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remove H5close call, introduce specific hdf5 object H5xclose calls #397

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merged 1 commit into from
Apr 8, 2019
Merged

remove H5close call, introduce specific hdf5 object H5xclose calls #397

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101 changes: 97 additions & 4 deletions ADApp/pluginSrc/NDFileHDF5.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -584,6 +584,9 @@ asynStatus NDFileHDF5::storeOnOpenCloseAttribute(hdf5::Element *element, bool op
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "%s::%s unable to create attribute: %s\n",
driverName, functionName, attr.get_name().c_str());
H5Sclose(hdfattrdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
} else {
herr_t hdfstatus = H5Awrite(hdfattr, hdfdatatype, datavalue);
if (hdfstatus < 0) {
Expand All @@ -592,6 +595,9 @@ asynStatus NDFileHDF5::storeOnOpenCloseAttribute(hdf5::Element *element, bool op
}
H5Aclose(hdfattr);
H5Sclose(hdfattrdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
}
} else if(dataType == NDAttrString){
// This is a string attribute
Expand Down Expand Up @@ -655,6 +661,7 @@ asynStatus NDFileHDF5::createTree(hdf5::Group* root, hid_t h5handle)
hid_t new_dset = this->createDataset(new_group, it_dsets->second);
if (new_dset <= 0) {
hdf5::Dataset *dset = it_dsets->second;
// HK I can see messages: Failed to create dataset: timestamp. Continuing to next.
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING,
"%s::%s Failed to create dataset: %s. Continuing to next.\n",
driverName, functionName, dset->get_name().c_str());
Expand Down Expand Up @@ -878,6 +885,9 @@ hid_t NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
epicsInt32 ival;
Expand All @@ -888,6 +898,9 @@ hid_t NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
driverName, functionName, name.c_str());
H5Dclose(hdfdset);
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
} else {
Expand All @@ -901,6 +914,9 @@ hid_t NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
for (int index = 0; index < (int)vect.size(); index++){
ivalues[index] = vect[index];
}
// HK test
H5Sclose(hdfdataspace);
// HK test
hdfdataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdfdataspace, 1, dims, NULL);
hdfdset = H5Dcreate2(element, name.c_str(), hdfdatatype, hdfdataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
Expand All @@ -909,6 +925,9 @@ hid_t NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
hdfstatus = H5Dwrite(hdfdset, hdfdatatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, ivalues);
Expand All @@ -918,11 +937,17 @@ hid_t NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
driverName, functionName, name.c_str());
H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
}
//H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return hdfdset;

}
Expand Down Expand Up @@ -959,6 +984,9 @@ hid_t NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, con
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
double fval;
Expand All @@ -969,6 +997,9 @@ hid_t NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, con
driverName, functionName, name.c_str());
H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
} else {
Expand All @@ -982,6 +1013,9 @@ hid_t NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, con
for (int index = 0; index < (int)vect.size(); index++){
fvalues[index] = vect[index];
}
// HK test
H5Sclose(hdfdataspace);
// HK test
hdfdataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdfdataspace, 1, dims, NULL);
hdfdset = H5Dcreate2(element, name.c_str(), hdfdatatype, hdfdataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
Expand All @@ -990,6 +1024,9 @@ hid_t NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, con
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
hdfstatus = H5Dwrite(hdfdset, hdfdatatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, fvalues);
Expand All @@ -999,11 +1036,17 @@ hid_t NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, con
driverName, functionName, name.c_str());
H5Dclose(hdfdset);
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return -1;
}
}
//H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
// HK test
H5Tclose(hdfdatatype);
// HK test
return hdfdset;

}
Expand Down Expand Up @@ -1056,6 +1099,9 @@ void NDFileHDF5::writeH5attrStr(hid_t element, const std::string &attr_name, con
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create attribute: %s\n",
driverName, functionName, attr_name.c_str());
H5Sclose(hdfattrdataspace);
// HK OK
H5Tclose(hdfdatatype);
// HK OK
return;
}

Expand All @@ -1065,10 +1111,16 @@ void NDFileHDF5::writeH5attrStr(hid_t element, const std::string &attr_name, con
driverName, functionName, attr_name.c_str());
H5Aclose (hdfattr);
H5Sclose(hdfattrdataspace);
// HK OK
H5Tclose(hdfdatatype);
// HK OK
return;
}
H5Aclose (hdfattr);
H5Sclose(hdfattrdataspace);
// HK OK
H5Tclose(hdfdatatype);
// HK OK
return;
}

Expand Down Expand Up @@ -1130,6 +1182,9 @@ void NDFileHDF5::writeH5attrInt32(hid_t element, const std::string &attr_name, c
for (int index = 0; index < (int)vect.size(); index++){
ivalues[index] = vect[index];
}
// HK OK
H5Sclose(hdfattrdataspace);
// HK OK
hdfattrdataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdfattrdataspace, 1, dims, NULL);
hdfattr = H5Acreate2(element, attr_name.c_str(), hdfdatatype, hdfattrdataspace, H5P_DEFAULT, H5P_DEFAULT);
Expand All @@ -1152,6 +1207,9 @@ void NDFileHDF5::writeH5attrInt32(hid_t element, const std::string &attr_name, c
}
H5Aclose (hdfattr);
H5Sclose(hdfattrdataspace);
// HK OK
H5Tclose(hdfdatatype);
// HK OK
return;
}

Expand Down Expand Up @@ -1213,6 +1271,9 @@ void NDFileHDF5::writeH5attrFloat64(hid_t element, const std::string &attr_name,
for (int index = 0; index < (int)vect.size(); index++){
fvalues[index] = vect[index];
}
// HK OK
H5Sclose(hdfattrdataspace);
// HK OK
hdfattrdataspace = H5Screate(H5S_SIMPLE);
H5Sset_extent_simple(hdfattrdataspace, 1, dims, NULL);
hdfattr = H5Acreate2(element, attr_name.c_str(), hdfdatatype, hdfattrdataspace, H5P_DEFAULT, H5P_DEFAULT);
Expand All @@ -1235,6 +1296,9 @@ void NDFileHDF5::writeH5attrFloat64(hid_t element, const std::string &attr_name,
}
H5Aclose (hdfattr);
H5Sclose(hdfattrdataspace);
// HK OK
H5Tclose(hdfdatatype);
// HK OK
return;
}

Expand Down Expand Up @@ -1301,6 +1365,10 @@ hid_t NDFileHDF5::createDatasetDetector(hid_t group, hdf5::Dataset *dset)
driverName, functionName, dsetname);
dataset = H5Dcreate2(group, dsetname, this->datatype, this->dataspace,
H5P_DEFAULT, this->cparms, dset_access_plist);

// HK OK
H5Pclose(dset_access_plist);
// HK OK

// Store the dataset into the detector dataset map
this->detDataMap[dset->get_full_name()] = new NDFileHDF5Dataset(this->pasynUserSelf, dset->get_name(), dataset);
Expand Down Expand Up @@ -1522,6 +1590,8 @@ asynStatus NDFileHDF5::writeFile(NDArray *pArray)
}
if (status != asynSuccess){
flushLock.unlock();
// HK is this a memory leak?
// compared to a couple of lines above where more is closed???
return status;
}
}
Expand Down Expand Up @@ -1551,6 +1621,8 @@ asynStatus NDFileHDF5::writeFile(NDArray *pArray)
}

if (status != asynSuccess){
// HK is this a memory leak?
// compared to a couple of lines above where more is closed???
hdfstatus = H5Fclose(this->file);
if (hdfstatus){
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR,
Expand Down Expand Up @@ -1624,9 +1696,17 @@ asynStatus NDFileHDF5::closeFile()

H5Tclose(this->datatype);

asynPrint(this->pasynUserSelf, ASYN_TRACE_FLOW,
"%s::%s closing HDF dataspace %ld\n",
driverName, functionName, (long int)this->datatype);

//HK OK
H5Sclose(this->dataspace);

asynPrint(this->pasynUserSelf, ASYN_TRACE_FLOW,
"%s::%s closing groups\n",
driverName, functionName);
//HK OK

// Iterate over the stored detector data sets and close them
std::map<std::string, NDFileHDF5Dataset *>::iterator it_dset;
Expand Down Expand Up @@ -1668,10 +1748,6 @@ asynStatus NDFileHDF5::closeFile()
// Close the HDF file
H5Fclose(this->file);
this->file = 0;
// Flush all data to disk, close all open HDF5 objects,
// and clean up all memory used by the HDF5 library
// to avoid memory leaks
H5close();

// At this point we can clear the SWMR active flag, whether we were running
// in SWMR mode or not
Expand Down Expand Up @@ -2561,12 +2637,18 @@ asynStatus NDFileHDF5::createPerformanceDataset()
if (!H5Iis_valid(this->perf_dataset_id)) {
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "NDFileHDF5::writePerformanceDataset: unable to create \'timestamp\' dataset.");
H5Sclose(dataspace_id);
// HK OK
H5Pclose(hdfcparm);
// HK OK
if(perf_group != NULL){
H5Gclose(group_performance);
}
return asynError;
}
H5Sclose(dataspace_id);
// HK OK
H5Pclose(hdfcparm);
// HK OK
if(perf_group != NULL){
H5Gclose(group_performance);
}
Expand Down Expand Up @@ -2940,6 +3022,9 @@ asynStatus NDFileHDF5::writeStringAttribute(hid_t element, const char * attrName
H5Awrite(hdfattr, hdfdatatype, attrStrValue);
H5Aclose(hdfattr);
H5Sclose(hdfattrdataspace);
// HK OK
H5Tclose(hdfdatatype);
// HK OK
}
return status;
}
Expand Down Expand Up @@ -3679,8 +3764,16 @@ asynStatus NDFileHDF5::createNewFile(const char *fileName)
"%s::%s Unable to create HDF5 file: %s\n",
driverName, functionName, fileName);
this->file = 0;
//HK OK
H5Pclose(create_plist);
H5Pclose(access_plist);
//HK OK
return asynError;
}
//HK OK
H5Pclose(create_plist);
H5Pclose(access_plist);
//HK OK
return asynSuccess;
}

Expand Down
5 changes: 5 additions & 0 deletions ADApp/pluginSrc/NDFileHDF5AttributeDataset.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -219,6 +219,11 @@ asynStatus NDFileHDF5AttributeDataset::closeAttributeDataset()
H5Sclose(memspace_);
H5Sclose(dataspace_);
H5Pclose(cparm_);
// HK test
if (type_ == NDAttrString) {
H5Tclose(datatype_);
}
// HK test
return asynSuccess;
}

Expand Down
9 changes: 9 additions & 0 deletions ADApp/pluginSrc/NDFileHDF5Dataset.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -267,6 +267,9 @@ asynStatus NDFileHDF5Dataset::writeFile(NDArray *pArray, hid_t datatype, hid_t d
asynPrint(this->pAsynUser_, ASYN_TRACE_ERROR,
"%s::%s ERROR Unable to select hyperslab\n",
fileName, functionName);
// HK test
H5Sclose(fspace);
// HK test
return asynError;
}

Expand Down Expand Up @@ -297,6 +300,9 @@ asynStatus NDFileHDF5Dataset::writeFile(NDArray *pArray, hid_t datatype, hid_t d
asynPrint(this->pAsynUser_, ASYN_TRACE_ERROR,
"%s::%s ERROR Unable to write pre-compressed data - mismatched chunk definition\n",
fileName, functionName);
// HK test
H5Sclose(fspace);
// HK test
return asynError;
}
asynPrint(this->pAsynUser_, ASYN_TRACE_FLOW,
Expand All @@ -309,6 +315,9 @@ asynStatus NDFileHDF5Dataset::writeFile(NDArray *pArray, hid_t datatype, hid_t d
asynPrint(this->pAsynUser_, ASYN_TRACE_ERROR,
"%s::%s ERROR Unable to write data to hyperslab\n",
fileName, functionName);
// HK test
H5Sclose(fspace);
// HK test
return asynError;
}

Expand Down
17 changes: 15 additions & 2 deletions ADApp/pluginSrc/NDFileHDF5Layout.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -311,6 +311,9 @@ namespace hdf5
{
for_each(this->datasets.begin(), this->datasets.end(), _delete_obj<Dataset>);
for_each(this->groups.begin(), this->groups.end(), _delete_obj<Group>);
// HK verify should this be done? Causes segfault..
// for_each(this->hardlinks.begin(), this->hardlinks.end(), _delete_obj<HardLink>);
// HK verify should this be done?
}

Group& Group::operator=(const Group& src)
Expand Down Expand Up @@ -372,7 +375,12 @@ namespace hdf5
std::pair<std::map<std::string, Group*>::iterator,bool> ret;
ret = this->groups.insert(std::pair<std::string, Group*>(name, grp));
// Check for successful insertion.
if (ret.second == false) return NULL;
if (ret.second == false) {
// HK test
delete grp;
// HK test
return NULL;
}
return grp;
}

Expand Down Expand Up @@ -402,7 +410,12 @@ namespace hdf5
std::pair<std::map<std::string, HardLink*>::iterator,bool> ret;
ret = this->hardlinks.insert(std::pair<std::string, HardLink*>(name, hardlink));
// Check for successful insertion.
if (ret.second == false) return NULL;
if (ret.second == false) {
// HK test
delete hardlink;
// HK test
return NULL;
}
return hardlink;
}

Expand Down
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