Re: Hdf-forum Digest, Vol 101, Issue 5

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Re: Hdf-forum Digest, Vol 101, Issue 5

guido
Hello Scot,

The subroutine that includes the declaration of arguments is bellow. The argument declaration is the following:

        integer(8)                 :: recl_test,flen_test,iolength_test
        integer                    :: error,hdferr,hdferr2,rank
        INTEGER(HID_T) :: file_id,dset_id,dataspace_id  
-----------------------------------------------------------------
 subroutine load_single_file(filename,filetype)
    
        ! loads particles into
        ! x(:),y(:),z(:),mass(:)
        ! and updates the variables
        ! npart = number of particles
    
        implicit none
        character(*),intent(in) :: filename
        integer*4,intent(in)    :: filetype
        logical*4               :: loadmasses
        integer*8               :: file_size
        integer*4               :: bytes_per_particle,i
        integer                 :: allocate_status

        ! guido debug
        integer(8)                 :: recl_test,flen_test,iolength_test
        integer                    :: error,hdferr,hdferr2,rank
        INTEGER(HID_T) :: file_id,dset_id,dataspace_id  
        
        if (allocated(x)) deallocate(x)
        if (allocated(y)) deallocate(y)
        if (allocated(z)) deallocate(z)
        if (allocated(mass)) deallocate(mass)
        
        loadmasses = filetype<0
        
        if (loadmasses) then
            bytes_per_particle = 16
        else
            bytes_per_particle = 12
        end if
        
        if (abs(filetype) == 2) then ! Simple binary file
    
            ! determine number of particles
            inquire(file=trim(filename), size=file_size)
            npart = file_size/int(bytes_per_particle,8)
            if (int(npart,8)*int(bytes_per_particle,8).ne.file_size) then
                write(*,'(A)')
                write(*,'(A)') 'Format of input file not recognized. Consider specifying a different format using -input.'
                stop
            end if
            
            ! load particles
            allocate(x(npart),y(npart),z(npart),mass(npart))
            open(1,file=trim(filename),action='read',form='unformatted',status='old',access='stream')
            if (loadmasses) then
                read(1) (x(i),y(i),z(i),mass(i),i=1,npart)
            else
                read(1) (x(i),y(i),z(i),i=1,npart)
                mass = 1.0
            end if
            close(1)
            
        else if (abs(filetype) == 3) then ! Simple ascii file
        
            ! determine number of particles
            npart = 0
            open(1,file=trim(filename),action='read',form='formatted',status='old')
            stat = 0
            do while (stat==0)
                read(1,*,IOSTAT=stat) xempty
                if (stat.ne.0) exit
                npart = npart+1
            end do
            close(1)
    
            allocate(x(npart),y(npart),z(npart),mass(npart))
            open(1,file=trim(filename),action='read',form='formatted',status='old')
            if (loadmasses) then
                do i = 1,npart
                    read(1,*) x(i),y(i),z(i),mass(i)
                end do
            else
                do i = 1,npart
                    read(1,*) x(i),y(i),z(i)
                end do
                mass = 1.0
            end if
            close(1)
            
        else if (abs(filetype) == 4) then ! Gadget file binary
    
            write(*,*) "The record length is: ",recl_test

            if(.true.) then 
                call h5open_f(error)
                call h5fopen_f(trim(filename)//'.hdf5',H5F_ACC_RDONLY_F,file_id,error)

                call h5dopen_f(file_id,'x',dset_id,error)
                call h5dget_space_f(dset_id,dataspace_id,hdferr)
                call h5sget_simple_extent_npoints_f(dataspace_id,npart,hdferr2) 
                write(*,*) 'The number of particles is :',npart             
                allocate(x(npart),y(npart),z(npart),mass(npart),stat=allocate_status) 
                call H5LTread_dataset_float_f(dset_id,'x',x)
                call h5dclose_f(dset_id,error)
 
                call h5dopen_f(file_id,'y',dset_id,error)
                call H5LTread_dataset_float_f(dset_id,'y',y)
                !call h5dread_f(dset_id,H5T_IEEE_F32BE,y,npart,error)
                call h5dclose_f(dset_id,error)
 
                call h5dopen_f(file_id,'z',dset_id,error)
                call H5LTread_dataset_float_f(dset_id,'z',z)
                !call h5dread_f(dset_id,H5T_IEEE_F32BE,z,npart,error)
                call h5dclose_f(dset_id,error)
 

                call h5fclose_f(file_id,error)
            endif 
            if(allocate_status /= 0) then
                 write(*,'(A)') 'memory problem.!'
            else
                 write(*,'(A)') 'memory is ok.'
            endif
            if (loadmasses) then
                read(1) (mass(i),i=1,npart)
            else
                mass = 1.0
            end if
            !close(1)
            
        end if
        
        if (npart==huge(npart)) then
            write(*,'(A)')
            write(*,'(A)') 'No single file can contain more than 2^31 particles.'
            stop   
        end if
      
    end subroutine load_single_file

2017-11-06 13:00 GMT-05:00 <[hidden email]>:
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Today's Topics:

   1. Memory allocation/deallocation (Andreas Derler)
   2. Re: no specific subroutine for the generic ?h5dread_f?
      (Scot Breitenfeld)


----------------------------------------------------------------------

Message: 1
Date: Mon, 6 Nov 2017 09:59:43 +0100
From: Andreas Derler <[hidden email]>
To: [hidden email].
Subject: [Hdf-forum] Memory allocation/deallocation
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=utf-8; format=flowed

Hi,

I am trying to use the Java HDF5 interface (JHI5) in an application server environment, where I am writing
to many different HDF5 files within a single JVM instance.

However, while using HDF5 I am running into memory issues. Basically, I am facing the issue that writing
to an HDF5 file causes memory to be allocated, which, even after successful writing and
closing the file is not deallocated.

So I would like to know if there is a way to clear all allocated memory after writing to the file using the JHI5 library.

I already made sure that everything is closed and also tried to limit the cache size using H5Pset_cache and H5Pset_chunk_cache.
However, changing cache sizes does not eliminate the problem, that the memory is not deallocated after closing the file.
Also calling the function H5garbage_collect does not seem to change this behaviour.
I saw in the docs that the native implementation provides the call H5Pset_evict_on_close (https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetEvictOnClose),
however, this call seems not to be available in the JHI5 version.

Is there any other way to make sure that all memory is deallocated, or am I doing something wrong? To this end, I am posting an example code I am using:

final long[] dims = { 0, 0 };
final long[] maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED };
final int RANK = 2;
long cache_size = 1024L*1024; // cache size in bytes

try {
   dims[0] = data.length; // num rows
   dims[1] = data[0].length; // num cols
   int file_id = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
   H5.H5Pset_cache(file_id, 0, 521L, cache_size, 1);
   file_id = H5.H5Fcreate(filename, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, file_id);
   int dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims);
   int dataset_access_property_list_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
   H5.H5Pset_chunk_cache(dataset_access_property_list_id, 521L, cache_size, 1);
   int dataset_creation_property_list_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
   long[] dim_chunk = { dims[1], 1 };
   H5.H5Pset_chunk(dataset_creation_property_list_id, RANK, dim_chunk);
   int dataset_id = H5.H5Dcreate(file_id, path, HDF5Constants.H5T_NATIVE_DOUBLE, dataspace_id,
                 HDF5Constants.H5P_DEFAULT, dataset_creation_property_list_id, dataset_access_property_list_id);
   H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
         HDF5Constants.H5P_DEFAULT, data);

   H5.H5Fflush(dataset_id, HDF5Constants.H5F_SCOPE_GLOBAL);
   H5.H5Dclose(dataset_id);
   H5.H5Sclose(dataspace_id);
   H5.H5Pclose(dataset_creation_property_list_id);
   H5.H5Pclose(dataset_access_property_list_id);
   H5.H5Fclear_elink_file_cache(file_id);
   H5.H5Pclose(file_id);
   H5.H5Fclose(file_id);
   H5.H5garbage_collect();
} catch (final Exception e) {
   e.printStackTrace();
}



------------------------------

Message: 2
Date: Mon, 6 Nov 2017 14:49:44 +0000
From: Scot Breitenfeld <[hidden email]>
To: HDF Users Discussion List <[hidden email]>
Subject: Re: [Hdf-forum] no specific subroutine for the generic
        ?h5dread_f?
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Can you include how you declared your arguments in h5dread_f? I would suspect that one of your arguments is wrong and the compiler is not finding the correct interface.

Scot

> On Nov 4, 2017, at 12:03 AM, Guido granda mu?oz <[hidden email]> wrote:
>
> Hello,
>
> I am having trouble with a code that uses hdf5. The code is written in fortran90 it consists of a main program(proccor.f90) and a module(module_correlation_functions.f90).
>
> After using the makefile to compile the code, I get the following error:
>
> gfortran -O3  -c module_correlation_functions.f90 -I/usr/local/hdf5/include -L/usr/local/hdf5/lib /usr/local/hdf5/lib/libhdf5hl_fortran.a /usr/local/hdf5/lib/libhdf5_hl.a /usr/local/hdf5/lib/libhdf5_fortran.a /usr/local/hdf5/lib/libhdf5.a -lz -ldl -lm -Wl,-rpath -Wl,/usr/local/hdf5/lib
> module_correlation_functions.f90:1583:68:
>
>                  call h5dread_f(dset_id,H5T_IEEE_F32BE,x,npart,error)
>                                                                     1
> Error: There is no specific subroutine for the generic ?h5dread_f? at (1)
> module_correlation_functions.f90:1588:68:
>
>                  call h5dread_f(dset_id,H5T_IEEE_F32BE,y,npart,error)
>                                                                     1
> Error: There is no specific subroutine for the generic ?h5dread_f? at (1)
> module_correlation_functions.f90:1593:68:
>
>                  call h5dread_f(dset_id,H5T_IEEE_F32BE,z,npart,error)
>                                                                     1
> Error: There is no specific subroutine for the generic ?h5dread_f? at (1)
> makefile:38: recipe for target 'module_correlation_functions.o' failed
> make: *** [module_correlation_functions.o] Error 1
>
>
> The makelife I used to compile the code includes the location of the hdf5 library :
>
>
> LIBSHDF=-I/usr/local/hdf5/include -L/usr/local/hdf5/lib /usr/local/hdf5/lib/libhdf5hl_fortran.a /usr/local/hdf5/lib/libhdf5_hl.a /usr/local/hdf5/lib/libhdf5_fortran.a /usr/local/hdf5/lib/libhdf5.a -lz -ldl -lm -Wl,-rpath -Wl,/usr/local/hdf5/lib
> FCFLAGS = -O3
> # List of executables to be built within the package
> PROGRAMS = procorr
>
> # "make" builds all
> all: $(PROGRAMS)
>
> procorr.o:      module_correlation_functions.o
> procorr:        module_correlation_functions.o
>
> # ======================================================================
> # And now the general rules, these should not require modification
> # ======================================================================
>
> # General rule for building prog from prog.o; $^ (GNU extension) is
> # used in order to list additional object files on which the
> # executable depends
> %: %.o
>         $(FC) $(FCFLAGS) -o $@ $^ $(LIBSHDF)
>
> # General rules for building prog.o from prog.f90 or prog.F90; $< is
> # used in order to list only the first prerequisite (the source file)
> # and not the additional prerequisites such as module or include files
> %.o: %.f90
>         $(FC) $(FCFLAGS) -c $^ $(LIBSHDF)
>
> # Utility targets
> .PHONY: clean veryclean
>
> clean:
>         rm -f *.o *.mod *.MOD
>         rm -f .last_fourier_transform
>         rm -f cdm_redshift0_*
>         rm -f *~ $(PROGRAMS)
>
> The call hdf5 statement is located on the module file (module_correlation_functions.f90)
>
> I am probably doing something wrong on the makefile because I used the same hdf5 library location to compile another fortran90+hdf5 code without any trouble. Could please help me ?
>
> The gfortran version used is: GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0
> and the hdf5 version is: hdf5-1.8.19 compiled with the enable fortran option.
>
>
> Kind Regards,
>
> --
> Guido
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5


------------------------------

Subject: Digest Footer

_______________________________________________
Hdf-forum is for HDF software users discussion.
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------------------------------

End of Hdf-forum Digest, Vol 101, Issue 5
*****************************************



--
Guido

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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Re: Hdf-forum Digest, Vol 101, Issue 5

Scot Breitenfeld
npart should be an array and not a scalar. If you use the F2003 interface, then you don’t need to supply npart.

Scot

On Nov 8, 2017, at 5:59 PM, Guido granda muñoz <[hidden email]> wrote:

Hello Scot,

The subroutine that includes the declaration of arguments is bellow. The argument declaration is the following:

        integer(8)                 :: recl_test,flen_test,iolength_test
        integer                    :: error,hdferr,hdferr2,rank
        INTEGER(HID_T) :: file_id,dset_id,dataspace_id  
-----------------------------------------------------------------
 subroutine load_single_file(filename,filetype)
    
        ! loads particles into
        ! x(:),y(:),z(:),mass(:)
        ! and updates the variables
        ! npart = number of particles
    
        implicit none
        character(*),intent(in) :: filename
        integer*4,intent(in)    :: filetype
        logical*4               :: loadmasses
        integer*8               :: file_size
        integer*4               :: bytes_per_particle,i
        integer                 :: allocate_status

        ! guido debug
        integer(8)                 :: recl_test,flen_test,iolength_test
        integer                    :: error,hdferr,hdferr2,rank
        INTEGER(HID_T) :: file_id,dset_id,dataspace_id  
        
        if (allocated(x)) deallocate(x)
        if (allocated(y)) deallocate(y)
        if (allocated(z)) deallocate(z)
        if (allocated(mass)) deallocate(mass)
        
        loadmasses = filetype<0
        
        if (loadmasses) then
            bytes_per_particle = 16
        else
            bytes_per_particle = 12
        end if
        
        if (abs(filetype) == 2) then ! Simple binary file
    
            ! determine number of particles
            inquire(file=trim(filename), size=file_size)
            npart = file_size/int(bytes_per_particle,8)
            if (int(npart,8)*int(bytes_per_particle,8).ne.file_size) then
                write(*,'(A)')
                write(*,'(A)') 'Format of input file not recognized. Consider specifying a different format using -input.'
                stop
            end if
            
            ! load particles
            allocate(x(npart),y(npart),z(npart),mass(npart))
            open(1,file=trim(filename),action='read',form='unformatted',status='old',access='stream')
            if (loadmasses) then
                read(1) (x(i),y(i),z(i),mass(i),i=1,npart)
            else
                read(1) (x(i),y(i),z(i),i=1,npart)
                mass = 1.0
            end if
            close(1)
            
        else if (abs(filetype) == 3) then ! Simple ascii file
        
            ! determine number of particles
            npart = 0
            open(1,file=trim(filename),action='read',form='formatted',status='old')
            stat = 0
            do while (stat==0)
                read(1,*,IOSTAT=stat) xempty
                if (stat.ne.0) exit
                npart = npart+1
            end do
            close(1)
    
            allocate(x(npart),y(npart),z(npart),mass(npart))
            open(1,file=trim(filename),action='read',form='formatted',status='old')
            if (loadmasses) then
                do i = 1,npart
                    read(1,*) x(i),y(i),z(i),mass(i)
                end do
            else
                do i = 1,npart
                    read(1,*) x(i),y(i),z(i)
                end do
                mass = 1.0
            end if
            close(1)
            
        else if (abs(filetype) == 4) then ! Gadget file binary
    
            write(*,*) "The record length is: ",recl_test

            if(.true.) then 
                call h5open_f(error)
                call h5fopen_f(trim(filename)//'.hdf5',H5F_ACC_RDONLY_F,file_id,error)

                call h5dopen_f(file_id,'x',dset_id,error)
                call h5dget_space_f(dset_id,dataspace_id,hdferr)
                call h5sget_simple_extent_npoints_f(dataspace_id,npart,hdferr2) 
                write(*,*) 'The number of particles is :',npart             
                allocate(x(npart),y(npart),z(npart),mass(npart),stat=allocate_status) 
                call H5LTread_dataset_float_f(dset_id,'x',x)
                call h5dclose_f(dset_id,error)
 
                call h5dopen_f(file_id,'y',dset_id,error)
                call H5LTread_dataset_float_f(dset_id,'y',y)
                !call h5dread_f(dset_id,H5T_IEEE_F32BE,y,npart,error)
                call h5dclose_f(dset_id,error)
 
                call h5dopen_f(file_id,'z',dset_id,error)
                call H5LTread_dataset_float_f(dset_id,'z',z)
                !call h5dread_f(dset_id,H5T_IEEE_F32BE,z,npart,error)
                call h5dclose_f(dset_id,error)
 

                call h5fclose_f(file_id,error)
            endif 
            if(allocate_status /= 0) then
                 write(*,'(A)') 'memory problem.!'
            else
                 write(*,'(A)') 'memory is ok.'
            endif
            if (loadmasses) then
                read(1) (mass(i),i=1,npart)
            else
                mass = 1.0
            end if
            !close(1)
            
        end if
        
        if (npart==huge(npart)) then
            write(*,'(A)')
            write(*,'(A)') 'No single file can contain more than 2^31 particles.'
            stop   
        end if
      
    end subroutine load_single_file

2017-11-06 13:00 GMT-05:00 <[hidden email]>:
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Today's Topics:

   1. Memory allocation/deallocation (Andreas Derler)
   2. Re: no specific subroutine for the generic ?h5dread_f?
      (Scot Breitenfeld)


----------------------------------------------------------------------

Message: 1
Date: Mon, 6 Nov 2017 09:59:43 +0100
From: Andreas Derler <[hidden email]>
To: [hidden email].
Subject: [Hdf-forum] Memory allocation/deallocation
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=utf-8; format=flowed

Hi,

I am trying to use the Java HDF5 interface (JHI5) in an application server environment, where I am writing
to many different HDF5 files within a single JVM instance.

However, while using HDF5 I am running into memory issues. Basically, I am facing the issue that writing
to an HDF5 file causes memory to be allocated, which, even after successful writing and
closing the file is not deallocated.

So I would like to know if there is a way to clear all allocated memory after writing to the file using the JHI5 library.

I already made sure that everything is closed and also tried to limit the cache size using H5Pset_cache and H5Pset_chunk_cache.
However, changing cache sizes does not eliminate the problem, that the memory is not deallocated after closing the file.
Also calling the function H5garbage_collect does not seem to change this behaviour.
I saw in the docs that the native implementation provides the call H5Pset_evict_on_close (https://support.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetEvictOnClose),
however, this call seems not to be available in the JHI5 version.

Is there any other way to make sure that all memory is deallocated, or am I doing something wrong? To this end, I am posting an example code I am using:

final long[] dims = { 0, 0 };
final long[] maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED };
final int RANK = 2;
long cache_size = 1024L*1024; // cache size in bytes

try {
   dims[0] = data.length; // num rows
   dims[1] = data[0].length; // num cols
   int file_id = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
   H5.H5Pset_cache(file_id, 0, 521L, cache_size, 1);
   file_id = H5.H5Fcreate(filename, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, file_id);
   int dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims);
   int dataset_access_property_list_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
   H5.H5Pset_chunk_cache(dataset_access_property_list_id, 521L, cache_size, 1);
   int dataset_creation_property_list_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
   long[] dim_chunk = { dims[1], 1 };
   H5.H5Pset_chunk(dataset_creation_property_list_id, RANK, dim_chunk);
   int dataset_id = H5.H5Dcreate(file_id, path, HDF5Constants.H5T_NATIVE_DOUBLE, dataspace_id,
                 HDF5Constants.H5P_DEFAULT, dataset_creation_property_list_id, dataset_access_property_list_id);
   H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
         HDF5Constants.H5P_DEFAULT, data);

   H5.H5Fflush(dataset_id, HDF5Constants.H5F_SCOPE_GLOBAL);
   H5.H5Dclose(dataset_id);
   H5.H5Sclose(dataspace_id);
   H5.H5Pclose(dataset_creation_property_list_id);
   H5.H5Pclose(dataset_access_property_list_id);
   H5.H5Fclear_elink_file_cache(file_id);
   H5.H5Pclose(file_id);
   H5.H5Fclose(file_id);
   H5.H5garbage_collect();
} catch (final Exception e) {
   e.printStackTrace();
}



------------------------------

Message: 2
Date: Mon, 6 Nov 2017 14:49:44 +0000
From: Scot Breitenfeld <[hidden email]>
To: HDF Users Discussion List <[hidden email]>
Subject: Re: [Hdf-forum] no specific subroutine for the generic
        ?h5dread_f?
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Can you include how you declared your arguments in h5dread_f? I would suspect that one of your arguments is wrong and the compiler is not finding the correct interface.

Scot

> On Nov 4, 2017, at 12:03 AM, Guido granda mu?oz <[hidden email]> wrote:
>
> Hello,
>
> I am having trouble with a code that uses hdf5. The code is written in fortran90 it consists of a main program(proccor.f90) and a module(module_correlation_functions.f90).
>
> After using the makefile to compile the code, I get the following error:
>
> gfortran -O3  -c module_correlation_functions.f90 -I/usr/local/hdf5/include -L/usr/local/hdf5/lib /usr/local/hdf5/lib/libhdf5hl_fortran.a /usr/local/hdf5/lib/libhdf5_hl.a /usr/local/hdf5/lib/libhdf5_fortran.a /usr/local/hdf5/lib/libhdf5.a -lz -ldl -lm -Wl,-rpath -Wl,/usr/local/hdf5/lib
> module_correlation_functions.f90:1583:68:
>
>                  call h5dread_f(dset_id,H5T_IEEE_F32BE,x,npart,error)
>                                                                     1
> Error: There is no specific subroutine for the generic ?h5dread_f? at (1)
> module_correlation_functions.f90:1588:68:
>
>                  call h5dread_f(dset_id,H5T_IEEE_F32BE,y,npart,error)
>                                                                     1
> Error: There is no specific subroutine for the generic ?h5dread_f? at (1)
> module_correlation_functions.f90:1593:68:
>
>                  call h5dread_f(dset_id,H5T_IEEE_F32BE,z,npart,error)
>                                                                     1
> Error: There is no specific subroutine for the generic ?h5dread_f? at (1)
> makefile:38: recipe for target 'module_correlation_functions.o' failed
> make: *** [module_correlation_functions.o] Error 1
>
>
> The makelife I used to compile the code includes the location of the hdf5 library :
>
>
> LIBSHDF=-I/usr/local/hdf5/include -L/usr/local/hdf5/lib /usr/local/hdf5/lib/libhdf5hl_fortran.a /usr/local/hdf5/lib/libhdf5_hl.a /usr/local/hdf5/lib/libhdf5_fortran.a /usr/local/hdf5/lib/libhdf5.a -lz -ldl -lm -Wl,-rpath -Wl,/usr/local/hdf5/lib
> FCFLAGS = -O3
> # List of executables to be built within the package
> PROGRAMS = procorr
>
> # "make" builds all
> all: $(PROGRAMS)
>
> procorr.o:      module_correlation_functions.o
> procorr:        module_correlation_functions.o
>
> # ======================================================================
> # And now the general rules, these should not require modification
> # ======================================================================
>
> # General rule for building prog from prog.o; $^ (GNU extension) is
> # used in order to list additional object files on which the
> # executable depends
> %: %.o
>         $(FC) $(FCFLAGS) -o $@ $^ $(LIBSHDF)
>
> # General rules for building prog.o from prog.f90 or prog.F90; $< is
> # used in order to list only the first prerequisite (the source file)
> # and not the additional prerequisites such as module or include files
> %.o: %.f90
>         $(FC) $(FCFLAGS) -c $^ $(LIBSHDF)
>
> # Utility targets
> .PHONY: clean veryclean
>
> clean:
>         rm -f *.o *.mod *.MOD
>         rm -f .last_fourier_transform
>         rm -f cdm_redshift0_*
>         rm -f *~ $(PROGRAMS)
>
> The call hdf5 statement is located on the module file (module_correlation_functions.f90)
>
> I am probably doing something wrong on the makefile because I used the same hdf5 library location to compile another fortran90+hdf5 code without any trouble. Could please help me ?
>
> The gfortran version used is: GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0
> and the hdf5 version is: hdf5-1.8.19 compiled with the enable fortran option.
>
>
> Kind Regards,
>
> --
> Guido
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5


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End of Hdf-forum Digest, Vol 101, Issue 5
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--
Guido
_______________________________________________
Hdf-forum is for HDF software users discussion.
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Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5