netcdf-c/libdap2/nccommon.h
Dennis Heimbigner 751300ec59 Fix more memory leaks in netcdf-c library
This is a follow up to PR https://github.com/Unidata/netcdf-c/pull/1173

Sorry that it is so big, but leak suppression can be complex.

This PR fixes all remaining memory leaks -- as determined by
-fsanitize=address, and with the exceptions noted below.

Unfortunately. there remains a significant leak that I cannot
solve. It involves vlens, and it is unclear if the leak is
occurring in the netcdf-c library or the HDF5 library.

I have added a check_PROGRAM to the ncdump directory to show the
problem.  The program is called tst_vlen_demo.c To exercise it,
build the netcdf library with -fsanitize=address enabled. Then
go into ncdump and do a "make clean check".  This should build
tst_vlen_demo without actually executing it.  Then do the
command "./tst_vlen_demo" to see the output of the memory
checker.  Note the the lost malloc is deep in the HDF5 library
(in H5Tvlen.c).

I am temporarily working around this error in the following way.
1. I modified several test scripts to not execute known vlen tests
   that fail as described above.
2. Added an environment variable called NC_VLEN_NOTEST.
   If set, then those specific tests are suppressed.

This should mean that the --disable-utilities option to
./configure should not need to be set to get a memory leak clean
build.  This should allow for detection of any new leaks.

Note: I used an environment variable rather than a ./configure
option to control the vlen tests. This is because it is
temporary (I hope) and because it is a bit tricky for shell
scripts to access ./configure options.

Finally, as before, this only been tested with netcdf-4 and hdf5 support.
2018-11-15 10:00:38 -07:00

316 lines
11 KiB
C

/*********************************************************************
* Copyright 1993, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
#ifndef NCCOMMON_H
#define NCCOMMON_H 1
#include "dapincludes.h"
/* Mnemonics */
#ifndef BOOL
#define BOOL int
#endif
#ifndef TRUE
#define TRUE 1
#define FALSE 0
#endif
#ifndef nullfree
#define nullfree(m) {if((m)!=NULL) {free(m);} else {}}
#endif
/* Misc. code controls */
#define FILLCONSTRAINT TRUE
/* Hopefully, this flag will someday not be needed */
#define COLUMBIA_HACK "columbia.edu"
/* Use an extended version of the netCDF-4 type system */
#define NC_URL 50
#define NC_SET 51
/* Merge relevant translations of OC types */
#define NC_Dataset 52
#define NC_Sequence 53
#define NC_Structure 54
#define NC_Grid 55
#define NC_Dimension 56
#define NC_Atomic 57
#undef OCCOMPILEBYDEFAULT
#define DEFAULTSTRINGLENGTH 64
/* The sequence limit default is zero because
most servers do not implement projections
on sequences.
*/
#define DEFAULTSEQLIMIT 0
/**************************************************/
/* sigh, do the forwards */
struct NCDAPCOMMON;
struct NCprojection;
struct NCselection;
struct Getvara;
struct NCcachenode;
struct NCcache;
struct NCslice;
struct NCsegment;
struct OClist;
struct NCTMODEL {
int translation;
char* model;
unsigned int flags;
};
/* Define the cache control flags */
/* Detail information about each cache item */
typedef struct NCcachenode {
int wholevariable; /* does this cache node only have wholevariables? */
int isprefetch;
off_t xdrsize;
DCEconstraint* constraint; /* as used to create this node */
NClist* vars; /* vars potentially covered by this cache node */
struct CDFnode* datadds;
OCddsnode ocroot;
OCdatanode content;
} NCcachenode;
/* All cache info */
typedef struct NCcache {
size_t cachelimit; /* max total size for all cached entries */
size_t cachesize; /* current size */
size_t cachecount; /* max # nodes in cache */
NCcachenode* prefetch;
NClist* nodes; /* cache nodes other than prefetch */
} NCcache;
/**************************************************/
/* The DAP packet info from OC */
typedef struct NCOC {
OClink conn;
char* rawurltext; /* as given to nc3d_open */
char* urltext; /* as modified by nc3d_open */
NCURI* url; /* parse of rawuritext */
OCdasnode ocdasroot;
DCEconstraint* dapconstraint; /* from url */
int inmemory; /* store fetched data in memory? */
} NCOC;
typedef struct NCCDF {
struct CDFnode* ddsroot; /* constrained dds */
struct CDFnode* fullddsroot; /* unconstrained dds */
NClist* projectedvars; /* vars appearing in nc_open url projections */
unsigned int defaultstringlength;
unsigned int defaultsequencelimit; /* global sequence limit;0=>no limit */
struct NCcache* cache;
size_t fetchlimit;
size_t smallsizelimit; /* what constitutes a small object? */
size_t totalestimatedsize;
const char* separator; /* constant; do not free */
/* Following fields should be set from the unconstrained dds only */
/* global string dimension */
struct CDFnode* globalstringdim;
char* recorddimname; /* From DODS_EXTRA */
struct CDFnode* recorddim;
} NCCDF;
/* Define a structure holding common info for NCDAP */
typedef struct NCDAPCOMMON {
NC* controller; /* Parent instance of NCDAPCOMMON */
NCCDF cdf;
NCOC oc;
NCCONTROLS controls; /* Control flags and parameters */
struct {
int realfile; /* 1 => we created actual temp file */
char* filename; /* of the substrate file */
int nc3id; /* substrate nc4 file ncid used to hold metadata; not same as external id */
} substrate;
} NCDAPCOMMON;
/**************************************************/
/* Create our own node tree to mimic ocnode trees*/
/* Each root CDFnode contains info about the whole tree */
typedef struct CDFtree {
OCddsnode ocroot;
OCdxd occlass;
NClist* nodes; /* all nodes in tree*/
struct CDFnode* root; /* cross link */
struct NCDAPCOMMON* owner;
/* Collected sets of useful nodes */
NClist* varnodes; /* nodes which can represent netcdf variables */
NClist* seqnodes; /* sequence nodes; */
NClist* gridnodes; /* grid nodes */
NClist* dimnodes; /* (base) dimension nodes */
/* Classification flags */
int restructed; /* Was this tree passed thru restruct? */
} CDFtree;
/* Track the kinds of dimensions */
typedef int CDFdimflags;
#define CDFDIMNORMAL 0x0
#define CDFDIMSEQ 0x1
#define CDFDIMSTRING 0x2
#define CDFDIMCLONE 0x4
#define CDFDIMRECORD 0x20
#define DIMFLAG(d,flag) ((d)->dim.dimflags & (flag))
#define DIMFLAGSET(d,flag) ((d)->dim.dimflags |= (flag))
#define DIMFLAGCLR(d,flag) ((d)->dim.dimflags &= ~(flag))
typedef struct CDFdim {
CDFdimflags dimflags;
struct CDFnode* basedim; /* for duplicate dimensions*/
struct CDFnode* array; /* parent array node */
size_t declsize; /* from constrained DDS*/
size_t declsize0; /* from unconstrained DDS*/
int index1; /* dimension name index +1; 0=>no index */
} CDFdim;
typedef struct CDFarray {
NClist* dimsetall; /* dimsetplus + inherited */
NClist* dimsettrans; /* dimset0 plus inherited(transitive closure) */
NClist* dimsetplus; /* dimset0 + pseudo */
NClist* dimset0; /* original dims from the dds */
struct CDFnode* stringdim;
/* Track sequence related information */
struct CDFnode* seqdim; /* if this node is a sequence */
/* note: unlike string dim; seqdim is also stored in dimensions vector */
struct CDFnode* sequence; /* containing usable sequence, if any */
struct CDFnode* basevar; /* for duplicate grid variables*/
} CDFarray;
typedef struct NCattribute {
char* name;
nc_type etype; /* dap type of the attribute */
NClist* values; /* strings come from the oc values */
int invisible; /* Do not materialize to the user */
} NCattribute;
/* Extend as additional DODS attribute values are defined */
typedef struct NCDODS {
size_t maxstrlen;
char* dimname;
} NCDODS;
typedef struct NCD2alignment {
unsigned long size; /* size of single instance of this type*/
unsigned long alignment; /* alignment of this field */
unsigned long offset; /* offset of this field in parent */
} NCD2alignment;
typedef struct NCtypesize {
BOOL aligned; /* have instance and field been defined? */
NCD2alignment instance; /* Alignment, etc for instance data */
NCD2alignment field; /* Alignment, etc WRT to parent */
} NCtypesize;
/* Closely mimics struct OCnode*/
typedef struct CDFnode {
nc_type nctype; /* e.g. var, dimension */
nc_type etype; /* e.g. NC_INT, NC_FLOAT if applicable,*/
char* ocname; /* oc base name */
char* ncbasename; /* generally cdflegalname(ocname) */
char* ncfullname; /* complete path name from root to this node*/
OCddsnode ocnode; /* oc mirror node*/
struct CDFnode* group; /* null => in root group */
struct CDFnode* container; /* e.g. struct or sequence, but not group */
struct CDFnode* root;
CDFtree* tree; /* root level metadata;only defined if root*/
CDFdim dim; /* nctype == dimension */
CDFarray array; /* nctype == grid,var,etc. with dimensions */
NClist* subnodes; /* if nctype == grid, sequence, etc. */
NClist* attributes; /*NClist<NCattribute*>*/
NCDODS dodsspecial; /* special attributes like maxStrlen */
nc_type externaltype; /* the type as represented to nc_inq*/
int ncid; /* relevant NC id for this object*/
unsigned long maxstringlength;
unsigned long sequencelimit; /* 0=>unlimited */
BOOL usesequence; /* If this sequence is usable */
BOOL elided; /* 1 => node does not partipate in naming*/
struct CDFnode* basenode; /* derived tree map to pattern tree */
BOOL invisible; /* 1 => do not show to user */
BOOL zerodim; /* 1 => node has a zero dimension */
/* These two flags track the effects on grids of constraints */
BOOL nc_virtual; /* node added by regrid */
struct CDFnode* attachment; /* DDS<->DATADDS cross link*/
struct CDFnode* pattern; /* temporary field for regridding */
/* Fields for use by libncdap4 */
NCtypesize typesize;
int typeid; /* when treating field as type */
int basetypeid; /* when typeid is vlen */
char* typename;
char* vlenname; /* for sequence types */
int singleton; /* for singleton sequences */
unsigned long estimatedsize; /* > 0 Only for var nodes */
BOOL whole; /* projected as whole node */
BOOL prefetchable; /* eligible to be prefetched (if whole) */
} CDFnode;
/**************************************************/
/* Shared procedures */
/* From error.c*/
extern NCerror ocerrtoncerr(OCerror);
extern NCerror attach(CDFnode* xroot, CDFnode* ddstarget);
extern void unattach(CDFnode*);
extern int nodematch(CDFnode* node1, CDFnode* node2);
extern int simplenodematch(CDFnode* node1, CDFnode* node2);
extern CDFnode* findxnode(CDFnode* target, CDFnode* xroot);
extern int constrainable(NCURI*);
extern char* makeconstraintstring(DCEconstraint*);
extern size_t estimatedataddssize(CDFnode* datadds);
extern void canonicalprojection(NClist*, NClist*);
extern NClist* getalldims(NCDAPCOMMON* nccomm, int visibleonly);
/* From cdf.c */
extern NCerror fixgrid(NCDAPCOMMON* drno, CDFnode* grid);
extern NCerror computecdfinfo(NCDAPCOMMON*, NClist*);
extern char* cdfname(char* basename);
extern NCerror augmentddstree(NCDAPCOMMON*, NClist*);
extern NCerror computecdfdimnames(NCDAPCOMMON*);
extern NCerror buildcdftree(NCDAPCOMMON*, OCddsnode, OCdxd, CDFnode**);
extern CDFnode* makecdfnode(NCDAPCOMMON*, char* nm, OCtype,
/*optional*/ OCddsnode ocnode, CDFnode* container);
extern void freecdfroot(CDFnode*);
extern NCerror dimimprint(NCDAPCOMMON*);
extern NCerror definedimsets(NCDAPCOMMON*,CDFtree*);
extern NCerror definedimsettrans(NCDAPCOMMON*,CDFtree*);
/* From cache.c */
extern int iscached(NCDAPCOMMON*, CDFnode* target, NCcachenode** cachenodep);
extern NCerror prefetchdata(NCDAPCOMMON*);
extern NCerror markprefetch(NCDAPCOMMON*);
extern NCerror buildcachenode(NCDAPCOMMON*,
DCEconstraint* constraint,
NClist* varlist,
NCcachenode** cachep,
NCFLAGS flags);
extern NCcachenode* createnccachenode(void);
extern void freenccachenode(NCDAPCOMMON*, NCcachenode* node);
extern NCcache* createnccache(void);
extern void freenccache(NCDAPCOMMON*, NCcache* cache);
/* Add an extra function whose sole purpose is to allow
configure(.ac) to test for the presence of thiscode.
*/
extern int nc__opendap(void);
/* Define accessors for the dispatchdata */
#define NCD2_DATA(nc) ((NCDAPCOMMON*)(nc)->dispatchdata)
#define NCD2_DATA_SET(nc,data) ((nc)->dispatchdata = (void*)(data))
#define getncid(drno) (((NC*)drno)->ext_ncid)
#define getdap(drno) ((NCDAPCOMMON*)((NC*)drno)->dispatchdata)
#define getnc3id(drno) (getdap(drno)->substrate.nc3id)
#endif /*NCCOMMON_H*/