Hi Roger,
On Jun 1, 2010, at 3:36 PM, Roger Martin wrote:
> 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.
Are you making the H5TBmake_table() calls from only one process in a
parallel application? If so, that's certainly the problem.
Quincey
> 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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