Bug 1155118

Summary:	libelpa.so needs mpi_wtime_ missing in openmpi
Product:	[Fedora] Fedora	Reporter:	marcindulak <Marcin.Dulak>
Component:	elpa	Assignee:	Dominik 'Rathann' Mierzejewski <dominik>
Status:	CLOSED ERRATA	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	unspecified	Docs Contact:
Priority:	unspecified
Version:	22	CC:	dominik, orion
Target Milestone:	---
Target Release:	---
Hardware:	Unspecified
OS:	Unspecified
Whiteboard:
Fixed In Version:	mpich-3.1.4-2.fc22	Doc Type:	Bug Fix
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2015-05-11 00:05:56 UTC	Type:	Bug
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:

Description marcindulak 2014-10-21 12:00:35 UTC

Description of problem:

libelpa.so contains the mpi_wtime_ reference missing in openmpi.
I'm not sure where the fault is (maybe just a question of recompiling elpa),
but on Fedora 20 mpi_wtime_ was in libmpi_usempi.so.

Version-Release number of selected component (if applicable):

elpa-openmpi-devel-2013.11-5.008.fc22.x86_64
openmpi-1.8.3-2.fc22.x86_64

How reproducible:


Steps to Reproduce:
1. $ nm -D /usr/lib64/openmpi/lib/libelpa.so | grep "mpi_wtime_"
   U mpi_wtime_
2. $ nm -D /usr/lib64/openmpi/lib/libmpi*.so | grep "T mpi_wtime_"
   0000003877c88660 T mpi_wtime_f90
   0000003877c88670 T mpi_wtime_f90_
   0000003877c88680 T mpi_wtime_f90__
3.

Actual results:

mpi_wtime_ is undefined

Expected results:


Additional info:

Comment 1 Jaroslav Reznik 2015-03-03 16:23:18 UTC

This bug appears to have been reported against 'rawhide' during the Fedora 22 development cycle.
Changing version to '22'.

More information and reason for this action is here:
https://fedoraproject.org/wiki/Fedora_Program_Management/HouseKeeping/Fedora22

Comment 2 Dominik 'Rathann' Mierzejewski 2015-03-17 12:43:12 UTC

Working on it.

Comment 3 Orion Poplawski 2015-03-18 20:37:35 UTC

I think you're missing the weak symbol in libmpi_mpifh.so:

0000000000047f10 W mpi_wtime_
/usr/lib64/openmpi/lib/libmpi_mpifh.so

Is there some other issue that prompted this bug?

Comment 4 marcindulak 2015-03-19 12:43:31 UTC

This happened some months ago during a build of https://bugzilla.redhat.com/show_bug.cgi?id=1156086

I've tried to reproduce this on fc22 now, but run into the problem
of gfortran modules incompatibility:
"
Fatal Error: Cannot read module file 'elpa1.mod' opened at (1), because it was created by a different version of GNU Fortran
"
See http://koji.fedoraproject.org/koji/taskinfo?taskID=9273242

I thought a mass rebuild for Fedora 23 was planned in order to introduce
the gfortran-4.9 -> 5.0? I guess more fortran mods may be broken - how would you suggest this new problem needs to be handled?

Comment 5 Orion Poplawski 2015-03-19 14:45:19 UTC

All fortran modules need to be rebuilt for gcc 5 in F22.  Unfortunately there's not an easy automatic check for which ones still need to be rebuilt.  Also unfortunately, elpa currently doesn't build in F22 due to a failing test on arm.

Comment 6 Orion Poplawski 2015-03-19 14:46:22 UTC

Dominik is working on an update to elpa, so perhaps that will help.  We *may* also update mpich in F22 as well, which might help.

Comment 7 Fedora Update System 2015-05-01 21:15:58 UTC

elpa-2015.02.002-2.fc22, scalapack-2.0.2-7.fc22 has been submitted as an update for Fedora 22.
https://admin.fedoraproject.org/updates/elpa-2015.02.002-2.fc22,scalapack-2.0.2-7.fc22

Comment 8 Fedora Update System 2015-05-02 18:07:38 UTC

Package elpa-2015.02.002-2.fc22, scalapack-2.0.2-7.fc22:
* should fix your issue,
* was pushed to the Fedora 22 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=updates-testing elpa-2015.02.002-2.fc22 scalapack-2.0.2-7.fc22'
as soon as you are able to.
Please go to the following url:
https://admin.fedoraproject.org/updates/FEDORA-2015-7426/elpa-2015.02.002-2.fc22,scalapack-2.0.2-7.fc22
then log in and leave karma (feedback).

Comment 9 Fedora Update System 2015-05-05 05:34:32 UTC

mpich-3.1.4-2.fc22, netcdf-fortran-4.4.1-3.fc22, elpa-2015.02.002-2.fc22, hdf5-1.8.14-3.fc22, scorep-1.3-4.fc22, netcdf-4.3.3.1-1.fc22, nwchem-6.5.26243-15.fc22.1, mathgl-2.3-4.fc22, gmsh-2.9.3-2.fc22, boost-1.57.0-6.fc22, gromacs-4.6.5-6.fc22, pypar-2.1.5_108-7.fc22, espresso-3.3.0-3.fc22, ga-5.3b-16.fc22, netcdf-cxx4-4.2.1-5.fc22, scalapack-2.0.2-7.fc22, mpi4py-1.3.1-6.fc22, paraview-4.3.1-4.fc22.1, Ray-2.3.1-7.fc22, freefem++-3.31-1.4.fc22, cp2k-2.6.0-2.fc22, netgen-mesher-5.3.1-4.fc22, dl_poly-1.9.20140324-8.fc22, scotch-6.0.4-2.fc22, orsa-0.7.0-30.fc22, elk-3.0.18-10.fc22, gpaw-0.10.0.11364-10.fc22 has been submitted as an update for Fedora 22.
https://admin.fedoraproject.org/updates/FEDORA-2015-4630/mpich-3.1.4-2.fc22,elpa-2015.02.002-2.fc22,scalapack-2.0.2-7.fc22,hdf5-1.8.14-3.fc22,mpi4py-1.3.1-6.fc22,scorep-1.3-4.fc22,paraview-4.3.1-4.fc22.1,netcdf-4.3.3.1-1.fc22,netcdf-fortran-4.4.1-3.fc22,netcdf-cxx4-4.2.1-5.fc22,Ray-2.3.1-7.fc22,nwchem-6.5.26243-15.fc22.1,freefem++-3.31-1.4.fc22,mathgl-2.3-4.fc22,cp2k-2.6.0-2.fc22,gmsh-2.9.3-2.fc22,netgen-mesher-5.3.1-4.fc22,boost-1.57.0-6.fc22,dl_poly-1.9.20140324-8.fc22,gromacs-4.6.5-6.fc22,scotch-6.0.4-2.fc22,pypar-2.1.5_108-7.fc22,orsa-0.7.0-30.fc22,espresso-3.3.0-3.fc22,elk-3.0.18-10.fc22,ga-5.3b-16.fc22,gpaw-0.10.0.11364-10.fc22

Comment 10 Fedora Update System 2015-05-08 07:28:24 UTC

Package mpich-3.1.4-2.fc22, netcdf-fortran-4.4.1-3.fc22, hdf5-1.8.14-3.fc22, scorep-1.3-4.fc22, netcdf-4.3.3.1-1.fc22, nwchem-6.5.26243-15.fc22.1, mathgl-2.3-4.fc22, gmsh-2.9.3-2.fc22, boost-1.57.0-6.fc22, gromacs-4.6.5-6.fc22, pypar-2.1.5_108-7.fc22, espresso-3.3.0-3.fc22, ga-5.3b-16.fc22, netcdf-cxx4-4.2.1-5.fc22, scalapack-2.0.2-7.fc22, mpi4py-1.3.1-6.fc22, paraview-4.3.1-4.fc22.1, Ray-2.3.1-7.fc22, freefem++-3.31-1.4.fc22, cp2k-2.6.0-2.fc22, netgen-mesher-5.3.1-4.fc22, dl_poly-1.9.20140324-8.fc22, scotch-6.0.4-2.fc22, orsa-0.7.0-30.fc22, elk-3.0.18-10.fc22, gpaw-0.10.0.11364-10.fc22, elpa-2015.02.002-4.fc22:
* should fix your issue,
* was pushed to the Fedora 22 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=updates-testing mpich-3.1.4-2.fc22 netcdf-fortran-4.4.1-3.fc22 hdf5-1.8.14-3.fc22 scorep-1.3-4.fc22 netcdf-4.3.3.1-1.fc22 nwchem-6.5.26243-15.fc22.1 mathgl-2.3-4.fc22 gmsh-2.9.3-2.fc22 boost-1.57.0-6.fc22 gromacs-4.6.5-6.fc22 pypar-2.1.5_108-7.fc22 espresso-3.3.0-3.fc22 ga-5.3b-16.fc22 netcdf-cxx4-4.2.1-5.fc22 scalapack-2.0.2-7.fc22 mpi4py-1.3.1-6.fc22 paraview-4.3.1-4.fc22.1 Ray-2.3.1-7.fc22 freefem++-3.31-1.4.fc22 cp2k-2.6.0-2.fc22 netgen-mesher-5.3.1-4.fc22 dl_poly-1.9.20140324-8.fc22 scotch-6.0.4-2.fc22 orsa-0.7.0-30.fc22 elk-3.0.18-10.fc22 gpaw-0.10.0.11364-10.fc22 elpa-2015.02.002-4.fc22'
as soon as you are able to.
Please go to the following url:
https://admin.fedoraproject.org/updates/FEDORA-2015-4630/mpich-3.1.4-2.fc22,elpa-2015.02.002-4.fc22,scalapack-2.0.2-7.fc22,hdf5-1.8.14-3.fc22,mpi4py-1.3.1-6.fc22,scorep-1.3-4.fc22,paraview-4.3.1-4.fc22.1,netcdf-4.3.3.1-1.fc22,netcdf-fortran-4.4.1-3.fc22,netcdf-cxx4-4.2.1-5.fc22,Ray-2.3.1-7.fc22,nwchem-6.5.26243-15.fc22.1,freefem++-3.31-1.4.fc22,mathgl-2.3-4.fc22,cp2k-2.6.0-2.fc22,gmsh-2.9.3-2.fc22,netgen-mesher-5.3.1-4.fc22,boost-1.57.0-6.fc22,dl_poly-1.9.20140324-8.fc22,gromacs-4.6.5-6.fc22,scotch-6.0.4-2.fc22,pypar-2.1.5_108-7.fc22,orsa-0.7.0-30.fc22,espresso-3.3.0-3.fc22,elk-3.0.18-10.fc22,ga-5.3b-16.fc22,gpaw-0.10.0.11364-10.fc22
then log in and leave karma (feedback).

Comment 11 Fedora Update System 2015-05-11 00:05:56 UTC

mpich-3.1.4-2.fc22, netcdf-fortran-4.4.1-3.fc22, hdf5-1.8.14-3.fc22, scorep-1.3-4.fc22, netcdf-4.3.3.1-1.fc22, nwchem-6.5.26243-15.fc22.1, mathgl-2.3-4.fc22, gmsh-2.9.3-2.fc22, boost-1.57.0-6.fc22, gromacs-4.6.5-6.fc22, pypar-2.1.5_108-7.fc22, espresso-3.3.0-3.fc22, ga-5.3b-16.fc22, netcdf-cxx4-4.2.1-5.fc22, scalapack-2.0.2-7.fc22, mpi4py-1.3.1-6.fc22, paraview-4.3.1-4.fc22.1, Ray-2.3.1-7.fc22, freefem++-3.31-1.4.fc22, cp2k-2.6.0-2.fc22, netgen-mesher-5.3.1-4.fc22, dl_poly-1.9.20140324-8.fc22, scotch-6.0.4-2.fc22, orsa-0.7.0-30.fc22, elk-3.0.18-10.fc22, gpaw-0.10.0.11364-10.fc22, elpa-2015.02.002-4.fc22 has been pushed to the Fedora 22 stable repository.  If problems still persist, please make note of it in this bug report.