content_faq.html

---
title: FAQ - SECONDO
description: Troubleshooting FAQ for SECONDO, covering profiling, macOS ARM/Intel linking errors, and BerkeleyDB memory allocation errors.
last_changed: 2026-07-21
---

<h1> FAQ </h1>

<p>
This page collects frequently asked questions, known problems and their solutions when
building, running, and operating <span class="secondo">Secondo</span>.
</p>


<h2> A operation in SECONDO is slow. How can I investigate this? </h2>

<p>
You can use a profiler like
<a href="https://valgrind.org/docs/manual/cl-manual.html" target="_blank">callgrind</a>
to investigate the problem.
</p>

<p>
In one shell, execute:
</p>
<pre>watch "callgrind_control -e -b"</pre>

<p>
In another shell, execute:
</p>
{% highlight bash %}
./SecondoTTYBDB --profile
{% endhighlight %}

<p>
You will now see in the first shell the current stack trace of
<span class="secondo">Secondo</span> while it is running. Execute the slow operation
and have a look at the stack trace, and you see in which operations the CPU time is
spent.
</p>

<p>
After you have finished your operation and you have quit
<span class="secondo">Secondo</span>, a file named <code>callgrind.out.&lt;pid&gt;</code>
is written into the current directory. This file contains the stack trace and can be
analyzed by executing <code>callgrind_annotate &lt;filename&gt;</code>.
</p>


<h2> ld: [...] building for macOS-arm64 but attempting to link with file built for macOS-x86_64 </h2>

<p>
It seems you are using a Mac with an ARM-based CPU, while your
<span class="secondo">Secondo</span>-SDK was built on an Intel CPU. Please delete your
old <span class="secondo">Secondo</span>-SDK (e.g., <code>rm ~/secondo-sdk</code>) and
reinstall the latest <span class="secondo">Secondo</span>-SDK. Please also re-install
your BerkeleyDB installation.
</p>


<h2> E_SMI_BDB sysErrCode=12 Cannot allocate memory </h2>

<pre>---------------------------
  Secondo-SMI Error Stack
---------------------------
E_SMI_BDB sysErrCode=12 Cannot allocate memory -&gt; [bdbFile.cpp:1622]</pre>

<p>
This error is most likely caused by a too small memory area for lock objects (more
information can be found
<a href="https://docs.oracle.com/cd/E17275_01/html/programmer_reference/lock_am_conv.html" target="_blank">here</a>
and
<a href="https://docs.oracle.com/database/bdb181/html/bdb-sql/lockingnotes.html" target="_blank">here</a>).
To solve this problem, two known solutions exist:
</p>

<ul>
  <li> Disable the transactions in <span class="secondo">Secondo</span>. This can be done
       by setting <code>RTFlags += SMI:NoTransactions</code> in your
       <code>SecondoConfig.ini</code>. </li>
  <li> Increase the memory area for locks. This is controlled by the following settings in
       the <code>SecondoConfig.ini</code>:
{% highlight ini %}
[BerkeleyDB]

MaxLockers=100
MaxLocks=5000
MaxLockObjects=5000
{% endhighlight %}
       In most cases the values for <code>MaxLocks</code> and <code>MaxLockObjects</code>
       need to be increased. </li>
</ul>


<h2> Compile error 'syntax error, unexpected string, expecting =' in *.y files </h2>

<p>
This error indicates that you are using an outdated version of Bison. Please ensure that
you have updated your
<a href="content_install.html">project dependencies</a>. At least Bison 3.0.4 is required
to build the project.
</p>


<h2> Compile error ''register' storage class specifier is deprecated and incompatible with C++17' </h2>

<p>
This error indicates that you are using an outdated version of Flex. Please ensure that you
have updated your
<a href="content_install.html">project dependencies</a>. At least Flex 2.6.4 is required to
build the project.
</p>


<h2> Compile error 'undefined reference to `TempRelation::BasicType[abi:cxx11]()' </h2>

<p>
A part of the project was built with an older C++ standard, another part with the C++17
standard (<code>-std=c++17</code>). The linker is unable to link these files. Please update
your <span class="secondo">Secondo</span> to the most recent version and run:
</p>
{% highlight bash %}
make clean
make
{% endhighlight %}


<h2> Compile error 'fatal error: libxml/xmlreader.h: No such file or directory' </h2>

<p>
The <i>GNOME XML library</i> was not found on the system. Please install the library and the
needed development files on the system. On Debian/Ubuntu based systems, this can be done by
executing <code>apt-get install libxml2-dev</code>.
</p>


<h2> How to run checkpd in git as a pre-commit check </h2>

<p>
Commits on GitHub are tested asynchronously by <code>checkpd</code> and a
<i>GitHub Action</i>. Due to the asynchronous execution, it may take some time before an
error is reported. To execute <code>checkpd</code> locally before a commit is made, use the
included <i>pre-commit check</i>. This check can be enabled by executing the command
<code>cp -av CM-Scripts/pre-commit .git/hooks/pre-commit</code> from the root directory of
your git repository.
</p>


<h2> How to speed up the compilation process? </h2>

<p>
You can use <code>ccache</code> to cache compilation units (even
<code>make clean / make -j $(nproc)</code> is quite fast afterwards). Simply add the
following lines to your <code>.secondorc</code> file:
</p>
{% highlight bash %}
export SECONDO_CC="ccache gcc"
export SECONDO_CPP="ccache g++"
{% endhighlight %}

<p>
The cache can be checked by running <code>ccache -s</code>.
</p>


<h2> How can I keep long-running queries alive on a remote system? </h2>

<p>
Executing queries on a large data set in <span class="secondo">Secondo</span> can take some
time. Usually, the secure shell (SSH) is used to connect to a remote system. Keeping an SSH
connection open for a long time can be challenging. The following tips can be used to keep a
connection open or prevent the termination of <span class="secondo">Secondo</span> when the
SSH connection is terminated.
</p>

<h3> Enabling the 'ServerAliveInterval' in the SSH Client </h3>

<p>
IP gateways (such as firewalls) can terminate idle TCP connections after some time. To prevent
a TCP connection from becoming idle, SSH can send some keep-alive packets in the background on
the TCP connection automatically. To enable the feature, add the following lines to your SSH
client configuration (e.g., <code>/etc/ssh/ssh_config</code> or
<code>~/.ssh/ssh_config</code>):
</p>

<pre>Host *
    ServerAliveInterval 60</pre>

<p>
The setting will send a keep-alive packet every 60 seconds. If the connection is terminated
earlier, please reduce the setting to a lower value (e.g., 15). Please note this is a setting
for the <i>SSH client</i> <code>ssh_config</code>, <b>not</b> for the <i>SSH server</i>
<code>sshd_config</code>.
</p>

<h3> Using screen to Execute SECONDO </h3>

<p>
<a href="https://www.gnu.org/software/screen/" target="_blank">screen</a> is a terminal
multiplexer for Linux. It allows the execution of multiple terminal sessions within one window
or SSH connection. Besides, the screen session (and all programs started from the session) is
not terminated when the SSH connection is lost. Another SSH session can be used to re-attach to
the previously opened session. <code>screen</code> can be used to start
<span class="secondo">Secondo</span> and to re-attach to the same
<span class="secondo">Secondo</span> session when the connection was lost. A complete overview
of the functionality of <code>screen</code> can be found
<a href="https://www.gnu.org/software/screen/manual/screen.html" target="_blank">here</a>.
</p>

<p>
Example:
</p>

<pre># Connect to the remote system
$ ssh user@remote.system.tld

# Start a new screen session and run SECONDO
$ screen
$ cd ~/secondo/bin
$ ./SecondoTTYBDB

# You can now detach from the SECONDO session by pressing CTRL-a and d
# (press CTRL-a first, then press d)

# Re-attach to the previously opened screen session
# This can also be done from another SSH session if the connection was lost
$ screen -x</pre>