md array with disk gone missing – recovering data

Had a server that decided to drop a disk (or disk went faulty) in a RAID5 array. On reboot the array didn’t want to start. Output of mdadm --detail /dev/md0

Version : 1.2
Creation Time : Wed May 22 18:17:58 2013
Raid Level : raid5
Used Dev Size : -1
Raid Devices : 3
Total Devices : 2
Persistence : Superblock is persistent

Update Time : Sun Jan 3 06:50:05 2021
State : active, degraded, Not Started
Active Devices : 2
Working Devices : 2
Failed Devices : 0
Spare Devices : 0

Layout : left-symmetric
Chunk Size : 512K

Name : nebula:0 (local to host nebula)
UUID : 962b8ff0:00d88161:5a030e1f:236466af
Events : 31168

Number Major Minor RaidDevice State
4 8 16 0 active sync /dev/sdb
1 0 0 1 removed
3 8 48 2 active sync /dev/sdd

Try to start array with mdadm --run /dev/md0

mdadm: failed to run array /dev/md0: Input/output error

As expected, given it didn’t autorun on boot.

Trying mdadm --assemble --run /dev/md0 /dev/sdb /dev/sdd

mdadm: /dev/sdb is busy - skipping
mdadm: /dev/sdd is busy - skipping

This is because the md device is using the disks. Stop it: with mdadm --stop /dev/md0

then reassemble with mdadm --assemble --run --force /dev/md0 /dev/sd[bd]

mdadm: Marking array /dev/md0 as 'clean'
mdadm: /dev/md0 has been started with 2 drives (out of 3).

Ran mount -a to rerun fstab. Took a few seconds but worked. Copy data off ASAP!


Running svnadmin verify as root permission issues on Berkeley DB repositories

After a system crash I ran svnadmin verify on some of the relevant repositories to check things were ok – this was done as root. Afterwards normal network access (via Apache) was broken with

Internal error: Berkeley DB error for filesystem

appearing in the logs. The fix was to chown -R www-data:www-data on the broken repositories. It looks like running svnadmin verify as root changes permissions on SVN repositories somewhere (at least Berkeley DB ones).

Lesson learned – check normal SVN access after doing this sort of thing!

Blocking or disabling autofs automounts with the -null map

Suppose you have a linux network setup with automounter maps that come from the network (via nis, sssd, LDAP etc.) and you want to block some of them acting on a particular system. In our case we have an automount map that acts on /opt and mounts various software packages from network shares. The problem with this is that you can’t then install your own stuff locally to /opt, which is what a lot of Debian/Ubuntu packages expect to be able to do.

It turns out there is a option in the automounter for this sort of situation. There is a built-in map called -null that blocks any further automounts to a particular mountpoint. In our case we want to block auto.opt, so we add a line to auto.master (somewhere before the bottom +auto.master line)

/opt  -null

Then restart the autofs service (if stuff was mounted on /opt then unmount it). Or reboot the system. You should find that you can put stuff in the local /opt.

To check the map is blocked you can also run

automount --dumpmaps

(also handy for checking what is actually meant to be mapped where).

Another way of doing this that leaves the system auto.master untouched is to create a file /etc/auto.master.d/opt.autofs (the first part of the name can be anything you want). Put the same contents in the file, e.g.

/opt  -null

Note that using this mechanism normally requires two files – one in /etc/auto.master.d/ and a map file that it refers to. In this case -null is a built-in map.

Unfortunately this option is not well documented. Places where it is referred to are:

There are also other built-in maps, e.g. -passwd, -hosts, -fedfs. Of these only the -hosts map is documented in the auto.master(5) man page.

-null is confirmed to work in CentOS 7, CentOS 8, Ubuntu 20.04, Debian 10.

OpenProject Apache reverse proxy with https secure connection

These are some notes on setting up OpenProject on a backend server (let’s call it, and accessing it via a front-end system ( Normally we’d do the SSL termination at the reverse proxy, and there is some documentation on this. In this case I wanted to do things properly, and protect the login credentials all the way. This means using an https connection between the reverse proxy and the back end server.

Firstly, the reverse proxy has to trust the SSL certificate that the back end uses. There are several ways to go about this. I chose to set up a local certificate authority using the easy-rsa scripts (using another small virtual machine set up only for this purpose). For one connection this is probably overkill, but for multiple backends in the future it will make the administration a lot easier.

  • Set up CA
    • Debian 10, install easy-rsa package, do required setup.
  • Copy CA root certificate to frontsrv
    • For Debian systems, copy to /usr/local/share/ca-certificates/ and run update-ca-certificates
  • Create CSR on backsrv, copy it to CA, sign it and copy resulting certificate to backsrv. Put cert and key in sensible places (/etc/ssl/private/ and /etc/ssl/local-certs/). Make sure permissions are correct.
  • Configure Apache on backsrv and check cert works (for OpenProject edit /etc/openproject/installer.dat to put in the correct certificate paths and run openproject configure to update the config).

Set up Apache to do proxy stuff on frontsrv. Here’s the beginning fragment of default-ssl.conf that should work:

<IfModule mod_ssl.c>
        <VirtualHost _default_:443>
                ServerAdmin webmaster@localhost

                DocumentRoot /var/www/html

                RequestHeader edit Destination ^https http early

                SSLProxyEngine on
                SSLProxyCheckPeerName off

                # To openproject server on backserv
                ProxyPass /openproject
                ProxyPassReverse /openproject
                <Location /openproject>
                        ProxyPreserveHost On
                        Require all granted

You also need to go to the OpenProject web interface admin area, go to System Settings – General and change the Host name to the reverse proxy, and set protocol to https. It will complain if there’s a hostname mismatch (case sensitive, even!). You may also want to go to EmailEmail notifications and change the Emission email address to be consistent.

Don’t forget, need SSLProxyEngine on!

For OpenProject the subdirectory locations on the front and back ends do need to match.

The ProxyPreserveHost On is required per the OpenProject documentation. Unfortunately, that means it tries to match the name to the back end cert, and the SSL handshake fails. This is the reason for the SSLProxyCheckPeerName off directive – it disables checking the certificate CN or Subject Alternative Names.

Apparently the SSLProxyCheckPeerName off can go in a <Proxy>...</Proxy> matching block with Apache 2.4.30 or newer, which would be nice. As it is this will turn it off for the whole vhost, which is a small lessening of security.

I suppose in principle we could create the certificate for the back end with the name of the front end, or add it to the SANs. I haven’t tried this and it seems like it could be a recipe for confusion and subtle bugs.

ANSI control codes in Jekyll output breaking emails

Also see Publishing websites with Jekyll, Apache and SVN

If you send console output via email (like, say the output of jekyll build as part of a SVN post-commit hook script) if there are ANSI control characters in the string (e.g. colour codes) this can break things. In this case the mail command (Debian 9 default exim) was only sending text up to the first ANSI code, which meant that the jekyll build error messages (which are yellow and red) were missing.

To fix this pipe the text through ansi2txt (comes with the colorized-logs package in Debian and Ubuntu). This strips out all ANSI control codes making the string email safe.

(After this I pipe it through unix2dos to convert to CRLF line endings, as this appears to be the standard for email. On Debian this comes with the dos2unix package.)

The last line in the hook script then becomes

echo "$LOGVAR" | /usr/bin/ansi2txt | /usr/bin/unix2dos | mail -s "$REPOS_BASENAME build $REV" "$BUILD_EMAIL"

Publishing websites with Jekyll, Apache and SVN

Now I’ve got this working to some extent here are some notes about setting up Jekyll with SVN and Apache:

Server – Debian 9 Stretch, normal command-line only install. Set up system to use email server (campus smarthost in our case).

Install SVN and Apache and set up accordingly.

Install Jekyll:

apt install jekyll

Create an SVN repository for the site files.

Create new project directories at a temporary location, e.g.

jekyll new /tmp/newsite

Commit these files to the SVN repository (I normally check out the repository on my local workstation, copy the directory in /tmp from the server into the working directory on the workstation, add them and commit). Delete the directory in /tmp.

On the server, create the actual website file location by exporting from the SVN via a temporary location:

svn export file:///path/to/repository /tmp/buildfiles
jekyll build --source /tmp/buildfiles /var/www/sitename
rm -Rf /tmp/buildfiles

Configure Apache to serve from /var/www/sitename. In our case we ultimately wanted to serve multiple sites through a reverse proxy, so we used a vhost serving on an alternate port. This can be a handy testing configuration – you don’t have to worry about fiddling with the other website settings. For example, using port 8081:

<VirtualHost *:8081>

    ServerAdmin webmaster@localhost
    DocumentRoot /var/www/sitename


(Remember to change ports.conf to listen on the new port!)

Test by pointing a webserver at server:8081

Once that’s all working, set up the post-commit hook script to automatically build the site on a commit. Our current setup is:



REPOS_BASENAME=$(/usr/bin/basename "$REPOS")

# These two need configured!

"$REPOS"/hooks/ commit "$REPOS" $REV "$REPOS"/hooks/mailer.conf

LOGVAR=$(/export0/svn_config/ "$REPOS" $REV "$TMP_SVN_EXPORT" "$PUBLIC_WWW" 2>&1)

echo "$LOGVAR" | /usr/bin/unix2dos | mail -s "$REPOS_BASENAME build $REV" "$BUILD_EMAIL"

(Note that on Debian you need to install the dos2unix package. Needed as plain text email expects CRLF line terminators as specified in RFC 2822.)



/usr/bin/svn export --quiet file:///"$REPOS" "$TMP_SVN_EXPORT"
/usr/bin/jekyll build --source "$TMP_SVN_EXPORT" --destination "$PUBLIC_WWW"

Note that the build process runs under the Apache user account, so set permissions appropriately. Also, when troubleshooting remember that on Debian 9 the Apache process is configured by default to use a private /tmp directory!

This works for our current needs, although it isn’t optimised. Improvements would be:

  • Unify the setup for the commit email and build email scripts.
  • Build the site in the background (although you’d have to tweak how the logging output works in that case).

Of course, the professionals would use something like a combination of GitLab and Jenkins to automate this stuff properly…


Private /tmp directories in Debian 9 Stretch with Apache

In Debian 9 Stretch Apache is configured to use systemd‘s PrivateTmp feature by default. This means that the Apache tmp directory actually lives in /tmp/systemd-private-BIGLONGSTRING--apache2.service-STRING.

So if you are running an SVN server that uses Apache for serving, anything written to /tmp in the hook scripts ends up in the private directory rather than the normal userspace one.

Dell Latitude 7490 freezing when unplugging USB3 WD15 dock

Setup – Dell Latitude 7490 running Ubuntu 18.04 Bionic and Dell WD15 USB-C dock.

Problem – system freezes when dock unplugged.

This problem started after updates. The solution found was to revert to the previous kernel (4.15.0-43-generic) from 4.15.0-44-generic. Did this by setting GRUB to remember the boot setting – change /etc/grub/grub with:


and run


Then hit esc at the loading screen to get to the grub menu.

Making nis authentication work with Ubuntu 16, Debian 8, Fedora 28 etc.

After updating anything to use systemd-235 NIS logins either don’t work at all (usually for GUI logins), or take a long time to login (console or ssh, sometimes). The culprit is a line in the systemd-logind.service:


This sandboxes the service and doesn’t allow it to talk to the network. Unfortunately this affects nis lookups done via the glibc NSS API. See the links at

The quick solution is to turn off the sandboxing, either by commenting out or changing the line in systemd-logind.service, or creating a drop-in snippet that overrides it. This can be done by creating a file /etc/systemd/system/systemd-logind.service.d/IPAddress_clear.conf with the contents:


The file can be called anything you like (.conf).

Then restart things:

systemctl daemon-reload
systemctl restart systemd-logind.service

You can check that the drop-in is being loaded with

systemctl status systemd-logind.service

In the output you should see something like:

   Loaded: loaded (/lib/systemd/system/systemd-logind.service; static; vendor preset: enabled)
  Drop-In: /etc/systemd/system/systemd-logind.service.d

The other test is to see if NIS logins work correctly, of course…

The slightly slower solution is to use nscd to cache the lookup requests, and apparently does so in a way that plays nicely with the sandboxing. The much slower solution is to switch to using sssd or similar and ditch NIS once and for all…

Note – this may also affect systemd-udevd.

Making Debian 9 (Stretch) configure GRUB to boot partitions with UUIDs

As per this bug:

Debian Bug report logs – #852323

The Debian 9 installer (up to v9.5 at least) does not always configure GRUB to find the boot partition using UUID, but leaves it pointing to /dev/sdb or whatever. This can be a problem if you change disks in the system. In particular, if you install from a USB stick and then remove it when the system reboots after the install this can change the disk /dev id. The result is a unbootable system. This can be a bit fiddly to fix (although the first thing that’s always worth trying is to reverse the changes you made and see if it boots, e.g. plug the install USB stick back in to the same usb slot).

You can check this by looking at the /boot/grub/grub.cfg file. A quick check is:

grep "/boot/v" /boot/grub/grub.cfg

The fix is easy. Let the system reboot while leaving the install media in place (obviously make sure you don’t boot from the install media again!). Log in to the system and run (as root/using sudo)


Compare the grub.cfg before and after. Then test by removing the install media and rebooting.