Problem with compiling HDF5 1.6 for parallel I/O

Hdf-forum archives
1

Hello:

I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop
running Ubuntu 9.10 on a virtual machine.

I have configured id with the following command:

$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/
FFLAGS=-I/usr/include/mpich2/ ./configure
--prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel
--enable-fortran |tee configure_parallel.log

But when I do $ make
I get the following error after some time :

make[3]: Entering directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
/usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c
thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:

     comm = MPI_COMM_WORLD
                          1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:

     info = MPI_INFO_NULL
                         1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type
make[3]: *** [thyperslab_wr.lo] Error 1
make[3]: Leaving directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'

Can you please tell me how to rectify this?

I am attaching the log file for configure for your reference.

Thanks & Regards,
Kunal

configure_parallel.log (19.2 KB)

2

Hi Kunal,

···

On Jun 5, 2010, at 7:19 PM, kunal rao wrote:

Hello:

I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop running Ubuntu 9.10 on a virtual machine.

I have configured id with the following command:

$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ FFLAGS=-I/usr/include/mpich2/ ./configure --prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel --enable-fortran |tee configure_parallel.log

But when I do $ make
I get the following error after some time :

make[3]: Entering directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
/usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:

     comm = MPI_COMM_WORLD
                          1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:

     info = MPI_INFO_NULL
                         1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type
make[3]: *** [thyperslab_wr.lo] Error 1
make[3]: Leaving directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'

Can you please tell me how to rectify this?

I am attaching the log file for configure for your reference.

  First, you probably want the 1.8.5 release of HDF5, which should be released next week. Here's the link for a release candidate:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

  Then, you should use the 'mpicc' command from MPICH2 as your compiler, instead of trying to get the MPI include files and libraries correct.

  Quincey

3

Perhaps this is a transcription error, but I think you have your
a typo or two in your environment variables:

% CC=mpicc FC=mpif90 ./configure --enable-fortran

( the --enable-parallel is ok to keep but it is enabled when HDF5 sees
you're building with an MPI compiler)

==rob

···

On Sat, Jun 05, 2010 at 08:19:13PM -0400, kunal rao wrote:

Hello:

I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop
running Ubuntu 9.10 on a virtual machine.

I have configured id with the following command:

$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/
FFLAGS=-I/usr/include/mpich2/ ./configure
--prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel
--enable-fortran |tee configure_parallel.log

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

4

Hi Quincey,

Thanks for your reply. I tried with mpicc as well..but still I got the same
error..

Regards,
Kunal

···

On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol <koziol@hdfgroup.org> wrote:

Hi Kunal,

On Jun 5, 2010, at 7:19 PM, kunal rao wrote:

Hello:

I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop
running Ubuntu 9.10 on a virtual machine.

I have configured id with the following command:

$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/
FFLAGS=-I/usr/include/mpich2/ ./configure
--prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel
--enable-fortran |tee configure_parallel.log

But when I do $ make
I get the following error after some time :

make[3]: Entering directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
/usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c
thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:

     comm = MPI_COMM_WORLD
                          1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:

     info = MPI_INFO_NULL
                         1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type
make[3]: *** [thyperslab_wr.lo] Error 1
make[3]: Leaving directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'

Can you please tell me how to rectify this?

I am attaching the log file for configure for your reference.

First, you probably want the 1.8.5 release of HDF5, which should be
released next week. Here's the link for a release candidate:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

Then, you should use the 'mpicc' command from MPICH2 as your compiler,
instead of trying to get the MPI include files and libraries correct.

Quincey

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

5

Hi Kunal,

Please make sure you have mpif.h under the include directories you specified. And it is better to use MPI fortran compiler (check if you have mpif90).

Elena

···

On Jun 5, 2010, at 10:07 PM, kunal rao wrote:

Hi Quincey,

Thanks for your reply. I tried with mpicc as well..but still I got the same error..

Regards,
Kunal

On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol <koziol@hdfgroup.org> wrote:
Hi Kunal,

On Jun 5, 2010, at 7:19 PM, kunal rao wrote:

Hello:

I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop running Ubuntu 9.10 on a virtual machine.

I have configured id with the following command:

$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/ FFLAGS=-I/usr/include/mpich2/ ./configure --prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel --enable-fortran |tee configure_parallel.log

But when I do $ make
I get the following error after some time :

make[3]: Entering directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
/usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:

     comm = MPI_COMM_WORLD
                          1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:

     info = MPI_INFO_NULL
                         1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type
make[3]: *** [thyperslab_wr.lo] Error 1
make[3]: Leaving directory `/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'

Can you please tell me how to rectify this?

I am attaching the log file for configure for your reference.

  First, you probably want the 1.8.5 release of HDF5, which should be released next week. Here's the link for a release candidate:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

  Then, you should use the 'mpicc' command from MPICH2 as your compiler, instead of trying to get the MPI include files and libraries correct.

  Quincey

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

6

Hi Elena,

I tried with mpif90..but still get this error..

configure_parallel.log (19.3 KB)

···

--------------------------------------------
make[3]: Leaving directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/test'
make[3]: Entering directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
mpif90 -I. -I. -I../src -c thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:

     comm = MPI_COMM_WORLD
                          1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:

     info = MPI_INFO_NULL
                         1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type

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

Attaching my configuration output for your reference..

Thanks & Regards,
Kunal

On Sat, Jun 5, 2010 at 11:58 PM, Elena Pourmal <epourmal@hdfgroup.org>wrote:

Hi Kunal,

Please make sure you have mpif.h under the include directories you
specified. And it is better to use MPI fortran compiler (check if you have
mpif90).

Elena

On Jun 5, 2010, at 10:07 PM, kunal rao wrote:

Hi Quincey,

Thanks for your reply. I tried with mpicc as well..but still I got the same
error..

Regards,
Kunal

On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol <koziol@hdfgroup.org>wrote:

Hi Kunal,

On Jun 5, 2010, at 7:19 PM, kunal rao wrote:

Hello:

I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop
running Ubuntu 9.10 on a virtual machine.

I have configured id with the following command:

$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/
FFLAGS=-I/usr/include/mpich2/ ./configure
--prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel
--enable-fortran |tee configure_parallel.log

But when I do $ make
I get the following error after some time :

make[3]: Entering directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
/usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c
thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:

     comm = MPI_COMM_WORLD
                          1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:

     info = MPI_INFO_NULL
                         1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type
make[3]: *** [thyperslab_wr.lo] Error 1
make[3]: Leaving directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'

Can you please tell me how to rectify this?

I am attaching the log file for configure for your reference.

First, you probably want the 1.8.5 release of HDF5, which should be
released next week. Here's the link for a release candidate:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

Then, you should use the 'mpicc' command from MPICH2 as your compiler,
instead of trying to get the MPI include files and libraries correct.

Quincey

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

7

Hi Quincey,

Thanks for your reply. I used the latest release 1.8.5 and mpicc for
compiling..and that worked fine..

Thanks a lot !!

Regards,
Kunal

···

On Sat, Jun 5, 2010 at 11:02 PM, Quincey Koziol <koziol@hdfgroup.org> wrote:

Hi Kunal,

On Jun 5, 2010, at 7:19 PM, kunal rao wrote:

Hello:

I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop
running Ubuntu 9.10 on a virtual machine.

I have configured id with the following command:

$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/
FFLAGS=-I/usr/include/mpich2/ ./configure
--prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel
--enable-fortran |tee configure_parallel.log

But when I do $ make
I get the following error after some time :

make[3]: Entering directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
/usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c
thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:

     comm = MPI_COMM_WORLD
                          1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:

     info = MPI_INFO_NULL
                         1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type
make[3]: *** [thyperslab_wr.lo] Error 1
make[3]: Leaving directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'

Can you please tell me how to rectify this?

I am attaching the log file for configure for your reference.

First, you probably want the 1.8.5 release of HDF5, which should be
released next week. Here's the link for a release candidate:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

Then, you should use the 'mpicc' command from MPICH2 as your compiler,
instead of trying to get the MPI include files and libraries correct.

Quincey

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org