netcdf-c/ncgen/genj.c

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/*********************************************************************
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* Copyright 2018, UCAR/Unidata
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* See netcdf/COPYRIGHT file for copying and redistribution conditions.
* $Header: /upc/share/CVS/netcdf-3/ncgen/genj.c,v 1.2 2010/05/17 23:26:44 dmh Exp $
*********************************************************************/
#include "includes.h"
#include <stddef.h>
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#ifdef ENABLE_JAVA
#undef EXCEPTWRAP
#undef TRACE
/*MNEMONIC*/
#define USEMEMORY 1
extern List* vlenconstants; /* List<Constant*>;*/
/* Forward */
static const char* jtypeallcaps(nc_type type);
static const char* jtypecap(nc_type type);
static const char* jtype(nc_type type);
static const char* jarraytype(nc_type type);
static const char* jname(Symbol* sym);
static void genj_defineattr(Symbol* asym);
static void genj_definevardata(Symbol*);
static void genj_write(Generator*,Symbol* sym, Bytebuffer* code,
int rank, size_t* start, size_t* count);
static void genj_writevar(Generator*,Symbol*,Bytebuffer*,int,size_t*,size_t*);
static void genj_writeattr(Generator*,Symbol*,Bytebuffer*,int,size_t*,size_t*);
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/*
* Generate code for creating netCDF from in-memory structure.
*/
void
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.
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genjava_netcdf(void)
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{
size_t idim, ivar, iatt;
int maxdims;
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.
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const char *filename = rootgroup->file.filename;
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size_t ndims = listlength(dimdefs);
size_t nvars = listlength(vardefs);
size_t natts = listlength(attdefs);
size_t ngatts = listlength(gattdefs);
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/* Construct the main class */
codeline("import java.util.*;");
codeline("import ucar.ma2.*;");
codeline("import ucar.nc2.*;");
codeline("import ucar.nc2.NetcdfFile.*;");
codeline("");
codepartial("public class ");
codeline(mainname);
codeline("{");
/* Now construct the main procedure*/
codeline("");
codeline("static public void main(String[] argv) throws Exception");
codeline("{");
/* create necessary declarations */
if(ndims > 0) {
codeline("");
codelined(1,"/* dimension lengths */");
for(idim = 0; idim < ndims; idim++) {
Symbol* dsym = (Symbol*)listget(dimdefs,idim);
if(dsym->dim.declsize == NC_UNLIMITED) {
bbprintf0(stmt,"%sfinal int %s_len = 0;\n",
indented(1),jname(dsym));
} else {
bbprintf0(stmt,"%sfinal int %s_len = %lu;\n",
indented(1),
jname(dsym),
(unsigned long) dsym->dim.declsize);
}
codedump(stmt);
}
}
codeflush();
maxdims = 0; /* most dimensions of any variable */
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
if(vsym->typ.dimset.ndims > maxdims)
maxdims = vsym->typ.dimset.ndims;
}
codeline("");
#ifdef EXCEPTWRAP
codelined(1,"try {");
#endif
/* create netCDF file, uses NC_CLOBBER mode */
codeline("");
codelined(1,"/* enter define mode */");
bbprintf0(stmt,
"%sNetcdfFileWriteable ncfile = NetcdfFileWriteable.createNew(\"%s\", %s);\n",
indented(1),filename,(nofill_flag?"false":"true"));
codedump(stmt);
codeflush();
/* define dimensions from info in dims array */
if(ndims > 0) {
codeline("");
codelined(1,"/* define dimensions */");
for(idim = 0; idim < ndims; idim++) {
Symbol* dsym = (Symbol*)listget(dimdefs,idim);
if(dsym->dim.declsize == NC_UNLIMITED) {
bbprintf0(stmt,"%sDimension %s_dim = ncfile.addUnlimitedDimension(\"%s\");\n",
indented(1),jname(dsym),jescapifyname(dsym->name));
} else {
bbprintf0(stmt,"%sDimension %s_dim = ncfile.addDimension(\"%s\", %s_len);\n",
indented(1),jname(dsym),jescapifyname(dsym->name), jname(dsym));
}
codedump(stmt);
}
codeflush();
}
/* define variables from info in vars array */
if(nvars > 0) {
codeline("");
codelined(1,"/* define variables */");
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
Symbol* basetype = vsym->typ.basetype;
Dimset* dimset = &vsym->typ.dimset;
codeline("");
bbprintf0(stmt,"%sArrayList %s_dimlist = new ArrayList();\n",
indented(1),jname(vsym));
codedump(stmt);
if(dimset->ndims > 0) {
for(idim = 0; idim < dimset->ndims; idim++) {
Symbol* dsym = dimset->dimsyms[idim];
bbprintf0(stmt,"%s%s_dimlist.add(%s_dim);\n",
indented(1),jname(vsym),jname(dsym));
codedump(stmt);
}
}
bbprintf0(stmt,
"%sncfile.addVariable(\"%s\", DataType.%s, %s_dimlist);\n",
indented(1),
jescapifyname(vsym->name),
jtypeallcaps(basetype->typ.typecode),
jname(vsym));
codedump(stmt);
}
codeflush();
}
/* Define the global attributes*/
if(ngatts > 0) {
codeline("");
codelined(1,"/* assign global attributes */");
for(iatt = 0; iatt < ngatts; iatt++) {
Symbol* gasym = (Symbol*)listget(gattdefs,iatt);
genj_defineattr(gasym);
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}
codeline("");
codeflush();
}
/* Define the variable specific attributes*/
if(natts > 0) {
codeline("");
codelined(1,"/* assign per-variable attributes */");
for(iatt = 0; iatt < natts; iatt++) {
Symbol* asym = (Symbol*)listget(attdefs,iatt);
genj_defineattr(asym);
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}
codeline("");
codeflush();
}
codelined(1,"ncfile.create();"); /* equiv to nc_enddef */
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if(!header_only) {
/* Load values into those variables with defined data */
if(nvars > 0) {
codeline("");
codelined(1,"/* assign variable data */");
for(ivar = 0; ivar < nvars; ivar++) {
Symbol* vsym = (Symbol*)listget(vardefs,ivar);
if(vsym->data != NULL) genj_definevardata(vsym);
}
codeline("");
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}
}
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codeflush();
}
void
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.
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genjava_close(void)
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{
codelined(1,"ncfile.close();");
codeline("");
#ifdef EXCEPTIONWRAP
codelined(1,"} catch(Exception e) {e.printStackTrace();};");
#endif
codelined(1,"}"); /* main */
codeline("}"); /* class Main */
codeflush();
}
const char*
jtypeallcaps(nc_type type)
{
switch (type) {
case NC_CHAR: return "CHAR";
case NC_BYTE: return "BYTE";
case NC_SHORT: return "SHORT";
case NC_INT: return "INT";
case NC_FLOAT: return "FLOAT";
case NC_DOUBLE: return "DOUBLE";
case NC_UBYTE: return "LONG";
case NC_USHORT: return "LONG";
case NC_UINT: return "LONG";
case NC_INT64: return "LONG";
case NC_UINT64: return "LONG";
case NC_STRING: return "STRING";
default: PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
static const char*
jtypecap(nc_type type)
{
switch (type) {
case NC_CHAR: return "Char";
case NC_BYTE: return "Byte";
case NC_SHORT: return "Short";
case NC_INT: return "Int";
case NC_FLOAT: return "Float";
case NC_DOUBLE: return "Double";
case NC_UBYTE: return "Long";
case NC_USHORT: return "Long";
case NC_UINT: return "Long";
case NC_INT64: return "Long";
case NC_UINT64: return "Long";
case NC_STRING: return "String";
case NC_ENUM: return "Int";
case NC_OPAQUE: return "String";
default: PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
void
jquotestring(Bytebuffer* databuf, char quote)
{
char* escaped = jescapify(bbContents(databuf),'"',bbLength(databuf));
bbClear(databuf);
bbAppend(databuf,quote);
if(escaped != NULL) bbCat(databuf,escaped);
bbAppend(databuf,quote);
}
/* Compute the name for a given symbol*/
/* Cache in symbol->lname*/
static const char*
jname(Symbol* sym)
{
char* name;
assert (sym->fqn != NULL);
/* convert to language form*/
name = codify(sym->fqn); /* convert to usable form*/
return name;
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}
/*
* Return java type name for netCDF type, given type code.
*/
static const char*
jtype(nc_type type)
{
switch (type) {
case NC_CHAR: return "char";
case NC_BYTE: return "byte";
case NC_SHORT: return "short";
case NC_INT: return "int";
case NC_FLOAT: return "float";
case NC_DOUBLE: return "double";
case NC_UBYTE: return "long";
case NC_USHORT: return "long";
case NC_UINT: return "long";
case NC_INT64: return "long";
case NC_UINT64: return "long";
case NC_STRING: return "String";
case NC_ENUM: return "int";
case NC_OPAQUE: return "String";
default: PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
/*
* Return a type name and dimensions for constant arrays
* for netCDF type, given type code.
*/
static const char*
jarraytype(nc_type type)
{
switch (type) {
case NC_CHAR:
return "String";
case NC_BYTE:
return "byte";
case NC_SHORT:
return "short";
case NC_INT:
return "int";
case NC_FLOAT:
return "float";
case NC_DOUBLE:
return "double";
case NC_UBYTE:
return "long";
case NC_USHORT:
return "long";
case NC_UINT:
return "long";
case NC_INT64:
return "long";
case NC_UINT64:
return "long";
case NC_STRING:
return "String";
case NC_ENUM:
return "int";
case NC_OPAQUE:
return "String";
default:
PANIC1("ncctype: bad type code:%d",type);
}
return 0;
}
/*
* Return netcdf interface type name for netCDF type suffix, given type code.
*/
const char*
jstype(nc_type nctype)
{
switch (nctype) {
case NC_CHAR:
return "text";
case NC_BYTE:
return "schar";
case NC_SHORT:
return "short";
case NC_INT:
return "int";
case NC_FLOAT:
return "float";
case NC_DOUBLE:
return "double";
case NC_UBYTE:
return "ubyte";
case NC_USHORT:
return "ushort";
case NC_UINT:
return "uint";
case NC_INT64:
return "longlong";
case NC_UINT64:
return "ulonglong";
case NC_STRING:
return "string";
case NC_OPAQUE:
return "opaque";
case NC_ENUM:
return "enum";
default:
derror("ncstype: bad type code: %d",nctype);
return 0;
}
}
static void
genj_defineattr(Symbol* asym)
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{
Bytebuffer* code; /* capture so we can dump vlens first */
ASSERT(asym->data != NULL);
code = bbNew();
generator_reset(j_generator,NULL);
generate_attrdata(asym,j_generator,(Writer)genj_write,code);
bbFree(code);
}
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static void
genj_definevardata(Symbol* vsym)
{
Bytebuffer* code; /* capture so we can dump vlens first */
if(vsym->data == NULL) return;
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code = bbNew();
generator_reset(j_generator,NULL);
generate_vardata(vsym,j_generator,(Writer)genj_write,code);
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bbFree(code);
}
static void
genj_write(Generator* generator, Symbol* sym, Bytebuffer* code,
int rank, size_t* start, size_t* count)
{
if(sym->objectclass == NC_ATT)
genj_writeattr(generator,sym,code,rank,start,count);
else if(sym->objectclass == NC_VAR)
genj_writevar(generator,sym,code,rank,start,count);
else
PANIC("illegal symbol for genj_write");
}
static void
genj_writevar(Generator* generator, Symbol* vsym, Bytebuffer* code,
int rank, size_t* start, size_t* count)
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{
Dimset* dimset = &vsym->typ.dimset;
int typecode = vsym->typ.basetype->typ.typecode;
int i;
codeline("");
codelined(1,"{"); /* Enclose in {...} for scoping */
if(rank == 0) {
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bbprintf0(stmt,"%sArray%s.D0 data = new Array%s.D0();\n",
indented(1),jtypecap(typecode), jtypecap(typecode));
codedump(stmt);
if(typecode == NC_CHAR) {
/* Construct the data Array */
jquotestring(code,'\'');
bbprintf0(stmt,"%sdata.set((char)%s);\n",
indented(1),bbContents(code));
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} else {
commify(code);
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bbprintf0(stmt,"%sdata.set((%s)%s);\n",
indented(1),jtype(typecode),bbContents(code));
}
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codedump(stmt);
/* do the actual write */
bbprintf0(stmt,"%sncfile.write(\"%s\",data);\n",
indented(1),jescapifyname(vsym->name));
codedump(stmt);
} else { /* array */
Bytebuffer* dimbuf = bbNew();
/* Construct the dimension set*/
bbCat(dimbuf,"new int[]{");
for(i=0;i<rank;i++) {
Symbol* dsym = dimset->dimsyms[i];
char tmp[32];
nprintf(tmp,sizeof(tmp),"%lu",dsym->dim.declsize);
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if(i>0) {bbCat(dimbuf,", ");}
bbCat(dimbuf,tmp);
}
bbCat(dimbuf,"}");
/* Construct the data array and capture its index */
if(typecode == NC_CHAR) {
jquotestring(code,'"');
bbprintf0(stmt,"%sString contents = ",
indented(1));
} else {
bbprintf0(stmt,"%s%s[] contents = new %s[] {",
indented(1),jtype(typecode),jtype(typecode));
commify(code);
}
codedump(stmt);
codedump(code);
if(typecode != NC_CHAR) codepartial("}");
codeline(";");
bbprintf0(stmt,"%sArray%s data = new Array%s(%s);\n",
indented(1),
jtypecap(typecode),
jtypecap(typecode),
bbContents(dimbuf));
codedump(stmt);
codelined(1,"IndexIterator iter = data.getIndexIterator();");
codelined(1,"int count = 0;");
codelined(1,"while(iter.hasNext())");
if(typecode == NC_CHAR)
bbprintf0(stmt,
"%siter.setCharNext(contents.charAt(count++));\n",indented(2));
else
bbprintf0(stmt,"%siter.set%sNext(contents[count++]);\n",
indented(2),jtypecap(typecode));
codedump(stmt);
bbFree(dimbuf);
/* Construct the origin set from the start set */
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bbprintf0(stmt,"%sint[] origin = new int[]{",indented(1));
for(i=0;i<rank;i++) {
bbprintf(stmt,"%s%lu",(i>0?", ":""),start[i]);
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}
bbCat(stmt,"};\n");
codedump(stmt);
/* do the actual write */
bbprintf0(stmt,"%sncfile.write(\"%s\",origin,data);\n",
indented(1),jescapifyname(vsym->name));
codedump(stmt);
}
codelined(1,"}"); /* Enclose in {...} for scoping */
codeflush();
}
static void
genj_writeattr(Generator* generator, Symbol* asym, Bytebuffer* code,
int rank, size_t* start, size_t* count)
{
Symbol* basetype = asym->typ.basetype;
nc_type typecode = basetype->typ.typecode;
/* default assumption */
size_t len = asym->data == NULL?0:asym->data->length;
codeprintf("%s/* attribute: %s */\n",indented(1),asym->name);
/* Handle NC_CHAR specially */
if(typecode == NC_CHAR) {
/* revise the length count */
len = bbLength(code);
if(len == 0) {
bbAppend(code,'\0'); len++;
bbClear(code);
bbCat(code,"\"\"");
len++;
} else
jquotestring(code,'"');
bbNull(code);
} else { /* not NC_CHAR*/
char* code2;
commify(code);
/* Convert to constant */
code2 = bbDup(code);
bbClear(code);
bbprintf0(stmt,"new %s[]",
jarraytype(typecode));
bbCatbuf(code,stmt);
bbCat(code,"{");
bbCat(code,code2);
bbCat(code,"}");
efree(code2);
}
switch (typecode) {
case NC_BYTE:
case NC_SHORT:
case NC_INT:
case NC_FLOAT:
case NC_DOUBLE:
codelined(1,"{");
bbprintf0(stmt,"%sArray data = Array.factory(%s.class, new int[]{%lu}, ",
indented(1),
jtype(basetype->typ.typecode),
len);
codedump(stmt);
codedump(code);
codeline(");");
if(asym->att.var == NULL) {
bbprintf0(stmt,"%sncfile.addGlobalAttribute(\"%s\",data);\n",
indented(1),jescapifyname(asym->name));
} else {
bbprintf0(stmt,"%sncfile.addVariableAttribute(\"%s\",\"%s\",data);\n",
indented(1),
jescapifyname(asym->att.var->name),
jescapifyname(asym->name));
}
codedump(stmt);
codelined(1,"}");
codeflush();
break;
case NC_CHAR:
if(asym->att.var == NULL) {
bbprintf0(stmt,"%sncfile.addGlobalAttribute(\"%s\",%s);\n",
indented(1),
jescapifyname(asym->name),
bbContents(code));
} else {
bbprintf0(stmt,"%sncfile.addVariableAttribute(\"%s\",\"%s\",%s);\n",
indented(1),
jescapifyname(asym->att.var->name),
jescapifyname(asym->name),
bbContents(code));
}
codedump(stmt);
codeflush();
break;
default: break;
}
codeflush();
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}
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#endif /*ENABLE_JAVA*/