Sage FAQ: Frequently Asked Questions

TableOfContents

1. Introduction

1.1. What is Sage?

Sage is a comprehensive open-source mathematics software suite that has the mission statement "Creating a viable free open source alternative to Magma, Maple, Mathematica, and Matlab." See http://www.sagemath.org/ for more details.

2. Getting Sage

2.1. Can I try out Sage without downloading anything?

Yes! Go to http://www.sagenb.org/ and set up a free account. If you log in, you will be working on a free Sage notebook server that will work identically to the one you get with Sage.

2.2. How do I get a Sage program I can run immediately?

Go to http://www.sagemath.org/download.html and click on the link for the binary for your operating system.

2.3. How do I get the Sage source code?

Go to http://www.sagemath.org/src/ to download the tar archive for any release of Sage.

2.4. How do I get a previous release of Sage?

Go to http://www.sagemath.org/src/ to download the tar archive for any release of Sage.

3. Installing and running Sage

3.1. How do I use the notebook with Firefox 3.0 beta 5?

There is [https://bugzilla.mozilla.org/show_bug.cgi?id=427081 a bug in Firefox 3.0 beta 5] that causes it to reject connections to the Sage notebook with the error "Certificate key usage inadequate for attempted operation. (Error code: sec_error_inadequate_key_usage)". One solution is to use a different browser, such as Firefox 2, Konqueror, Safari, Opera, or even Internet Explorer. Another solution is to run the notebook in insecure mode by using the command inotebook() instead of notebook(); then Firefox 3.0b5 will work. Finally, there is a rather tedious workaround:

1. Go to a notebook with a certificate which fails
2. Click on the warning sign next to the location bar, then "more information"
3. Click "View Certificate", and go to the Details tab # Click "Export", and save the file to your local machine

4. Open Firefox Preferences -> Advanced -> Encryption

5. Click "View Certificates", then "Import"
6. Import the file that you saved in step 4
7. Reload the notebook, you should see another warning message, which has a link "Or you can add an exception..." and the rest is straightforward.

3.2. How do I compile the source to Sage?

Download the source tar archive, extract the archive, change your directory to be inside of it, and read the README.txt file there. Basically, after making sure you have the proper prerequisite tools installed, you type make.

3.3. How do I run Sage on a platform other than VMWare or Windows?

Change your directory to the sage directory and run ./sage

To start an online notebook server, start Sage and type notebook() at the sage command prompt.

3.4. How do I run Sage with VMWare?

You must install the VMWare software (the free VMWare Player should work). Simply start the virtual machine using the VMWare software, wait for the virtual machine to boot up, then type notebook at the prompt.

3.5. How do I run Sage in Windows?

Windows is currently supported via the VMWare image, so see the instructions for running Sage under VMWare.

3.6. How do I run a parallel build?

export MAKE="make -j8" will enable 8 threads for parts of the build that support parallelism.

3.7. How do I run Sage in a browser that is not the system default

Issue this command "env SAGE_BROWSER=opera /usr/bin/sage -notebook" either from the command prompt or as a menu command for Sage. Assumes a Linux operating system, Opera as the browser, and I happen to use KDE as my desktop.

4. Developing in Sage

4.1. What tools do I need to develop in Sage?

You need the prerequisite tools listed in the README.txt file in the root directory of Sage.

4.2. Where is the source code to Sage?

You can browse the complete source code to everything in Sage at http://www.sagemath.org/hg/. This is a web interface to the Mercurial repository. The main source files are at http://www.sagemath.org/hg/sage-main?cmd=manifest;manifest=-1;path=/sage/. The other directories include docs directories, the package system, etc.

5. Working in Sage

5.1. How do I save an object so I don't have to compute it each time I open a worksheet?

The save and load commands will save and load an object, respectively. In the notebook, the DATA variable is the location of the data storage area of the worksheet. To save the object my_stuff in a worksheet, you could do save(my_stuff, DATA+"my_stuff") and to reload it, you would just do my_stuff = load(my_stuff, DATA+"my_stuff")

6. Getting help

6.1. How do I get help?

Sage has two very active email lists: http://groups.google.com/group/sage-devel and http://groups.google.com/group/sage-support. There are also two very active IRC channels: #sage-devel and #sage-support on freenode. Many developers also actively blog and also post other Sage-related tutorials and talks. See http://www.sagemath.org/help.html for a listing of these resources.

7. Other questions

---

• QUESTION: I'm using scipy or cvxopt or numpy from Sage and get type errors, e.g., "TypeError: function not supported for these types, and can't coerce safely to supported types."

• ANSWER: Redefine RealNumber to change the behavior of the Sage preparser, so decimal literals are floats instead of Sage arbitrary precision real numbers, for example:

  sage: from scipy import stats
  sage: RealNumber=float
  sage: stats.ttest_ind(list([1,2,3,4,5]),list([2,3,4,5,.6]))
  (array(0.076752955645333687), 0.940704902474)

---

• QUESTION: I created the file SAGE_ROOT/devel/sage/sage/calculus/stokes.py, and have changed my mind and want to completely delete it from Sage, but it keeps coming back (i.e. it is still importable) when I type sage -br. What do I do?

• ANSWER: Delete both SAGE_ROOT/devel/sage/build/sage/calculus/stokes.py and SAGE_ROOT/devel/sage/build/lib.*/sage/calculus/stokes.py.

---

• QUESTION: Does sage contain a function similar to Mathematica's ToCharacterCode[]? That is, I'd like to covert something like "Big Mac" to ascii numerals for further processing. Thanks

• ANSWER: Yes, use ord, e.g., map(ord,'abcde') outputs [97, 98, 99, 100, 101].

---

• QUESTION: Is there anything so Sage can be made to automatically execute commands on startup?

• ANSWER: Yes, just make a file $HOME/.sage/init.sage and it will be executed any time you start sage.

---

• QUESTION: My Sage upgrade failed with missing gmp symbols on OSX 10.4. What can I do?
• ANSWER: Moving a sage install on OSX 10.4 and then upgrading anything that is linked against NTL leads to link errors due to missing gmp symbols. The problem is the link mode with which the dynamic NTL is created. I have a fix, but I am currently verifying that it really fixes the issue. Everything that is linked against NTL needs to be recompiled, i.e. singular and cremona at the moment. To add to the confusion: This is not an issue on OSX 10.5. A fix for this issue went into 2.8.15, so please report if you see this with a more current Sage release.

---

• QUESTION: When I compile Sage my computer beeps and shuts down or hangs.
• ANSWER 1: Compiling Sage is quite taxing on the CPU. The above behavior usually indicates that your computer has overheated. In many cases this can be fixed by cleaning the CPU fan and assuring proper ventilation of the system. Please ask your system administrator or a professional to do this in case you have never done this since you can potentially damage your system.
• ANSWER 2: For Linux users, if you suspect that the compilation fails because of a resource issue, a fix might be to edit your /etc/inittab so that Linux boots into run level 3. The file /etc/inittab usually contains something similar to the following snippet:

  #   0 - halt (Do NOT set initdefault to this)
  #   1 - Single user mode
  #   2 - Multiuser, without NFS (The same as 3, if you do not have networking)
  #   3 - Full multiuser mode
  #   4 - unused
  #   5 - X11
  #   6 - reboot (Do NOT set initdefault to this)
  # 
  id:5:initdefault:

  which directs your Linux distribution to boot into a graphical login screen. Comment out the line "id:5:initdefault:" and add the line "id:3:initdefault:", so that you now have something like:

  #   0 - halt (Do NOT set initdefault to this)
  #   1 - Single user mode
  #   2 - Multiuser, without NFS (The same as 3, if you do not have networking)
  #   3 - Full multiuser mode
  #   4 - unused
  #   5 - X11
  #   6 - reboot (Do NOT set initdefault to this)
  # 
  # id:5:initdefault:
  id:3:initdefault:

  Now if you reboot your system, you'll be greeted with a text based login screen. This allows you to log into your system with a text based session from within a virtual terminal, which doesn't consume as much system resources as would be the case with a graphical session. Then build your Sage source distribution from within your text based session.

---

• QUESTION: When I run doctests on OSX I see the following messages, but in the end Sage reports that everything went fine:

  sage -t  devel/sage-main/sage/libs/pari/gen.pyx
  python(4563) malloc: *** vm_allocate(size=4096000000) failed (error code=3)
  python(4563) malloc: *** error: can't allocate region
  python(4563) malloc: *** set a breakpoint in szone_error to debug

• ANSWER: The issue above isn't a doctest failure, it is an error message printed by the system and it is exactly what one expects to see -- in that particular doctest, we try to allocate a very large list in Pari that doesn't fit into physical memory (it is at least 100GB in size). So OSX tells you that it couldn't allocate a chunk of memory roughly 4 GB in size, which is expected, since Sage is still a 32 bit application on OSX.

---

• QUESTION: Sage 2.9 and higher fails compiling ATLAS on Linux. How can I fix this?

• ANSWER: The most likely cause is enabled power management. Disabling it should fix the problem. Depending on your flavor of distribution, this might either be possible with some nice GUI tool or not. On the command line do the following as root for each CPU you have: /usr/bin/cpufreq-selector -g performance -c #number CPU. On Ubuntu try disabling "Power Manager" via "System --> Preferences --> Sessions" under the "Startup Programs" or using cpufreq-set via command line.

---

• QUESTION: Sage fails with the error message restore segment prot after reloc: Permission denied. What is wrong?

• ANSWER: The problem is related to SELinux: http://www.ittvis.com/services/techtip.asp?ttid=3092. We are currently tracking this issue at http://www.sagetrac.org/sage_trac/ticket/480.

---

• QUESTION: When I start Sage, SELinux complains that '/path/to/libpari-gmp.so.2' requires text-relocation. How can I fix it?
• ANSWER: The problem can be fixed by running the following command "chcon -t textrel_shlib_t /path/to/libpari-gmp.so.2"

---

• QUESTION: Upgrading Sage went fine, but now the banner still shows the old version. How can I fix this?

• ANSWER: Try doing sage: hg_scripts.merge() followed by sage: hg_scripts.commit(). As an alternative, you can simply try hg_scripts.pull().

---

• QUESTION: How do I run sage in daemon mode, i.e. as a service?

• ANSWER: We currently do not have a ready-to-go solution. There are several possibilities: Use screen, nohup or disown. We are tracking the issue at http://www.sagetrac.org/sage_trac/ticket/381 - so stay tuned.

---

• QUESTION: I downloaded a Sage binary and it crashes on startup with Illegal instruction. What can I do?

• ANSWER: The binaries have been built for a newer architecture than you have. We want to acquire an older machine and install a bunch of minimal Linux images on it for building Sage binaries to avoid this, but it hasn't happened yet. One solution is to build from source. Another solution is to have your distribution's ATLAS package installed. That package has to provide a dynamic version of the ATLAS libaries from the 3.8 release. Then go into $SAGE_LOCAL/lib and delete libatlas.*, libf77blas.* and libcblas.*. That needs to be repeated every time you update Sage. Certain Via CPUs like Nehemiah also seem to have trouble with the binaries we provide and the solution seems to be to build from source since ATLAS isn't the culprit in that case. We are investigating the issue.

---

• QUESTION: I just downloaded version 2.8.15 for Mac OSX and tried to run notebook() and dyld is unable to load libintl.3.dylib. I don't have a libintl.3.dylib in usr/local/lib and I didn't find it in $SAGE_ROOT/local/lib. Is there a workaround?

• ANSWER: Yes, put the libintl3.dylib from http://sagemath.org/SAGEbin/apple_osx/intel/10.4-extra_files/ in SAGE_ROOT/local/lib/. Sage 2.8.15 and later contain a copy of the library, so please let us know if you experience the problem with any later release.

---

• QUESTION: I am using Mac OSX. Where do I put the jsMath "font" directory to eliminate the red box?

• ANSWER: See http://www.math.union.edu/~dpvc/jsMath/download/jsMath-fonts.html where it says "For Mac OS X users: download and unpack the archive, then drag the fonts to your Library/Fonts folder (or to the FontBook, or just double-click them and press the "install" button).".

---

• QUESTION: The show command for plotting 3D objects does not work.
• ANSWER 1: Since Sage 2.9.2 we have switched to using jmol, a Java applet, for 3D plotting. There are several possibilities for the cause of the malfunction: You do not have Java installed at all or the Java installed is an older GNU based alternative Java implementation, which causes some yet to determine problem. A solution to both issues is to either install Sun's Java SDK or to update the GNU based Java implementation. As of January 2008 Debian's Java in testing works, but stable does have problems.

• ANSWER 2: If you are running a brand new (as of April 2008) Ubuntu 8.04, they ship the Java Plugin by IcedTea. This is basically a good idea, but a bit too early since it is broken. Either wait for an update or uninstall the IcedTea Plugin and install the "SUN Java 6 Plugin". Later, switch back to IcedTea, since it is based on OpenJDK 7 (or SUNs Java 7) which is the next Java version. You can check for the used plugin in Firefox 3 by typing "about:plugins" into the URL bar. [https://bugs.launchpad.net/ubuntu/+source/icedtea-java7/ read more here at launchpad]

---

• QUESTION: May I use Sage tools in a commercial environment?
• ANSWER: YES! Absolutely! Basically the *only* constraint is that if you make changes to Sage itself and redistribute this changed version of Sage publicly, then you must make these changes available to us so that we can put them into the standard version of Sage (if we want). Otherwise, you are free to use as many copies of Sage as you want completely for free to make money, etc., without paying any license fees at all.

---

• QUESTION: I want to write some Cython code that uses finite field arithmetic but cimport sage.rings.finite_field_givaro fails. What can I do?

• ANSWER: You need to give hints to Sage so that it uses C++ (both Givaro and NTL are C++ libraries), and it also needs the GMP and STDC C++ libraries. Here is a small example:

  # These comments are hints to Sage/Pyrex about the compiler and
  # libraries needed for the Givaro library:
  #
  #clang c++
  #clib givaro gmpxx gmp m stdc++
  cimport sage.rings.finite_field_givaro
  # Construct a finite field of order 11.
  cdef sage.rings.finite_field_givaro.FiniteField_givaro K
  K = sage.rings.finite_field_givaro.FiniteField_givaro(11)
  print "K is a", type(K)
  print "K cardinality =", K.cardinality()
  # Construct two values in the field:
  cdef sage.rings.finite_field_givaro.FiniteField_givaroElement x
  cdef sage.rings.finite_field_givaro.FiniteField_givaroElement y
  x = K(3)
  y = K(6)
  print "x is a", type(x)
  print "x =", x
  print "y =", y
  print "x has multiplicative order =", x.multiplicative_order()
  print "y has multiplicative order =", y.multiplicative_order()
  print "x*y =", x*y
  # Show that x behaves like a finite field element:
  for i in range(1, x.multiplicative_order() + 1):
      print i, x**i
  assert x*(1/x) == K.one_element()

  To find out more, type sage.rings.finite_field_givaro.FiniteField_givaro. at the Sage prompt and hit tab, then use ?? to get more information on each function. For example: sage.rings.finite_field_givaro.FiniteField_givaro.one_element?? tells you more about the multiplicative unit element in the finite field.

---

• QUESTION: How do I make the VMware appliance for Windows automatically login as "sage"?

• ANSWER: Follow http://ubuntu-utah.ubuntuforums.org/showthread.php?t=303319. Short version: put in the file /usr/bin/autologin the text

  /bin/login -f sage

  and make this file executable; then edit /etc/event.d/tty1, comment out

  respawn /sbin/getty 38400 tty1

  and add

  respawn /sbin/getty -n -1 /usr/bin/autologin 38400 tty1

  Now every time the appliance reboots, it will automatically load directly to the sage: prompt. Warning: This will make it nearly impossible to get a terminal prompt! So only do this if you don't plan on any further management.

---

• QUESTION: When running Sage under VMware, if you log in under manage you are not given the permissions to create a file!
• ANSWER: Type "sudo su" before creating files.

---

• QUESTION: I'm getting weird build failures on OSX. How do I fix this?
• ANSWER: Search the build log (install.log) to see if you're getting "fork: Resource temporarily unavailable.". If so, try the following. Create (or edit) /etc/launchd.conf and include the following:

  limit maxproc 512 2048

• then reboot. See [http://www.macosxhints.com/article.php?story=20050709233920660 this page] for more details.

---

• QUESTION: How do I use the bitwise XOR operator in Sage?

• ANSWER: Define two variables, for example a = 5; b = 8, and evaluate a.__xor__(b), 13. You can also do (5).__xor__(8) (the parentheses are necessary so that Sage doesn't think you have a real number). There are several ways to define a function: xor = lambda x, y: x.__xor__(y) and then do xor(3, 8). Another option, which sneaks around the Sage preparser, is def xor(a,b):  return eval("%s^%s"%(a,b)). You can also turn off the Sage preparser with preparser(False) -- then ^ will work just like in Python, and you can later turn on the preparser with preparser(True). (That only works in command-line Sage; in a notebook, switch to Python mode.)

---

• QUESTION: When I try to use LaTeX in the notebook, it says it cannot find fullpage.sty!

• ANSWER: That's not a question. But we can help you solve your problem. The general -- but perhaps not very helpful -- answer is that you need to install fullpage.sty into a directory searched by TeX. In Ubuntu (and probably many other Linux distributions), you should install the texlive-latex-extra package. If that's not available, try installing the tetex-extra package. If you are using OS X, you will have to use whatever TeX distribution you use to get fullpage.sty (if you use [http://www.tug.org/mactex MacTeX], it's likely already installed). If you are using the VMware image in Windows, you'll need to log into the VMware image and install texlive-latex-extra there.

ToDo

• QUESTION: Sage fails to compile on OSX 10.4
• ANSWER: Most likely resource issue.
• QUESTION: Notebook doesn't work
• ANSWER: networking issues, firewall blocking, proxy setting screwed up

• Individual FAQ entries should be referable by a URL, possibly http://wiki.sagemath.org/faq?someid=something

• You can do that with page anchors: http://wiki.sagemath.org/faq?#something. MoinMoin [http://moinmo.in/HelpOnLinking can insert page anchors] but it doesn't seem like that facility is turned on for this installation. If we could get that enabled, we could insert anchors for all the questions on this page.