Dac Chartrand wrote:
Yum is broken.
I have the priorities plug-in setup. I did `yum update` before messing around with 3rd party repositories. The only modules I installed from the 3rd party sties are PHP related.
Isn't there php in the CentOS plus repo? What repo is that you messed about with? ATRPMS or Livna?
Regards, Vandaman.
Vandaman wrote:
Dac Chartrand wrote:
Yum is broken.
Please check your version of python and mysql as I can not imagine that mysql itself is effecting yum, at least not the way CentOS builds it.
I have the priorities plug-in setup. I did `yum update` before messing around with 3rd party repositories. The only modules I installed from the 3rd party sties are PHP related.
Again, do:
rpm -q mysql mysql-server python
Johnny Hughes wrote:
Vandaman wrote:
Dac Chartrand wrote:
Yum is broken.
Please check your version of python and mysql as I can not imagine that mysql itself is effecting yum, at least not the way CentOS builds it.
It probably is. As already mailed: I suspect a VPS with a strong limitation on the threads which can be started. yum with fastestmirror uses up quite a bit of threads, mysql can do so too.
Turn of fastestmirror and try again.
Ralph
Hi all. Thanks for reading and replying.
Isn't there php in the CentOS plus repo? What repo is that you messed about with? ATRPMS or Livna?
These don't have the latest versions of PHP5, the repo I am using is "Jason's Utter Ramblings Repo" @ www.jasonlitka.com and the only files I pulled from it are:
php.i386 5.2.6-jason.1 php-bcmath.i386 5.2.6-jason.1 php-cli.i386 5.2.6-jason.1 php-common.i386 5.2.6-jason.1 php-gd.i386 5.2.6-jason.1 php-mbstring.i386 5.2.6-jason.1 php-mysql.i386 5.2.6-jason.1 php-pdo.i386 5.2.6-jason.1 php-pgsql.i386 5.2.6-jason.1
Again, do:
rpm -q mysql mysql-server python
Results are as expected:
$ rpm -q mysql mysql-server python mysql-5.0.45-7.el5 mysql-server-5.0.45-7.el5 python-2.4.3-21.el5
$ yum list installed mysql.i386 5.0.45-7.el5 mysql-server.i386 5.0.45-7.el5 python.i386 2.4.3-21.el5
I'll re-iterate for good measure: `yum list php` doesn't work if mysqld is turned on. If I do `/etc/init.d/mysqld stop` (or `services mysqld stop`), `yum list php` works fine. So it's only failing when mysqld is turned on. (?!) And only on some commands. For example `yum list installed` works all the time.
Here's the full error:
]$ yum list php Loading "fastestmirror" plugin Loading "priorities" plugin Loading mirror speeds from cached hostfile * utterramblings: www.jasonlitka.com Traceback (most recent call last): File "/usr/bin/yum", line 29, in ? yummain.main(sys.argv[1:]) File "/usr/share/yum-cli/yummain.py", line 105, in main result, resultmsgs = base.doCommands() File "/usr/share/yum-cli/cli.py", line 289, in doCommands self._getTs() File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 85, in _getTs self._getTsInfo() File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 91, in _getTsInfo self._tsInfo.setDatabases(self.rpmdb, self.pkgSack) File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 537, in <lambda> pkgSack = property(fget=lambda self: self._getSacks(), File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 392, in _getSacks self.repos.populateSack(which=repos) File "/usr/lib/python2.4/site-packages/yum/repos.py", line 214, in populateSack self.doSetup() File "/usr/lib/python2.4/site-packages/yum/repos.py", line 66, in doSetup self.ayum.plugins.run('postreposetup') File "/usr/lib/python2.4/site-packages/yum/plugins.py", line 169, in run func(conduitcls(self, self.base, conf, **kwargs)) File "/usr/lib/yum-plugins/fastestmirror.py", line 90, in postreposetup_hook repomirrors[str(repo)] = FastestMirror(repo.urls).get_mirrorlist() File "/usr/lib/yum-plugins/fastestmirror.py", line 142, in get_mirrorlist self._poll_mirrors() File "/usr/lib/yum-plugins/fastestmirror.py", line 155, in _poll_mirrors pollThread.start() File "/usr/lib/python2.4/threading.py", line 416, in start _start_new_thread(self.__bootstrap, ()) thread.error: can't start new thread
Other than installing packages using yum, and modified /etc/services and removed /etc/rpc for security reasons, nothing much has been done with this system. I'm at a loss to understand why it doesn't work when mysqld is turned on.
Any other ideas?
On 4-Oct-08, at 7:06 PM, Stephen Harris wrote:
On Sat, Oct 04, 2008 at 07:02:18PM -0400, Dac Chartrand wrote:
- utterramblings: www.jasonlitka.com
Do you have this added to your yum repo list? What happens if you remove it?
Yes, it's in /etc/yum.repos.d/utterramblings.repo
Looks like:
[utterramblings] name=Jason's Utter Ramblings Repo baseurl=http://www.jasonlitka.com/media/EL$releasever/$basearch/ enabled=1 gpgcheck=1 gpgkey=http://www.jasonlitka.com/media/RPM-GPG-KEY-jlitka priority=99
Here's the same result trying to remove it
yum list php --disablerepo=utterramblings Loading "fastestmirror" plugin Loading "priorities" plugin Loading mirror speeds from cached hostfile Traceback (most recent call last): File "/usr/bin/yum", line 29, in ? yummain.main(sys.argv[1:]) File "/usr/share/yum-cli/yummain.py", line 85, in main base.getOptionsConfig(args) File "/usr/share/yum-cli/cli.py", line 178, in getOptionsConfig (opts, self.cmds) = self.optparser.setupYumConfig() File "/usr/share/yum-cli/cli.py", line 1238, in setupYumConfig self.base._getRepos(doSetup=True) File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 356, in _getRepos self._repos.doSetup(thisrepo) File "/usr/lib/python2.4/site-packages/yum/repos.py", line 66, in doSetup self.ayum.plugins.run('postreposetup') File "/usr/lib/python2.4/site-packages/yum/plugins.py", line 169, in run func(conduitcls(self, self.base, conf, **kwargs)) File "/usr/lib/yum-plugins/fastestmirror.py", line 90, in postreposetup_hook repomirrors[str(repo)] = FastestMirror(repo.urls).get_mirrorlist() File "/usr/lib/yum-plugins/fastestmirror.py", line 142, in get_mirrorlist self._poll_mirrors() File "/usr/lib/yum-plugins/fastestmirror.py", line 155, in _poll_mirrors pollThread.start() File "/usr/lib/python2.4/threading.py", line 416, in start _start_new_thread(self.__bootstrap, ()) thread.error: can't start new thread
Here's the command, after i delete /etc/yum.repos.d/utterramblings.repo
$ yum list php Loading "fastestmirror" plugin Loading "priorities" plugin Loading mirror speeds from cached hostfile Traceback (most recent call last): File "/usr/bin/yum", line 29, in ? yummain.main(sys.argv[1:]) File "/usr/share/yum-cli/yummain.py", line 105, in main result, resultmsgs = base.doCommands() File "/usr/share/yum-cli/cli.py", line 289, in doCommands self._getTs() File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 85, in _getTs self._getTsInfo() File "/usr/lib/python2.4/site-packages/yum/depsolve.py", line 91, in _getTsInfo self._tsInfo.setDatabases(self.rpmdb, self.pkgSack) File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 537, in <lambda> pkgSack = property(fget=lambda self: self._getSacks(), File "/usr/lib/python2.4/site-packages/yum/__init__.py", line 392, in _getSacks self.repos.populateSack(which=repos) File "/usr/lib/python2.4/site-packages/yum/repos.py", line 214, in populateSack self.doSetup() File "/usr/lib/python2.4/site-packages/yum/repos.py", line 66, in doSetup self.ayum.plugins.run('postreposetup') File "/usr/lib/python2.4/site-packages/yum/plugins.py", line 169, in run func(conduitcls(self, self.base, conf, **kwargs)) File "/usr/lib/yum-plugins/fastestmirror.py", line 90, in postreposetup_hook repomirrors[str(repo)] = FastestMirror(repo.urls).get_mirrorlist() File "/usr/lib/yum-plugins/fastestmirror.py", line 142, in get_mirrorlist self._poll_mirrors() File "/usr/lib/yum-plugins/fastestmirror.py", line 155, in _poll_mirrors pollThread.start() File "/usr/lib/python2.4/threading.py", line 416, in start _start_new_thread(self.__bootstrap, ()) thread.error: can't start new thread
Again, only when mysqld is running.
PS:
z00dax in irc made a good point, that I should mention that this is a VPS and i have root access. No one else is on this machine.
Furthermore, disabling the fastestmirror plugin solves the problem for now. (thanks z00dax)
If anything else weird happens i'll write back.
Thanks for the help.
z00dax in irc made a good point, that I should mention that this is a VPS and i have root access. No one else is on this machine.
Furthermore, disabling the fastestmirror plugin solves the problem for now. (thanks z00dax)
If anything else weird happens i'll write back.
Thanks for the help.
Dac
Interesting...
Why does disabling something that the centos website says is "highly recommended" (multiple times) fix this issue?
For those that do not know, you can disable this plugin by removing it or by going to the /etc/yum directory, and then go to the plugin directory below there and editing the proper file and zeroing out the enable line
-rh
RobertH wrote on Sun, 5 Oct 2008 13:39:26 -0700:
Why does disabling something that the centos website says is "highly recommended" (multiple times) fix this issue?
Because he has a non-standard setup. In case you didn't recognize: stopping mysqld also fixes his problem! He installed some software that affects threading and it's likely other things (that he didn't notice yet) are also affected. It's still weird, though. If you do not overwrite any base files you won't hit this problem.
Kai
He installed some software that affects threading and it's likely other things (that he didn't notice yet) are also affected. It's still weird, though. If you do not overwrite any base files you won't hit this problem.
Woah.
Well, here's where I disagree What's non standard in my install other than PHP? Furthermore, uninstalling PHP does nothing?
I submit yum.log for further scrutiny. Note the part where I removed PHP and the problem still persisted.
Oct 03 20:13:12 Installed: nano.i386 1.3.12-1.1 Oct 03 20:28:42 Installed: make.i386 1:3.81-3.el5 Oct 03 20:29:58 Updated: libgcc.i386 4.1.2-42.el5 Oct 03 20:30:04 Updated: glibc-common.i386 2.5-24 Oct 03 20:30:10 Updated: glibc.i686 2.5-24 Oct 03 20:30:10 Installed: glibc-headers.i386 2.5-24 Oct 03 20:30:10 Installed: glibc-devel.i386 2.5-24 Oct 03 20:30:10 Installed: binutils.i386 2.17.50.0.6-6.el5 Oct 03 20:30:10 Installed: cpp.i386 4.1.2-42.el5 Oct 03 20:30:10 Installed: libgomp.i386 4.1.2-42.el5 Oct 03 20:30:11 Installed: gcc.i386 4.1.2-42.el5 Oct 03 20:39:36 Updated: bash.i386 3.2-21.el5 Oct 03 20:39:36 Updated: chkconfig.i386 1.3.30.1-2 Oct 03 20:39:36 Updated: popt.i386 1.10.2-48.el5 Oct 03 20:39:36 Updated: audit-libs.i386 1.6.5-9.el5 Oct 03 20:39:36 Updated: bzip2-libs.i386 1.0.3-4.el5_2 Oct 03 20:39:39 Updated: perl.i386 4:5.8.8-15.el5_2.1 Oct 03 20:39:39 Updated: libacl.i386 2.2.39-3.el5 Oct 03 20:39:40 Updated: libxml2.i386 2.6.26-2.1.2.6 Oct 03 20:39:40 Updated: freetype.i386 2.2.1-20.el5_2 Oct 03 20:39:40 Updated: libpng.i386 2:1.2.10-7.1.el5_0.1 Oct 03 20:39:40 Updated: libstdc++.i386 4.1.2-42.el5 Oct 03 20:39:40 Updated: libtiff.i386 3.8.2-7.el5_2.2 Oct 03 20:39:40 Updated: pcre.i386 6.6-2.el5_1.7 Oct 03 20:39:40 Updated: procps.i386 3.2.7-9.el5 Oct 03 20:39:40 Installed: nspr.i386 4.7.1-1.el5 Oct 03 20:40:11 Installed: nss.i386 3.12.1.1-1.el5.centos.1 Oct 03 20:40:11 Updated: file.i386 4.17-13 Oct 03 20:40:11 Updated: gnutls.i386 1.4.1-3.el5_1 Oct 03 20:40:11 Updated: cups-libs.i386 1:1.2.4-11.18.el5_2.1 Oct 03 20:40:11 Updated: tcp_wrappers.i386 7.6-40.4.el5 Oct 03 20:40:12 Updated: libX11.i386 1.0.3-9.el5 Oct 03 20:40:12 Updated: diffutils.i386 2.8.1-15.2.3.el5 Oct 03 20:40:12 Updated: iproute.i386 2.6.18-7.el5 Oct 03 20:40:12 Updated: pkgconfig.i386 1:0.21-2.el5 Oct 03 20:40:12 Updated: centos-release-notes.i386 5.2-2 Oct 03 20:40:12 Updated: centos-release.i386 10:5-2.el5.centos Oct 03 20:40:12 Updated: cracklib-dicts.i386 2.8.9-3.3 Oct 03 20:40:12 Updated: libxslt.i386 1.1.17-2.el5_2.2 Oct 03 20:40:13 Updated: kernel-headers.i386 2.6.18-92.1.13.el5 Oct 03 20:40:13 Installed: keyutils-libs.i386 1.2-1.el5 Oct 03 20:40:13 Updated: bzip2.i386 1.0.3-4.el5_2 Oct 03 20:40:13 Updated: iptables.i386 1.3.5-4.el5 Oct 03 20:40:13 Updated: gzip.i386 1.3.5-10.el5.centos Oct 03 20:40:13 Updated: telnet.i386 1:0.17-39.el5 Oct 03 20:40:14 Updated: man-pages.noarch 2.39-10.el5 Oct 03 20:40:14 Updated: tzdata.noarch 2008e-1.el5 Oct 03 20:40:14 Updated: traceroute.i386 3:2.0.1-3.el5 Oct 03 20:40:15 Updated: libselinux.i386 1.33.4-5.el5 Oct 03 20:40:15 Updated: coreutils.i386 5.97-14.el5 Oct 03 20:40:18 Updated: python.i386 2.4.3-21.el5 Oct 03 20:40:18 Updated: pam.i386 0.99.6.2-3.27.el5 Oct 03 20:40:18 Updated: shadow-utils.i386 2:4.0.17-13.el5 Oct 03 20:40:18 Updated: newt.i386 0.52.2-10.el5 Oct 03 20:40:18 Updated: device-mapper.i386 1.02.24-1.el5 Oct 03 20:40:18 Updated: e2fsprogs-libs.i386 1.39-15.el5 Oct 03 20:40:19 Updated: openssl.i686 0.9.8b-10.el5 Oct 03 20:40:19 Updated: krb5-libs.i386 1.6.1-25.el5 Oct 03 20:40:19 Updated: openldap.i386 2.3.27-8.el5_2.4 Oct 03 20:40:19 Updated: util-linux.i386 2.13-0.47.el5 Oct 03 20:40:19 Updated: psmisc.i386 22.2-6 Oct 03 20:40:19 Updated: libuser.i386 0.54.7-2.el5.5 Oct 03 20:40:20 Updated: samba-common.i386 3.0.28-1.el5_2.1 Oct 03 20:40:20 Updated: postgresql-libs.i386 8.1.11-1.el5_1.1 Oct 03 20:40:20 Updated: apr-util.i386 1.2.7-7.el5 Oct 03 20:40:20 Updated: bind-libs.i386 30:9.3.4-6.0.2.P1.el5_2 Oct 03 20:40:22 Updated: fontconfig.i386 2.4.1-7.el5 Oct 03 20:40:22 Updated: cracklib.i386 2.8.9-3.3 Oct 03 20:40:22 Updated: usermode.i386 1.88-3.el5.1 Oct 03 20:40:22 Updated: e2fsprogs.i386 1.39-15.el5 Oct 03 20:40:22 Updated: audit-libs-python.i386 1.6.5-9.el5 Oct 03 20:40:22 Updated: libselinux-python.i386 1.33.4-5.el5 Oct 03 20:40:22 Updated: libxml2-python.i386 2.6.26-2.1.2.6 Oct 03 20:40:23 Updated: dbus.i386 1.0.0-7.el5 Oct 03 20:40:23 Updated: module-init-tools.i386 3.3-0.pre3.1.37.el5 Oct 03 20:40:23 Updated: net-tools.i386 1.60-78.el5 Oct 03 20:40:23 Updated: initscripts.i386 8.45.19.1.EL-1.el5.centos Oct 03 20:40:23 Updated: openssh.i386 4.3p2-26.el5_2.1 Oct 03 20:40:23 Updated: sysklogd.i386 1.4.1-44.el5 Oct 03 20:40:23 Updated: mcstrans.i386 0.2.7-1.el5 Oct 03 20:40:23 Updated: logrotate.i386 3.7.4-8 Oct 03 20:40:26 Updated: samba.i386 3.0.28-1.el5_2.1 Oct 03 20:40:26 Updated: httpd.i386 2.2.3-11.el5_1.centos.3 Oct 03 20:40:26 Updated: gd.i386 2.0.33-9.4.el5_1.1 Oct 03 20:40:26 Installed: yum-metadata-parser.i386 1.1.2-2.el5 Oct 03 20:40:26 Installed: python-iniparse.noarch 0.2.3-4.el5 Oct 03 20:40:26 Updated: httpd-manual.i386 2.2.3-11.el5_1.centos.3 Oct 03 20:40:27 Updated: samba-swat.i386 3.0.28-1.el5_2.1 Oct 03 20:40:27 Updated: vixie-cron.i386 4:4.1-72.el5 Oct 03 20:40:27 Updated: openssh-server.i386 4.3p2-26.el5_2.1 Oct 03 20:40:27 Updated: openssh-clients.i386 4.3p2-26.el5_2.1 Oct 03 20:40:27 Updated: authconfig.i386 5.3.21-3.el5 Oct 03 20:40:28 Updated: samba-client.i386 3.0.28-1.el5_2.1 Oct 03 20:40:28 Updated: sudo.i386 1.6.8p12-12.el5 Oct 03 20:40:28 Updated: fetchmail.i386 6.3.6-1.1.el5 Oct 03 20:40:28 Updated: m2crypto.i386 0.16-6.el5.2 Oct 03 20:40:28 Updated: tcpdump.i386 14:3.9.4-12.el5 Oct 03 20:40:28 Updated: ntsysv.i386 1.3.30.1-2 Oct 03 20:40:28 Updated: tar.i386 2:1.15.1-23.0.1.el5 Oct 03 20:40:28 Updated: rpm.i386 4.4.2-48.el5 Oct 03 20:40:29 Updated: rpm-libs.i386 4.4.2-48.el5 Oct 03 20:40:29 Updated: rpm-python.i386 4.4.2-48.el5 Oct 03 20:40:29 Updated: policycoreutils.i386 1.33.12-14.el5 Oct 03 20:40:29 Updated: bind.i386 30:9.3.4-6.0.2.P1.el5_2 Oct 03 20:40:29 Installed: yum-fastestmirror.noarch 1.1.10-9.el5.centos Oct 03 20:40:29 Updated: caching-nameserver.i386 30:9.3.4-6.0.2.P1.el5_2 Oct 03 20:40:29 Updated: yum.noarch 3.2.8-9.el5.centos.2.1 Oct 03 20:51:41 Installed: logwatch - 7.3-6.el5.noarch Oct 03 21:50:16 Installed: aspell - 12:0.60.3-7.1.i386 Oct 03 21:50:16 Installed: gmp - 4.1.4-10.el5.i386 Oct 03 21:50:16 Installed: php-common - 5.2.6-jason.1.i386 Oct 03 21:50:17 Installed: php-cli - 5.2.6-jason.1.i386 Oct 03 21:50:17 Installed: aspell-en - 50:6.0-2.1.i386 Oct 03 21:50:17 Installed: php - 5.2.6-jason.1.i386 Oct 03 21:56:43 Installed: php-mbstring - 5.2.6-jason.1.i386 Oct 03 21:57:59 Installed: php-bcmath - 5.2.6-jason.1.i386 Oct 03 21:59:03 Installed: php-pdo - 5.2.6-jason.1.i386 Oct 03 21:59:25 Installed: php-gd - 5.2.6-jason.1.i386 Oct 03 23:14:53 Installed: perl-DBI - 1.52-1.fc6.i386 Oct 03 23:14:54 Installed: mysql - 5.0.58-jason.2.i386 Oct 03 23:18:19 Installed: perl-DBD-MySQL - 3.0007-1.fc6.i386 Oct 03 23:18:20 Installed: mysql-server - 5.0.58-jason.2.i386 Oct 03 23:26:00 Installed: keyutils-libs-devel - 1.2-1.el5.i386 Oct 03 23:26:00 Installed: libsepol-devel - 1.15.2-1.el5.i386 Oct 03 23:26:00 Installed: libselinux-devel - 1.33.4-5.el5.i386 Oct 03 23:26:01 Installed: e2fsprogs-devel - 1.39-15.el5.i386 Oct 03 23:26:01 Installed: krb5-devel - 1.6.1-25.el5.i386 Oct 03 23:26:01 Installed: zlib-devel - 1.2.3-3.i386 Oct 03 23:26:01 Installed: openssl-devel - 0.9.8b-10.el5.i386 Oct 03 23:26:01 Installed: mysql-devel - 5.0.58-jason.2.i386 Oct 03 23:37:50 Erased: perl-DBD-MySQL Oct 03 23:37:50 Erased: mysql-server Oct 03 23:37:50 Erased: mysql Oct 03 23:37:50 Erased: mysql-devel Oct 03 23:40:26 Installed: mysql - 5.0.45-7.el5.i386 Oct 03 23:40:26 Installed: perl-DBD-MySQL - 3.0007-1.fc6.i386 Oct 03 23:40:27 Installed: mysql-devel - 5.0.45-7.el5.i386 Oct 03 23:40:27 Installed: mysql-server - 5.0.45-7.el5.i386 Oct 03 23:42:25 Erased: mysql-devel Oct 03 23:42:25 Erased: perl-DBD-MySQL Oct 03 23:42:25 Erased: mysql-server Oct 03 23:42:25 Erased: mysql Oct 03 23:51:31 Installed: yum-priorities - 1.1.10-9.el5.centos.noarch Oct 04 00:21:56 Installed: mysql - 5.0.45-7.el5.i386 Oct 04 00:21:57 Installed: perl-DBD-MySQL - 3.0007-1.fc6.i386 Oct 04 00:21:57 Installed: mysql-server - 5.0.45-7.el5.i386 Oct 04 01:57:17 Erased: mysql-server Oct 04 01:58:13 Erased: perl-DBD-MySQL Oct 04 01:58:13 Erased: mysql Oct 04 01:58:50 Installed: mysql - 5.0.45-7.el5.i386 Oct 04 01:58:50 Installed: perl-DBD-MySQL - 3.0007-1.fc6.i386 Oct 04 01:58:50 Installed: mysql-server - 5.0.45-7.el5.i386 Oct 04 02:56:26 Installed: mx - 2.0.6-2.2.2.i386 Oct 04 02:56:26 Installed: MySQL-python - 1.2.1-1.i386 Oct 04 02:57:37 Erased: MySQL-python Oct 04 02:57:37 Erased: mx Oct 04 03:12:36 Installed: php-mysql - 5.2.6-jason.1.i386 Oct 04 03:14:37 Installed: php-pgsql - 5.2.6-jason.1.i386 Oct 05 00:05:50 Installed: mx - 2.0.6-2.2.2.i386 Oct 05 00:05:50 Installed: MySQL-python - 1.2.1-1.i386 Oct 05 00:49:04 Installed: nmap - 2:4.11-1.1.i386 Oct 05 01:08:37 Erased: php-pdo Oct 05 01:08:37 Erased: php-mbstring Oct 05 01:08:37 Erased: php-mysql Oct 05 01:08:37 Erased: php-pgsql Oct 05 01:08:37 Erased: php-bcmath Oct 05 01:08:37 Erased: php-cli Oct 05 01:08:37 Erased: php-common Oct 05 01:08:37 Erased: php-gd Oct 05 01:08:37 Erased: php Oct 05 01:12:56 Installed: php-common - 5.2.6-2.el5s2.i386 Oct 05 01:12:56 Installed: php-pdo - 5.2.6-2.el5s2.i386 Oct 05 01:12:58 Updated: postgresql-libs - 8.2.9-1.el5s2.i386 Oct 05 01:12:58 Installed: php-cli - 5.2.6-2.el5s2.i386 Oct 05 01:12:58 Installed: postgresqlclient81 - 8.1.11-1.el5s2.i386 Oct 05 01:12:58 Installed: php-mysql - 5.2.6-2.el5s2.i386 Oct 05 01:12:58 Installed: php-gd - 5.2.6-2.el5s2.i386 Oct 05 01:12:58 Installed: php-mbstring - 5.2.6-2.el5s2.i386 Oct 05 01:12:58 Installed: php-bcmath - 5.2.6-2.el5s2.i386 Oct 05 01:12:58 Installed: php-pgsql - 5.2.6-2.el5s2.i386 Oct 05 01:12:58 Installed: php - 5.2.6-2.el5s2.i386
Dac Chartrand wrote:
Well, here's where I disagree What's non standard in my install other than PHP? Furthermore, uninstalling PHP does nothing?
Are there any packages installed that weren't part of the *base* CentOS?
Perhaps you should use a distribution that includes all of the packages you need rather than trying to bolt a bunch of 3rd party stuff on to CentOS.
I install a bunch of 3rd party packages myself, though they are all built from source, and all installed/tested via RPM, I never, ever directly use 3rd party repositories. Never have had a problem. I even download mysql from mysql.com and build it from source, even go so far as rebuilding php to link against the newer mysql(in CentOS 4's case). No problems.
nate
On 5-Oct-08, at 10:10 PM, nate wrote:
Perhaps you should use a distribution that includes all of the packages you need rather than trying to bolt a bunch of 3rd party stuff on to CentOS.
Only a the PHP packages came from a 3rd party, Everything else as far as I know comes from CentOS-Base.repo. I later removed the 3rd party PHP rpms (see log) and re-installed what was available from CentOS- Testing.repo
I never, ever directly use 3rd party repositories. Never have had a problem. I even download mysql from mysql.com and build it from source, even go so far as rebuilding php to link against the newer mysql(in CentOS 4's case). No problems.
Well. this is definitely good advice. But for the rest of us looking to use yum, you know, the default CentOS package management software, it seems a bit odd top to say "you shouldn't have used yum" when all the documentation I searched for led to it?
Dac Chartrand wrote:
Well. this is definitely good advice. But for the rest of us looking to use yum, you know, the default CentOS package management software, it seems a bit odd top to say "you shouldn't have used yum" when all the documentation I searched for led to it?
I didn't mean don't use yum, I meant if you want a really stable system don't use 3rd party repos. Stick to what is in base, or use a distribution that has the apps/versions that are closer to what your needs are.
nate
nate wrote:
I didn't mean don't use yum, I meant if you want a really stable system don't use 3rd party repos. Stick to what is in base, or use a distribution that has the apps/versions that are closer to what your needs are.
That doesn't have anything to do with this problem.
Ralph
On 5-Oct-08, at 10:10 PM, nate wrote:
Are there any packages installed that weren't part of the *base* CentOS?
PS: I can't answer this question. I inherited a CentOS 5.2 VPS and moved forward from there.
I wrote support and they looked into it. None of their other installs exhibit the same behavior.
I accept I could have messed up the system somehow, but I equally submit that yum broke something while I followed standard procedure.
Accusing me of screwing something up when I pretty much did `yum update`, all the while setting up and obeying priorities as outlined in the docs, and pretty much nothing else, is a bit overzealous IMHO. See log and the rest of this thread for a full scrutiny of my activities.
Anyway, for now. Disabling fastestmirror works, full yum log is there for people to review, the pyhthon error is easily reproducible (happens when mysqld is on, and only when fastmirror is enabled).
Don't know what else I can add here.
Dac Chartrand wrote:
On 5-Oct-08, at 10:10 PM, nate wrote:
Are there any packages installed that weren't part of the *base* CentOS?
PS: I can't answer this question. I inherited a CentOS 5.2 VPS and moved forward from there.
Accusing me of screwing something up when I pretty much did `yum update`, all the while setting up and obeying priorities as outlined in the docs, and pretty much nothing else, is a bit overzealous IMHO.
I don't recall accusing you of that, you mention above you inherited that system, it's possible that whoever had it before you screwed it up before you got it.
Did I mention I don't trust VPS either ?:) I pay a bit extra and co-lo my own server a local facility so I have complete control over it and knowledge of what is/is not installed (Runs Debian stable instead of CentOS since Debian has more packages that I want/need/like).
I inherited more than 300 RHEL 3/4 systems earlier this year in various states of dysfunction. So I do have somewhat of an idea of how you feel!
The previous admin didn't really know what they were doing in many cases. It'll probably be another 6-8 months before I have everything cleaned up at this rate(getting downtime to re-install each system fresh takes a while amongst my other projects). I'd rather not try to hunt down and fix every system, just backup, re-install and start fresh so everything is in a known good, consistent state.
My habits generally involve more work up front but once that work is done the long term benefits more than compensate for it.
nate
I don't recall accusing you of that, you mention above you inherited that system, it's possible that whoever had it before you screwed it up before you got it.
Sorry, the statement of feeling 'accused' falls under reply-to-all. I didn't mean that you accused me. I just felt that thread was heading in an odd persecutive direction considering I am looking for support, not a trial by fire.
That said. I appreciate all the help and insight provided. By everyone.
Turning off fastmirror solves the problem for me. I will keep my eye on the system and report any other weirdness that may be suspect, as suggested.
Thanks!
On Sun, 2008-10-05 at 22:52 -0400, Dac Chartrand wrote:
On 5-Oct-08, at 10:10 PM, nate wrote:
Are there any packages installed that weren't part of the *base* CentOS?
Could please you possibly do a list of all the installed RPMs on the system in question. Just for cause do a grep to list any packages like "rf" = rpmforge, "jason or "litka" "centos"
Anyway, for now. Disabling fastestmirror works, full yum log is there for people to review, the pyhthon error is easily reproducible (happens when mysqld is on, and only when fastmirror is enabled).
Don't know what else I can add here.
-------------------
JohnStanley Writes: Just by thought and maybe this is going to far off the subject. If it is I appologize. What lets yum run the correct way when fastest mirror is not loaded as a plugin? That there in sense does not sound right at all. The thing that makes me think is a possible botched yum update that yums meta data was hijacked and in turn got packages that were bugged or malwared? IE...The Lateness of the update from the mirrors. Makes me think. I know I know it's just a question.
On 6-Oct-08, at 1:52 AM, John wrote:
Could please you possibly do a list of all the installed RPMs on the system in question. Just for cause do a grep to list any packages like "rf" = rpmforge, "jason or "litka" "centos"
There no longer any rpm packages with "jason" or "litka", there are a few with "centos"
$ rpm -qa | grep -i centos filesystem-2.4.0-1.el5.centos basesystem-8.0-5.1.1.el5.centos procmail-3.22-17.1.el5.centos setuptool-1.19.2-1.el5.centos nss-3.12.1.1-1.el5.centos.1 centos-release-5-2.el5.centos yum-priorities-1.1.10-9.el5.centos centos-release-notes-5.2-2 gzip-1.3.5-10.el5.centos initscripts-8.45.19.1.EL-1.el5.centos httpd-2.2.3-11.el5_1.centos.3 httpd-manual-2.2.3-11.el5_1.centos.3 yum-fastestmirror-1.1.10-9.el5.centos yum-3.2.8-9.el5.centos.2.1
See end of email for list of all packages.
Just by thought and maybe this is going to far off the subject. If it is I appologize. What lets yum run the correct way when fastest mirror is not loaded as a plugin? That there in sense does not sound right at all. The thing that makes me think is a possible botched yum update that yums meta data was hijacked and in turn got packages that were bugged or malwared? IE...The Lateness of the update from the mirrors. Makes me think. I know I know it's just a question.
I'll keep my eye out for this. For the record, the one and only "non- standard" repo I used was http://www.jasonlitka.com/yum-repository/ - It was recommended in the CentOS forums. People seem to know the guy and trust him from what I read. Later, I removed all the packages I installed from that site (*.jason) and re-installed similar packages from CentOS-Testing repo.
-=-=-
$ rpm -qa filesystem-2.4.0-1.el5.centos basesystem-8.0-5.1.1.el5.centos libtermcap-2.0.8-46.1 ncurses-5.5-24.20060715 sed-4.1.5-5.fc6 libsepol-1.15.2-1.el5 gawk-3.1.5-14.el5 elfutils-libelf-0.125-3.el5 sqlite-3.3.6-2 gdbm-1.8.0-26.2.1 libattr-2.4.32-1.1 libgpg-error-1.4-2 libgcrypt-1.2.3-1 libcap-1.10-26 groff-1.18.1.1-11.1 m4-1.4.5-3.el5.1 iputils-20020927-43.el5 procmail-3.22-17.1.el5.centos libXau-1.0.1-3.1 mingetty-1.07-5.2.2 wireless-tools-28-2.el5 mailcap-2.1.23-1.fc6 sharutils-4.6.1-2 cyrus-sasl-plain-2.1.22-4 ed-0.2-38.2.2 cpio-2.6-20 unzip-5.52-2.2.1 crontabs-1.10-8 mailx-8.1.1-44.2.2 unixODBC-2.2.11-7.1 netpbm-10.35-6.fc6 finger-0.17-32.2.1.1 rootfiles-8.1-1.1.1 findutils-4.2.27-4.1 passwd-0.73-1 rhpl-0.194.1-1 libsemanage-1.9.1-3.el5 curl-7.15.5-2.el5 SysVinit-2.86-14 sendmail-8.13.8-2.el5 vim-minimal-7.0.109-3.el5.3 sendmail-cf-8.13.8-2.el5 sendmail-doc-8.13.8-2.el5 talk-server-0.17-29.2.2 quota-3.13-1.2.3.2.el5 gnupg-1.4.5-13 setuptool-1.19.2-1.el5.centos tmpwatch-2.9.7-1.1.el5.1 wget-1.10.2-7.el5 lynx-2.8.5-28.1 cyrus-sasl-gssapi-2.1.22-4 sgml-common-0.6.3-18 tcsh-6.14-12.el5 MAKEDEV-3.23-1.2 python-elementtree-1.2.6-5 python-urlgrabber-3.1.0-2 nano-1.3.12-1.1 libgcc-4.1.2-42.el5 glibc-2.5-24 glibc-devel-2.5-24 cpp-4.1.2-42.el5 gcc-4.1.2-42.el5 chkconfig-1.3.30.1-2 audit-libs-1.6.5-9.el5 perl-5.8.8-15.el5_2.1 libxml2-2.6.26-2.1.2.6 libpng-1.2.10-7.1.el5_0.1 libtiff-3.8.2-7.el5_2.2 procps-3.2.7-9.el5 nss-3.12.1.1-1.el5.centos.1 gnutls-1.4.1-3.el5_1 tcp_wrappers-7.6-40.4.el5 diffutils-2.8.1-15.2.3.el5 pkgconfig-0.21-2.el5 centos-release-5-2.el5.centos libxslt-1.1.17-2.el5_2.2 keyutils-libs-1.2-1.el5 iptables-1.3.5-4.el5 telnet-0.17-39.el5 tzdata-2008e-1.el5 libselinux-1.33.4-5.el5 python-2.4.3-21.el5 shadow-utils-4.0.17-13.el5 device-mapper-1.02.24-1.el5 openssl-0.9.8b-10.el5 util-linux-2.13-0.47.el5 libuser-0.54.7-2.el5.5 bind-libs-9.3.4-6.0.2.P1.el5_2 cracklib-2.8.9-3.3 e2fsprogs-1.39-15.el5 libselinux-python-1.33.4-5.el5 dbus-1.0.0-7.el5 net-tools-1.60-78.el5 openssh-4.3p2-26.el5_2.1 mcstrans-0.2.7-1.el5 samba-3.0.28-1.el5_2.1 gd-2.0.33-9.4.el5_1.1 python-iniparse-0.2.3-4.el5 samba-swat-3.0.28-1.el5_2.1 openssh-server-4.3p2-26.el5_2.1 authconfig-5.3.21-3.el5 sudo-1.6.8p12-12.el5 m2crypto-0.16-6.el5.2 ntsysv-1.3.30.1-2 rpm-4.4.2-48.el5 rpm-python-4.4.2-48.el5 bind-9.3.4-6.0.2.P1.el5_2 caching-nameserver-9.3.4-6.0.2.P1.el5_2 logwatch-7.3-6.el5 aspell-0.60.3-7.1 aspell-en-6.0-2.1 perl-DBI-1.52-1.fc6 keyutils-libs-devel-1.2-1.el5 libselinux-devel-1.33.4-5.el5 openssl-devel-0.9.8b-10.el5 yum-priorities-1.1.10-9.el5.centos perl-DBD-MySQL-3.0007-1.fc6 mx-2.0.6-2.2.2 nmap-4.11-1.1 php-common-5.2.6-2.el5s2 postgresql-libs-8.2.9-1.el5s2 postgresqlclient81-8.1.11-1.el5s2 php-gd-5.2.6-2.el5s2 php-bcmath-5.2.6-2.el5s2 php-5.2.6-2.el5s2 krb5-devel-1.6.1-25.el5_2.1 gpg-pubkey-e8562897-459f07a4 setup-2.5.58-1.el5 termcap-5.5-1.20060701.1 zlib-1.2.3-3 mktemp-1.5-23.2.2 info-4.8-14.el5 readline-5.1-1.1 db4-4.3.29-9.fc6 cyrus-sasl-lib-2.1.22-4 glib2-2.12.3-2.fc6 expat-1.95.8-8.2.1 libidn-0.6.5-1.1 libjpeg-6b-37 beecrypt-4.1.2-10.1.1 grep-2.5.1-54.2.el5 less-394-5.el5 hesiod-3.1.0-8 elfutils-libs-0.125-3.el5 libusb-0.1.12-5.1 xorg-x11-filesystem-7.1-2.fc6 slang-2.0.6-4.el5 libXdmcp-1.0.1-2.1 libXpm-3.5.5-3 ethtool-5-1.el5 elfutils-0.125-3.el5 rsync-2.6.8-3.1 jwhois-3.2.3-8.el5 ftp-0.17-33.fc6 time-1.7-27.2.2 talk-0.17-29.2.2 tcl-8.4.13-3.fc6 libtool-ltdl-1.5.22-6.1 libdbi-0.8.1-2.1 ncompress-4.2.4-47 vzdev-3.3.13-1.4.swsoft apr-1.2.7-11 xinetd-2.3.14-10.el5 cyrus-sasl-2.1.22-4 finger-server-0.17-32.2.1.1 portmap-4.0-65.2.2.1 stunnel-4.15-2 screen-4.0.3-1.el5 xml-common-0.6.3-18 mlocate-0.15-1.el5 libutempter-1.1.4-3.fc6 lsof-4.78-3 man-1.6d-1.1 python-sqlite-1.1.7-1.2.1 make-3.81-3.el5 glibc-common-2.5-24 glibc-headers-2.5-24 binutils-2.17.50.0.6-6.el5 libgomp-4.1.2-42.el5 bash-3.2-21.el5 popt-1.10.2-48.el5 bzip2-libs-1.0.3-4.el5_2 libacl-2.2.39-3.el5 freetype-2.2.1-20.el5_2 libstdc++-4.1.2-42.el5 pcre-6.6-2.el5_1.7 nspr-4.7.1-1.el5 file-4.17-13 cups-libs-1.2.4-11.18.el5_2.1 libX11-1.0.3-9.el5 iproute-2.6.18-7.el5 centos-release-notes-5.2-2 cracklib-dicts-2.8.9-3.3 kernel-headers-2.6.18-92.1.13.el5 bzip2-1.0.3-4.el5_2 gzip-1.3.5-10.el5.centos man-pages-2.39-10.el5 traceroute-2.0.1-3.el5 coreutils-5.97-14.el5 pam-0.99.6.2-3.27.el5 newt-0.52.2-10.el5 e2fsprogs-libs-1.39-15.el5 openldap-2.3.27-8.el5_2.4 psmisc-22.2-6 samba-common-3.0.28-1.el5_2.1 apr-util-1.2.7-7.el5 fontconfig-2.4.1-7.el5 usermode-1.88-3.el5.1 audit-libs-python-1.6.5-9.el5 libxml2-python-2.6.26-2.1.2.6 module-init-tools-3.3-0.pre3.1.37.el5 initscripts-8.45.19.1.EL-1.el5.centos sysklogd-1.4.1-44.el5 logrotate-3.7.4-8 httpd-2.2.3-11.el5_1.centos.3 yum-metadata-parser-1.1.2-2.el5 httpd-manual-2.2.3-11.el5_1.centos.3 vixie-cron-4.1-72.el5 openssh-clients-4.3p2-26.el5_2.1 samba-client-3.0.28-1.el5_2.1 fetchmail-6.3.6-1.1.el5 tcpdump-3.9.4-12.el5 tar-1.15.1-23.0.1.el5 rpm-libs-4.4.2-48.el5 policycoreutils-1.33.12-14.el5 yum-fastestmirror-1.1.10-9.el5.centos yum-3.2.8-9.el5.centos.2.1 gpg-pubkey-0d4306ef-45f6bc30 gmp-4.1.4-10.el5 libsepol-devel-1.15.2-1.el5 e2fsprogs-devel-1.39-15.el5 zlib-devel-1.2.3-3 gpg-pubkey-6b8d79e6-3f49313d mysql-5.0.45-7.el5 mysql-server-5.0.45-7.el5 MySQL-python-1.2.1-1 gpg-pubkey-7203f491-437e9cd3 php-pdo-5.2.6-2.el5s2 php-cli-5.2.6-2.el5s2 php-mysql-5.2.6-2.el5s2 php-mbstring-5.2.6-2.el5s2 php-pgsql-5.2.6-2.el5s2 krb5-libs-1.6.1-25.el5_2.1
Dac Chartrand wrote:
On 6-Oct-08, at 1:52 AM, John wrote:
Could please you possibly do a list of all the installed RPMs on the system in question. Just for cause do a grep to list any packages like "rf" = rpmforge, "jason or "litka" "centos"
There no longer any rpm packages with "jason" or "litka", there are a few with "centos"
As said: Your problem isn't with non-standard repositories, your problem lies in the way your hoster handles the VPS by limiting the number of threads on the guests.
Ralph
On 6-Oct-08, at 9:34 AM, Ralph Angenendt wrote:
As said: Your problem isn't with non-standard repositories, your problem lies in the way your hoster handles the VPS by limiting the number of threads on the guests.
Ok, understood.
Thank you for the help and clarification.
On Sun, Oct 5, 2008 at 22:10, nate centos@linuxpowered.net wrote:
Perhaps you should use a distribution that includes all of the packages you need rather than trying to bolt a bunch of 3rd party stuff on to CentOS.
Agreed.
I install a bunch of 3rd party packages myself, though they are all built from source, and all installed/tested via RPM, I never, ever directly use 3rd party repositories. Never have had a problem. I even download mysql from mysql.com and build it from source, even go so far as rebuilding php to link against the newer mysql(in CentOS 4's case). No problems.
How is this not "trying to bolt a bunch of 3rd party stuff on to CentOS"?
And I don't agree with you that using 3rd party repositories is not advisable. Many 3rd party repositories have very high quality standards and many useful packages. Not using them means a lot more work in packaging and updating that others will do for you if you use them. http://wiki.centos.org/AdditionalResources/Repositories
Filipe
On Mon, Oct 6, 2008 at 11:41 AM, Filipe Brandenburger filbranden@gmail.com wrote:
On Sun, Oct 5, 2008 at 22:10, nate centos@linuxpowered.net wrote:
<snip>
And I don't agree with you that using 3rd party repositories is not advisable. Many 3rd party repositories have very high quality standards and many useful packages. Not using them means a lot more work in packaging and updating that others will do for you if you use them. http://wiki.centos.org/AdditionalResources/Repositories
Probably the majority of the people in this mailing list use one or more 3rd party repositories. After you read the above, please read this one too: http://wiki.centos.org/PackageManagement/Yum/Priorities yum-priorities can help you prevent your box from being hosed. Please use it.
Dac Chartrand wrote on Sun, 5 Oct 2008 21:44:10 -0400:
Well, here's where I disagree
You already admitted that you have a non-standard setup. Besides of that it's a "VPS" of unknown origin and type. Do you consider this standard? Nobody here can know which parts are non-standard. But it's obvious that there is more non-standard than you think. Remember, others do not have this problem.
What's non standard in my install other
than PHP? Furthermore, uninstalling PHP does nothing?
I already told you what *I* would check *first*. This may not be the right track, but nevertheless: Did you?
Apart from that, as you have "inherited" a VPS. What is that? Do you rent it from a hosting provider? If so, and keeping in mind that there's obviously a problem with opening more threads (fastestmirror will open simultaneous download threads to several repo's to find out the fastest): Have you considered asking your provider the obvious?
Kai
On Mon, Oct 6, 2008 at 5:31 AM, Kai Schaetzl maillists@conactive.comwrote:
Apart from that, as you have "inherited" a VPS. What is that? Do you rent it from a hosting provider? If so, and keeping in mind that there's obviously a problem with opening more threads (fastestmirror will open simultaneous download threads to several repo's to find out the fastest): Have you considered asking your provider the obvious?
Inherited means a provider (networkredux.com) is sponsoring a project of mine (sf.net/projects/sux0r) with a free VPS so I can host the demo and other development initiatives. I was using shared hosting before as provided by them. I like them, they are helpful, I would recommend them regardless of the issue I am currently having.
I wrote the provider. They looked into it. I didn't give any answer about threads. All they could say is that this behavior didn't happen on their other similarly configured systems and as fastmirror solved the problem they consider the issue closed.
Dac Chartrand wrote on Mon, 6 Oct 2008 08:48:36 -0400:
I didn't give any answer about threads.
I don't know what this means, but I hope you are now aware that the issue stems from a limit on threads/processes?
Kai
On 6-Oct-08, at 9:31 AM, Kai Schaetzl wrote:
Dac Chartrand wrote on Mon, 6 Oct 2008 08:48:36 -0400:
I didn't give any answer about threads.
I don't know what this means, but I hope you are now aware that the issue stems from a limit on threads/processes?
Haha, woops, typo. I meant "They (the provider) didn't give any answer about threads."
And yes, I am now aware that the that the issue stems from a limit on threads/processes.
Thank you for your help.
FA0C171DBC@gmail.com> X-Rcpt-To: centos@centos.org
Dac Chartrand wrote on Mon, 6 Oct 2008 09:37:27 -0400:
Haha, woops, typo. I meant "They (the provider) didn't give any answer about threads."
Ok, that makes it clear :-) I would think that putting some senseful limits on a VPS is a normal business procedure. So you are certainly right with your statement "I would recommend them regardless of the issue".
Kai
Kai Schaetzl wrote:
RobertH wrote on Sun, 5 Oct 2008 13:39:26 -0700:
Why does disabling something that the centos website says is "highly recommended" (multiple times) fix this issue?
Because he has a non-standard setup. In case you didn't recognize: stopping mysqld also fixes his problem! He installed some software that affects threading and it's likely other things (that he didn't notice yet) are also affected. It's still weird, though. If you do not overwrite any base files you won't hit this problem.
That is not true. He is running on a VPS which probably does limiting on threads he can use. mysqld uses up quite a bit of threads, and yum's fastestmirror plugin uses up even more. So he hits a limit there - and yes, this happens with standard repositories (the php doesn't account for that behaviour). It's all the fault of the VPS he is running on.
Ralph
Ralph Angenendt wrote on Mon, 6 Oct 2008 11:50:39 +0200:
That is not true.
Well, my point was that he's not using a standard setup, that includes not only repo's. I already pointed out in my first reply that he may hit some limit, but he didn't follow up on that. In case there are no limits one of the few options left is that some third-party software affects behavior. Normal operation of fastest-mirror in a normal environment doesn't exhibit this behavior, that's what I wanted to clarify.
Kai
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Dac Chartrand -
Filipe Brandenburger -
John -
Johnny Hughes -
Kai Schaetzl -
Lanny Marcus -
nate -
Ralph Angenendt -
RobertH -
Stephen Harris -
Vandaman