Your message dated Tue, 16 Oct 2007 09:17:06 +0000
with message-id <[EMAIL PROTECTED]>
and subject line Bug#442886: fixed in gromacs 3.3.2-1
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--- Begin Message ---
Package: gromacs
Version: 3.3.1-5
Severity: normal
Dear Nicholas,
I have trouble compiling GROMACS with DEB_BUILD_OPTIONS="double" on amd64. The
buildlog reads:
/bin/sh ../../libtool --tag=CC --mode=link x86_64-linux-gnu-gcc -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops
-o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o
splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o
grompp.o ../mdlib/libmd_d.la ../gmxlib/libgmx_d.la -lnsl -lfftw3 -lm -lXm
-lXt -lSM -lICE -lXext -lXp -lX11
x86_64-linux-gnu-gcc -O3 -fomit-frame-pointer -finline-functions -Wall
-Wno-unused -funroll-all-loops -o .libs/grompp topio.o toppush.o topcat.o
topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o
add_par.o topexcl.o toputil.o topdirs.o grompp.o ../mdlib/.libs/libmd_d.so
../gmxlib/.libs/libgmx_d.so -lnsl /usr/lib/libfftw3.so -lm -lXm -lXt -lSM -lICE
-lXext -lXp -lX11
../gmxlib/.libs/libgmx_d.so: undefined reference to `_nb_kerne010_x86_64_sse2'
collect2: ld returned 1 exit status
make[4]: *** [grompp] Error 1
This happens if I build in a clean sid chroot using pbuilder and with a simple
dpkg-buildpackage on testing. Running "./configure --enable-double && make &&
make install" works fine. I wasn't able to track it down so far. If you need
more information, please let me know!
Best regards
Manuel
-- System Information:
Debian Release: lenny/sid
APT prefers testing
APT policy: (500, 'testing'), (500, 'stable'), (200, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.21-2-amd64 (SMP w/2 CPU cores)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Versions of packages gromacs depends on:
ii fftw3 3.1.2-2 library for computing Fast Fourier
ii lesstif2 1:0.95.0-2 OSF/Motif 2.1 implementation relea
ii libc6 2.6.1-1 GNU C Library: Shared libraries
ii libice6 2:1.0.4-1 X11 Inter-Client Exchange library
ii libsm6 2:1.0.3-1+b1 X11 Session Management library
ii libx11-6 2:1.0.3-7 X11 client-side library
ii libxext6 1:1.0.3-2 X11 miscellaneous extension librar
ii libxp6 1:1.0.0.xsf1-1 X Printing Extension (Xprint) clie
ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library
Versions of packages gromacs recommends:
ii gromacs-doc 3.3.1-5 GROMACS molecular dynamics sim, do
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: gromacs
Source-Version: 3.3.2-1
We believe that the bug you reported is fixed in the latest version of
gromacs, which is due to be installed in the Debian FTP archive:
gromacs-dev_3.3.2-1_i386.deb
to pool/main/g/gromacs/gromacs-dev_3.3.2-1_i386.deb
gromacs-doc_3.3.2-1_all.deb
to pool/main/g/gromacs/gromacs-doc_3.3.2-1_all.deb
gromacs-lam_3.3.2-1_i386.deb
to pool/main/g/gromacs/gromacs-lam_3.3.2-1_i386.deb
gromacs-mpich_3.3.2-1_i386.deb
to pool/main/g/gromacs/gromacs-mpich_3.3.2-1_i386.deb
gromacs_3.3.2-1.diff.gz
to pool/main/g/gromacs/gromacs_3.3.2-1.diff.gz
gromacs_3.3.2-1.dsc
to pool/main/g/gromacs/gromacs_3.3.2-1.dsc
gromacs_3.3.2-1_i386.deb
to pool/main/g/gromacs/gromacs_3.3.2-1_i386.deb
gromacs_3.3.2.orig.tar.gz
to pool/main/g/gromacs/gromacs_3.3.2.orig.tar.gz
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.
Nicholas Breen <[EMAIL PROTECTED]> (supplier of updated gromacs 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: SHA1
Format: 1.7
Date: Mon, 15 Oct 2007 14:39:30 -0700
Source: gromacs
Binary: gromacs gromacs-lam gromacs-dev gromacs-mpich gromacs-doc
Architecture: source i386 all
Version: 3.3.2-1
Distribution: unstable
Urgency: low
Maintainer: Nicholas Breen <[EMAIL PROTECTED]>
Changed-By: Nicholas Breen <[EMAIL PROTECTED]>
Description:
gromacs - Molecular dynamics simulator, with building and analysis tools
gromacs-dev - GROMACS molecular dynamics sim, development kit
gromacs-doc - GROMACS molecular dynamics sim, documentation
gromacs-lam - Molecular dynamics sim, binaries for LAM-MPI parallelization
gromacs-mpich - Molecular dynamics sim, binaries for MPICH parallelization
Closes: 442139 442886 446760
Changes:
gromacs (3.3.2-1) unstable; urgency=low
.
* New upstream release. (Closes: #446760)
- Incorporates fix for amd64 double-precision builds.
(Closes: #442886)
- Remove obsolete patches 50_gmx_order, 51_libxdrf_trajectory,
52_genion_compiler_workaround, 60_amd64_double.
* Add a Recommends: cpp to gromacs binary package, and improve the error
message given by grompp when no preprocessor is installed to clarify
the "-pp" option. (Closes: #442139)
* Update Build-Depends to reflect fftw3-dev -> libfftw3-dev renaming.
* Conflict with radiance (<= 3R8+20070924.dfsg-1) due to overlapping
/usr/bin/genbox. Related to #446726, which will be closed by a
future upload of radiance.
* src/gmxlib/xtcio.c: import upstream fix for range checking failures
when running both parallel and double-precision simulations. (cf.
http://www.gromacs.org/pipermail/gmx-users/2007-October/029990.html)
Files:
c153c012838f08e766085119fc658d26 803 science extra gromacs_3.3.2-1.dsc
f25853fefdbfbe7f4e8667a16c495736 8019795 science extra
gromacs_3.3.2.orig.tar.gz
1ed5f549966db2218b18dcee1372caef 1730428 science extra gromacs_3.3.2-1.diff.gz
d157f9473553ccad0a059e2940a8151a 2121772 doc extra gromacs-doc_3.3.2-1_all.deb
3f1d41e647728dab49a8e624d7c6fd54 3538510 science extra gromacs_3.3.2-1_i386.deb
8234e589fbac878111802c1db94bb04f 5537338 devel extra
gromacs-dev_3.3.2-1_i386.deb
068a103d13f488e8da0b85208040f079 1637194 science extra
gromacs-mpich_3.3.2-1_i386.deb
dd1cb1b2928f8445395fb7913d07ad7e 1383522 science extra
gromacs-lam_3.3.2-1_i386.deb
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