Your message dated Thu, 30 Nov 2017 18:35:59 +0000
with message-id <[email protected]>
and subject line Bug#883042: fixed in scalapack 2.0.2-4
has caused the Debian Bug report #883042,
regarding scalapack: Filter -Wl,-Bsymbolic-functions out of LDFLAGS for more
robust builds
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
883042: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=883042
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: scalapack
Version: 2.0.2-3
Severity: minor
Tags: patch
User: [email protected]
Usertags: origin-ubuntu bionic ubuntu-patch
Dear Muammar,
In Ubuntu, scalapack 2.0.2-3 was failing its tests during build:
[...]
Running tests for libscalapack-openmpi
************************************************
****** TESTING openmpi BUILD
************************************************
cd build-openmpi && make -j4 test ARGS\+=-j4
make[2]: Entering directory '/<<PKGBUILDDIR>>/build-openmpi'
Running tests...
/usr/bin/ctest --force-new-ctest-process -j4
Test project /<<PKGBUILDDIR>>/build-openmpi
Start 1: xCbtest
Start 2: xFbtest
Start 3: spb1tst
Start 4: dpb1tst
1/96 Test #4: dpb1tst ..........................***Failed 1.13 sec
--------------------------------------------------------------------------
[[3011,1],1]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: lgw01-amd64-045
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
Level 1 PBLAS testing program.
'Intel iPSC/860 hypercube, gamma model.'
Tests of the real double precision Level 1 PBLAS
The following parameter values will be used:
Number of Tests : 4
Number of process grids : 4
P : 2 1 2 1
Q : 2 2 1 4
Stop on failure flag : F
Test for error exits flag : T
Leading dimension gap : 10
Verbosity level : 0
Alpha : 2.00000
Routines to be tested : PDSWAP ... Yes
PDSCAL ... Yes
PDCOPY ... Yes
PDAXPY ... Yes
PDDOT ... Yes
PDNRM2 ... Yes
PDASUM ... Yes
PDAMAX ... Yes
Relative machine precision (eps) is taken to be 0.111022E-15
Tests started.
PBLAS ERROR 'Illegal length of sub( X ) = -1, it must be at least 0'
from {0,1}, pnum=1, Contxt=0, in routine 'PDSWAP'.
PBLAS ERROR 'Illegal length of sub( Y ) = -1, it must be at least 0'
from {0,1}, pnum=1, Contxt=0, in routine 'PDSWAP'.
PBLAS ERROR 'Parameter number 1 had an illegal value'
from {0,1}, pnum=1, Contxt=0, in routine 'PDSWAP'.
{0,1}, pnum=1, Contxt=0, killed other procs, exiting with error #-1.
PBLAS ERROR 'Illegal length of sub( X ) = -1, it must be at least 0'
from {0,2}, pnum=2, Contxt=0, in routine 'PDSWAP'.
PBLAS ERROR 'Illegal length of sub( Y ) = -1, it must be at least 0'
from {0,2}, pnum=2, Contxt=0, in routine 'PDSWAP'.
PBLAS ERROR 'Parameter number 1 had an illegal value'
from {0,2}, pnum=2, Contxt=0, in routine 'PDSWAP'.
{0,2}, pnum=2, Contxt=0, killed other procs, exiting with error #-1.
PBLAS ERROR 'Illegal length of sub( X ) = -1, it must be at least 0'
from {0,0}, pnum=0, Contxt=0, in routine 'PDSWAP'.
PBLAS ERROR 'Illegal length of sub( Y ) = -1, it must be at least 0'
from {0,0}, pnum=0, Contxt=0, in routine 'PDSWAP'.
PBLAS ERROR 'Parameter number 1 had an illegal value'
from {0,0}, pnum=0, Contxt=0, in routine 'PDSWAP'.
{0,0}, pnum=0, Contxt=0, killed other procs, exiting with error #-1.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[lgw01-amd64-045:02004] 3 more processes have sent help message
help-mpi-btl-base.txt / btl:no-nics
[lgw01-amd64-045:02004] Set MCA parameter "orte_base_help_aggregate" to 0 to
see all help / error messages
[lgw01-amd64-045:02004] 2 more processes have sent help message
help-mpi-api.txt / mpi-abort
[...]
https://launchpad.net/ubuntu/+source/scalapack/2.0.2-3/+build/13662891
This build failure does not happen in Debian, and I tracked it down to a
difference in the default dpkg-buildflags used in Debian vs Ubuntu. Ubuntu
includes -Wl,-Bsymbolic-functions in its LDFLAGS, and Debian does not.
The attached patch filters -Wl,-Bsymbolic-functions out of LDFLAGS, allowing
the package to build in Ubuntu. Although this is a no-op on Debian, it does
make the package more robust against differences in user-configured build
flags, so I think it makes sense to apply it in Debian.
Perhaps you would also prefer to work with upstream to understand why this
flag causes the tests to fail. Previous versions of scalapack did not fail
when built with this flag, and it is a sensible default in Ubuntu for some
time.
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer http://www.debian.org/
[email protected] [email protected]
diff -Nru scalapack-2.0.2/debian/rules scalapack-2.0.2/debian/rules
--- scalapack-2.0.2/debian/rules 2017-09-10 09:26:09.000000000 -0700
+++ scalapack-2.0.2/debian/rules 2017-11-28 17:37:43.000000000 -0800
@@ -5,6 +5,7 @@
export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
export DEB_CXXFLAGS_MAINT_APPEND = -Wall -pedantic
export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+export DEB_LDFLAGS_MAINT_STRIP = -Wl,-Bsymbolic-functions
export DEB_HOST_MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
export DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
export DEB_BUILD_ARCH_OS := $(shell dpkg-architecture -qDEB_BUILD_ARCH_OS)
--- End Message ---
--- Begin Message ---
Source: scalapack
Source-Version: 2.0.2-4
We believe that the bug you reported is fixed in the latest version of
scalapack, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (supplier of updated scalapack package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 01 Dec 2017 01:49:53 +0800
Source: scalapack
Binary: libscalapack-openmpi2.0 libscalapack-mpich2.0 libscalapack-mpi-dev
libscalapack-mpich-dev libscalapack-openmpi-dev scalapack-mpi-test
scalapack-test-common
Architecture: source
Version: 2.0.2-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Drew Parsons <[email protected]>
Description:
libscalapack-mpi-dev - Scalable Linear Algebra Package - Dev. files for MPICH
libscalapack-mpich-dev - Scalable Linear Algebra Package - Dev. files for MPICH
libscalapack-mpich2.0 - Scalable Linear Algebra Package - Shared libs. for
MPICH
libscalapack-openmpi-dev - Scalable Linear Algebra Package - Dev. files for
OPENMPI
libscalapack-openmpi2.0 - Scalable Linear Algebra Package - Shared libs. for
OpenMPI
scalapack-mpi-test - Scalable Linear Algebra Package - Test files for MPI
scalapack-test-common - Test data for ScaLAPACK testers
Closes: 883042
Changes:
scalapack (2.0.2-4) unstable; urgency=medium
.
* Team upload.
* Standards-Version: 4.1.1
* List OpenBLAS and ATLAS as alternative Build-Deps to provide BLAS
and LAPACK.
* Ubuntu uses linker flag -Bsymbolic-functions at build time, but it
causes tests to fail. So strip it from LDFLAGS.
Thanks Steve Langasek. Closes: #883042.
* Priority: optional not extra.
* debian/rules: conditionally define Debian build variables using ?=
Checksums-Sha1:
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ad6729ae441f6f931279954310272d8675de4202 15520 scalapack_2.0.2-4.debian.tar.xz
Checksums-Sha256:
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scalapack_2.0.2-4.dsc
93497d205935b7ce7d20fb56ad03d21f807ef5f9581831f10215de2f61d96908 15520
scalapack_2.0.2-4.debian.tar.xz
Files:
aad99eb4e11914e5fc4b3c77ce528592 2731 devel optional scalapack_2.0.2-4.dsc
0288b99217cd8577b49399f9fd0d9193 15520 devel optional
scalapack_2.0.2-4.debian.tar.xz
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