Bug#848574: mpgrafic-0.3.7.8-1 and 0.3.10-1 mips64el builds seg-faulted too
This may affect mpgrafic, which depends on mpi-default-dev and mpi-default-bin, i.e. effectively on openmpi. mipsel-manda-01 (mips64el) had a segmentation violation fault for the code regression test on mpgrafic-0.3.10-1 and 0.3.7.8-1: https://buildd.debian.org/status/logs.php?pkg=mpgrafic=mips64el but two other mipsel/mips64el machines built successfully with mpgrafic-0.3.8-1 and mpgrafic-0.3.9-1. https://buildd.debian.org/status/fetch.php?pkg=mpgrafic=mips64el=0.3.10-1=1485682537=0 This looks like a debian openmpi system. Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0xffe95a70a3 in ??? -- mpirun noticed that process rank 0 with PID 0 on node mipsel-manda-01 exited on signal 11 (Segmentation fault).
Bug#852076: mpgrafic: mips build of mpgrafic gives zero record size
Package: mpgrafic
Version: 0.3.7.8-1
Severity: serious
Tags: upstream
Justification: fails to build from source
Dear Maintainer,
Description:
After installing mpgrafics-0.3.7.8-1 on mips by the debian buildd system,
`make check' runs `regression-test-0.3.7.8.sh', which runs
`mpirun -n 1 --mca plm_rsh_agent sh ${srcdir}/src/mpgrafic --np=32 <
${srcdir}/Input.stdin
and gives the output:
Record size0 is different from expected4096
and then fatally exits (as it should in such a case).
Log:
https://buildd.debian.org/status/fetch.php?pkg=mpgrafic=mips=0.3.7.8-1=1484927169=0
(line 1010 of the raw html file)
Analysis:
The error is presumably triggered at line 308 (v0.3.7.8-1) of
src/grafic_io.f90 - taille_tampon is read by f77_parallel_read() in
src/parallel_io.c . The function f77_parallel_read() is a front end to
parallel_read(), in the same .c file, which calls pread() to read
bytes from a disk file into a buffer.
The disk file is (previously to this) written by a similar hierarchy
of f90 and C functions to `white-outfile.dat' (assuming that
`Input.stdin' is the source package input file above).
Hypothesis:
This looks like an endianness/word size problem - bytes are written to
disk and read from disk as a raw sequence of bytes without any
casting, neither in writing nor in reading.
Proposed solution method:
On a real or emulated mips machine, a quick hack would be to play
around with casting and byte-swapping to find a way that the test
script is successful.
An acceptable solution would be to make changes that are not
machine dependent. The AC_C_BIGENDIAN should probably be added to configure.ac
and then the preprocessor macro WORDS_BIGENDIAN could be used.
See the autoconf documentation for details.
Appropriate use of casting and USE_ISO_C in src/grafic_io.f90 would
probably give a more elegant and robust solution in terms of
portability.
-- System Information:
Debian Release: sid
Architecture: mips
Bug#851071: running dh_auto_test as fakeroot would cause openmpi test runs to fail
There's a discussion thread starting here: https://lists.debian.org/debian-mentors/2017/01/msg00322.html about mpirun (a front end provided by openmpi to run a user program) refusing, by default, to run as root for mpgrafic, a program that uses mpi. This would affect any other debian package using openmpi if that package has a test run under dh_auto_test, unless that package explicitly adds an option --allow-run-as-root. Either having lots of failed builds, or having lots of packages run with a default option --allow-run-as-root, both sound like bad choices to me. Cheers Boud
Bug#851923: mpgrafic: MPI_Comm_dup error on s390x, ppc64, sparc64 builds of mpgrafic
Package: mpgrafic Version: 0.3.7.6-2 Severity: serious Justification: fails to build from source In this debian automated build of mpgrafic-0.3.7.6-2 (debian downstream version) on an s390x architecture, `make check' calls `regression-test-0.3.7.sh', which gives this fatal error: * lines 878-884 of the html source of https://buildd.debian.org/status/fetch.php?pkg=mpgrafic=s390x=0.3.7.6-2=1484854191=0 878 This looks like a debian openmpi system. 879 [zandonai:4650] *** An error occurred in MPI_Comm_dup 880 [zandonai:4650] *** reported by process [4180410369,0] 881 [zandonai:4650] *** on communicator MPI_COMM_WORLD 882 [zandonai:4650] *** MPI_ERR_COMM: invalid communicator 883 [zandonai:4650] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, 884 [zandonai:4650] ***and potentially your MPI job) Version 0.3.7.6-2 is presently set up so that the build is not blocked by make check errors - I need the logs on different architectures in order to understand portability problems. I will soon prepare an updated version in which this will lead to a build failure. So strictly speaking, the "Justification:" tag above is not correct for 0.3.7.6-2, but I expect that it will be a build failure on s390x, ppc64 and sparc64 for the next version of mpgrafic, probably 0.3.7.7-1 , unless this bug is sorted out before that. Since mpgrafic does not call MPI_Comm_dup directly, I suspect that the error comes from openmpi or fftw2 - after discussing this on #debian-mentors with James Clarke, I've put a block against openmpi source bug #851918 = https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=851918 . Hope this is right in terms of bug dependencies - if not feel free to make corrections. Cheers Boud -- System Information: Debian Release: sid Architecture: s390x
Bug#447156: browser says Unable to bring up wimslogd Permission denied
On Mon, 22 Oct 2007, Georges Khaznadar wrote: Boud Roukema a écrit : ANALYSIS: From the command line: as user wims: cd /var/lib/wims/public_html/ ./wims outputs a correct html page. as user www-data, same command: cd /var/lib/wims/public_html/ ./wims outputs: Status: 500 WIMS Internal Error The command ./wims, in this context, should be executed with the identity of the user wims, since the post-installation package is supposed to set the permission bit as stated below: salut Georges and the bug-tracker, i found some more chmod commands sufficient to make wims work sufficiently correctly for me to copy/paste old classes, do some appropriate mkdir/chown/chmod/cp operations on them and satisfy students' needs. :) However, i suspect that the setup of user/group/suid and so on that i have is not the one intended. Regarding the wims web-based management functions, i'll reply independently to bug 447896 in order to not mess up the bug tracking structure. Here are the commands i found sufficient (in addition to my previous comments): chmod g+rx public_html/scripts/adm/ chmod g+rx bin chmod g+rx public_html/bin public_html/msg/ chmod g+rx public_html/bases/d[io]c public_html/bases/sheet/ public_html/bases/site/ public_html/bases/sys/ chmod g-x log/classes/.[hiw]* chmod g+w tmp/forall/ tmp/sessions/ # This was needed since otherwise the exercises have key information in italian! chmod g+rx public_html/modules/adm/sheet.??/ chmod g+rx public_html/modules/adm/* The group in each case is wims, which includes both wims and www-data. i hope this helps. i guess for testing (sorry, i'm unlikely to have much time on any short time scale, but at least i'd like my feedback here to be available), the best solution would be to create a chroot jail and install etch from scratch there, then test the installation from aptitude. i'm not a debian developer, so i'm only guessing here what would be best. As to whether or not the bug is closed, it's hard to say. For me personally, the above and my previous list of chmod/chown commands are a hack, which is not enough to close the bug. Maybe the bug severity could just be downgraded. In a moment i'll reply to the other bug report. bon courage boud
Bug#447156: browser says Unable to bring up wimslogd Permission denied
On Thu, 18 Oct 2007, Georges Khaznadar wrote: Hello Boud, the package wims_3.62-8 will be available shortly, which fixes this bug and many others. hi Georges, i think that this bug is not yet closed... And i have another one which seems to be independent so i'll file it independently. amities boud -- PROBLEM: i updated to wims-3.62-8 from debian.ofset.org i once again get: WIMS panick! Unable to bring up wimslogd. Permission denied ANALYSIS: From the command line: as user wims: cd /var/lib/wims/public_html/ ./wims outputs a correct html page. as user www-data, same command: cd /var/lib/wims/public_html/ ./wims outputs: Status: 500 WIMS Internal Error Cache-Control: no-cache Pragma: no-cache Content-type: text/plain WIMS panick! Unable to bring up wimslogd. Permission denied wims: Unable to bring up wimslogd. Permission denied i tried the following in the order below: /var/lib/wims# chmod g+rx bin chmod -R g+rw log/ chmod -R g+x log/account/ log/[cf]* log/modules/ log/referer # directories chmod g+rwx tmp/log/ # key step to solution After this last line, user www-data *was* able to correctly do cd /var/lib/wims/public_html/ ./wims The web interface then gives: WIMS panick! cannot_create_session_directory Permission denied chmod g+w tmp/sessions/ pwd /var/lib/wims chmod g+rwx sessions/ # key step to solution This second problem is now resolved after this chmod. SUGGESTED SOLUTION: i don't have the time to check which chmods are necessary or optional among the above list - i would suggest just doing chmod g+rwx tmp/log/ # key step to solution chmod g+rwx sessions/ # key step to solution and then if there's a problem trying some of the others. -- -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#447156: browser says Unable to bring up wimslogd Permission denied
Package: wims Version: 3.60-6 Severity: grave Justification: renders package unusable -- System Information: Debian Release: 4.0 APT prefers stable APT policy: (500, 'stable') Architecture: i386 (i686) Shell: /bin/sh linked to /bin/bash Kernel: Linux 2.6.18-5-686 Locale: LANG=pl_PL.ISO-8859-2, LC_CTYPE=pl_PL.ISO-8859-2 (charmap=ANSI_X3.4-1968) (ignored: LC_ALL set to C) Versions of packages wims depends on: ii adduser 3.102Add and remove users and groups ii apache 1.3.34-4.1 versatile, high-performance HTTP s ii chemeq 1.9 Parser for chemical formula and eq ii debconf [debconf-2. 1.5.11 Debian configuration management sy ii fortunes1:1.99.1-3 Data files containing fortune cook ii gnuplot 4.0.0-5 A command-line driven interactive ii imagemagick 7:6.2.4.5.dfsg1-0.14 Image manipulation programs ii libc6 2.3.6.ds1-13etch2GNU C Library: Shared libraries ii libgd2-xpm 2.0.33-5.2 GD Graphics Library version 2 ii maxima 5.10.0-6 A computer algebra system -- base ii octave 1:2.1.73-13 GNU Octave language for numerical ii octave2.0 [octave] 2.0.17-9 The GNU Octave language for numeri ii octave2.1 [octave] 1:2.1.73-13 GNU Octave language for numerical ii octave2.9 [octave] 2.9.9-8etch1 GNU Octave language for numerical ii pari-gp 2.3.1-2 PARI/GP Computer Algebra System bi ii tetex-bin 3.0-30 The teTeX programs ii tetex-extra 3.0.dfsg.3-5etch1Additional TeX input files of teTe ii units-filter2.6-1Parser for expressions concerning ii wims-modules3.60-6 modules used by the WIMS server Versions of packages wims recommends: ii gap 4r4p9-1Groups, Algorithms and Programming pn wims-extranone (no description available) ii yacas 1.0.57-2 Computer Algebra System -- debconf information: * wims/reconfigure-webserver: apache * wims/restart-webserver: true PROBLEM: Installing: installing wims-3.60-6 from debian etch, on a system with a pre-existing wims-3.58 installed by hand gave an error message regarding the pre-existence of the wims user and something about a wims group being needed (i didn't record the exact message). i did: addgroup wims adduser wims wims IIRC, i then didaptitude install wims again. The installation finished without errors (after about 10-15 minutes...) The problem: my browser at the page http://mydomain.com/wims gave the error message: WIMS panick! Unable to bring up wimslogd. Permission denied Eventually (after many, many hours, including reading src/log.c and learning about sockets) i found that by doing some chown + chmod's this problem was solved. My guess is that www-data (the apache user) did not have the authorisation to create files and/or directories in wims' area. SUGGESTION: The debian package for wims should either * give the sysadmin some interactive hints about the possible need to fix things with chmod chown (it is not enough just to say that the group wims must be created), or * a comment about this could be added to README.Debian, or * it should redo some chmod/chown-ing in the post-installation phase in case the installation got stopped half-way and then continued as happened in my case. DETAILS: DIAGNOSTICS: uname -a Linux mydomain 2.6.18-5-686 #1 SMP Wed Oct 3 00:12:50 UTC 2007 i686 GNU/Linux dpkg -l |grep wims ii wims 3.60-6 WWW Interactive Mathematics Server (WIMS) ii wims-modules 3.60-6 modules used by the WIMS server As shown above, this is still using apache-1.3. grep wims /var/log/dpkg.log# local times :P 2007-10-18 03:56:04 install wims-modules none 3.60-6 2007-10-18 03:56:04 status half-installed wims-modules 3.60-6 2007-10-18 03:56:14 status unpacked wims-modules 3.60-6 2007-10-18 03:56:14 status unpacked wims-modules 3.60-6 2007-10-18 03:56:15 install wims none 3.60-6 2007-10-18 03:56:15 status half-installed wims 3.60-6 2007-10-18 03:56:19 status unpacked wims 3.60-6 2007-10-18 03:56:19 status unpacked wims 3.60-6 2007-10-18 03:56:21 status unpacked wims-modules 3.60-6 2007-10-18 03:56:21 status half-configured wims-modules 3.60-6 2007-10-18 03:56:26 status half-configured wims-modules 3.60-6 2007-10-18 03:58:43 status half-configured wims-modules 3.60-6 2007-10-18 04:01:59 status installed wims-modules 3.60-6 2007-10-18 04:01:59 status unpacked wims 3.60-6 2007-10-18 04:01:59 status unpacked wims 3.60-6 2007-10-18 04:01:59 status half-configured wims 3.60-6 2007-10-18 04:17:25 status installed wims 3.60-6 grep www-data\|wims
