PHDF5 Installation Issue - Make errors

Vaibhav_Thakore · January 6, 2011, 7:43pm

Hi Elena,

Thank you for your prompt response. First answers to your questions:

On which platforms do you build and which compilers do you use?
I am using OpenSuse Linux 11.1, kernel 2.6.27.56-0.1. I am using gcc(version: 4.3.2) and gfortran(version: 4.3.2)

Can you see *.mod files in the fortran/src directory?
Yes I can see the *.mod files in the fortran/src directory.

Any chance that they were left their from the previous build?
Nope as this is the first time I am trying to use HDF5 or PHDF5.

Action Items:
I followed your instructions to do the build again.
Step 1:
- make distclean starting from the top directory

Step2:
- configuring with the simplified command
./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-parallel

Outcome:
- configuring succeeded as earlier.
- make failed with similar errors as earlier.

I am attaching the console outputs for ./configure and make in two separate text files respectively:

- vtconfiglogfile-hdf5-1.6.10
- vtmakelogfile-hdf5-1.6.10.

As per your suggestion I also tried building hdf5-1.8.5-patch1 but again configure succeeded but make failed. The console outputs for ./configure and make (partial output as write to the output file could not complete) in two separate text files respectively:
- vtconfiglogfile-hdf5-1.8.5-patch1
- vtmakelogfile-hdf5-1.8.5-patch1.

I had earlier avoided installing the latest release hdf5-1.8.5-patch1 because there had been some bugs/problems reported in release notes with regard to using certain number of processors with PHDF5.

Looking forward to your response. Thanks once again.

Regards.
Vaibhav

Vaibhav Thakore
Graduate Research Assistant
416 NanoScience Technology Center
12424 Research Parkway
Orlando, FL 32826
Phone: 864 506 6563

Elena Pourmal <epourmal@hdfgroup.org> 01/06/11 9:54 AM >>>

Hi Vaibhav,

It looks to me as mpif90 cannot find HDF5 modules when it links Fortran tests. On which platforms do you build and which compilers do you use? Can you see *.mod files in the fortran/src directory? Any chance that they were left their from the previous build?

Could you please try

- make distclean starting from the top directory
- configuring with the simplified command

./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-parallel

make
make check

Please save outputs of the configure command and make commands; if build doesn't work, we will need to look at the output.

I would also recommend to use 1.8.5-patch1 instead of 1.6.10. If your application uses 1.6 API, you can use --with-default-api-version=v16 configure flag when you configure and build the 1.8.5-patch1 library, or use -DH5_USE_16_API flag when you compile your application (and build the library as discussed above).

Thank you!

Elena

vtconfiglogfile-hdf5-1.6.10 (19.8 KB)

vtmakelogfile-hdf5-1.6.10 (122 KB)

vtconfiglogfile-hdf5-1.8.5-patch1 (21.7 KB)

vtmakelogfile-hdf5-1.8.5-patch1 (623 KB)

···

On Jan 5, 2011, at 4:26 PM, vthakore wrote:

Hi,

I have been trying to install hdf5 with the parallel option and ran
configure using the following options:

./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-linux-lfs --enable-debug=all
--enable-parallel

Also set environment variables using

export CC=mpicc and export FC=mpif90

After successful configuration, I ran make which failed due to errors.
Please see output below. I already had mpich2 installed on my system and I
have sucessfully used mpi calls several times in my Fortran programs.

Can someone please point out as to what the issue might be and how can it be
remedied? Thanks a lot for your time and effort.

Regards.

Vaibhav.

epourmal · January 13, 2011, 9:44pm

Vaibhav,

Hmm... I don't see the error in "make" output for 1.6.10, looks like it finished building Fortran tests
........

mpif90 -I. -I. -I../src -c tH5E.f90 -o tH5E.o
echo timestamp > tH5E.lo
mpif90 -I. -I. -o fortranlib_test fortranlib_test.o tH5F.o tH5D.o tH5R.o tH5S.o tH5T.o tH5VL.o tH5Z.o tH5Sselect.o tH5P.o tH5A.o tH5I.o tH5G.o tH5E.o tf.o t.o ./.libs/libh5test_fortran.a ../../test/.libs/libh5test.a ../src/.libs/libhdf5_fortran.a ../../src/.libs/libhdf5.a -lz -lm
make[3]: Leaving directory `/home/vthakore/My_Downloads/hdf5-1.6.10/fortran/test'
make[2]: Leaving directory `/home/vthakore/My_Downloads/hdf5-1.6.10/fortran'
make[1]: Leaving directory `/home/vthakore/My_Downloads/hdf5-1.6.10'

make output for 1.8.5-patch 1 stops when trying to build C tests with this error

virtual memory exhausted: Cannot allocate memory
make[1]: *** [tselect.o] Error 1

Elena

···

On Jan 6, 2011, at 1:43 PM, Vaibhav Thakore wrote:

Hi Elena,

Thank you for your prompt response. First answers to your questions:

On which platforms do you build and which compilers do you use?
I am using OpenSuse Linux 11.1, kernel 2.6.27.56-0.1. I am using gcc(version: 4.3.2) and gfortran(version: 4.3.2)

Can you see *.mod files in the fortran/src directory?
Yes I can see the *.mod files in the fortran/src directory.

Any chance that they were left their from the previous build?
Nope as this is the first time I am trying to use HDF5 or PHDF5.

Action Items:
I followed your instructions to do the build again.
Step 1:
- make distclean starting from the top directory

Step2:
- configuring with the simplified command
./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-parallel

Outcome:
- configuring succeeded as earlier.
- make failed with similar errors as earlier.

I am attaching the console outputs for ./configure and make in two separate text files respectively:

- vtconfiglogfile-hdf5-1.6.10
- vtmakelogfile-hdf5-1.6.10.

As per your suggestion I also tried building hdf5-1.8.5-patch1 but again configure succeeded but make failed. The console outputs for ./configure and make (partial output as write to the output file could not complete) in two separate text files respectively:
- vtconfiglogfile-hdf5-1.8.5-patch1
- vtmakelogfile-hdf5-1.8.5-patch1.

I had earlier avoided installing the latest release hdf5-1.8.5-patch1 because there had been some bugs/problems reported in release notes with regard to using certain number of processors with PHDF5.

Looking forward to your response. Thanks once again.

Regards.
Vaibhav

Vaibhav Thakore
Graduate Research Assistant
416 NanoScience Technology Center
12424 Research Parkway
Orlando, FL 32826
Phone: 864 506 6563

Elena Pourmal <epourmal@hdfgroup.org> 01/06/11 9:54 AM >>>

Hi Vaibhav,

It looks to me as mpif90 cannot find HDF5 modules when it links Fortran tests. On which platforms do you build and which compilers do you use? Can you see *.mod files in the fortran/src directory? Any chance that they were left their from the previous build?

Could you please try

- make distclean starting from the top directory
- configuring with the simplified command

./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-parallel

make
make check

Please save outputs of the configure command and make commands; if build doesn't work, we will need to look at the output.

I would also recommend to use 1.8.5-patch1 instead of 1.6.10. If your application uses 1.6 API, you can use --with-default-api-version=v16 configure flag when you configure and build the 1.8.5-patch1 library, or use -DH5_USE_16_API flag when you compile your application (and build the library as discussed above).

Thank you!

Elena

On Jan 5, 2011, at 4:26 PM, vthakore wrote:

Hi,

I have been trying to install hdf5 with the parallel option and ran
configure using the following options:

./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-linux-lfs --enable-debug=all
--enable-parallel

Also set environment variables using

export CC=mpicc and export FC=mpif90

After successful configuration, I ran make which failed due to errors.
Please see output below. I already had mpich2 installed on my system and I
have sucessfully used mpi calls several times in my Fortran programs.

Can someone please point out as to what the issue might be and how can it be
remedied? Thanks a lot for your time and effort.

Regards.

Vaibhav.

<vtconfiglogfile-hdf5-1.6.10><vtmakelogfile-hdf5-1.6.10><vtconfiglogfile-hdf5-1.8.5-patch1><vtmakelogfile-hdf5-1.8.5-patch1>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

brtnfld · January 14, 2011, 5:09am

I can verify that compiling hdf5-1.8.5-patch1 on Suse 11.1, with gnu compilers (4.3) and just:
./configure
fails during make by running out of virtual memory compiling tselect.c.

The trunk also fails due to __h5global_MOD_ for
./configure --enable-fortran --enable-parallel --with-default-api-version=v16

Compiling hdf5-1.6.10 on Suse 11.1, with gnu compilers (4.3) and just:
./configure --enable-fortran
cause the complaints about the undefined __h5global_MOD_ as described.

···

*********

On OpenSuse 11.3 with gnu compilers 4.5 (mpich2-1.2.p1) it has no problems with either 1.8.5 or 1.6.10
(I tested ./configure --enable-fortran --enable-parallel for 1.6.10 and had no problems).

Maybe updating to a newer gnu compiler will help or it's a problem with Suse 11.1, but I'm not sure.

It might be easier (and advised) to upgrade your OpenSUSE since OpenSuse 11.1 has reached its service lifetime last month anyway.

Quoting Vaibhav Thakore <thakore@mail.ucf.edu>:

Hi Elena,

    Thank you for your prompt response. First answers to your questions:

On which platforms do you build and which compilers do you use?
I am using OpenSuse Linux 11.1, kernel 2.6.27.56-0.1. I am using gcc(version: 4.3.2) and gfortran(version: 4.3.2)

Can you see *.mod files in the fortran/src directory?
Yes I can see the *.mod files in the fortran/src directory.

Any chance that they were left their from the previous build?
Nope as this is the first time I am trying to use HDF5 or PHDF5.

Action Items:
I followed your instructions to do the build again.
Step 1:
- make distclean starting from the top directory

Step2:
- configuring with the simplified command
./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-parallel

Outcome:
- configuring succeeded as earlier.
- make failed with similar errors as earlier.

I am attaching the console outputs for ./configure and make in two separate text files respectively:

- vtconfiglogfile-hdf5-1.6.10
- vtmakelogfile-hdf5-1.6.10.

As per your suggestion I also tried building hdf5-1.8.5-patch1 but again configure succeeded but make failed. The console outputs for ./configure and make (partial output as write to the output file could not complete) in two separate text files respectively:
- vtconfiglogfile-hdf5-1.8.5-patch1
- vtmakelogfile-hdf5-1.8.5-patch1.

I had earlier avoided installing the latest release hdf5-1.8.5-patch1 because there had been some bugs/problems reported in release notes with regard to using certain number of processors with PHDF5.

   Looking forward to your response. Thanks once again.

Regards.
Vaibhav

Vaibhav Thakore
Graduate Research Assistant
416 NanoScience Technology Center
12424 Research Parkway
Orlando, FL 32826
Phone: 864 506 6563

Elena Pourmal <epourmal@hdfgroup.org> 01/06/11 9:54 AM >>>

Hi Vaibhav,

It looks to me as mpif90 cannot find HDF5 modules when it links Fortran tests. On which platforms do you build and which compilers do you use? Can you see *.mod files in the fortran/src directory? Any chance that they were left their from the previous build?

Could you please try

- make distclean starting from the top directory
- configuring with the simplified command

./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-parallel

  make
  make check

Please save outputs of the configure command and make commands; if build doesn't work, we will need to look at the output.

I would also recommend to use 1.8.5-patch1 instead of 1.6.10. If your application uses 1.6 API, you can use --with-default-api-version=v16 configure flag when you configure and build the 1.8.5-patch1 library, or use -DH5_USE_16_API flag when you compile your application (and build the library as discussed above).

Thank you!

Elena

On Jan 5, 2011, at 4:26 PM, vthakore wrote:

Hi,

I have been trying to install hdf5 with the parallel option and ran
configure using the following options:

./configure --prefix=/opt/hdf5-1.6.10 --with-szlib=/opt/szip-2.1
--with-zlib=/lib64 --enable-fortran --enable-linux-lfs --enable-debug=all
--enable-parallel

Also set environment variables using

export CC=mpicc and export FC=mpif90

After successful configuration, I ran make which failed due to errors.
Please see output below. I already had mpich2 installed on my system and I
have sucessfully used mpi calls several times in my Fortran programs.

Can someone please point out as to what the issue might be and how can it be
remedied? Thanks a lot for your time and effort.

Regards.

Vaibhav.