Create & open groups with several process

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1

Hi,

In my computer code, I want to create several groups. Basically, the process of rank 0 should create my groups. Then all the process should access to these groups in order to write data in the dataset.

This is a piece of my code to illustrate my request:

#include "hdf5.h"
#define H5FILE_NAME "File.h5"
#define DATASETNAME "My_Array"

int main(int argc, char **argv){
      //declare variables
      hid_t file_id, group_id, plist_id;
      int world_rank, world_size;

      MPI_Init(&argc, &argv);
      MPI_Comm_rank(MPI_COMM_WORLD, & world_rank);
      MPI_Comm_size(MPI_COMM_WORLD, &world_size);

     //All process have to access to file
      plist_id = H5Pcreate(H5P_FILE_ACCESS);
      H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);

      //Create my file
      file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

      //Only process of rank 0 can create my groups, here we have one group
      if(world_rank == 0){
         group_id = H5Gcreate(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
      }
       //I want to synchronize my process
       MPI_Barrier(MPI_COMM_WORLD);
       hid_t grp;
       //All process can access on my groups
       grp = H5Gopen2(file_id, "/MyGroup", H5P_DEFAULT);

       //release ressources
       H5Gclose(grp);
       H5Gclose(group_id);
       H5Fclose(file_id);
       H5Pclose(plist_id);

      MPI_Finalize();

return 0;

}

My code compiles, but it doesn't run. In particular, I can't open my group. I have a problem about groups here.

What is my mistake in this program?

Thanks to you

Rolih

2

Rohlih, several APIs in parallel HDF5 must be called collectively.
H5Gcreate is one of them. A complete list can be found here:

https://www.hdfgroup.org/HDF5/doc/RM/CollectiveCalls.html

G.

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of MEYNARD Rolih
Sent: Wednesday, June 29, 2016 7:31 AM
To: Hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Create & open groups with several process

Hi,

In my computer code, I want to create several groups. Basically, the process of rank 0 should create my groups. Then all the process should access to these groups in order to write data in the dataset.

This is a piece of my code to illustrate my request:

#include "hdf5.h"
#define H5FILE_NAME "File.h5"
#define DATASETNAME "My_Array"

int main(int argc, char **argv){
      //declare variables
      hid_t file_id, group_id, plist_id;
      int world_rank, world_size;

      MPI_Init(&argc, &argv);
      MPI_Comm_rank(MPI_COMM_WORLD, & world_rank);
      MPI_Comm_size(MPI_COMM_WORLD, &world_size);

     //All process have to access to file
      plist_id = H5Pcreate(H5P_FILE_ACCESS);
      H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);

      //Create my file
      file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

      //Only process of rank 0 can create my groups, here we have one group
      if(world_rank == 0){
         group_id = H5Gcreate(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
      }
       //I want to synchronize my process
       MPI_Barrier(MPI_COMM_WORLD);
       hid_t grp;
       //All process can access on my groups
       grp = H5Gopen2(file_id, "/MyGroup", H5P_DEFAULT);

       //release ressources
       H5Gclose(grp);
       H5Gclose(group_id);
       H5Fclose(file_id);
       H5Pclose(plist_id);

      MPI_Finalize();

return 0;

}

My code compiles, but it doesn't run. In particular, I can't open my group. I have a problem about groups here.

What is my mistake in this program?

Thanks to you

Rolih

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Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

3

If you want one process to create the file’s groups then you need to close the file before all the processors access the file again, this is what you would do:

#include "hdf5.h"
#define H5FILE_NAME "File.h5"
#define DATASETNAME "My_Array"

int main(int argc, char **argv){
     //declare variables
     hid_t file_id, group_id, plist_id;
     int world_rank, world_size;

     MPI_Init(&argc, &argv);
     MPI_Comm_rank(MPI_COMM_WORLD, & world_rank);
     MPI_Comm_size(MPI_COMM_WORLD, &world_size);

    //All process have to access to file
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);

     //Create my file
     if(world_rank == 0){
       file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

     //Only process of rank 0 can create my groups, here we have one group
       group_id = H5Gcreate(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

       H5Gclose(group_id);
       H5Fclose(file_id);
     }
      //I want to synchronize my process
      MPI_Barrier(MPI_COMM_WORLD);

      file_id = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, plist_id);

      hid_t grp;
      //All process can access on my groups
      grp = H5Gopen2(file_id, "/MyGroup", H5P_DEFAULT);

      //release ressources
      H5Gclose(grp);
      H5Fclose(file_id);
      H5Pclose(plist_id);

     MPI_Finalize();

return 0;

}

4

Thank you very much Scot, it works )
Quoting Scot Breitenfeld <brtnfld@hdfgroup.org>:

···

If you want one process to create the file’s groups then you need to close the file before all the processors access the file again, this is what you would do:

#include "hdf5.h"
#define H5FILE_NAME "File.h5"
#define DATASETNAME "My_Array"

int main(int argc, char **argv){
     //declare variables
     hid_t file_id, group_id, plist_id;
     int world_rank, world_size;

     MPI_Init(&argc, &argv);
     MPI_Comm_rank(MPI_COMM_WORLD, & world_rank);
     MPI_Comm_size(MPI_COMM_WORLD, &world_size);

    //All process have to access to file
     plist_id = H5Pcreate(H5P_FILE_ACCESS);
     H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);

     //Create my file
     if(world_rank == 0){
       file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

     //Only process of rank 0 can create my groups, here we have one group
       group_id = H5Gcreate(file_id, "/MyGroup", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

       H5Gclose(group_id);
       H5Fclose(file_id);
     }
      //I want to synchronize my process
      MPI_Barrier(MPI_COMM_WORLD);

      file_id = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, plist_id);

      hid_t grp;
      //All process can access on my groups
      grp = H5Gopen2(file_id, "/MyGroup", H5P_DEFAULT);

      //release ressources
      H5Gclose(grp);
      H5Fclose(file_id);
      H5Pclose(plist_id);

     MPI_Finalize();

return 0;

}

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Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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