diff --git a/GNUmakefile b/GNUmakefile
index 3182a7d0bcabe0a6e3e13da2dc25719f649c7e8d..cbc419922850707850f01331c099c7f24c41d969 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -59,7 +59,7 @@ BLOSC_CPPFLAGS := \
-Ithirdparty/blosc/internal-complibs/zstd-0.7.4/dictBuilder \
-Ithirdparty/blosc/internal-complibs/zstd-0.7.4/decompress
-BASE_CPPFLAGS := $(BLOSC_CPPFLAGS) -D__STDC_CONSTANT_MACROS
+BASE_CPPFLAGS := $(BLOSC_CPPFLAGS) -I. -D__STDC_CONSTANT_MACROS
FEDIR = frontend
FE_CFLAGS := -g -fPIC -O3 -fopenmp
@@ -141,7 +141,14 @@ FE_SHARED := -bundle
else
FE_SHARED := -shared
endif
-$(FEDIR)/GenericIOSQLite.so: $(FEDIR)/GenericIOSQLite.o $(FEDIR)/GenericIO.o
+
+$(FEDIR)/libpygio.so: $(FEDIR)/GenericIO.o $(FEDIR)/python/lib/gio.o $(FE_BLOSC_O)
+ $(CXX) $(FE_CFLAGS) $(FE_SHARED) -o $@ $^
+
+$(FEDIR)/gio.py: python/gio.py
+ cp -f $< $@
+
+$(FEDIR)/GenericIOSQLite.so: $(FEDIR)/GenericIOSQLite.o $(FEDIR)/GenericIO.o $(FE_BLOSC_O)
$(CXX) $(FE_CFLAGS) $(FE_SHARED) -o $@ $^
SQLITE_CPPFLAGS := -DSQLITE_ENABLE_COLUMN_METADATA=1 -DSQLITE_DISABLE_DIRSYNC=1 -DSQLITE_ENABLE_FTS3=3 -DSQLITE_ENABLE_RTREE=1 -DSQLITE_ENABLE_UNLOCK_NOTIFY=1 -DSQLITE_ENABLE_LOAD_EXTENSION=1 -DHAVE_READLINE=1
@@ -183,7 +190,7 @@ $(MPIDIR)/GenericIOBenchmarkWrite: $(MPIDIR)/GenericIOBenchmarkWrite.o $(MPIDIR)
$(MPIDIR)/GenericIORewrite: $(MPIDIR)/GenericIORewrite.o $(MPIDIR)/GenericIO.o $(MPI_BLOSC_O)
$(MPICXX) $(MPI_CFLAGS) -o $@ $^
-frontend-progs: $(FEDIR)/GenericIOPrint $(FEDIR)/GenericIOVerify
+frontend-progs: $(FEDIR)/GenericIOPrint $(FEDIR)/GenericIOVerify $(FEDIR)/libpygio.so $(FEDIR)/gio.py
fe-progs: frontend-progs
mpi-progs: $(MPIDIR)/GenericIOPrint $(MPIDIR)/GenericIOVerify $(MPIDIR)/GenericIOBenchmarkRead $(MPIDIR)/GenericIOBenchmarkWrite $(MPIDIR)/GenericIORewrite
diff --git a/python/gio.py b/python/gio.py
new file mode 100644
index 0000000000000000000000000000000000000000..3125d299ba819c3aa6c6e19662c7c97904b49480
--- /dev/null
+++ b/python/gio.py
@@ -0,0 +1,101 @@
+# Copyright (C) 2015, UChicago Argonne, LLC
+# All Rights Reserved
+#
+# Generic IO (ANL-15-066)
+# Hal Finkel, Argonne National Laboratory
+#
+# OPEN SOURCE LICENSE
+#
+# Under the terms of Contract No. DE-AC02-06CH11357 with UChicago Argonne,
+# LLC, the U.S. Government retains certain rights in this software.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice,
+# this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# 3. Neither the names of UChicago Argonne, LLC or the Department of Energy
+# nor the names of its contributors may be used to endorse or promote
+# products derived from this software without specific prior written
+# permission.
+#
+# *****************************************************************************
+#
+# DISCLAIMER
+# THE SOFTWARE IS SUPPLIED “AS IS†WITHOUT WARRANTY OF ANY KIND. NEITHER THE
+# UNTED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT OF ENERGY, NOR
+# UCHICAGO ARGONNE, LLC, NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY,
+# EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE
+# ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, DATA, APPARATUS,
+# PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE
+# PRIVATELY OWNED RIGHTS.
+#
+# *****************************************************************************
+
+import numpy as np
+import ctypes as ct
+import os
+
+#Define where the library is and load it
+_path = os.path.dirname('__file__')
+libpygio = ct.CDLL(os.path.abspath('libpygio.so'))
+#we need to define the return type ("restype") and
+#the argument types
+libpygio.get_elem_num.restype=ct.c_int64
+libpygio.get_elem_num.argtypes=[ct.c_char_p]
+
+libpygio.get_variable_type.restype=ct.c_int
+libpygio.get_variable_type.argtypes=[ct.c_char_p,ct.c_char_p]
+
+libpygio.read_gio_int32.restype=None
+libpygio.read_gio_int32.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_int)]
+
+libpygio.read_gio_int64.restype=None
+libpygio.read_gio_int64.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_int64)]
+
+libpygio.read_gio_float.restype=None
+libpygio.read_gio_float.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_float)]
+
+libpygio.read_gio_double.restype=None
+libpygio.read_gio_double.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_double)]
+
+libpygio.inspect_gio.restype=None
+libpygio.inspect_gio.argtypes=[ct.c_char_p]
+
+def gio_read(file_name,var_name):
+ var_size = libpygio.get_elem_num(file_name)
+ var_type = libpygio.get_variable_type(file_name,var_name)
+ if(var_type==10):
+ print "Variable not found"
+ return
+ elif(var_type==9):
+ print "variable type not known (not int32/int64/float/double)"
+ elif(var_type==0):
+ #float
+ result = np.ndarray(var_size,dtype=np.float32)
+ libpygio.read_gio_float(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_float)))
+ return result
+ elif(var_type==1):
+ #double
+ result = np.ndarray(var_size,dtype=np.float64)
+ libpygio.read_gio_double(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_double)))
+ return result
+ elif(var_type==2):
+ #int32
+ result = np.ndarray(var_size,dtype=np.int32)
+ libpygio.read_gio_int32(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_int32)))
+ return result
+ elif(var_type==3):
+ #int64
+ result = np.ndarray(var_size,dtype=np.int64)
+ libpygio.read_gio_int64(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_int64)))
+ return result
+
+def gio_inspect(file_name):
+ libpygio.inspect_gio(file_name)
+
diff --git a/python/lib/gio.cxx b/python/lib/gio.cxx
new file mode 100644
index 0000000000000000000000000000000000000000..82cebd4cb4dcb376a434d09aab08099899f2ce35
--- /dev/null
+++ b/python/lib/gio.cxx
@@ -0,0 +1,117 @@
+/*
+ * Copyright (C) 2015, UChicago Argonne, LLC
+ * All Rights Reserved
+ *
+ * Generic IO (ANL-15-066)
+ * Hal Finkel, Argonne National Laboratory
+ *
+ * OPEN SOURCE LICENSE
+ *
+ * Under the terms of Contract No. DE-AC02-06CH11357 with UChicago Argonne,
+ * LLC, the U.S. Government retains certain rights in this software.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the distribution.
+ *
+ * 3. Neither the names of UChicago Argonne, LLC or the Department of Energy
+ * nor the names of its contributors may be used to endorse or promote
+ * products derived from this software without specific prior written
+ * permission.
+ *
+ * *****************************************************************************
+ *
+ * DISCLAIMER
+ * THE SOFTWARE IS SUPPLIED “AS IS†WITHOUT WARRANTY OF ANY KIND. NEITHER THE
+ * UNTED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT OF ENERGY, NOR
+ * UCHICAGO ARGONNE, LLC, NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY,
+ * EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE
+ * ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, DATA, APPARATUS,
+ * PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE
+ * PRIVATELY OWNED RIGHTS.
+ *
+ * *****************************************************************************
+ */
+
+#include "gio.h"
+#include <iostream>
+
+ void read_gio_float(char* file_name, char* var_name, float* data){
+ read_gio<float>(file_name,var_name,data);
+ }
+ void read_gio_double(char* file_name, char* var_name, double* data){
+ read_gio<double>(file_name,var_name,data);
+ }
+ void read_gio_int32(char* file_name, char* var_name, int* data){
+ read_gio<int>(file_name,var_name,data);
+ }
+ void read_gio_int64(char* file_name, char* var_name, int64_t* data){
+ read_gio<int64_t>(file_name,var_name,data);
+ }
+
+ int64_t get_elem_num(char* file_name){
+ gio::GenericIO reader(file_name);
+ reader.openAndReadHeader(gio::GenericIO::MismatchAllowed);
+ int num_ranks = reader.readNRanks();
+ uint64_t size = 0;
+ for(int i =0;i<num_ranks;++i)
+ size +=reader.readNumElems(i);
+ reader.close();
+ return size;
+ }
+
+ var_type get_variable_type(char* file_name,char* var_name){
+ gio::GenericIO reader(file_name);
+ std::vector<gio::GenericIO::VariableInfo> VI;
+ reader.openAndReadHeader(gio::GenericIO::MismatchAllowed);
+ reader.getVariableInfo(VI);
+
+ int num =VI.size();
+ for(int i =0;i<num;++i){
+ gio::GenericIO::VariableInfo vinfo = VI[i];
+ if(vinfo.Name == var_name){
+ if(vinfo.IsFloat && vinfo.Size == 4)
+ return float_type;
+ else if(vinfo.IsFloat && vinfo.Size == 8)
+ return double_type;
+ else if(!vinfo.IsFloat && vinfo.Size == 4)
+ return int32_type;
+ else if(!vinfo.IsFloat && vinfo.Size == 8)
+ return int64_type;
+ else
+ return type_not_found;
+ }
+ }
+ return var_not_found;
+
+ }
+
+extern "C" void inspect_gio(char* file_name){
+ int64_t size = get_elem_num(file_name);
+ gio::GenericIO reader(file_name);
+ std::vector<gio::GenericIO::VariableInfo> VI;
+ reader.openAndReadHeader(gio::GenericIO::MismatchAllowed);
+ reader.getVariableInfo(VI);
+ std::cout<<"Number of Elements: "<<size<<std::endl;
+ int num =VI.size();
+ std::cout<<"[data type] Variable name"<<std::endl;
+ std::cout<<"---------------------------------------------"<<std::endl;
+ for(int i =0;i<num;++i){
+ gio::GenericIO::VariableInfo vinfo = VI[i];
+
+ if(vinfo.IsFloat)
+ std::cout<<"[f";
+ else
+ std::cout<<"[i";
+ std::cout<<" "<<vinfo.Size*8<<"] ";
+ std::cout<<vinfo.Name<<std::endl;
+ }
+ std::cout<<"\n(i=integer,f=floating point, number bits size)"<<std::endl;
+}
+
diff --git a/python/lib/gio.h b/python/lib/gio.h
new file mode 100644
index 0000000000000000000000000000000000000000..fcfa8cf35ad35cc565dd7318bbdd0e3ec14b53db
--- /dev/null
+++ b/python/lib/gio.h
@@ -0,0 +1,85 @@
+/*
+ * Copyright (C) 2015, UChicago Argonne, LLC
+ * All Rights Reserved
+ *
+ * Generic IO (ANL-15-066)
+ * Hal Finkel, Argonne National Laboratory
+ *
+ * OPEN SOURCE LICENSE
+ *
+ * Under the terms of Contract No. DE-AC02-06CH11357 with UChicago Argonne,
+ * LLC, the U.S. Government retains certain rights in this software.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ * this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the distribution.
+ *
+ * 3. Neither the names of UChicago Argonne, LLC or the Department of Energy
+ * nor the names of its contributors may be used to endorse or promote
+ * products derived from this software without specific prior written
+ * permission.
+ *
+ * *****************************************************************************
+ *
+ * DISCLAIMER
+ * THE SOFTWARE IS SUPPLIED “AS IS†WITHOUT WARRANTY OF ANY KIND. NEITHER THE
+ * UNTED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT OF ENERGY, NOR
+ * UCHICAGO ARGONNE, LLC, NOR ANY OF THEIR EMPLOYEES, MAKES ANY WARRANTY,
+ * EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPONSIBILITY FOR THE
+ * ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, DATA, APPARATUS,
+ * PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE
+ * PRIVATELY OWNED RIGHTS.
+ *
+ * *****************************************************************************
+ */
+
+#include <GenericIO.h>
+
+#include <stdint.h>
+#include <sstream>
+
+template <class T>
+void read_gio(char* file_name, std::string var_name, T*& data){
+ gio::GenericIO reader(file_name);
+ reader.openAndReadHeader(gio::GenericIO::MismatchAllowed);
+ int num_ranks = reader.readNRanks();
+ uint64_t max_size = 0;
+ uint64_t rank_size[num_ranks];
+ for(int i =0;i<num_ranks;++i){
+ rank_size[i] = reader.readNumElems(i);
+ if(max_size < rank_size[i])
+ max_size = rank_size[i];
+ }
+ T* rank_data = new T[max_size+reader.requestedExtraSpace()/sizeof(T)];
+ int64_t offset =0;
+ reader.addVariable(var_name,rank_data,true);
+ for(int i=0;i<num_ranks;++i){
+ reader.readData(i,false);
+ std::copy(rank_data,rank_data+rank_size[i],data+offset);
+ offset +=rank_size[i];
+ }
+ delete [] rank_data;
+ reader.close();
+}
+extern "C" int64_t get_elem_num(char* file_name);
+
+extern "C" void read_gio_float (char* file_name, char* var_name, float* data);
+extern "C" void read_gio_double(char* file_name, char* var_name, double* data);
+extern "C" void read_gio_int32 (char* file_name, char* var_name, int* data);
+extern "C" void read_gio_int64 (char* file_name, char* var_name, int64_t* data);
+enum var_type{
+ float_type=0,
+ double_type=1,
+ int32_type=2,
+ int64_type=3,
+ type_not_found=9,
+ var_not_found=10
+};
+extern "C" var_type get_variable_type(char* file_name,char* var_name);
+extern "C" void inspect_gio(char* file_name);