On Fri, Aug 21, 2020 at 8:04 AM Malcolm wrote:

On Fri 21 Aug 2020 07:43:58 AM CDT, Christoph Junghans wrote:

...

Hi,

Can somebody give me a hand to convert python3-espressomd to a new HPC-style package? Background is that, espresso's cmake recently failed to detect hdf5 [ 33s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5_hl.a: No such file or directory [ 33s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5.a: No such file or directory (from https://build.opensuse.org/package/live_build_log/devel:languages:python:num...) and I am a bit helpless on how to fix this.

If this is the wrong mailing list, please point me in the right direction!

Thanks,

Christoph

Hi That would require hdf5-openmpi2-devel-static as a build requires, are you sure you need static libs, if not disable the static build and only use shared libs.

It worked with the shared libs in the past, this is a more recent error. In Espresso's CMake it does: set(HDF5_PREFER_PARALLEL 1) find_package(HDF5 "1.8" COMPONENTS C) which is pretty standard. Christoph

-- Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890) Tumbleweed 20200819 | GNOME Shell 3.36.5 | 5.8.0-1-default Intel DQ77MK MB | Xeon E3-1245 V2 X8 @ 3.40 GHz | Intel/Nvidia up 11:42, 2 users, load average: 0.79, 0.58, 0.62 -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org

-- Christoph Junghans Web: http://www.compphys.de -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org

On Fri, Aug 21, 2020 at 9:08 AM Malcolm wrote:

On Fri 21 Aug 2020 08:13:54 AM CDT, Christoph Junghans wrote:

...

On Fri, Aug 21, 2020 at 8:04 AM Malcolm wrote:

...

On Fri 21 Aug 2020 07:43:58 AM CDT, Christoph Junghans wrote:

...

Hi,

Can somebody give me a hand to convert python3-espressomd to a new HPC-style package? Background is that, espresso's cmake recently failed to detect hdf5 [ 33s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5_hl.a: No such file or directory [ 33s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5.a: No such file or directory (from https://build.opensuse.org/package/live_build_log/devel:languages:python:num...) and I am a bit helpless on how to fix this.

If this is the wrong mailing list, please point me in the right direction!

Thanks,

Christoph

Hi That would require hdf5-openmpi2-devel-static as a build requires, are you sure you need static libs, if not disable the static build and only use shared libs.

It worked with the shared libs in the past, this is a more recent error. In Espresso's CMake it does: set(HDF5_PREFER_PARALLEL 1) find_package(HDF5 "1.8" COMPONENTS C) which is pretty standard.

Christoph

...

-- Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890) Tumbleweed 20200819 | GNOME Shell 3.36.5 | 5.8.0-1-default Intel DQ77MK MB | Xeon E3-1245 V2 X8 @ 3.40 GHz | Intel/Nvidia up 11:42, 2 users, load average: 0.79, 0.58, 0.62 -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org

Hi If you look at the build log for Tumbleweed, it doesn't find them there either, even though the build succeeds? I think there is also something wrong with the OpenMPI version checks as I would have thought it would use 3 and not 2 for Tumbleweed?

You are right, hence I was asking about the new HPC-style for multiple mpi implementations. The header of the spec is: %if 0%{?sle_version} == 0 %define mpiver openmpi2 %else %if 0%{?sle_version} <= 120300 %define mpiver openmpi %else %if 0%{?sle_version} <= 150000 %define mpiver openmpi2 %else %define mpiver openmpi3 %endif %endif This might be outdated.

[ 73s] /home/abuild/rpmbuild/BUILD/espresso/build/CMakeFiles/hdf5/cmake_hdf5_test.c: In function 'main': [ 73s] /home/abuild/rpmbuild/BUILD/espresso/build/CMakeFiles/hdf5/cmake_hdf5_test.c:13:9: warning: variable 'fid' set but not used [-Wunused-but-set-variable] [ 73s] 13 | hid_t fid; [ 73s] | ^~~ [ 73s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5_hl.a: No such file or directory [ 73s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5.a: No such file or directory [ 73s] -- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program. [ 73s] -- Could NOT find HDF5: Found unsuitable version "", but required is at least "1.8" (found HDF5_hdf5_LIBRARY-NOTFOUND)

-- Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890) Tumbleweed 20200819 | GNOME Shell 3.36.5 | 5.8.0-1-default Intel DQ77MK MB | Xeon E3-1245 V2 X8 @ 3.40 GHz | Intel/Nvidia up 12:46, 2 users, load average: 0.60, 0.45, 0.32 -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org

-- Christoph Junghans Web: http://www.compphys.de -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org

On Fri, Aug 21, 2020 at 9:32 AM Christoph Junghans wrote:

On Fri, Aug 21, 2020 at 9:19 AM Christoph Junghans wrote:

...

On Fri, Aug 21, 2020 at 9:08 AM Malcolm wrote:

...

On Fri 21 Aug 2020 08:13:54 AM CDT, Christoph Junghans wrote:

...

On Fri, Aug 21, 2020 at 8:04 AM Malcolm wrote:

...

On Fri 21 Aug 2020 07:43:58 AM CDT, Christoph Junghans wrote:

...

Hi,

Can somebody give me a hand to convert python3-espressomd to a new HPC-style package? Background is that, espresso's cmake recently failed to detect hdf5 [ 33s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5_hl.a: No such file or directory [ 33s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5.a: No such file or directory (from https://build.opensuse.org/package/live_build_log/devel:languages:python:num...) and I am a bit helpless on how to fix this.

If this is the wrong mailing list, please point me in the right direction!

Thanks,

Christoph

Hi That would require hdf5-openmpi2-devel-static as a build requires, are you sure you need static libs, if not disable the static build and only use shared libs.

It worked with the shared libs in the past, this is a more recent error. In Espresso's CMake it does: set(HDF5_PREFER_PARALLEL 1) find_package(HDF5 "1.8" COMPONENTS C) which is pretty standard.

Christoph

...

-- Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890) Tumbleweed 20200819 | GNOME Shell 3.36.5 | 5.8.0-1-default Intel DQ77MK MB | Xeon E3-1245 V2 X8 @ 3.40 GHz | Intel/Nvidia up 11:42, 2 users, load average: 0.79, 0.58, 0.62 -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org

Hi If you look at the build log for Tumbleweed, it doesn't find them there either, even though the build succeeds? I think there is also something wrong with the OpenMPI version checks as I would have thought it would use 3 and not 2 for Tumbleweed?

You are right, hence I was asking about the new HPC-style for multiple mpi implementations. The header of the spec is: %if 0%{?sle_version} == 0 %define mpiver openmpi2 %else %if 0%{?sle_version} <= 120300 %define mpiver openmpi %else %if 0%{?sle_version} <= 150000 %define mpiver openmpi2 %else %define mpiver openmpi3 %endif %endif

This might be outdated.

Ok, I think it is issue with hdf5. Even without mpi, I reproduce the error: cat CMakeLists.txt cmake_minimum_required(VERSION 3.10) project(test) find_package(HDF5 COMPONENTS C) junghans@pn1806404-opensuse:/tmp> cmake . /tmp/CMakeFiles/hdf5/cmake_hdf5_test.c: In function ‘main’: /tmp/CMakeFiles/hdf5/cmake_hdf5_test.c:13:9: warning: variable ‘fid’ set but not used [-Wunused-but-set-variable] 13 | hid_t fid; | ^~~ gcc: error: /usr/lib64/libhdf5_hl.a: No such file or directory gcc: error: /usr/lib64/libhdf5.a: No such file or directory -- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program. -- Found HDF5: /usr/lib64/libhdf5.so (found version "1.10.5") found components: C

Looking at h5cc: $ h5cc -echo ... ++ gcc -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -Werror=return-type -flto=auto -ffat-lto-objects -g -L/usr/lib64 /usr/lib64/libhdf5_hl.a /usr/lib64/libhdf5.a -flto=auto -ffat-lto-objects -lpthread -lz -ldl -lm -Wl,-rpath -Wl,/usr/lib64 gcc: error: /usr/lib64/libhdf5_hl.a: No such file or directory gcc: error: /usr/lib64/libhdf5.a: No such file or directory

There we go the static lib get injected by h5cc. I guess export HDF5_USE_SHLIB=yes should help, let me try.

Conclusion, that fixed it. Christoph

Christoph

...

...

[ 73s] /home/abuild/rpmbuild/BUILD/espresso/build/CMakeFiles/hdf5/cmake_hdf5_test.c: In function 'main': [ 73s] /home/abuild/rpmbuild/BUILD/espresso/build/CMakeFiles/hdf5/cmake_hdf5_test.c:13:9: warning: variable 'fid' set but not used [-Wunused-but-set-variable] [ 73s] 13 | hid_t fid; [ 73s] | ^~~ [ 73s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5_hl.a: No such file or directory [ 73s] gcc: error: /usr/lib64/mpi/gcc/openmpi2/lib64/libhdf5.a: No such file or directory [ 73s] -- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program. [ 73s] -- Could NOT find HDF5: Found unsuitable version "", but required is at least "1.8" (found HDF5_hdf5_LIBRARY-NOTFOUND)

-- Cheers Malcolm °¿° SUSE Knowledge Partner (Linux Counter #276890) Tumbleweed 20200819 | GNOME Shell 3.36.5 | 5.8.0-1-default Intel DQ77MK MB | Xeon E3-1245 V2 X8 @ 3.40 GHz | Intel/Nvidia up 12:46, 2 users, load average: 0.60, 0.45, 0.32 -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org

-- Christoph Junghans Web: http://www.compphys.de

-- Christoph Junghans Web: http://www.compphys.de

-- Christoph Junghans Web: http://www.compphys.de -- To unsubscribe, e-mail: opensuse-packaging+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-packaging+owner@opensuse.org