Hello,
I am trying to build HDF5 1.8.11 with PGI 13.2-0 and mvapich2 1.8 and am getting a link error. I haven't been able to find any references to this issue in my searching thus far.
The error:
FCLD fortranlib_test_F03
tH5F_F03.o: In function `test_get_file_image_':
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
make[3]: *** [fortranlib_test_F03] Error 2
make[3]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8'
make: *** [/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8] Error 2
In looking at ...fortran/test/./tH5F_F03.f90 I see that there is a RETURN statement at the top of the subroutine with a comment indicating that there is a PGI bug. How do I disable the compilation of this unusable test?
This is how I am configuring it:
export CC=mpicc
export CXX=mpicxx
export F77=mpif90
export F90=mpif90
export FC=mpif90
export LDFLAGS=" -Wl,--rpath -Wl,/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6/lib"
./configure --with-szlib=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6 --enable-parallel --enable-fortran --enable-fortran2003 --enable-shared --prefix=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8
This does not occur when I build HDF5 without parallel support.
Let me know if I did not supply enough information.
Chris
···
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
I noticed this too and observed that when using pgi to build a parallel variant (with hdf5 1.8.12) the symbols where part of HF5_PROVISIONAL. So I was able to make it build by applying the following mod:
Index: fortran/test/tH5F_F03.f90
···
===================================================================
--- fortran/test/tH5F_F03.f90 (revision 1324)
+++ fortran/test/tH5F_F03.f90 (working copy)
@@ -41,6 +41,7 @@
! Tests the wrapper for h5fget_file_image
!
USE HDF5
+ USE H5F_PROVISIONAL
USE ISO_C_BINDING
IMPLICIT NONE
I'm not sure if this was appropriate.
Sean B.
________________________________________
From: Hdf-forum [hdf-forum-bounces@lists.hdfgroup.org] on behalf of Christopher Harrop - NOAA Affiliate [christopher.w.harrop@noaa.gov]
Sent: Tuesday, January 07, 2014 11:19 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] HDF5-1.8.11 PGI link error
Hello,
I am trying to build HDF5 1.8.11 with PGI 13.2-0 and mvapich2 1.8 and am getting a link error. I haven't been able to find any references to this issue in my searching thus far.
The error:
FCLD fortranlib_test_F03
tH5F_F03.o: In function `test_get_file_image_':
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
make[3]: *** [fortranlib_test_F03] Error 2
make[3]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8'
make: *** [/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8] Error 2
In looking at ...fortran/test/./tH5F_F03.f90 I see that there is a RETURN statement at the top of the subroutine with a comment indicating that there is a PGI bug. How do I disable the compilation of this unusable test?
This is how I am configuring it:
export CC=mpicc
export CXX=mpicxx
export F77=mpif90
export F90=mpif90
export FC=mpif90
export LDFLAGS=" -Wl,--rpath -Wl,/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6/lib"
./configure --with-szlib=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6 --enable-parallel --enable-fortran --enable-fortran2003 --enable-shared --prefix=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8
This does not occur when I build HDF5 without parallel support.
Let me know if I did not supply enough information.
Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Sean,
Thank you for that patch. It does indeed solve the build problem for me.
Chris
···
I noticed this too and observed that when using pgi to build a parallel variant (with hdf5 1.8.12) the symbols where part of HF5_PROVISIONAL. So I was able to make it build by applying the following mod:
Index: fortran/test/tH5F_F03.f90
--- fortran/test/tH5F_F03.f90 (revision 1324)
+++ fortran/test/tH5F_F03.f90 (working copy)
@@ -41,6 +41,7 @@
! Tests the wrapper for h5fget_file_image
!
USE HDF5
+ USE H5F_PROVISIONAL
USE ISO_C_BINDING
IMPLICIT NONE
I'm not sure if this was appropriate.
Sean B.
________________________________________
From: Hdf-forum [hdf-forum-bounces@lists.hdfgroup.org] on behalf of Christopher Harrop - NOAA Affiliate [christopher.w.harrop@noaa.gov]
Sent: Tuesday, January 07, 2014 11:19 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] HDF5-1.8.11 PGI link error
Hello,
I am trying to build HDF5 1.8.11 with PGI 13.2-0 and mvapich2 1.8 and am getting a link error. I haven't been able to find any references to this issue in my searching thus far.
The error:
FCLD fortranlib_test_F03
tH5F_F03.o: In function `test_get_file_image_':
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
make[3]: *** [fortranlib_test_F03] Error 2
make[3]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8'
make: *** [/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8] Error 2
In looking at ...fortran/test/./tH5F_F03.f90 I see that there is a RETURN statement at the top of the subroutine with a comment indicating that there is a PGI bug. How do I disable the compilation of this unusable test?
This is how I am configuring it:
export CC=mpicc
export CXX=mpicxx
export F77=mpif90
export F90=mpif90
export FC=mpif90
export LDFLAGS=" -Wl,--rpath -Wl,/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6/lib"
./configure --with-szlib=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6 --enable-parallel --enable-fortran --enable-fortran2003 --enable-shared --prefix=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8
This does not occur when I build HDF5 without parallel support.
Let me know if I did not supply enough information.
Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
Thank you for information.
The HDF Group is looking into the problem.
Elena
···
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Jan 7, 2014, at 12:52 PM, Christopher Harrop - NOAA Affiliate <christopher.w.harrop@noaa.gov> wrote:
Sean,
Thank you for that patch. It does indeed solve the build problem for me.
Chris
I noticed this too and observed that when using pgi to build a parallel variant (with hdf5 1.8.12) the symbols where part of HF5_PROVISIONAL. So I was able to make it build by applying the following mod:
Index: fortran/test/tH5F_F03.f90
--- fortran/test/tH5F_F03.f90 (revision 1324)
+++ fortran/test/tH5F_F03.f90 (working copy)
@@ -41,6 +41,7 @@
! Tests the wrapper for h5fget_file_image
!
USE HDF5
+ USE H5F_PROVISIONAL
USE ISO_C_BINDING
IMPLICIT NONE
I'm not sure if this was appropriate.
Sean B.
________________________________________
From: Hdf-forum [hdf-forum-bounces@lists.hdfgroup.org] on behalf of Christopher Harrop - NOAA Affiliate [christopher.w.harrop@noaa.gov]
Sent: Tuesday, January 07, 2014 11:19 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] HDF5-1.8.11 PGI link error
Hello,
I am trying to build HDF5 1.8.11 with PGI 13.2-0 and mvapich2 1.8 and am getting a link error. I haven't been able to find any references to this issue in my searching thus far.
The error:
FCLD fortranlib_test_F03
tH5F_F03.o: In function `test_get_file_image_':
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
make[3]: *** [fortranlib_test_F03] Error 2
make[3]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8'
make: *** [/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8] Error 2
In looking at ...fortran/test/./tH5F_F03.f90 I see that there is a RETURN statement at the top of the subroutine with a comment indicating that there is a PGI bug. How do I disable the compilation of this unusable test?
This is how I am configuring it:
export CC=mpicc
export CXX=mpicxx
export F77=mpif90
export F90=mpif90
export FC=mpif90
export LDFLAGS=" -Wl,--rpath -Wl,/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6/lib"
./configure --with-szlib=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6 --enable-parallel --enable-fortran --enable-fortran2003 --enable-shared --prefix=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8
This does not occur when I build HDF5 without parallel support.
Let me know if I did not supply enough information.
Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Thank you for the report, H5F_provisional was missing from HDF5mpi.f90, which is used when --enable-parallel is specified. The fix will be in the next release, but for now the patch is:
--- HDF5mpio.f90 (revision 24616)
+++ HDF5mpio.f90 (working copy)
@@ -28,6 +28,7 @@
MODULE HDF5
USE H5GLOBAL
USE H5F
+ USE H5F_PROVISIONAL
USE H5G
USE H5E
USE H5E_PROVISIONAL
Scot
···
_______________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of Christopher Harrop - NOAA Affiliate <christopher.w.harrop@noaa.gov>
Sent: Tuesday, January 07, 2014 12:52 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] HDF5-1.8.11 PGI link error
Sean,
Thank you for that patch. It does indeed solve the build problem for me.
Chris
I noticed this too and observed that when using pgi to build a parallel variant (with hdf5 1.8.12) the symbols where part of HF5_PROVISIONAL. So I was able to make it build by applying the following mod:
Index: fortran/test/tH5F_F03.f90
--- fortran/test/tH5F_F03.f90 (revision 1324)
+++ fortran/test/tH5F_F03.f90 (working copy)
@@ -41,6 +41,7 @@
! Tests the wrapper for h5fget_file_image
!
USE HDF5
+ USE H5F_PROVISIONAL
USE ISO_C_BINDING
IMPLICIT NONE
I'm not sure if this was appropriate.
Sean B.
________________________________________
From: Hdf-forum [hdf-forum-bounces@lists.hdfgroup.org] on behalf of Christopher Harrop - NOAA Affiliate [christopher.w.harrop@noaa.gov]
Sent: Tuesday, January 07, 2014 11:19 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] HDF5-1.8.11 PGI link error
Hello,
I am trying to build HDF5 1.8.11 with PGI 13.2-0 and mvapich2 1.8 and am getting a link error. I haven't been able to find any references to this issue in my searching thus far.
The error:
FCLD fortranlib_test_F03
tH5F_F03.o: In function `test_get_file_image_':
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
make[3]: *** [fortranlib_test_F03] Error 2
make[3]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8'
make: *** [/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8] Error 2
In looking at ...fortran/test/./tH5F_F03.f90 I see that there is a RETURN statement at the top of the subroutine with a comment indicating that there is a PGI bug. How do I disable the compilation of this unusable test?
This is how I am configuring it:
export CC=mpicc
export CXX=mpicxx
export F77=mpif90
export F90=mpif90
export FC=mpif90
export LDFLAGS=" -Wl,--rpath -Wl,/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6/lib"
./configure --with-szlib=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6 --enable-parallel --enable-fortran --enable-fortran2003 --enable-shared --prefix=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8
This does not occur when I build HDF5 without parallel support.
Let me know if I did not supply enough information.
Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
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All,
Thank you for the quick help. Much appreciated. Applying that simple patch in the interim is easy to do.
Chris
···
Thank you for the report, H5F_provisional was missing from HDF5mpi.f90, which is used when --enable-parallel is specified. The fix will be in the next release, but for now the patch is:
--- HDF5mpio.f90 (revision 24616)
+++ HDF5mpio.f90 (working copy)
@@ -28,6 +28,7 @@
MODULE HDF5
USE H5GLOBAL
USE H5F
+ USE H5F_PROVISIONAL
USE H5G
USE H5E
USE H5E_PROVISIONAL
Scot
_______________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of Christopher Harrop - NOAA Affiliate <christopher.w.harrop@noaa.gov>
Sent: Tuesday, January 07, 2014 12:52 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] HDF5-1.8.11 PGI link error
Sean,
Thank you for that patch. It does indeed solve the build problem for me.
Chris
I noticed this too and observed that when using pgi to build a parallel variant (with hdf5 1.8.12) the symbols where part of HF5_PROVISIONAL. So I was able to make it build by applying the following mod:
Index: fortran/test/tH5F_F03.f90
--- fortran/test/tH5F_F03.f90 (revision 1324)
+++ fortran/test/tH5F_F03.f90 (working copy)
@@ -41,6 +41,7 @@
! Tests the wrapper for h5fget_file_image
!
USE HDF5
+ USE H5F_PROVISIONAL
USE ISO_C_BINDING
IMPLICIT NONE
I'm not sure if this was appropriate.
Sean B.
________________________________________
From: Hdf-forum [hdf-forum-bounces@lists.hdfgroup.org] on behalf of Christopher Harrop - NOAA Affiliate [christopher.w.harrop@noaa.gov]
Sent: Tuesday, January 07, 2014 11:19 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] HDF5-1.8.11 PGI link error
Hello,
I am trying to build HDF5 1.8.11 with PGI 13.2-0 and mvapich2 1.8 and am getting a link error. I haven't been able to find any references to this issue in my searching thus far.
The error:
FCLD fortranlib_test_F03
tH5F_F03.o: In function `test_get_file_image_':
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: undefined reference to `h5fget_file_image_f_'
make[3]: *** [fortranlib_test_F03] Error 2
make[3]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8'
make: *** [/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8] Error 2
In looking at ...fortran/test/./tH5F_F03.f90 I see that there is a RETURN statement at the top of the subroutine with a comment indicating that there is a PGI bug. How do I disable the compilation of this unusable test?
This is how I am configuring it:
export CC=mpicc
export CXX=mpicxx
export F77=mpif90
export F90=mpif90
export FC=mpif90
export LDFLAGS=" -Wl,--rpath -Wl,/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6/lib"
./configure --with-szlib=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6 --enable-parallel --enable-fortran --enable-fortran2003 --enable-shared --prefix=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8
This does not occur when I build HDF5 without parallel support.
Let me know if I did not supply enough information.
Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop email: christopher.w.harrop@noaa.gov
Global Systems Division voice: (303) 497-6808
NOAA Earth System Research Laboratory fax: (303) 497-7259
325 Broadway R/GSD2
Boulder, CO 80303
