Hi,
I'm testing 1.8.4 and 1.8.5 pre2 on CentOS 5.4 nfs v3 64 bit with shared
libraries (is there additional info that'd be useful ?). Both build
successfully with
----
./configure
--prefix=/net/frodo/home/roger/Software/hdf5-1.8.5-pre2/dist
--disable-fortran --enable-parallel
--with-zlib=/net/frodo/home/roger/sourceforge/zlib-1.2.4/dist
--without-szlib --enable-shared=yes --enable-static=no
make
#make check
make install
----
All processes do the collective H5Fcreate and then the rank=0 begins to
create tables using the H5TBmake_table method while the others wait.
1) It goes for 28 tables and then stalls while headed to 196 tables.
2) If the chunk_size is changed from 10 to 1000 it then goes to 44
tables and then stalls.
I'll try to make a small app that reveals the same stall but for now
here is the portion of code that sets up the table:
----------
typedef struct Particle
{
char element[3];
char atomName[16];
char residueName[16];
double x;
double y;
double z;
int formalCharge;
} Particle;
Particle dst_buf[elements.size()];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof ( Particle);
size_t dst_offset[7] = {HOFFSET(Particle, element),
HOFFSET(Particle, atomName),
HOFFSET(Particle, residueName),
HOFFSET(Particle, x),
HOFFSET(Particle, y),
HOFFSET(Particle, z),
HOFFSET(Particle, formalCharge)};
size_t dst_sizes[7] = {sizeof ( dst_buf[0].element),
sizeof ( dst_buf[0].atomName),
sizeof ( dst_buf[0].residueName),
sizeof ( dst_buf[0].x),
sizeof ( dst_buf[0].y),
sizeof ( dst_buf[0].z),
sizeof ( dst_buf[0].formalCharge)};
/* Define an array of Particles */
Particle p_data[elements.size()];
for (int index = 0; index < elements.size(); index++)
{
std::strncpy(p_data[index].element, elements[index].c_str(), 3);
std::strncpy(p_data[index].atomName, atomNames[index].c_str(), 16);
std::strncpy(p_data[index].residueName,
residueNames[index].c_str(), 16);
p_data[index].x = (*xyz)[0][index];
p_data[index].y = (*xyz)[1][index];
p_data[index].z = (*xyz)[2][index];
p_data[index].formalCharge = formalCharge[index];
}
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 1;
if(parallel)compress = 0;
/* Define field information */
const char *field_names[7] = {"Element", "AtomName", "ResidueName",
"X", "Y", "Z", "FormalCharge"};
/* Initialize field_type */
hid_t string_element_type = H5Tcopy(H5T_C_S1);
hid_t string_type = H5Tcopy(H5T_C_S1);
H5Tset_size(string_element_type, 3);
H5Tset_size(string_type, 16);
hid_t field_type[7];
field_type[0] = string_element_type;
field_type[1] = string_type;
field_type[2] = string_type;
field_type[3] = H5T_NATIVE_DOUBLE;
field_type[4] = H5T_NATIVE_DOUBLE;
field_type[5] = H5T_NATIVE_DOUBLE;
field_type[6] = H5T_NATIVE_INT;
std::cout<<"create table "<<datasetName<<"
"<<elements.size()<<std::endl;
herr_t status = H5TBmake_table(title.c_str(), currentFileID,
datasetName.c_str(), 7, elements.size(),
dst_size, field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data);
std::cout<<"create table "<<status<<std::endl;
...
H5Tclose( string_type );
H5Tclose( string_element_type );
---------------
The only things closed during this loop of 196 table making calls is the
string_type and string_element_type. There are two attributes set on
the tables but the same stall happens without these extra attributes too.
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