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Red Hat OS Specific Issues

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Obtaining Red Hat

At UCB, http://software.berkeley.edu, has a "Software" link, then under "Operating Systems" is http://software.berkeley.edu/operating-systems#RedHat, which as a "Downloads" link https://ucbrhn.berkeley.edu/iso/ which has https://ucbrhn.berkeley.edu/iso/UC-RHN-FAQ-v6.pdf

Searching the web for "UC Berkeley Red Hat Enterprise Linux License Service - FAQ" yields https://kb.berkeley.edu/ist/page.php?id=24796, which is more up to date than https://ucbrhn.berkeley.edu/iso/UC-RHN-FAQ-v6.pdf

  1. Go to https://ucbrhn.berkeley.edu/iso/, login with your Calnet ID and download the appropriate image. I downloaded https://ucbrhn.berkeley.edu/iso/rhel-server-6.1-x86_64-dvd.iso
  2. Email your name, your login and your status (Staff/Student/Faculty) to the address listed in the FAQ above. Don't forget to have the Optional Channel enabled.
  3. Once Red Hat is running use the key provided:
    /usr/sbin/rhnreg_ks --force --activationkey PLACEKEYHERE \
    --serverUrl https://ucbrhn.berkeley.edu/XMLRPC \
    --sslCACert /etc/pki/tls/certs/ca-bundle.crt

Optional Channel

The Red Hat Network (RHN) has a number of channels. The Server Optional channel is well, um, optional. When you request a key, ask that the Server Optional channel be enabled. If the Server Optional channel is added after your initial installation, run yum makecache

To install PhpMyAdmin requires the Optional channel, see: https://www.linuxquestions.org/questions/red-hat-31/rhel6-no-php-mcrypt-support-846251/

There was a thread about this: http://micronet-at-uc-berkeley.840177.n3.nabble.com/Micronet-php-devel-on-redhat-linux-tp4025779p4025785.html

SSH

I could not log in using my id_rsa and id_rsa.pub keys. I opened up port 666 on the firewall by (as root) running system-config-firewall and then ran /usr/sbin/sshd -d -p 666 as root.

On the non-rhel client, I ran ssh -v sisyphus -p 666 date and the connection worked!

<Looking at a diff of the output from ssh -v sisyphus -p 22 date, I could see:

bash-3.2$ diff -rwb /tmp/6 /tmp/2
4c4
> debug1: Connecting to sisyphus [128.32.32.221] port 666.
---
< debug1: Connecting to sisyphus [128.32.32.221] port 22.
22d21
> debug1: checking without port identifier
25d23
< debug1: found matching key w/out port
36,39c34,38
> debug1: Server accepts key: pkalg ssh-rsa blen 149
> debug1: read PEM private key done: type RSA
> debug1: Authentication succeeded (publickey).
> Authenticated to sisyphus ([128.32.32.221]:666).
---
< debug1: Authentications that can continue: publickey,gssapi-keyex,gssapi-with-mic,password
< debug1: Trying private key: /Users/cxh/.ssh/id_dsa
< debug1: Next authentication method: password
< debug1: Authentication succeeded (password).
< Authenticated to sisyphus ([128.32.32.221]:22).

So, with port 22, ssh-rsa is not enabled?

Also, ssh-keygen was failing?>

-bash-4.1$ ssh-keygen
Generating public/private rsa key pair.

Enter file in which to save the key (/home/cxh/.ssh/id_rsa): Enter passphrase (empty for no passphrase):

Enter same passphrase again:

open /home/cxh/.ssh/id_rsa failed: Permission denied.
Saving the key failed: /home/cxh/.ssh/id_rsa.

The fix was to do:

sudo yum remove selinux*

Problem: There was an error parsing the RHN proxy settings, RHN Satellite or RHN Classic support will be disabled.

[root@sisyphus yum.repos.d]# yum repolist all
Loaded plugins: product-id, refresh-packagekit, rhnplugin, security,
: subscription-manager
Updating certificate-based repositories.
There was an error parsing the RHN proxy settings.
RHN Satellite or RHN Classic support will be disabled.
ftp://ftp.redhat.com/pub/redhat/linux/beta/6Server/en/os/SRPMS/repodata/repomd.xml: [Errno 14] PYCURL ERROR 9 - "Server denied you to change to the given directory"
Trying other mirror.
repo id repo name status
adobe-linux-x86_64 Adobe Systems Incorporated enabled: 2
hudson Hudson enabled: 5
rhel-source Red Hat Enterprise Linux 6Server - x86_64 - So enabled: 0
rhel-source-beta Red Hat Enterprise Linux 6Server Beta - x86_64 enabled: 3,825
repolist: 3,832

See https://www.linuxquestions.org/questions/linux-newbie-8/rhn-satellite-or-rhn-classic-support-will-be-disabled-882847/ which suggested editing /etc/sysconfig/rhn/up2date. I ended up changing:

enableProxy[comment]=Use a HTTP Proxy
enableProxy=1

to

enableProxy[comment]=Use a HTTP Proxy
enableProxy=0

yum update fails with "Server denied you to change to the given directory" on ftp.redhat.com

yum update failed with:

ftp://ftp.redhat.com/pub/redhat/linux/beta/6Server/en/os/SRPMS/repodata/filelists.xml.gz: [Errno 14] PYCURL ERROR 9 - "Server denied you to change to the given directory"
Trying other mirror.
Error: failure: repodata/filelists.xml.gz from rhel-source-beta: [Errno 256] No more mirrors to try.

My solution was

mv /etc/yum.repos.d rhel-source.repo ..

Other packages to install

sudo yum install expat-devel.i686
sudo yum install expat-devel.x86_64

Installing Xvfb

Xfvb is a virtual frame buffer that we use as part of the nightly build.

http://serverfault.com/questions/344793/install-xvfb-via-yum-yum-repository-for-xvfb says:

"It's available on the Client, Workstation, and Server Optional Channels inside RHN"

Unfortunately, at the time, I did not know how to request the Optional Channel, so I did the below steps:

[root@sisyphus ~]# yum -v repolist all
Loading "rhnplugin" plugin
Loading "product-id" plugin
Loading "refresh-packagekit" plugin
Loading "security" plugin
Loading "subscription-manager" plugin
Updating certificate-based repositories.
Config time: 0.396
Looking for repo options for [main]
Looking for repo options for [rhel-x86_64-server-6]
Repo 'rhel-x86_64-server-6' setting option 'enabled' = '1'
Repo 'rhel-x86_64-server-6' setting option 'gpgcheck' = '1'
Looking for repo options for [rhel-x86_64-server-6-beta]
Repo 'rhel-x86_64-server-6-beta' setting option 'enabled' = '1'
Repo 'rhel-x86_64-server-6-beta' setting option 'gpgcheck' = '1'
Looking for repo options for [rhn-tools-rhel-x86_64-server-6]
Repo 'rhn-tools-rhel-x86_64-server-6' setting option 'enabled' = '1'
Repo 'rhn-tools-rhel-x86_64-server-6' setting option 'gpgcheck' = '1'
Yum Version: 3.2.29
Setting up Package Sacks
pkgsack time: 0.017
Repo-id : adobe-linux-x86_64
Repo-name : Adobe Systems Incorporated
Repo-status : enabled
Repo-updated : Fri May 11 08:52:28 2012
Repo-pkgs : 2
Repo-size : 6.9 M
Repo-baseurl : http://linuxdownload.adobe.com/linux/x86_64/
Repo-expire : 21,600 second(s) (last: Wed Jul 11 18:13:19 2012)

Repo-id : hudson
Repo-name : Hudson
Repo-status : enabled
Repo-revision: 1338420354
Repo-updated : Wed May 30 16:26:01 2012
Repo-pkgs : 5
Repo-size : 283 M
Repo-baseurl : http://hudson-ci.org/redhat/
Repo-expire : 21,600 second(s) (last: Wed Jul 11 18:13:20 2012)

Repo-id : rhel-source
Repo-name : Red Hat Enterprise Linux 6Server - x86_64 - Source
Repo-status : disabled
Repo-baseurl : ftp://ftp.redhat.com/pub/redhat/linux/enterprise/6Server/en/os/SRPMS/
Repo-expire : 21,600 second(s) (last: Fri Jun 29 14:10:42 2012)

Repo-id : rhel-source-beta
Repo-name : Red Hat Enterprise Linux 6Server Beta - x86_64 - Source
Repo-status : disabled
Repo-baseurl : ftp://ftp.redhat.com/pub/redhat/linux/beta/6Server/en/os/SRPMS/
Repo-expire : 21,600 second(s) (last: Fri Jun 29 13:36:43 2012)

Repo-id : rhel-x86_64-server-6
Repo-name : Red Hat Enterprise Linux Server (v. 6 for 64-bit x86_64)
Repo-status : enabled
Repo-updated : Wed Jul 11 06:21:04 2012
Repo-pkgs : 8,255
Repo-size : 11 G
Repo-baseurl : https://ucbrhn.berkeley.edu/XMLRPC/GET-REQ/rhel-x86_64-server-6
Repo-expire : 21,600 second(s) (last: Wed Jul 11 18:13:20 2012)

Repo-id : rhel-x86_64-server-6-beta
Repo-name : Red Hat Enterprise Linux Server Beta (v. 6 for 64-bit x86_64)
Repo-status : enabled
Repo-updated : Wed Jun 20 09:50:58 2012
Repo-pkgs : 1,062
Repo-size : 1.5 G
Repo-baseurl : https://ucbrhn.berkeley.edu/XMLRPC/GET-REQ/rhel-x86_64-server-6-beta
Repo-expire : 21,600 second(s) (last: Wed Jul 11 18:13:20 2012)

Repo-id : rhn-tools-rhel-x86_64-server-6
Repo-name : RHN Tools for RHEL (v. 6 for 64-bit x86_64)
Repo-status : enabled
Repo-updated : Mon May 14 06:25:14 2012
Repo-pkgs : 64
Repo-size : 9.6 M
Repo-baseurl : https://ucbrhn.berkeley.edu/XMLRPC/GET-REQ/rhn-tools-rhel-x86_64-server-6
Repo-expire : 21,600 second(s) (last: Wed Jul 11 18:13:20 2012)

repolist: 9,388
[root@sisyphus ~]#

So, my workaround was to install the Centos 6.2 package at http://rpmfind.net/linux/RPM/centos/updates/6.2/x86_64/Packages/xorg-x11-server-Xvfb-1.10.4-6.el6.centos.3.x86_64.html

Here's what's in it.

root@sisyphus ~]# rpm -qpl xorg-x11-server-Xvfb-1.10.4-6.el6.centos.3.x86_64.rpm
warning: xorg-x11-server-Xvfb-1.10.4-6.el6.centos.3.x86_64.rpm: Header V3 RSA/SHA1 Signature, key ID c105b9de: NOKEY
/usr/bin/Xvfb
/usr/bin/xvfb-run
/usr/share/man/man1/Xvfb.1.gz

Resizing a partition

I want to split the /home partition and keep it ext4. I have:

[root@moog ~]# ls
anaconda-ks.cfg install.log install.log.syslog
[root@moog ~]# df -k
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/vg_moog-lv_root
51606140 2335452 46649248 5% /
tmpfs 49527296 0 49527296 0% /dev/shm
/dev/sda2 495844 63497 406747 14% /boot
/dev/sda1 204580 256 204324 1% /boot/efi

1671861364 201168 1586734552 1% /home
[root@moog ~]# ls
anaconda-ks.cfg install.log install.log.syslog
[root@moog ~]# ls /home
lost+found
[root@moog ~]# umount /home
[root@moog ~]# mount
/dev/mapper/vg_moog-lv_root on / type ext4 (rw)
proc on /proc type proc (rw)
sysfs on /sys type sysfs (rw)
devpts on /dev/pts type devpts (rw,gid=5,mode=620)
tmpfs on /dev/shm type tmpfs (rw,rootcontext="system_u:object_r:tmpfs_t:s0")
/dev/sda2 on /boot type ext4 (rw)
/dev/sda1 on /boot/efi type vfat (rw,umask=0077,shortname=winnt)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
[root@moog ~]# df -k
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/mapper/vg_moog-lv_root
51606140 2335452 46649248 5% /
tmpfs 49527296 0 49527296 0% /dev/shm
/dev/sda2 495844 63497 406747 14% /boot
/dev/sda1 204580 256 204324 1% /boot/efi
[root@moog ~]# parted /dev/mapper/vg_moog-lv_home
GNU Parted 2.1
Using /dev/mapper/vg_moog-lv_home
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) print
Model: Linux device-mapper (linear) (dm)
Disk /dev/mapper/vg_moog-lv_home: 1739GB
Sector size (logical/physical): 512B/4096B
Partition Table: loop

Number Start End Size File system Flags
1 0.00B 1739GB 1739GB ext4

Getting system-config-lvm to run

https://access.redhat.com/knowledge/docs/en-US/Red_Hat_Enterprise_Linux/6/html/Storage_Administration_Guide/ch-lvm.html suggests system-config-lvm. To get this to work I had to install various xorg-x11 packages including yum install xorg-x11-xauth.

Enable process accounting

chkconfig psacct on
/etc/init.d/psacct start

Problems with yum update

--> Finished Dependency Resolution
Error: Multilib version problems found. This often means that the root
cause is something else and multilib version checking is just
pointing out that there is a problem. Eg.:

1. You have an upgrade for gd which is missing some
dependency that another package requires. Yum is trying to
solve this by installing an older version of gd of the
different architecture. If you exclude the bad architecture
yum will tell you what the root cause is (which package
requires what). You can try redoing the upgrade with
--exclude gd.otherarch ... this should give you an error
message showing the root cause of the problem.

2. You have multiple architectures of gd installed, but
yum can only see an upgrade for one of those arcitectures.
If you don't want/need both architectures anymore then you
can remove the one with the missing update and everything
will work.

3. You have duplicate versions of gd installed already.
You can use "yum check" to get yum show these errors.

...you can also use --setopt=protected_multilib=false to remove
this checking, however this is almost never the correct thing to
do as something else is very likely to go wrong (often causing
much more problems).

Protected multilib versions: gd-2.0.35-11.el6.x86_64 != gd-2.0.35-10.el6.i686
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
yum update --exclude gd-2.0.35-10.el6.i686 --skip-broken

Package does not match intended download

yum failed with:

Error Downloading Packages:
libstdc++-4.4.7-4.el6.x86_64: failed to retrieve getPackage/libstdc++-4.4.7-4.el6.x86_64.rpm from rhel-x86_64-server-6-beta
error was [Errno -1] Package does not match intended download. Suggestion: run yum --enablerepo=rhel-x86_64-server-6-beta clean metadata

My workaround was to do

yum update --disablerepo=rhel-x86_64-server-6-beta --exclude gd-2.0.35-10.el6.i686 --skip-broken

Note that this dependency was probably from: php-mb, the yum command included:

Skipped (dependency problems):
php-mbstring x86_64 5.3.3-26.el6 rhel-x86_64-server-optional-6-beta
455 k

Setup NSF

http://cassjohnston.wordpress.com/2011/12/22/rhel-6-as-nfs-client/

yum install rpcbind nfs-utils
service rpcbind start
service nfslock start
chkconfig rpcbind on
chkconfig nfslock on

Check that the mount works:

[root@sisyphus ~]# mkdir /x
[root@sisyphus ~]# mount project:/vol/proj/ptolemy /x
[root@sisyphus ~]# ls /x
cvs dumper eal eecs20n gabriel johnr @LongLink neuendor ptdesign ptmail ptolemy tycho
[root@sisyphus ~]# umount /x

If mount does not work, email help@eecs and ask that the machine be added to the netgroup for that partition. I typically run showmount and email the results:


!!! Automounter
The automounter mounts files automatically as needed.  /projects/eesww and /projects/ptolemy are both automounted.

To set up the automounter: add to @@/etc/auto.master@@
(:source:)
/projects       /etc/auto.projects

Create /etc/auto.projects

+auto_projects
* project:/vol/proj/&

Restart the automounter:

[root@sisyphus etc]# service autofs restart
Stopping automount: ^[[60G[ OK ]
Starting automount: ^[[60G[ OK ]
[root@sisyphus etc]# cd /projects/ptolemy
[root@sisyphus ptolemy]# ls
cvs dumper eal eecs20n gabriel johnr @LongLink neuendor ptdesign ptmail ptolemy tycho
[root@sisyphus ptolemy]#

Problem installing the bash patch

On Sisyphus and moog, the problem was that yum update bash was not working because I was getting the beta channel.

yum info bash was returning

[root@moog yum.repos.d]# yum info bash
Loaded plugins: product-id, rhnplugin, security, subscription-manager
This system is not registered to Red Hat Subscription Management. You can use subscription-manager to register.
This system is receiving updates from RHN Classic or RHN Satellite.
rhel-x86_64-server-6 | 1.5 kB 00:00
rhel-x86_64-server-6/primary | 19 MB 00:00
rhel-x86_64-server-6 12947/12947
rhel-x86_64-server-optional-6 | 1.5 kB 00:00
rhel-x86_64-server-optional-6/primary | 1.8 MB 00:00
rhel-x86_64-server-optional-6 7284/7284
Installed Packages
Name : bash
Arch : x86_64
Version : 4.1.2
Release : 26.el6
Size : 3.0 M
Repo : installed
From repo : rhel-x86_64-server-6-beta
Summary : The GNU Bourne Again shell
URL : http://www.gnu.org/software/bash
License : GPLv3+
Description : The GNU Bourne Again shell (Bash) is a shell or command language
: interpreter that is compatible with the Bourne shell (sh). Bash
: incorporates useful features from the Korn shell (ksh) and the C
: shell (csh). Most sh scripts can be run by bash without
: modification.

Note that the version is after the version bash-4.1.2-15.el6_5.2 listed at https://access.redhat.com/solutions/1207723.

yum-config-manager --disable rhel-x86_64-server-6-beta was failing:

timeout = 60.0
up2date_cfg = <up2date_client.config.Config instance at 0x1360050>
username =

Traceback (most recent call last):
File "/usr/bin/yum-config-manager", line 186, in <module>
repo.cfg.options, repo.iteritems, repo.optionobj,
AttributeError: 'RhnRepo' object has no attribute 'cfg'

https://bugzilla.redhat.com/show_bug.cgi?format=multiple&id=982241 suggested editing /etc/yum/pluginconf.d/rhnplugin.conf:

[rhel-x86_64-server-6-beta]
enabled=0

[testing-1.1-devtools-6]
enabled=0

Then, this worked:

[root@moog yum.repos.d]# yum downgrade bash
Loaded plugins: product-id, rhnplugin, security, subscription-manager
This system is not registered to Red Hat Subscription Management. You can use subscription-manager to register.
This system is receiving updates from RHN Classic or RHN Satellite.
Setting up Downgrade Process
Resolving Dependencies
--> Running transaction check
---> Package bash.x86_64 0:4.1.2-15.el6_5.2 will be a downgrade
---> Package bash.x86_64 0:4.1.2-26.el6 will be erased
--> Finished Dependency Resolution

...

Setting the time

To set the clock, look at the end of /etc/ntp.conf

server 128.32.48.21 # added by /sbin/dhclient-script
server 128.32.48.23 # added by /sbin/dhclient-script

Below we use the -q flag to query the server to verify that it is on, then call ntpdate to use the two servers, then enable the ntpdate daemon across reboots.

[root@terratest ~]# date
Thu Nov 13 07:31:35 PST 2014
[root@terratest ~]# ps -auxgww | grep ntp
Warning: bad syntax, perhaps a bogus '-'? See /usr/share/doc/procps-3.2.8/FAQ
root 7777 0.0 0.0 103252 848 pts/1 S+ 07:31 0:00 grep ntp
[root@terratest ~]# ntpdate -q 128.32.48.21
server 128.32.48.21, stratum 4, offset 29298.608744, delay 0.02571
13 Nov 07:31:59 ntpdate[7795]: step time server 128.32.48.21 offset 29298.608744 sec
[root@terratest ~]# ntpdate 128.32.48.21 128.32.48.23
13 Nov 15:40:34 ntpdate[7809]: step time server 128.32.48.21 offset 29298.609240 sec
[root@terratest ~]# chkconfig ntpdate on
[root@terratest ~]# date
Thu Nov 13 15:40:47 PST 2014
[root@terratest ~]#

Building gcc-4.8.4

12/2014 - terra

As root:

   yum install gmp-devel.x86_64
   yum install mpfr-devel.x86_64
   yum install libmpc-devel.x86_64

As a fix for "/usr/include/gnu/stubs.h:7:27: fatal error: gnu/stubs-32.h: No such file or directory":

   yum install glibc-devel.i686

Not as root:

   wget http://www.netgull.com/gcc/releases/gcc-4.8.4/gcc-4.8.4.tar.gz
   tar -zxf gcc-4.8.4.tar.gz
   cd gcc-4.8.4
   mkdir build
   cd build
   ../configure --prefix=/usr/local/gcc-4.8.4.tar.gz
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