diff options
Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 391 |
1 files changed, 222 insertions, 169 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 5180461..11b08b2 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -33,6 +33,7 @@ extern char *progname; if (A!=0) \ per = (double) fabs( (double)(B-A) / (double)A ); \ } +#define USERBLOCK_XFER_SIZE 512 /* Size of buffer/# of bytes to xfer at a time when copying userblock */ /*------------------------------------------------------------------------- * local functions @@ -41,7 +42,7 @@ extern char *progname; static void print_dataset_info(hid_t dcpl_id,char *objname,double per); static int do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options); static int copy_attr(hid_t loc_in,hid_t loc_out,pack_opt_t *options); -static int copy_user_block(char *infile, char *outfile, hsize_t size); +static int copy_user_block(const char *infile, const char *outfile, hsize_t size); /*------------------------------------------------------------------------- * Function: copy_objects @@ -69,167 +70,196 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options) { - hid_t fidin; - hid_t fidout=-1; - trav_table_t *travt=NULL; - hsize_t ub_size=0; /* Size of user block */ - hid_t fapl=H5P_DEFAULT; /* File access property list ID */ - hid_t fcpl=H5P_DEFAULT; /* File creation property list ID */ + hid_t fidin; + hid_t fidout = -1; + trav_table_t *travt = NULL; + hsize_t ub_size = 0; /* Size of user block */ + hid_t fapl = H5P_DEFAULT; /* File access property list ID */ + hid_t fcpl = H5P_DEFAULT; /* File creation property list ID */ -/*------------------------------------------------------------------------- - * open the files - *------------------------------------------------------------------------- - */ - if ((fidin=h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, 0))<0 ){ - error_msg(progname, "<%s>: %s\n", fnamein, H5FOPENERROR ); - goto out; - } + /*------------------------------------------------------------------------- + * open the files + *------------------------------------------------------------------------- + */ + if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0) { + error_msg(progname, "<%s>: %s\n", fnamein, H5FOPENERROR ); + goto out; + } - /* get user block size */ - { - hid_t fcpl_in = H5Fget_create_plist(fidin); - H5Pget_userblock(fcpl_in, &ub_size); - if (fcpl_in != H5P_DEFAULT) - H5Pclose(fcpl_in); - } + /* get user block size */ + { + hid_t fcpl_in; /* File creation property list ID for input file */ + + if((fcpl_in = H5Fget_create_plist(fidin)) < 0) { + error_msg(progname, "failed to retrieve file creation property list\n"); + goto out; + } /* end if */ + + if(H5Pget_userblock(fcpl_in, &ub_size) < 0) { + error_msg(progname, "failed to retrieve userblock size\n"); + goto out; + } /* end if */ + + if(H5Pclose(fcpl_in) < 0) { + error_msg(progname, "failed to close property list\n"); + goto out; + } /* end if */ + } /* end block */ + + /* Check if we need to create a non-default file creation property list */ + if(options->latest || ub_size > 0) { + /* Create file creation property list */ + if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { + error_msg(progname, "fail to create a file creation property list\n"); + goto out; + } /* end if */ + + if(ub_size > 0) + if(H5Pset_userblock(fcpl, ub_size) < 0) { + error_msg(progname, "failed to set non-default userblock size\n"); + goto out; + } /* end if */ + + if(options->latest) { + unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5]; + + /* Adjust group creation parameters for root group */ + /* (So that it is created in "dense storage" form) */ + if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) { + error_msg(progname, "fail to adjust group creation parameters for root group\n"); + goto out; + } /* end if */ + + for(i = 0; i < 5; i++) { + if(options->msg_size[i] > 0) { + switch(i) { + case 0: + mesg_type_flags[nindex] = H5O_MESG_SDSPACE_FLAG; + break; + + case 1: + mesg_type_flags[nindex] = H5O_MESG_DTYPE_FLAG; + break; + + case 2: + mesg_type_flags[nindex] = H5O_MESG_FILL_FLAG; + break; + + case 3: + mesg_type_flags[nindex] = H5O_MESG_PLINE_FLAG; + break; + + case 4: + mesg_type_flags[nindex] = H5O_MESG_ATTR_FLAG; + break; + } /* end switch */ + min_mesg_sizes[nindex] = (unsigned)options->msg_size[i]; + + nindex++; + } /* end if */ + } /* end for */ + + if(nindex > 0) { + if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { + error_msg(progname, "fail to set the number of shared object header message indexes\n"); + goto out; + } /* end if */ + + /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ + for(i = 0; i < (nindex - 1); i++) { + if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) { + error_msg(progname, "fail to configure the specified shared object header message index\n"); + goto out; + } /* end if */ + } /* end for */ + } /* if (nindex>0) */ + + /* Create file access property list */ + if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { + error_msg(progname, "Could not create file access property list\n"); + goto out; + } /* end if */ + + if(H5Pset_latest_format(fapl, TRUE) < 0) { + error_msg(progname, "Could not set property for using latest version of the format\n"); + goto out; + } /* end if */ + } /* end if */ + } /* end if */ - if (options->latest || ub_size>=512) { - /* Create file creation property list */ - if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0){ - error_msg(progname, "fail to create a file creation property list\n"); + if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0) { + error_msg(progname, "<%s>: Could not create file\n", fnameout ); goto out; - } - } + } /* end if */ - if (ub_size>=512) { - H5Pset_userblock(fcpl, ub_size); - } + if(options->verbose) + printf("Making file <%s>...\n",fnameout); - if (options->latest) { - unsigned i=0, nindex=0, mesg_type_flags[5], min_mesg_sizes[5]; + /* init table */ + trav_table_init(&travt); - /* Adjust group creation parameters for root group */ - /* (So that it is created in "dense storage" form) */ - if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) { - error_msg(progname, "fail to adjust group creation parameters for root group\n"); + /* get the list of objects in the file */ + if(h5trav_gettable(fidin, travt) < 0) goto out; - } - - for (i=0; i<5; i++) { - if (options->msg_size[i]>0) { - switch (i) { - case 0: mesg_type_flags[nindex]=H5O_MESG_SDSPACE_FLAG; break; - case 1: mesg_type_flags[nindex]=H5O_MESG_DTYPE_FLAG; break; - case 2: mesg_type_flags[nindex]=H5O_MESG_FILL_FLAG; break; - case 3: mesg_type_flags[nindex]=H5O_MESG_PLINE_FLAG; break; - case 4: mesg_type_flags[nindex]=H5O_MESG_ATTR_FLAG; break; - } - min_mesg_sizes[nindex] = (unsigned)options->msg_size[i]; - - nindex++; - } - } - - if (nindex>0) { - nindex++; /* add one for default size */ - if (H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { - error_msg(progname, "fail to set the number of shared object header message indexes\n"); - goto out; - } - /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ - for (i=0; i<nindex-1; i++) { - if (H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i])<0) { - error_msg(progname, "fail to configure the specified shared object header message index\n"); - goto out; - } - } - } /* if (nindex>0) */ - /* Create file access property list */ - if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { - error_msg(progname, "Could not create file access property list\n"); + /*------------------------------------------------------------------------- + * do the copy + *------------------------------------------------------------------------- + */ + if(do_copy_objects(fidin, fidout, travt, options) < 0) { + error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout); goto out; } /* end if */ - if(H5Pset_latest_format(fapl, TRUE) < 0) { - error_msg(progname, "Could not set property for using latest version of the format\n"); + /*------------------------------------------------------------------------- + * do the copy of referenced objects + * and create hard links + *------------------------------------------------------------------------- + */ + if(do_copy_refobjs(fidin, fidout, travt, options) < 0) { + printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); goto out; } /* end if */ - } - - if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl))<0 ){ - error_msg(progname, "<%s>: Could not create file\n", fnameout ); - goto out; - } - - if (options->verbose) - printf("Making file <%s>...\n",fnameout); - - /* init table */ - trav_table_init(&travt); - - /* get the list of objects in the file */ - if (h5trav_gettable(fidin,travt)<0) - goto out; - -/*------------------------------------------------------------------------- - * do the copy - *------------------------------------------------------------------------- - */ - if(do_copy_objects(fidin,fidout,travt,options)<0) { - error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout); - goto out; - } -/*------------------------------------------------------------------------- - * do the copy of referenced objects - * and create hard links - *------------------------------------------------------------------------- - */ - if(do_copy_refobjs(fidin,fidout,travt,options)<0) { - printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); - goto out; - } + /* free table */ + trav_table_free(travt); - /* free table */ - trav_table_free(travt); + /*------------------------------------------------------------------------- + * close + *------------------------------------------------------------------------- + */ -/*------------------------------------------------------------------------- - * close - *------------------------------------------------------------------------- - */ - - if (fapl>0) - H5Pclose(fapl); + if(fapl > 0) + H5Pclose(fapl); - if (fcpl>0) - H5Pclose(fcpl); + if(fcpl > 0) + H5Pclose(fcpl); - H5Fclose(fidin); - H5Fclose(fidout); + H5Fclose(fidin); + H5Fclose(fidout); - if (ub_size >= 512) - copy_user_block(fnamein, fnameout, ub_size); + if(ub_size > 0) + copy_user_block(fnamein, fnameout, ub_size); - return 0; + return 0; -/*------------------------------------------------------------------------- - * out - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * out + *------------------------------------------------------------------------- + */ out: - H5E_BEGIN_TRY { - H5Pclose(fapl); - H5Pclose(fcpl); - H5Fclose(fidin); - H5Fclose(fidout); - } H5E_END_TRY; - if (travt) - trav_table_free(travt); + H5E_BEGIN_TRY { + H5Pclose(fapl); + H5Pclose(fcpl); + H5Fclose(fidin); + H5Fclose(fidout); + } H5E_END_TRY; + if(travt) + trav_table_free(travt); - return -1; + return -1; } /*------------------------------------------------------------------------- @@ -892,7 +922,7 @@ int copy_attr(hid_t loc_in, goto error; /* get name */ - if (H5Aget_name( attr_id, 255, name )<0) + if (H5Aget_name( attr_id, (size_t)255, name )<0) goto error; /* get the file datatype */ @@ -938,7 +968,7 @@ int copy_attr(hid_t loc_in, *------------------------------------------------------------------------- */ - buf=(void *) HDmalloc((unsigned)(nelmts*msize)); + buf=(void *) HDmalloc((size_t)(nelmts*msize)); if ( buf==NULL){ error_msg(progname, "cannot read into memory\n" ); goto error; @@ -1104,7 +1134,7 @@ static void print_dataset_info(hid_t dcpl_id, } /* switch */ }/*i*/ - if (strcmp(strfilter,"\0")==0) + if(*strfilter == '\0') printf(FORMAT_OBJ,"dset",objname ); else { @@ -1130,51 +1160,74 @@ static void print_dataset_info(hid_t dcpl_id, * *------------------------------------------------------------------------- */ -static int copy_user_block(char *infile, char *outfile, hsize_t size) +static int +copy_user_block(const char *infile, const char *outfile, hsize_t size) { - int infid=-1, outfid=-1, status=0; - off_t offset; - ssize_t how_much_left = (ssize_t)size; - ssize_t nchars; - char buf[512]; - + int infid = -1, outfid = -1; /* File descriptors */ + int status = 0; /* Return value */ /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */ - if (size<512) - return 0; + assert(size > 0); - if ((infid = HDopen(infile,O_RDONLY,0)) < 0) { + /* Open files */ + if((infid = HDopen(infile, O_RDONLY, 0)) < 0) { status = -1; goto done; } - - - if ((outfid = HDopen(outfile,O_WRONLY,0644)) < 0) { + if((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) { status = -1; goto done; } - offset = 0; - while (how_much_left > 0) { - HDlseek(infid,offset,SEEK_SET); - if (how_much_left > 512) - nchars = HDread(infid,buf,(unsigned)512); + /* Copy the userblock from the input file to the output file */ + while(size > 0) { + ssize_t nread, nbytes; /* # of bytes transfered, etc. */ + char rbuf[USERBLOCK_XFER_SIZE]; /* Buffer for reading */ + const char *wbuf; /* Pointer into buffer, for writing */ + + /* Read buffer from source file */ + if(size > USERBLOCK_XFER_SIZE) + nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE); else - nchars = HDread(infid,buf,(unsigned)how_much_left); - HDlseek(outfid, offset, SEEK_SET); - HDwrite(outfid, buf, (unsigned)nchars); - how_much_left -= nchars; - offset += nchars; - } + nread = HDread(infid, rbuf, (size_t)size); + if(nread < 0) { + status = -1; + goto done; + } /* end if */ + + /* Write buffer to destination file */ + /* (compensating for interrupted writes & checking for errors, etc.) */ + nbytes = nread; + wbuf = rbuf; + while(nbytes > 0) { + ssize_t nwritten; /* # of bytes written */ + + do { + nwritten = HDwrite(outfid, wbuf, (size_t)nbytes); + } while(-1 == nwritten && EINTR == errno); + if(-1 == nwritten) { /* error */ + status = -1; + goto done; + } /* end if */ + assert(nwritten > 0); + assert(nwritten <= nbytes); + + /* Update # of bytes left & offset in buffer */ + nbytes -= nwritten; + wbuf += nwritten; + assert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE)); + } /* end while */ + + /* Update size of userblock left to transfer */ + size -= nread; + } /* end while */ done: - if (infid > 0) - close(infid); - - if (outfid > 0) - close (outfid); + if(infid > 0) + HDclose(infid); + if(outfid > 0) + HDclose(outfid); return status; } - |