bigint offset = 0;
for (int i = 0; i < n; i++) {
@ -989,7 +989,8 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
offset += insize;
}
all2all1_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) + n*insize;
all2all1_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint)
+ (bigint)n*insize;
} else {
procs_a2a = procs;
@ -1085,7 +1086,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
offsets[0] = 0;
for (int i = 1; i < nprocs; i++)
offsets[i] = offsets[i-1] + outsize*procs_a2a[i-1];
offsets[i] = offsets[i-1] + (bigint)outsize*procs_a2a[i-1];
bigint offset = 0;
for (int i = 0; i < nrvous_out; i++) {
@ -1096,7 +1097,7 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
}
all2all2_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) +
nrvous_out*outsize;
(bigint)nrvous_out*outsize;
} else {
procs_a2a = procs_rvous;

2
src/compute_orientorder_atom.cpp
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@ -258,7 +258,7 @@ void ComputeOrientOrderAtom::compute_peratom()
double **x = atom->x;
int *mask = atom->mask;
memset(&qnarray[0][0],0,nmax*ncol*sizeof(double));
memset(&qnarray[0][0],0,sizeof(double)*nmax*ncol);
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];

10
src/memory.h
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@ -410,18 +410,18 @@ class Memory : protected Pointers {
nbytes = ((bigint) sizeof(TYPE ***)) * n1;
array = (TYPE ****) smalloc(nbytes,name);
int i,j,k;
bigint i,j,k;
bigint m1,m2;
bigint n = 0;
for (i = 0; i < n1; i++) {
m2 = ((bigint) i) * n2;
m2 = i * n2;
array[i] = &plane[m2];
for (j = 0; j < n2; j++) {
m1 = ((bigint) i) * n2 + j;
m2 = ((bigint) i) * n2*n3 + j*n3;
m1 = i * n2 + j;
m2 = i * n2*n3 + j*n3;
plane[m1] = &cube[m2];
for (k = 0; k < n3; k++) {
m1 = ((bigint) i) * n2*n3 + j*n3 + k;
m1 = i * n2*n3 + j*n3 + k;
cube[m1] = &data[n];
n += n4;
}