Bug 757050
| Summary: | hdf5-static does not provide mpi support... | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | eyurtese |
| Component: | hdf5 | Assignee: | Orion Poplawski <orion> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | high | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | 16 | CC: | c.david86, orion, pertusus |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | x86_64 | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Fixed In Version: | hdf5-1.8.7-3.fc16 | Doc Type: | Bug Fix |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2011-12-17 20:53:56 UTC | Type: | --- |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
hdf5-1.8.7-3.fc16 has been submitted as an update for Fedora 16. https://admin.fedoraproject.org/updates/hdf5-1.8.7-3.fc16 While I hardly think it is necessary to use static libraries for mpi (simply make sure you have loaded the proper environment module), this update should provide them. Package hdf5-1.8.7-3.fc16: * should fix your issue, * was pushed to the Fedora 16 testing repository, * should be available at your local mirror within two days. Update it with: # su -c 'yum update --enablerepo=updates-testing hdf5-1.8.7-3.fc16' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2011-16450/hdf5-1.8.7-3.fc16 then log in and leave karma (feedback). It might be required on clusters where the files/libraries are not shared on all nodes or if you are using your program on a remote system which does not have same version of hdf5 installed. Also, I actually couldnt manage to build shared libraries with HDF5 at all and actually it defaults to using static libraries and shared libraries are not supported on all platforms. http://www.hdfgroup.org/hdf5-quest.html#fshare In either case, these are important stuff :) hdf5-1.8.7-3.fc16 has been pushed to the Fedora 16 stable repository. If problems still persist, please make note of it in this bug report. |
HDF5 packages seem to be not very useful... The hdf5 does not seem to have mpi support with static libraries. hdf5-mpich2 package installs dynamic libraries with mpi support, however this lacks the static libraries. Fedora needs to supply hdf5-mpich2-static or include mpi support in hdf5-static. in Ubuntu, the static libraries arrive when the libhdf5-mpich-dev package is installed by default. It does not make much sense to not have MPI support in HDF5 since in my opinion many people who use HDF5 use it in programs which also use MPI. $ nm /usr/lib64/libhdf5_fortran.a |grep mpi 0000000000000010 T __h5t_MOD_h5tcompiler_conv_f U h5tcompiler_conv_c_ U H5Tcompiler_conv 0000000000001a9c T h5tcompiler_conv_c_ $ objdump -T /usr/lib64/mpich2/lib/libhdf5_fortran.so |grep mpi /usr/lib64/mpich2/lib/libhdf5_fortran.so: file format elf64-x86-64 0000000000000000 DF *UND* 0000000000000000 H5Tcompiler_conv 0000000000000000 DF *UND* 0000000000000000 H5Pset_dxpl_mpio 0000000000000000 DF *UND* 0000000000000000 H5FD_mpio_init 0000000000000000 DF *UND* 0000000000000000 H5Pget_fapl_mpiposix 0000000000000000 DF *UND* 0000000000000000 H5Pset_fapl_mpio 0000000000000000 DF *UND* 0000000000000000 H5Pget_fapl_mpio 0000000000000000 DF *UND* 0000000000000000 H5Pget_dxpl_mpio 0000000000000000 DF *UND* 0000000000000000 H5Pset_fapl_mpiposix 00000000000341a0 g DF .text 000000000000003e Base __h5fdmpio_MOD_h5pget_fapl_mpiposix_f 0000000000034250 g DF .text 000000000000000f Base __h5fdmpio_MOD_h5pset_fapl_mpio_f 0000000000033f08 g DF .text 0000000000000073 Base h5pset_fapl_mpio_c_ 0000000000034122 g DF .text 0000000000000078 Base h5pget_fapl_mpiposix_c_ 0000000000034220 g DF .text 000000000000000f Base __h5fdmpio_MOD_h5pget_dxpl_mpio_f 0000000000034240 g DF .text 000000000000000f Base __h5fdmpio_MOD_h5pget_fapl_mpio_f 0000000000034230 g DF .text 000000000000000f Base __h5fdmpio_MOD_h5pset_dxpl_mpio_f 0000000000033ff1 g DF .text 000000000000005d Base h5pset_dxpl_mpio_c_ 00000000000341e0 g DF .text 0000000000000032 Base __h5fdmpio_MOD_h5pset_fapl_mpiposix_f 00000000000340af g DF .text 0000000000000073 Base h5pset_fapl_mpiposix_c_ 000000000003404e g DF .text 0000000000000061 Base h5pget_dxpl_mpio_c_ 00000000000218b0 g DF .text 000000000000003d Base __h5t_MOD_h5tcompiler_conv_f 0000000000033f7b g DF .text 0000000000000076 Base h5pget_fapl_mpio_c_ 0000000000033d34 g DF .text 000000000000005f Base h5tcompiler_conv_c_