diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/compression/bwt.c | 14 | ||||
| -rw-r--r-- | src/compression/coder.c | 8 | ||||
| -rw-r--r-- | src/compression/tng_compress.c | 22 | ||||
| -rw-r--r-- | src/compression/xtc3.c | 32 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 215 | ||||
| -rw-r--r-- | src/tests/tng_io_testing.c | 38 | ||||
| -rw-r--r-- | src/tests/tng_parallel_read.c | 31 |
7 files changed, 206 insertions, 154 deletions
diff --git a/src/compression/bwt.c b/src/compression/bwt.c index ea75199..e5cb5ce 100644 --- a/src/compression/bwt.c +++ b/src/compression/bwt.c @@ -37,8 +37,8 @@ static int compare_index(int i1,int i2,int nvals,unsigned int *vals,unsigned int int k1=(int)(nrepeat[i1]&0xFFU); int repeat2=(int)(nrepeat[i2]>>8); int k2=(int)(nrepeat[i2]&0xFFU); - - if ((repeat1>1) && (repeat1>1) && (k1==k2)) + + if ((repeat1>1) && (repeat2>1) && (k1==k2)) { int maxskip=0; /* Yes. Compare the repeating patterns. */ @@ -88,7 +88,7 @@ void Ptngc_bwt_merge_sort_inner(int *indices, int nvals,unsigned int *vals, middle=start+(end-start)/2; #if 0 printf("For start %d end %d obtained new middle: %d\n",start,end,middle); -#endif +#endif Ptngc_bwt_merge_sort_inner(indices,nvals,vals, start,middle, nrepeat, @@ -126,7 +126,7 @@ void Ptngc_bwt_merge_sort_inner(int *indices, int nvals,unsigned int *vals, if (compare_index(indices[ileft],indices[iright],nvals,vals,nrepeat)>0) { workarray[i]=indices[iright]; - iright++; + iright++; } else { @@ -221,7 +221,7 @@ void Ptngc_comp_to_bwt(unsigned int *vals, int nvals, pattern. */ #ifdef SHOWIT printf("Best j and k is now %d and %d\n",good_j,good_k); -#endif +#endif } } else @@ -257,7 +257,7 @@ void Ptngc_comp_to_bwt(unsigned int *vals, int nvals, nrepeat[i+m]=((unsigned int) (good_k)) | (((unsigned int) (repeat))<<8); } /* If no repetition was found for this value signal that here. */ - if (!nrepeat[i]) + if (!nrepeat[i]) nrepeat[i+m]=257U; /* This is 1<<8 | 1 */ } } @@ -334,4 +334,4 @@ void Ptngc_comp_from_bwt(unsigned int *input, int nvals, int index, free(p); free(c); } - + diff --git a/src/compression/coder.c b/src/compression/coder.c index 270e4d3..ca3de86 100644 --- a/src/compression/coder.c +++ b/src/compression/coder.c @@ -171,7 +171,6 @@ static int pack_stopbits_item(struct coder *coder_inst,int item, unsigned char * else if (item<0) s=2+(-item-1)*2; return write_stop_bit_code(coder_inst,s,coding_parameter,output); - return 0; } static int pack_triplet(struct coder *coder_inst,unsigned int *s, unsigned char **output, int coding_parameter, @@ -194,7 +193,6 @@ static int pack_triplet(struct coder *coder_inst,unsigned int *s, unsigned char { if (this_base>max_base) return 1; - this_base=max_base; bits_per_value=maxbits; jbase=3; } @@ -332,7 +330,7 @@ unsigned char *Ptngc_pack_array(struct coder *coder_inst,int *input, int *length static int unpack_array_stop_bits(struct coder *coder_inst,unsigned char *packed,int *output, int length, int coding_parameter) { - (void)coder_inst; + (void) coder_inst; int i,j; unsigned int extract_mask=0x80; unsigned char *ptr=packed; @@ -385,7 +383,7 @@ static int unpack_array_stop_bits(struct coder *coder_inst,unsigned char *packed static int unpack_array_triplet(struct coder *coder_inst,unsigned char *packed,int *output, int length, int coding_parameter) { - (void)coder_inst; + (void) coder_inst; int i,j; unsigned int extract_mask=0x80; unsigned char *ptr=packed; @@ -457,7 +455,7 @@ static int unpack_array_triplet(struct coder *coder_inst,unsigned char *packed,i static int unpack_array_bwlzh(struct coder *coder_inst,unsigned char *packed,int *output, int length, int natoms) { - (void)coder_inst; + (void) coder_inst; int i,j,k,n=length; unsigned int *pval=warnmalloc(n*sizeof *pval); int nframes=n/natoms/3; diff --git a/src/compression/tng_compress.c b/src/compression/tng_compress.c index ebd495b..2578336 100644 --- a/src/compression/tng_compress.c +++ b/src/compression/tng_compress.c @@ -481,13 +481,14 @@ static void compress_quantized_vel(int *quant, int *quant_inter, if (data) bufferfix((unsigned char*)data+bufloc,prec_hi,4); bufloc+=4; + + length=natoms*3; /* The initial frame */ if ((initial_coding==TNG_COMPRESS_ALGO_VEL_STOPBIT_ONETOONE) || (initial_coding==TNG_COMPRESS_ALGO_VEL_TRIPLET_ONETOONE) || (initial_coding==TNG_COMPRESS_ALGO_VEL_BWLZH_ONETOONE)) { struct coder *coder=Ptngc_coder_init(); - length=natoms*3; datablock=(char*)Ptngc_pack_array(coder,quant,&length, initial_coding,initial_coding_parameter,natoms,speed); Ptngc_coder_deinit(coder); @@ -497,10 +498,12 @@ static void compress_quantized_vel(int *quant, int *quant_inter, bufferfix((unsigned char*)data+bufloc,(fix_t)length,4); bufloc+=4; /* The actual data block. */ - if (data) - memcpy(data+bufloc,datablock,length); - free(datablock); - bufloc+=length; + if (data && datablock) + { + memcpy(data+bufloc,datablock,length); + free(datablock); + bufloc+=length; + } /* The remaining frames */ if (nframes>1) { @@ -683,7 +686,6 @@ static void determine_best_pos_initial_coding(int *quant, int *quant_intra, int { best_coding=current_coding; best_coding_parameter=current_coding_parameter; - best_code_size=current_code_size; } } *initial_coding=best_coding; @@ -846,7 +848,6 @@ static void determine_best_pos_coding(int *quant, int *quant_inter, int *quant_i { best_coding=current_coding; best_coding_parameter=current_coding_parameter; - best_code_size=current_code_size; } } *coding=best_coding; @@ -950,7 +951,6 @@ static void determine_best_vel_initial_coding(int *quant, int natoms, int speed, { best_coding=current_coding; best_coding_parameter=current_coding_parameter; - best_code_size=current_code_size; } } *initial_coding=best_coding; @@ -1090,7 +1090,6 @@ static void determine_best_vel_coding(int *quant, int *quant_inter, int natoms, if (current_code_size<best_code_size) { best_coding=current_coding; - best_code_size=current_code_size; best_coding_parameter=current_coding_parameter; } } @@ -1492,7 +1491,6 @@ int DECLSPECDLLEXPORT tng_compress_inquire(char *data,int *vel, int *natoms, prec_lo=readbufferfix((unsigned char *)data+bufloc,4); bufloc+=4; prec_hi=readbufferfix((unsigned char *)data+bufloc,4); - bufloc+=4; *precision=PRECISION(prec_hi, prec_lo); algo[0]=initial_coding; algo[1]=initial_coding_parameter; @@ -1583,8 +1581,6 @@ static int tng_compress_uncompress_pos_gen(char *data,double *posd,float *posf,i /* The remaining frames. */ if (nframes>1) { - /* The data block length. */ - length=(int)readbufferfix((unsigned char *)data+bufloc,4); bufloc+=4; coder=Ptngc_coder_init(); rval=Ptngc_unpack_array(coder,(unsigned char *)data+bufloc,quant+natoms*3,(nframes-1)*natoms*3, @@ -1721,8 +1717,6 @@ static int tng_compress_uncompress_vel_gen(char *data,double *veld,float *velf,i /* The remaining frames. */ if (nframes>1) { - /* The data block length. */ - length=(int)readbufferfix((unsigned char *)data+bufloc,4); bufloc+=4; coder=Ptngc_coder_init(); rval=Ptngc_unpack_array(coder,(unsigned char *)data+bufloc,quant+natoms*3,(nframes-1)*natoms*3, diff --git a/src/compression/xtc3.c b/src/compression/xtc3.c index 197cc12..297e948 100644 --- a/src/compression/xtc3.c +++ b/src/compression/xtc3.c @@ -512,7 +512,6 @@ static void buffer_large(struct xtc3_context *xtc3_context, int *input, int inpd thislen=compute_intlen(interdelta); if (thislen*TRESHOLD_INTRA_INTER_DIRECT<minlen) { - minlen=thislen; best_type=2; /* Inter delta */ } } @@ -730,7 +729,6 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output) while (nvals_left) { int n; - int numints; if (basegiven==0) { base=(unsigned int)(input[0])| @@ -755,24 +753,26 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output) #ifdef SHOWIT fprintf(stderr,"Reading largeint: "); #endif - for (j=0; j<numbytes; j++) - { - int ilarge=j/4; - int ibyte=j%4; - largeint[ilarge]|=((unsigned int)input[j])<<(ibyte*8); + if (numbytes/4 < maxbasevals+1) + { + for (j=0; j<numbytes; j++) + { + int ilarge=j/4; + int ibyte=j%4; + largeint[ilarge]|=((unsigned int)input[j])<<(ibyte*8); #ifdef SHOWIT - fprintf(stderr,"%02x",(unsigned int)input[j]); + fprintf(stderr,"%02x",(unsigned int)input[j]); #endif + } } #ifdef SHOWIT - fprintf(stderr,"\n"); + fprintf(stderr,"\n"); #endif input+=numbytes; /* Do the long division required to get the output values. */ n=maxbasevals; if (n>nvals_left) n=nvals_left; - numints=(numbytes+3)/4; for (i=n-1; i>=0; i--) { output[outvals+i*3]=Ptngc_largeint_div(base,largeint,largeint_tmp,maxbasevals+1); @@ -1699,21 +1699,21 @@ static void unpack_one_large(struct xtc3_context *xtc3_context, int natoms, int current_large_type) { int large_ints[3]={0,0,0}; - if (current_large_type==0) + if (current_large_type==0 && xtc3_context->large_direct) { large_ints[0]=(int)xtc3_context->large_direct[(*ilargedir)]+minint[0]; large_ints[1]=(int)xtc3_context->large_direct[(*ilargedir)+1]+minint[1]; large_ints[2]=(int)xtc3_context->large_direct[(*ilargedir)+2]+minint[2]; (*ilargedir)+=3; } - else if (current_large_type==1) + else if (current_large_type==1 && xtc3_context->large_intra_delta) { large_ints[0]=unpositive_int(xtc3_context->large_intra_delta[(*ilargeintra)])+prevcoord[0]; large_ints[1]=unpositive_int(xtc3_context->large_intra_delta[(*ilargeintra)+1])+prevcoord[1]; large_ints[2]=unpositive_int(xtc3_context->large_intra_delta[(*ilargeintra)+2])+prevcoord[2]; (*ilargeintra)+=3; } - else + else if (xtc3_context->large_inter_delta) { large_ints[0]=unpositive_int(xtc3_context->large_inter_delta[(*ilargeinter)]) +output[outdata-natoms*3+didswap*3]; @@ -1838,7 +1838,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n prevcoord[1]=minint[1]; prevcoord[2]=minint[2]; - while (ntriplets_left>0) + while (ntriplets_left>0 && iinstr<xtc3_context.ninstr) { int instr=xtc3_context.instructions[iinstr++]; #ifdef SHOWIT @@ -1895,7 +1895,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n outdata+=runlength*3; } } - else if (instr==INSTR_LARGE_RLE) + else if (instr==INSTR_LARGE_RLE && irle<xtc3_context.nrle) { int large_rle=xtc3_context.rle[irle++]; #ifdef SHOWIT @@ -1910,7 +1910,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n outdata+=3; } } - else if (instr==INSTR_SMALL_RUNLENGTH) + else if (instr==INSTR_SMALL_RUNLENGTH && irle<xtc3_context.nrle) { runlength=xtc3_context.rle[irle++]; #ifdef SHOWIT diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 9acd857..725e4b6 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -965,7 +965,6 @@ static tng_function_status tng_block_header_read __FILE__, __LINE__); } } - offset += sizeof(block->block_version); return(TNG_SUCCESS); } @@ -992,7 +991,7 @@ static tng_function_status tng_block_header_read // __FILE__, __LINE__); // return(TNG_CRITICAL); // } -// +// // if(!block->block_contents) // { // printf("No block data to write. %s: %d\n", @@ -1133,7 +1132,6 @@ static tng_function_status tng_block_header_write __FILE__, __LINE__); } } - offset += sizeof(block->block_version); if(fwrite(block->header_contents, block->header_contents_size, 1, tng_data->output_file) != 1) @@ -2362,7 +2360,8 @@ static tng_function_status tng_molecules_block_read tng_chain_data_read(tng_data, block, chain, &offset); - chain->residues = residue; + chain->residues = molecule->residues; + residue = chain->residues; /* Read the residues of the chain */ for(k=chain->n_residues; k--;) @@ -2436,64 +2435,67 @@ static tng_function_status tng_molecules_block_read } offset += sizeof(molecule->n_bonds); - molecule->bonds = malloc(molecule->n_bonds * - sizeof(struct tng_bond)); - if(!molecule->bonds) + if(molecule->n_bonds > 0) { - printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", - molecule->n_bonds * sizeof(struct tng_bond), - __FILE__, __LINE__); - if(molecule->chains) - { - free(molecule->chains); - molecule->chains = 0; - } - if(molecule->residues) - { - free(molecule->residues); - molecule->residues = 0; - } - if(molecule->bonds) + molecule->bonds = malloc(molecule->n_bonds * + sizeof(struct tng_bond)); + if(!molecule->bonds) { - free(molecule->bonds); - molecule->bonds = 0; + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + molecule->n_bonds * sizeof(struct tng_bond), + __FILE__, __LINE__); + if(molecule->chains) + { + free(molecule->chains); + molecule->chains = 0; + } + if(molecule->residues) + { + free(molecule->residues); + molecule->residues = 0; + } + if(molecule->atoms) + { + free(molecule->atoms); + molecule->atoms = 0; + } + return(TNG_CRITICAL); } - return(TNG_CRITICAL); - } - bond = molecule->bonds; + bond = molecule->bonds; - for(j=molecule->n_bonds; j--;) - { - memcpy(&bond->from_atom_id, block->block_contents+offset, - sizeof(bond->from_atom_id)); - if(tng_data->input_endianness_swap_func_64) + for(j=molecule->n_bonds; j--;) { - if(tng_data->input_endianness_swap_func_64(tng_data, - &bond->from_atom_id) - != TNG_SUCCESS) + memcpy(&bond->from_atom_id, block->block_contents+offset, + sizeof(bond->from_atom_id)); + if(tng_data->input_endianness_swap_func_64) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->input_endianness_swap_func_64(tng_data, + &bond->from_atom_id) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } - } - offset += sizeof(bond->from_atom_id); + offset += sizeof(bond->from_atom_id); - memcpy(&bond->to_atom_id, block->block_contents+offset, - sizeof(bond->to_atom_id)); - if(tng_data->input_endianness_swap_func_64) - { - if(tng_data->input_endianness_swap_func_64(tng_data, - &bond->to_atom_id) - != TNG_SUCCESS) + memcpy(&bond->to_atom_id, block->block_contents+offset, + sizeof(bond->to_atom_id)); + if(tng_data->input_endianness_swap_func_64) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->input_endianness_swap_func_64(tng_data, + &bond->to_atom_id) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } - } - offset += sizeof(bond->to_atom_id); + offset += sizeof(bond->to_atom_id); - bond++; + bond++; + } } } @@ -2621,7 +2623,6 @@ static tng_function_status tng_molecules_block_write atom++; } - bond = molecule->bonds; for(j = molecule->n_bonds; j--;) { len += sizeof(bond->from_atom_id) + sizeof(bond->to_atom_id); @@ -3191,7 +3192,6 @@ static tng_function_status tng_frame_set_block_read __FILE__, __LINE__); } } - offset += sizeof(tng_data->time_per_frame); } else { @@ -3429,7 +3429,6 @@ static tng_function_status tng_frame_set_block_write __FILE__, __LINE__); } } - offset += sizeof(tng_data->time_per_frame); if(tng_block_header_write(tng_data, block, hash_mode) != TNG_SUCCESS) { @@ -3760,8 +3759,6 @@ static tng_function_status tng_particle_data_block_create return(TNG_CRITICAL); } frame_set->tr_particle_data = data; - data = &frame_set->tr_particle_data[frame_set-> - n_particle_data_blocks - 1]; } else { @@ -3779,8 +3776,6 @@ static tng_function_status tng_particle_data_block_create return(TNG_CRITICAL); } tng_data->non_tr_particle_data = data; - data = &tng_data->non_tr_particle_data[tng_data-> - n_particle_data_blocks - 1]; } return(TNG_SUCCESS); @@ -4209,6 +4204,11 @@ static tng_function_status tng_allocate_particle_data_mem void ***values; int64_t i, j, k, size, frame_alloc; + if(n_particles == 0 || n_values_per_frame == 0) + { + return(TNG_FAILURE); + } + if(data->strings && data->datatype == TNG_CHAR_DATA) { for(i = data->n_frames; i--;) @@ -5208,7 +5208,6 @@ static tng_function_status tng_data_block_create return(TNG_CRITICAL); } frame_set->tr_data = data; - data = &frame_set->tr_data[frame_set->n_data_blocks - 1]; } else { @@ -5224,7 +5223,6 @@ static tng_function_status tng_data_block_create return(TNG_CRITICAL); } tng_data->non_tr_data = data; - data = &tng_data->non_tr_data[tng_data->n_data_blocks - 1]; } return(TNG_SUCCESS); @@ -6888,6 +6886,7 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_w_id_add sizeof(int64_t) * (tng_data->n_molecules + 1), __FILE__, __LINE__); free(tng_data->molecule_cnt_list); + free(new_molecules); return(TNG_CRITICAL); } @@ -7206,7 +7205,7 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_w_id_add int curr_index; tng_residue_t new_residues, temp_residue, last_residue; tng_molecule_t molecule = chain->molecule; - tng_function_status stat; + tng_function_status stat = TNG_SUCCESS; if(chain->n_residues) { @@ -7342,7 +7341,7 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_atom_w_id_add int64_t i; tng_atom_t new_atoms; tng_molecule_t molecule = residue->chain->molecule; - tng_function_status stat; + tng_function_status stat = TNG_SUCCESS; if(!residue->n_atoms) { @@ -9320,8 +9319,6 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frame_sets_get ++cnt; - file_pos = tng_data->current_trajectory_frame_set_input_file_pos; - long_stride_length = tng_data->long_stride_length; medium_stride_length = tng_data->medium_stride_length; @@ -9444,6 +9441,11 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_nr_find stat = tng_num_frame_sets_get(tng_data, &n_frame_sets); + if(stat != TNG_SUCCESS) + { + return(stat); + } + if(nr >= n_frame_sets) { return(TNG_FAILURE); @@ -11972,6 +11974,11 @@ static tng_function_status tng_data_values_alloc int64_t i; tng_function_status stat; + if(n_frames == 0 || n_values_per_frame == 0) + { + return(TNG_FAILURE); + } + if(*values) { stat = tng_data_values_free(tng_data, *values, n_frames, @@ -11984,7 +11991,7 @@ static tng_function_status tng_data_values_alloc return(stat); } } - *values = malloc(sizeof(union data_values **) * n_frames); + *values = malloc(sizeof(union data_values *) * n_frames); if(!*values) { printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", @@ -12060,6 +12067,11 @@ static tng_function_status tng_particle_data_values_alloc int64_t i, j; tng_function_status stat; + if(n_particles == 0 || n_values_per_frame == 0) + { + return(TNG_FAILURE); + } + if(*values) { stat = tng_particle_data_values_free(tng_data, *values, n_frames, @@ -12387,6 +12399,7 @@ tng_function_status tng_data_vector_get(tng_trajectory_t tng_data, printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", data_size, __FILE__, __LINE__); free(*values); + *values = 0; return(TNG_CRITICAL); } @@ -12694,6 +12707,12 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get stat = tng_frame_set_read_next(tng_data, hash_mode); if(stat != TNG_SUCCESS) { + if(current_values) + { + free(current_values); + } + free(*values); + *values = 0; return(stat); } @@ -12729,7 +12748,10 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get } } - free(current_values); + if(current_values) + { + free(current_values); + } return(TNG_SUCCESS); } @@ -13361,7 +13383,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get &n_frames, stride_length, n_particles, n_values_per_frame, type); - if(stat != TNG_SUCCESS) + if(stat != TNG_SUCCESS || *n_particles == 0) { if(current_values) { @@ -13443,6 +13465,12 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get stat = tng_frame_set_read_next(tng_data, hash_mode); if(stat != TNG_SUCCESS) { + if(current_values) + { + free(current_values); + } + free(*values); + *values = 0; return(stat); } @@ -13478,7 +13506,10 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get } } - free(current_values); + if(current_values) + { + free(current_values); + } return(TNG_SUCCESS); } @@ -13553,14 +13584,14 @@ tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_close tng_function_status DECLSPECDLLEXPORT tng_util_trajectory_molecules_get (tng_trajectory_t tng_data, int64_t *n_mols, - int64_t *molecule_cnt_list, + int64_t **molecule_cnt_list, tng_molecule_t *mols) { /* FIXME: This should return a copy of the molecules instead */ *n_mols = tng_data->n_molecules; - molecule_cnt_list = tng_data->molecule_cnt_list; - mols = &tng_data->molecules; + *molecule_cnt_list = tng_data->molecule_cnt_list; + *mols = tng_data->molecules; return(TNG_SUCCESS); } @@ -13601,10 +13632,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get *n_particles = mol->n_atoms; - **names = malloc(sizeof(char *) * *n_particles); - **types = malloc(sizeof(char *) * *n_particles); - **res_names = malloc(sizeof(char *) * *n_particles); - **chain_names = malloc(sizeof(char *) * *n_particles); + *names = malloc(sizeof(char *) * *n_particles); + *types = malloc(sizeof(char *) * *n_particles); + *res_names = malloc(sizeof(char *) * *n_particles); + *chain_names = malloc(sizeof(char *) * *n_particles); *res_ids = malloc(sizeof(int64_t) * *n_particles); *chain_ids = malloc(sizeof(int64_t) * *n_particles); @@ -13613,16 +13644,16 @@ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get atom = &mol->atoms[i]; res = atom->residue; chain = res->chain; - *names[i] = malloc(strlen(atom->name)); + (*names)[i] = malloc(strlen(atom->name)); strcpy(*names[i], atom->name); - *types[i] = malloc(strlen(atom->atom_type)); + (*types)[i] = malloc(strlen(atom->atom_type)); strcpy(*types[i], atom->atom_type); - *res_names[i] = malloc(strlen(res->name)); + (*res_names)[i] = malloc(strlen(res->name)); strcpy(*res_names[i], res->name); - *chain_names[i] = malloc(strlen(chain->name)); + (*chain_names)[i] = malloc(strlen(chain->name)); strcpy(*chain_names[i], chain->name); - *res_ids[i] = res->id; - *chain_ids[i] = chain->id; + (*res_ids)[i] = res->id; + (*chain_ids)[i] = chain->id; } return(TNG_SUCCESS); @@ -13923,6 +13954,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set stat = tng_allocate_particle_data_mem(tng_data, p_data, n_frames, f, n_particles, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } else { @@ -13947,6 +13984,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write_frequency_set n_data_blocks - 1]; stat = tng_allocate_data_mem(tng_data, np_data, n_frames, f, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } else { @@ -14098,6 +14141,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write stat = tng_allocate_particle_data_mem(tng_data, p_data, n_frames, stride_length, n_particles, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } if(block_type_flag == TNG_TRAJECTORY_BLOCK) @@ -14142,6 +14191,12 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write } stat = tng_allocate_data_mem(tng_data, np_data, n_frames, stride_length, n_values_per_frame); + if(stat != TNG_SUCCESS) + { + printf("Error allocating particle data memory. %s: %d\n", + __FILE__, __LINE__); + return(stat); + } } if(block_type_flag == TNG_TRAJECTORY_BLOCK) diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c index 96b53f7..0f67ccc 100644 --- a/src/tests/tng_io_testing.c +++ b/src/tests/tng_io_testing.c @@ -136,7 +136,7 @@ static tng_function_status tng_test_read_and_write_file } stat = tng_frame_set_write(traj, TNG_USE_HASH); } - + return(stat); } @@ -148,11 +148,11 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) int64_t frame_nr; double box_shape[9]; char atom_type[16], annotation[128]; - tng_function_status stat; + tng_function_status stat = TNG_SUCCESS; tng_medium_stride_length_set(traj, 10); tng_long_stride_length_set(traj, 100); - + /* Create molecules */ if(tng_test_setup_molecules(traj) == TNG_CRITICAL) { @@ -200,7 +200,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) printf("Failed setting partial charges.\n"); return(TNG_CRITICAL); } - + stat = tng_particle_data_block_add(traj, TNG_TRAJ_PARTIAL_CHARGES, "PARTIAL CHARGES", TNG_FLOAT_DATA, TNG_NON_TRAJECTORY_BLOCK, 1, 1, 1, 0, n_particles, @@ -230,9 +230,9 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) printf("Cannot write file headers.\n"); } - + tng_num_frames_per_frame_set_get(traj, &n_frames_per_frame_set); - + data = malloc(sizeof(float) * n_particles * n_frames_per_frame_set * 3); if(!data) @@ -366,9 +366,9 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) return(TNG_CRITICAL); } } - + /* Write two more frame sets one frame at a time */ - cnt = 0; + /* Make a new frame set - if always using the same mapping blocks * it is not necessary to explicitly add a new frame set - it will * be added automatically when adding data for a frame */ @@ -383,7 +383,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) } frame_nr = i * n_frames_per_frame_set; - + for(k=0; k<300; k++) { mapping[k]=k; @@ -470,7 +470,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) } } } - + free(molpos); free(data); @@ -481,7 +481,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) #endif stat = tng_file_headers_read(traj, TNG_SKIP_HASH); - + while(stat == TNG_SUCCESS) { stat = tng_frame_set_read_next(traj, TNG_SKIP_HASH); @@ -582,7 +582,7 @@ int main() tng_trajectory_t traj; tng_function_status stat; char time_str[TNG_MAX_DATE_STR_LEN]; - + if(tng_trajectory_init(&traj) != TNG_SUCCESS) { tng_trajectory_destroy(&traj); @@ -614,7 +614,7 @@ int main() { printf("Test Read and write file:\t\t\tSucceeded.\n"); } - + if(tng_test_get_box_data(traj) != TNG_SUCCESS) { printf("Test Get data:\t\t\t\t\tFailed. %s: %d\n", @@ -635,7 +635,7 @@ int main() { printf("Test Destroy and init trajectory:\t\tSucceeded.\n"); } - + #ifdef EXAMPLE_FILES_DIR tng_output_file_set(traj, EXAMPLE_FILES_DIR "tng_test.tng"); @@ -652,7 +652,7 @@ int main() { printf("Test Write and read file:\t\t\tSucceeded.\n"); } - + if(tng_test_get_positions_data(traj) != TNG_SUCCESS) { printf("Test Get particle data:\t\t\t\tFailed. %s: %d\n", @@ -674,7 +674,7 @@ int main() printf("Test Destroy trajectory:\t\t\tSucceeded.\n"); } - + #ifdef EXAMPLE_FILES_DIR stat = tng_util_trajectory_open(EXAMPLE_FILES_DIR "tng_test.tng", 'r', &traj); #else @@ -691,7 +691,7 @@ int main() printf("Test Utility function open:\t\t\tSucceeded.\n"); } - stat = tng_util_trajectory_close(&traj); + stat = tng_util_trajectory_close(&traj); if(stat != TNG_SUCCESS) { printf("Test Utility function close:\t\t\tFailed. %s: %d.\n", @@ -702,8 +702,8 @@ int main() { printf("Test Utility function close:\t\t\tSucceeded.\n"); } - + printf("Tests finished\n"); - + exit(0); }
\ No newline at end of file diff --git a/src/tests/tng_parallel_read.c b/src/tests/tng_parallel_read.c index d0aaa15..58863b0 100644 --- a/src/tests/tng_parallel_read.c +++ b/src/tests/tng_parallel_read.c @@ -21,7 +21,7 @@ /* N.B. this code is for testing parallel reading of trajectory frame sets. The * performance is not improved very much and is to a large extent limited by * disk i/o. It can however be used as inspiration for writing parallel code - * using the TNG library. */ + * using the TNG library. The code is NOT fully tested and may behave strangely. */ int main(int argc, char **argv) { @@ -29,7 +29,7 @@ int main(int argc, char **argv) union data_values ***local_positions = 0; // A 3-dimensional array to be populated union data_values **particle_pos = 0; int64_t n_particles, n_values_per_frame, n_frame_sets, n_frames; - int64_t n_frames_per_frame_set; + int64_t n_frames_per_frame_set, tot_n_frames = 0; char data_type; int i, j; int64_t particle = 0, local_first_frame, local_last_frame; @@ -66,7 +66,7 @@ int main(int argc, char **argv) tng_num_frame_sets_get(traj, &n_frame_sets); tng_num_frames_per_frame_set_get(traj, &n_frames_per_frame_set); - particle_pos = malloc(sizeof(union data_values **) * n_frame_sets * + particle_pos = malloc(sizeof(union data_values *) * n_frame_sets * n_frames_per_frame_set); for(i = n_frame_sets * n_frames_per_frame_set; i--;) { @@ -94,7 +94,7 @@ int main(int argc, char **argv) private (n_frames, n_particles, n_values_per_frame, \ local_first_frame, local_last_frame, j) \ firstprivate (local_traj, local_positions, frame_set)\ -shared(data_type, traj, n_frame_sets, particle_pos, particle, i)\ +shared(data_type, traj, n_frame_sets, particle_pos, particle, i, tot_n_frames)\ default(none) { /* Each tng_trajectory_t keeps its own file pointers and i/o positions. @@ -106,17 +106,22 @@ default(none) if(tng_frame_set_nr_find(local_traj, i) != TNG_SUCCESS) { printf("FAILED finding frame set %d!\n", i); + tot_n_frames = 0; + break; } if(tng_particle_data_get(local_traj, TNG_TRAJ_POSITIONS, &local_positions, &n_frames, &n_particles, &n_values_per_frame, &data_type) != TNG_SUCCESS) { printf("FAILED getting particle data\n"); + tot_n_frames = 0; + break; } tng_current_frame_set_get(local_traj, &frame_set); tng_frame_set_frame_range_get(local_traj, frame_set, &local_first_frame, &local_last_frame); // printf("Frame %"PRId64"-%"PRId64":\n", local_first_frame, local_last_frame); // printf("%"PRId64" %"PRId64" %"PRId64"\n", n_frames, n_particles, n_values_per_frame); + tot_n_frames += n_frames; for(j = 0; j < n_frames; j++) { particle_pos[local_first_frame + j][0] = local_positions[j][particle][0]; @@ -136,24 +141,24 @@ default(none) switch(data_type) { case TNG_INT_DATA: - for(i = 0; i < n_frame_sets * n_frames_per_frame_set; i++) + for(j = 0; j < tot_n_frames; j++) { - printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", particle_pos[i][0].i, - particle_pos[i][1].i, particle_pos[i][2].i); + printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", particle_pos[j][0].i, + particle_pos[j][1].i, particle_pos[j][2].i); } break; case TNG_FLOAT_DATA: - for(i = 0; i < n_frame_sets * n_frames_per_frame_set; i++) + for(j = 0; j < tot_n_frames; j++) { - printf("\t%f\t%f\t%f\n", particle_pos[i][0].f, - particle_pos[i][1].f, particle_pos[i][2].f); + printf("\t%f\t%f\t%f\n", particle_pos[j][0].f, + particle_pos[j][1].f, particle_pos[j][2].f); } break; case TNG_DOUBLE_DATA: - for(i = 0; i < n_frame_sets * n_frames_per_frame_set; i++) + for(j = 0; j < tot_n_frames; j++) { - printf("\t%f\t%f\t%f\n", particle_pos[i][0].d, - particle_pos[i][1].d, particle_pos[i][2].d); + printf("\t%f\t%f\t%f\n", particle_pos[j][0].d, + particle_pos[j][1].d, particle_pos[j][2].d); } break; default: |