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Matlab #1142

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merged 16 commits into from
Feb 6, 2019
Merged

Matlab #1142

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a2d001c
added a serial python test code for producing test data for matlab
pnorbert Jan 28, 2019
adc9719
Fix const - non-const discrepancy
pnorbert Jan 28, 2019
9d100af
fix python write example, offset of array was wrong
pnorbert Jan 30, 2019
f85cec4
Fixes in Matlab wrapper to use C api correctly.
pnorbert Jan 31, 2019
c0267a6
Read attributes including array attributes and strings. Missing: stri…
pnorbert Feb 5, 2019
56e3a1f
Support min/max of variables. Support attribute string arrays.
pnorbert Feb 5, 2019
379a60f
added a serial python test code for producing test data for matlab
pnorbert Jan 28, 2019
51c1b78
Fix const - non-const discrepancy
pnorbert Jan 28, 2019
b97fcb5
fix python write example, offset of array was wrong
pnorbert Jan 30, 2019
a36d6d8
Fixes in Matlab wrapper to use C api correctly.
pnorbert Jan 31, 2019
5084305
Read attributes including array attributes and strings. Missing: stri…
pnorbert Feb 5, 2019
91093c1
Support min/max of variables. Support attribute string arrays.
pnorbert Feb 5, 2019
2b0f257
Fix reading string variable's value to create min/max
pnorbert Feb 6, 2019
a7ade88
Merge branch 'matlab' of https://github.com/ornladios/adios2 into matlab
pnorbert Feb 6, 2019
c56bc69
update python scripts for Codacy
pnorbert Feb 6, 2019
5988b23
flake python scripts
pnorbert Feb 6, 2019
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14 changes: 8 additions & 6 deletions bindings/Matlab/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,19 +5,21 @@
#MEXLIBS="LDFLAGS=${ADIOS_LIBS}"

### TITAN
#ADIOS_DIR=/ccs/proj/e2e/pnorbert/ADIOS/ADIOS2/build.titan.gnu-nompi-shared/install
ADIOS_DIR=/ccs/proj/e2e/pnorbert/ADIOS/ADIOS2/build.titan.gnu-nompi/install
#ADIOS_DIR=/ccs/proj/e2e/pnorbert/ADIOS/ADIOS2/build.rhea.gnu-nompi/install
#ADIOS_LIBS=-Wl,-rpath=${ADIOS_DIR}/lib -L${ADIOS_DIR}/lib -ladios2
ADIOS_LIBS=-L${ADIOS_DIR}/lib -ladios2
#ADIOS_INC=-I${ADIOS_DIR}/include
#MEXLIBS=${ADIOS_LIBS}
MEXLIBS=${ADIOS_LIBS}

### Kathleen's PC
ADIOS_DIR=/opt/adios/2.2-lean
ADIOS_LIBS=-Wl,-rpath=${ADIOS_DIR}/lib -L${ADIOS_DIR}/lib -ladios2
#ADIOS_DIR=/opt/adios/2.2-lean
#ADIOS_LIBS=-Wl,-rpath=${ADIOS_DIR}/lib -L${ADIOS_DIR}/lib -ladios2
ADIOS_INC=-I${ADIOS_DIR}/include
MEXLIBS="LDFLAGS=${ADIOS_LIBS}"
#MEXLIBS="LDFLAGS=${ADIOS_LIBS}"


MEXOPTS=-largeArrayDims -DDEBUG CFLAGS="-g -std=c99 -fPIC"
MEXOPTS=-largeArrayDims -DDEBUG CFLAGS="-g -std=c99 -fPIC -O0"
default:
@echo "ADIOS reader methods for MATLAB"
@echo "Have 'mex' compiler in the path and run"
Expand Down
225 changes: 198 additions & 27 deletions bindings/Matlab/adiosopenc.c
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Original file line number Diff line number Diff line change
Expand Up @@ -49,10 +49,13 @@
static int verbose = 0;

mxClassID adiostypeToMatlabClass(int adiostype, mxComplexity *complexity);
size_t adiostypeToMemSize(adios2_type adiostype);
mxClassID adiostypestringToMatlabClass(const char *type,
mxComplexity *complexity);
mxArray *valueToMatlabValue(const void *data, mxClassID mxtype,
mxComplexity complexFlag);
mxArray *arrayToMatlabArray(const void *data, const size_t nelems, mxClassID mxtype,
mxComplexity complexFlag);
void errorCheck(int nlhs, int nrhs, const mxArray *prhs[]);
char *getString(const mxArray *mxstr);
static size_t *swap_order(size_t n, const size_t *array);
Expand Down Expand Up @@ -232,17 +235,18 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
mexPrintf(" Variables\n");
for (vi = 0; vi < nvars; vi++)
{
const adios2_variable *avar = adios_vars[vi];
adios2_variable *avar = adios_vars[vi];
/* field NAME */
size_t namelen;
const char varname[adios2_string_array_element_max_size];
char varname[adios2_string_array_element_max_size];

adios2_variable_name(varname, &namelen, avar);
varname[namelen] = '\0';
mxSetFieldByNumber(vars, vi, var_field_Name, mxCreateString(varname));
/* field TYPE */
adios2_type *adiostype;
adios2_variable_type(adiostype, avar);
mxtype = adiostypeToMatlabClass(*adiostype, &complexFlag);
adios2_type adiostype;
adios2_variable_type(&adiostype, avar);
mxtype = adiostypeToMatlabClass(adiostype, &complexFlag);
arr = mxCreateNumericMatrix(1, 1, mxtype, complexFlag);
mxSetFieldByNumber(vars, vi, var_field_Type,
mxCreateString(mxGetClassName(arr)));
Expand Down Expand Up @@ -292,16 +296,31 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
arr = valueToMatlabValue((void *)(&stepsCount), mxINT64_CLASS, mxREAL);
mxSetFieldByNumber(vars, vi, var_field_StepsCount, arr);

/* field GLOBALMIN */
// FIXME arr = valueToMatlabValue(vinfo->gmin, mxtype, complexFlag);
double fakemin = 0.0;
arr = valueToMatlabValue(&fakemin, mxDOUBLE_CLASS, complexFlag);
mxSetFieldByNumber(vars, vi, var_field_GlobalMin, arr);

/* field GLOBALMAX */
// FIXME arr = valueToMatlabValue(vinfo->gmax, mxtype, complexFlag);
arr = valueToMatlabValue(&fakemin, mxDOUBLE_CLASS, complexFlag);
mxSetFieldByNumber(vars, vi, var_field_GlobalMax, arr);
/* fields GLOBALMIN and GLOBALMAX */
if (adiostype == adios2_type_string)
{
char *str1 = (char *)mxCalloc(65536, sizeof(char));
adios2_get(fp, avar, str1, adios2_mode_sync);
arr = valueToMatlabValue(str1, mxtype, complexFlag);
mxSetFieldByNumber(vars, vi, var_field_GlobalMin, arr);
/* must make another copy to avoid double free corruption
* at exit of Matlab */
arr = valueToMatlabValue(str1, mxtype, complexFlag);
mxSetFieldByNumber(vars, vi, var_field_GlobalMax, arr);
mxFree(str1);
}
else
{
size_t typesize = adiostypeToMemSize(adiostype);
char value[typesize];
adios2_variable_min(value, avar);
arr = valueToMatlabValue(value, mxtype, complexFlag);
mxSetFieldByNumber(vars, vi, var_field_GlobalMin, arr);

adios2_variable_max(value, avar);
arr = valueToMatlabValue(value, mxtype, complexFlag);
mxSetFieldByNumber(vars, vi, var_field_GlobalMax, arr);
}

free(dims);
}
Expand All @@ -316,31 +335,84 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
const adios2_attribute *aa = adios_attrs[ai];
/* field NAME */
size_t namelen;
const char attrname[adios2_string_array_element_max_size];
char attrname[adios2_string_array_element_max_size];
adios2_attribute_name(attrname, &namelen, aa);
attrname[namelen] = '\0';

mxSetFieldByNumber(attrs, ai, attr_field_Name,
mxCreateString(attrname));
/* field TYPE */
size_t typelen;
const char atype[adios2_string_array_element_max_size];
adios2_type adiostype;
adios2_attribute_type(&adiostype, aa);

/*char atype[adios2_string_array_element_max_size];
adios2_attribute_type_string(atype, &typelen, aa);
atype[namelen] = '\0';*/

mxtype = adiostypestringToMatlabClass(atype, &complexFlag);
// mxtype = adiostypeToMatlabClass(adiostype, &complexFlag);
mxtype = adiostypeToMatlabClass(adiostype, &complexFlag);
arr = mxCreateNumericMatrix(1, 1, mxtype, complexFlag);
mxSetFieldByNumber(attrs, ai, attr_field_Type,
mxCreateString(mxGetClassName(arr)));
mxDestroyArray(arr);
/* field VALUE */
size_t asize;
const void *data;
adios2_attribute_data(data, &asize, aa);
arr = valueToMatlabValue(data, mxtype, complexFlag);
mxSetFieldByNumber(attrs, ai, attr_field_Value, arr);
size_t aelems;
mexPrintf(" get field Data\n");
adios2_attribute_size(&aelems, aa);
size_t atypesize = adiostypeToMemSize(adiostype);
mexPrintf(" field Data nelems = %zu, type size=%zu\n", aelems, atypesize);
void *data;
if (adiostype == adios2_type_string)
{
if (aelems == 1)
{
/* single string attribute */
/* FIXME: get the size of string from ADIOS first */
data = mxCalloc(4096, 1);
size_t nelems;
adios2_attribute_data(data, &nelems, aa);
mexPrintf(" field Data ptr=%p data=%s\n", data, data);
arr = valueToMatlabValue(data, mxtype, complexFlag);
}
else
{
/* string array attribute */
char **dataArray = mxCalloc(aelems, sizeof(char*));
size_t i;
for (i = 0; i < aelems; ++i)
{
dataArray[i] = mxCalloc(4096, 1);
}
size_t nelems;
data = (void *) dataArray;
adios2_attribute_data(data, &nelems, aa);
mexPrintf(" field Data ptr=%p data[0]=%s\n", data, *(char**)data);
arr = arrayToMatlabArray(data, aelems, mxtype, complexFlag);
}
mxSetFieldByNumber(attrs, ai, attr_field_Value, arr);
}
else
{
data = mxCalloc(atypesize, aelems);
size_t nelems;
adios2_attribute_data(data, &nelems, aa);
mexPrintf(" field Data ptr=%p nelems=%zu\n", data, nelems);
if (aelems == 1)
{
/* single element attribute */
arr = valueToMatlabValue(data, mxtype, complexFlag);
}
else
{
/* array attribute */
arr = arrayToMatlabArray(data, aelems, mxtype, complexFlag);
}
mxSetFieldByNumber(attrs, ai, attr_field_Value, arr);
}
if (verbose > 1)
mexPrintf(" %s: adios type=%s size=%zu\n", attrname, atype,
asize);
mexPrintf(" %s: adios type=%s size=%zu\n", attrname, mxGetClassName(arr),
aelems);
mxFree(data);
}

if (verbose)
Expand Down Expand Up @@ -385,6 +457,45 @@ mxArray *valueToMatlabValue(const void *data, mxClassID mxtype,
return arr;
}

mxArray *arrayToMatlabArray(const void *data, const size_t nelems, mxClassID mxtype,
mxComplexity complexFlag)
{
/* copies values in all cases, so one can free(data) later */
mxArray *arr;
if (data == NULL)
{
arr = mxCreateString("undefined");
}
else if (mxtype == mxCHAR_CLASS)
{
arr = mxCreateCharMatrixFromStrings(nelems, (const char**)data);
}
else if (complexFlag == mxCOMPLEX)
{
arr = mxCreateDoubleMatrix(1, nelems, mxCOMPLEX);
size_t i;
for (i = 0; i < nelems; ++i)
{
if (mxtype == mxSINGLE_CLASS)
{
((float *)mxGetPr(arr))[i] = ((const float *)data)[2*i];
((float *)mxGetPi(arr))[i] = ((const float *)data)[2*i+1];
}
else
{
((double *)mxGetPr(arr))[i] = ((const double *)data)[2*i];
((double *)mxGetPi(arr))[i] = ((const double *)data)[2*i+1];
}
}
}
else
{
arr = mxCreateNumericMatrix(1, nelems, mxtype, mxREAL);
memcpy(mxGetData(arr), data, nelems*mxGetElementSize(arr));
}
return arr;
}

void errorCheck(int nlhs, int nrhs, const mxArray *prhs[])
{
/* Assume that we are called from adiosread.m which checks the arguments
Expand Down Expand Up @@ -447,7 +558,7 @@ mxClassID adiostypeToMatlabClass(adios2_type adiostype,
return mxINT8_CLASS;

case adios2_type_string:
case adios2_type_string_array:
/* case adios2_type_string_array: */
return mxCHAR_CLASS;

case adios2_type_unsigned_short:
Expand Down Expand Up @@ -503,6 +614,66 @@ mxClassID adiostypeToMatlabClass(adios2_type adiostype,
return 0; /* just to avoid warnings. never executed */
}

/** return the appropriate class for an adios type (and complexity too) */
size_t adiostypeToMemSize(adios2_type adiostype)
{
switch (adiostype)
{
case adios2_type_unsigned_char:
case adios2_type_uint8_t:
case adios2_type_char:
case adios2_type_signed_char:
case adios2_type_int8_t:
return sizeof(char);

case adios2_type_string:
/* case adios2_type_string_array: */
return sizeof(char);

case adios2_type_unsigned_short:
case adios2_type_uint16_t:
case adios2_type_short:
case adios2_type_int16_t:
return sizeof(int16_t);

case adios2_type_unsigned_int:
case adios2_type_uint32_t:
case adios2_type_int:
case adios2_type_int32_t:
return sizeof(int32_t);

case adios2_type_unsigned_long_int:
case adios2_type_long_int:
if (sizeof(long int) == 4)
return sizeof(int32_t);
else
return sizeof(int64_t);

case adios2_type_unsigned_long_long_int:
case adios2_type_uint64_t:
case adios2_type_long_long_int:
case adios2_type_int64_t:
return sizeof(int64_t);

case adios2_type_float:
return sizeof(float);
case adios2_type_double:
return sizeof(double);

case adios2_type_float_complex: /* 8 bytes */
return 2*sizeof(float);
case adios2_type_double_complex: /* 16 bytes */
return 2*sizeof(double);

default:
mexErrMsgIdAndTxt("MATLAB:adiosopenc.c:dimensionTooLarge",
"Adios type id=%d not supported in matlab.\n",
adiostype);
break;
}
return 0; /* just to avoid warnings. never executed */
}

/** return the appropriate class for an adios type (and complexity too) */
mxClassID adiostypestringToMatlabClass(const char *type,
mxComplexity *complexity)
Expand Down
12 changes: 9 additions & 3 deletions bindings/Matlab/adiosreadc.c
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Original file line number Diff line number Diff line change
Expand Up @@ -208,7 +208,8 @@ mxArray *readdata(adios2_engine *fp, adios2_io *group, const char *path,
if (adiostype == adios2_type_string)
{
/* Matlab string != char array of C, so handle separately */
data = (void *)mxCalloc(varDim[0], sizeof(char));
data = (void *)mxCalloc(65536, sizeof(char));
mexPrintf("Create C string reading in a string with ptr %p\n", data);
}
else
{
Expand Down Expand Up @@ -237,7 +238,11 @@ mxArray *readdata(adios2_engine *fp, adios2_io *group, const char *path,
mexPrintf("Set step-selection for variable: start = %zu count = %zu\n",
qstepstart, qstepcount);
}
adios2_set_selection(avar, varNdim, qoffsets, qcounts);

if (varNdim > 0)
{
adios2_set_selection(avar, varNdim, qoffsets, qcounts);
}
adios2_set_step_selection(avar, qstepstart, qstepcount);

/* read in data */
Expand All @@ -248,6 +253,7 @@ mxArray *readdata(adios2_engine *fp, adios2_io *group, const char *path,

if (adiostype == adios2_type_string)
{
mexPrintf("Create Matlab string from C string [%s]\n", (char*)data);
out = mxCreateString((char *)data);
mxFree(data);
}
Expand Down Expand Up @@ -343,7 +349,7 @@ mxClassID adiostypeToMatlabClass(adios2_type adiostype,
return mxINT8_CLASS;

case adios2_type_string:
case adios2_type_string_array:
/* case adios2_type_string_array: */
return mxCHAR_CLASS;

case adios2_type_unsigned_short:
Expand Down
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