Tag Archives: bug

On variable renumbering

Variable renumbering in SAT solvers keeps a mapping between the external variable numbers that is visible to the users and the internal variable numbers that is visible the to the system. The trivial mapping that most SAT solvers use is the one-to-one mapping where there is no difference between outer and internal variables. A smart mapping doesn’t keep track of all data related to variables that have been set or eliminated internally, so the internal datastructures can be smaller.


Having smaller internal data structures help in achieving a lower memory footprint and better cache usage.

The memory savings are useful because some CNFs have tens of millions of variables. If the solver uses the typical watched literal scheme, it needs 2 arrays for each variable. If we are using 64b pointers and 32b array sizes, it’s 32B for each variable, so 32MB for every million variable only to keep the watching literal array(!). I have seen people complaining that their 100M variable problem runs out of memory — if we count that right that’s 3.2GB of memory only to hold the watching literal array pointers and sizes, not any data at all.

As for the CPU cache benefits: modern CPUs work using cache lines which are e.g. 64B long on Intel Sandy Bridge. If half of the variables are set already, the array holding the variable values — which will be accessed non-stop during propagation — will contain 50% useless data. In practice the speedup achieved can be upwards of 10%.

The simple problems

One problem with having a renumbering scheme is that you need to keep track of which datastructure is numbered in which way. The easy solution is to renumber absolutely everything. This is costly, however, as the mapping has to change every once in a while when new variables have been set. In this case, if everything is renumbered, then the eliminated variables‘ data needs to be updated according to the new mapping every time. This might be quite significant. So, it’s best not to renumber that. Similarly, if disconnected component analysis is used, then the disconnected components’ saved solutions need to be renumbered as well, along with the clauses that have been moved to the components.

An approach I have found to be satisfying is to keep every dynamic datastructure such as variable states (eliminated/decomposed/etc.), variable values (True/False/Unknown), clauses’ literals, etc. renumbered, while keeping mostly static datastructures such as eliminated clauses or equivalent literal maps non-renumbered. This works very well in practice as it allows the main system to shuffle the mapping around while not caring about all the other systems’ data.

The hard problem

The above is all fine and dandy until bounded variable addition (BVA) comes to the scene. This technique adds new variables to the problem to simplify it. These new variables will look like new outer variables, which seems good at first sight: the system could simply print the solution to all variables except the last N that were added by BVA and are not part of the original problem. However, if the caller adds new variables after the call to solve(), what can we do? The actual variables by the caller and the BVA variables will be mixed up: start with a bunch of original variables, sprinkle the end with some BVA, then some original variables, then some BVA…

The trivial solution to this is to have another mapping, one that translates variable numbers between the BVA and non-BVA system. As you might imagine, this complicates everything. Another solution is to forcibly eliminate all BVA variables after the call to solve(), let the user add the new clauses, and perform BVA again. Another even more complicated solution is to keep track of the variables being added, then re-number all variables inside all datastructures to move all BVA variables to the end of the variable array. This is expensive but only needs to be done once after the call to solve(), which may be acceptable. Currently, CryptoMiniSat uses the trivial scheme. Maybe I’ll move to the last (and most complicated) system later on.


Variable renumbering is not for the faint of heart. Bugs become significantly harder to track, as all debug messages need to be translated to a common variable numbering or they make no sense at all. It’s also very easy to introduce bugs through variable renumbering. A truly difficult bug I had was when the disconnected component finder’s sub-solver renumbered its internal variables and when I tried to import some values from the sub-solver back to the main solver, I used the wrong variable numbers.

My SAT solver fuzzing setup

Since the SAT solver fuzzing paper by Brummayer, Lonsing and Biere, SAT solver fuzzing has been quite the thing in the SAT community. Many bugs have since been discovered in almost all SAT solvers, including those of this author. In this blog post I will detail my SAT fuzzing setup: what fuzzers I use and how I use them.

My fuzzers

The most obvious fuzzers to use are those present in the paper and accompanying website: CNFFuzz and FuzzSAT. These fuzzers randomly genereate high-quality structured problem instances. The emphasis here is on the word structured. Randomly generated instances, as the authors of the original paper note, do not excercise SAT solvers enough. SAT solvers are written with very specific problem types in mind: problems containing long chains of binary clauses, gates, etc.

Over the year(s) I have found, however, that these fuzzers are not enough. One of the revelations came when Vegard sent me lots of bugreports about CryptoMiniSat failing when Gaussian elimination was enabled. It turned out that although I ran the fuzzer for long hours, I only ran it with the default option, Gaussian turned off. So default options are sometimes not enough and when off-the track, systems can fail.

Vegard then sent me a fuzzer that wasn’t using CNFFuzz or FuzzSAT, but instead his own CNF generator for SHA-1 hash functions. Instances thus generated are not only structured, they are also very picky about the solution: they either have exactly one or zero. This helped fuzz solution reconstruction, which after blocked clause elimination may not be exactly easy. In fact, it’s so good at fuzzing that it finds a bug I have never been able to fix in CryptoMiniSat, to this day, about binary clauses. Whenever I block them, I cannot reconstruct the solution, ever, unless I disable equivalent literal replacement. The authors of the paper give a pretty complicated proof about why it should work in the presence of equivalent literal replacement, which I still haven’t understood.

When I implemented disconnected component analysis into CryptoMiniSat 3, I knew I had to be careful. In the SAT Competition’11 I failed terribly with it: CryptoMiniSat 2 memory-outed and crashed on many instances with disconnected components. The solution I came up with was to make a program that could concatenate two or more problems into one problem, renumbering the variables. This meta-fuzzer (that used fuzzers as inputs) was then used to fuzz the disconnected component handling system. Although this sounds sufficient, it is in fact far from it. Firstly, the problems generated are disconnected at toplevel — whereas problems in the real world sometimes disconnect later during the search. Secondly, it took 2, maybe 4 CNF inputs, but real problems sometimes have thousands of disconnected components. Both of these issues had to be addressed.

One of the most difficult parts of modern SAT solvers is time-outs of complicated algorithms. Time-outs sometimes make code quite convoluted, and thus are a source of bugs. However, most fuzzers generate problems that are too small for any time-outs to occur, thus severely limiting the scope of the fuzzer. So, the fuzzers don’t exercise a part of the system that is fully exercised by real-world problems. To fix this, I have written a short fuzzer script that generates enormous, but simple problems with millions of variables. This helped me fix a lot of issues in timeouts. I advise having a RAM-disk when using it though, as it writes gigabyte-size CNFs.

I also use some other fuzzers, namely one that excercise XOR-manipulation and the sgen4 CNF generator by Ivor Spence (PDF, pages 85-86) that generates problems of tuneable hardness.

My fuzzing system

Fuzz CNF generators are nice, but not enough on their own. A system around them is necessary for the full benefit. Writing one sounds trivial at first, but my system around the fuzzers is about 1000 lines of python code, so maybe it’s not that trivial after all. It has to do a number of things to be truly useful.

First, it needs to test the solutions given by the solver. If the solution is SAT, it needs to read the (gzipped) CNF file, and check the (partial) solution. Second, if the solution is UNSAT, it either needs to call the DRUP checker to verify the proof, and/or it needs to call another solver to see if it finds a solution or not — and verify that the other solver’s solution is correct. I actually run both DRUP and the other solver, you can never be sure enough. Note that solution verification also complicates time-limiting: we don’t want to wait 30 minutes because a fuzz CNF is too complicated, and we don’t want to indicate an error just because the problem is hard.

Secondly, fuzzing is not only about generating CNFs that trigger bugs, but also about saving these problematic cases for later, as a form of regression tests. These regression tests need to be ran regularly, so that bugs that came up before don’t come up again. I have a large set of regression tests that I have accumulated over the years. These help me increase confidence that when I improve the solver, I don’t accidentally re-introduce bugs. My fuzzer system helps manage and run these regression tests.

Finally, we don’t just want to fuzz the solver through the CNF interface. SAT solvers typically expose a library interface where one can add clauses, solve (with assumptions) and check the conflict returned in terms of the assumptions given. For now, CryptoMiniSat’s library is fuzzed through a specialized CNF format, where “c Solver::solve()” lines are interspersed with the regular clauses. These lines indicate for the solver to call the solve() method and output the solution to a file. This file is then read by the fuzzing system and verified by copying parts of the file into another CNF and using the DRUP-checker and another SAT solver to verify the results. This simulates library usage without assumptions. Thanks to Lukas Prokop who alerted me to bugs in assumptions usage, assumptions-based solving is also simulated through “c Solver::solve( LIT LIT LIT…)” calls, where LITs are replaced with a random literals.

Future work

I want to do two things related to testing and fuzzing. First, I want to improve the checker so that it checks for more problems. I want to check the conflict returned when assumptions are used. Further, I want to check timeouts — this will require some coordination between the fuzzer system and the solver where times are printed that are later checked for correctness. Some optimisations must never take more than N seconds on a fast enough machine, and this could be checked relatively easily.

Second, I want to move CryptoMiniSat into a test-driven system. This will require some quite extensive code re-writing so that test-harnesses will be easier to write. However, it will help fix one issue that hasn’t been talked about, kind of like the elephant in the room: performance bugs. They are quite prevalent, and cannot be caught by simple fuzzing. They plague many SAT solvers, I’m sure, as I keep on finding them at every corner. They are the silent bugs that prevent solvers to be more performant, yet they don’t diminish the resulting solution — only the time takes to find it.

CryptoMiniSat 3.3 released

This is just a short note that CryptoMiniSat 3.3 has been released. This is mainly a bugfix release. I have managed to make a fuzzer that simulates library usage of the system by interspersing the CNF with “c Solver::solve()” calls and then checking the intermediate solutions. Checking is either performed by verifying that all clauses are satisfied, or if the solution is UNSAT, by using a standard SAT solver (I use lingeling). This turned up a surprising number of bugs. I have also fixed the web-based statistics printing which should now work without a hitch.

The non-bugfix part of the release is that CryptoMiniSat now saves memory by dynamically shortening and reallocating the watchlist pointer array and some other data structures. This can save quite a bit of memory on large, sparse instances.

GCC 4.5.2 at the SAT Competition’13

(Note update below)

Just a short note. All MiniSat-derived SAT solvers might give wrong results during the competition. No, MiniSat doesn’t have a bug. GCC has a giant bug. Vegard reported this years ago — I personally put about 12h tracking it down, posted it to the CryptoMiniSat mailing list, and Vegard took it up, stripped it down and reported it.

This is a well-known bug, there is a thread about it on the MiniSat mailing list and I personally asked the competition organizers back in 2011 not to use the 4.5.2(or .3?) they wanted to use. I used to have code to check for this bug (there is a handy check attached to the bug report), but I removed it, though maybe I should add it back. It’s fixed in 4.5.4+, still present in 4.5.3 where Vegard&me found it. I hope I will be able to convince the organisers this time around, too :) By the way, the option you need to pass to gcc to avoid the bug is “-fno-tree-pre” — though of course this turns off an optimisation and so slows down the final executable.

Update: The organisers decided to move to gcc 4.8.0. This is very good news. They also note that the speed of the solvers is better, which is also very good news. I am happy I contributed to this welcome improvement and I hope it doesn’t cause any delays or inconveniences to anyone.

Q-DIMM, an “innovation” by ASUS

Lately, I have been having boot problems with my computer: the system would sometimes fail to boot, and at other times, it displayed the wrong memory readings. I was puzzled, so I took a look. I have six memory DIMMs installed in an ASUS motherboard. Memory modules are usually retained in their slots using two latches:

The point of these latches is to keep the memory modules in place when the computer is moved around. They thus serve the same purpose as the screws for PCIe slots or the mounting holes for the CPU coolers. My motherboard, however, is made by ASUS, and it has a “feature” called Q-DIMM, which is supposed to ease the installation of memory modules when the system has the video card already installed. This “feature” is rather simple: the latch on the right is completely missing:

Unsurprisingly, over time, some of my memory modules simply came out from their slots, making the system completely unstable. And I am far from being the only one who has had this problem.

Most probably the person who came up with this “feature” wasn’t an engineer, but a PR person. It is however rather sad that a technological company such as ASUS should make technical decisions based on PR. By the above logic, I wonder why they didn’t remove both latches. And while they were at it, get rid of all those pesky screw holes for the PCIe slots, and the mounting holes for the CPU cooler, too — things would be much easier to install!

Seriously, though, this is just unbelievable. Fun part is, ASUS sells this “feature” as an innovation that is available only to their high-end (and more expensive) motherboards. I don’t know whether to laugh or cry that you have to spend less to get a more robust, stable system.