On Tue, Oct 20, 2009 at 11:22 AM, mhampton <hampto...@gmail.com> wrote: > > OK, I can reproduce that - I got an error after the first cell. > > After saving & quitting, and deleting the line: > reset() > > then re-launching that worksheet everything seems to work fine. So I > think this is something about the reset() function. I've never used > it before, so I am not sure what it is doing that messes things up. > > Do your problem-causing worksheets always have reset() in them > somewhere?
Reset would do things like deleting sagenb from the globals() namespace, which would exactly cause the problem you suggest! This can certainly be fixed though, i.e., by making reset a little more intelligent. > -Marshall > > On Oct 20, 12:02 pm, William Stein <wst...@gmail.com> wrote: >> On Tue, Oct 20, 2009 at 10:37 AM, lutusp <lut...@gmail.com> wrote: >> >> > Hello all: >> >> > Today I decided to try out the new VirtualBox/PuppyLinux virtual >> > machine for Windows users. It seems much nicer than the prior version >> > and I want to update my tutorial to make reference to it. >> >> > Also I wanted to see if I experienced the same issue I've been >> > experiencing with 4.1.2 running (or not running) my existing 4.1.1 >> > worksheets, e.g. a message saying "NameError: name 'sagenb' is not >> > defined" on execution of a rather complex cell. >> >> Can you enter your example athttp://demo.sagenb.orgor paste it to >> pastebin, or paste a link to it online. By just pasting it in an >> email it gets word wrapped, which yields it suspect. >> >> William >> >> >> >> >> >> > Imagine my surprise when I ran the new VM using VirtualBox under >> > Windows, uploaded my worksheets into it, and got the same result as on >> > my usual Fedora 11 platform: "NameError: name 'sagenb' is not >> > defined". This is true for any worksheet cell above a certain >> > complexity level (or a series of such cells). >> >> > So I tried a few different ways to transfer the worksheets. I used the >> > 4.1.2 "download all" feature to create a zip file of all my worksheets >> > and uploaded them all into the PuppyLinux/VirtualBox Sage VM runnin >> > gunder Windows, but with the same result. >> >> > Then I ran Sage 4.1.1 and created a zip archive of the old (4.1.1) >> > versions of the worksheets and tried uploading them into the >> > VirtualBox/PuppyLinux Sage 4.1.2 version, but that caused Sage to lock >> > up with a message saying "Searching for Sage Server ...". Things went >> > downhill from there and I finally had to reinstall the Sage VM under >> > VirtualBox. Which leads me to offer this warning -- don't try to >> > transfer pre-4.1.2 worksheets using the browser-based download/upload >> > cycle, as this may well disable the VM under Windows and require >> > reinstallation. >> >> The install of Sage in the virtual machine is read only, so it cannot >> be "messed up". >> I guess in theory the notebook state file in >> /root/sage_notebook.sagenb could get >> messed up though in some way that could make it so the server doesn't >> startup properly (say after a reboot), though I can't imagine anyway >> that could possibly happen through the notebook. >> >> How many worksheets are you uploading at once? The code is certainly >> there (I wrote it and many of us tested it) so one can upload <= 4.1.1 >> worksheets into 4.1.2. >> >> >> >> > Summary of the problem: basically, for any invocation of Sage 4.1.2, >> > it seems some worksheets, above a certain complexity level, will / >> > always/ cause the error described above. >> >> > Here is a simple duplication procedure for anyone running Sage 4.1.2 >> > -- it involves creating a new, empty worksheet, pasting the two cell >> > contents below into it, and executing them. >> >> > 1. Create a new, empty worksheet under Sage 4.1.2. >> >> > 2. Copy the content shown below between the asterisk lines into two >> > separate Sage worksheet cells. >> >> > 3. Execute the first cell -- sometimes this causes the error message, >> > sometimes not. >> >> > 4. Execute the second cell -- this always creates the error message >> > (in my experience). >> >> > ******************* BEGIN Cell 1 content >> > ******************************** >> > %auto >> > reset() >> > forget() >> > # special equation rendering >> > def render(x,name = "temp.png",size = "normal"): >> > if(type(x) != type("")): x = latex(x) >> > latex.eval("\\" + size + " $" + x + "$",{},"",name) >> > var('a b c d e f g h j k l x y z') >> >> > class Pair: >> > def __init__(self,d): >> > self.x = d[0] >> > self.y = d[1] >> > def __repr__(self): >> > return "%e,%e" % (self.x,self.y) >> >> > def show_mat(data): >> > yt = len(data) >> > xt = len(data[0]) >> > for y in range(yt): >> > for x in range(xt): >> > sys.stdout.write("%12g " % data[y][x]) >> > print("") >> > print("****") >> >> > def show_mat_latex(data,fn): >> > yt = len(data) >> > xt = len(data[0]) >> > ya = [] >> > for y in range(yt): >> > xa = [] >> > for x in range(xt): >> > xa.append("%12g " % data[y][x]) >> > ya.append(join(xa," & ")) >> > ys = join(ya,"\\\\") >> > # specify right justification >> > cstr = "r" * xt >> > mat = "$\\left( \\begin{array}{%s}" % cstr >> > mat += ys >> > mat += "\\end{array}\\right)$" >> > render(mat,fn) >> > print "" >> >> > # example data >> > data1 = [ >> > [-1,-1], >> > [0,3], >> > [1,2.5], >> > [2,5], >> > [3,4], >> > [5,2], >> > [7,5], >> > [9,4] >> > ] >> >> > def set_data(x): >> > return [Pair(n) for n in x] >> >> > # polynomial regression of order "p" >> > def polyregress(data,p,debug = False): >> > # matrix rows and columns = p+1 >> > p += 1 >> > n = len(data) >> > # precalculate matrix cell data array >> > mda = [n] + [sum(data[a].x^b for a in range(n)) for b in range >> > (1,2*p-1)] >> > # create/populate square matrix with appended column >> > m = [[mda[r+c] for c in range(p)] + [0.0] for r in range(p)] >> > if debug: show_mat_latex(m,"nmat2.png") >> > # populate RH appended column >> > for v in data: m[0][p] += v.y >> > for r in range(1,p): >> > m[r][p] = sum(v.x^r*v.y for v in data) >> > if debug: show_mat_latex(m,"nmat3.png") >> > # reduce matrix >> > mm=Matrix(RR,m) >> > mm.echelonize() >> > if debug: show_mat_latex(mm.rows(),"nmat4.png") >> > # extract result column >> > a = mm.column(p).list() >> > # build term list >> > y = 0 >> > for j in range(p): >> > y += a[j]*x^j >> > return y >> >> > # correlation coefficient (r^2) >> > def corr_coeff(data,fy): >> > r = 0 >> > sx = sx2 = sy = sy2 = sxy = 0 >> > n = len(data) >> > for v in data: >> > x = fy(x=v.x) >> > y = v.y >> > sx += x >> > sy += y >> > sxy += x * y >> > sx2 += x * x >> > sy2 += y * y >> > divisor = sqrt((sx2 - (sx*sx)/n) * (sy2 - (sy*sy)/n)) >> > if(divisor != 0): >> > r = ((sxy-(sx*sy)/n)/divisor)^2 >> > return r >> >> > # standard error >> > def std_error(data,fy): >> > r = 0 >> > n = len(data); >> > if(n > 2): >> > a = 0 >> > for v in data: >> > a += (fy(x=v.x) - v.y)^2 >> > r = sqrt(a/(n-2)) >> > return r >> >> > # data range >> > def list_minmax(data): >> > max = -1e6 >> > min = 1e6 >> > for v in data: >> > if(max < v.x): max = v.x >> > if(min > v.x): min = v.x >> > return(min,max) >> > ******************* END Cell 1 content >> > ********************************** >> >> > ******************* BEGIN Cell 2 content >> > ******************************** >> > # interactive version >> > data = set_data(data1) >> > mp = len(data)-1 >> > @interact >> > def _(p = (0..mp)): >> > y = polyregress(data,p) >> > dp = list_plot([[data[n].x,data[n].y] for n in range(len >> > (data))],rgbcolor='red') >> > lp = plot(y,x,list_minmax(data)) >> > cc = corr_coeff(data,y) >> > se = std_error(data,y) >> > lbl = text("correlation coefficient (r^2): %f\nStandard error: %f" >> > % (cc,se),(5,-2),rgbcolor='black',fontsize=10) >> > show(dp+lp+lbl,ymin=-5,ymax=7) >> > ******************* END Cell 2 content >> > ********************************** >> >> > After copying, pasting and running the two cells, you should see the >> > error message "NameError: name 'sagenb' is not defined" after either >> > running the first or second cell. And once the message has appeared, >> > it will appear on an attempt to run any subsequent cell, like this >> > one: >> >> > 2^32 >> >> > I think this is an actual bug, not a transient artifact of a >> > particular installation. >> >> > Other notes: >> >> > 1. The file README.txt bundled with the new Sage/Puppy Linux/ >> > VirtualBox virtual machine has Linux line endings, needs to be >> > converted using "unix2dos" for Windows users. The file is an important >> > rundown on how to install the VM, and the default Windows text editor >> > is too dumb to sort out line endings. >> >> > 2. Under Windows and while using MSIE 8, on creating a new worksheet, >> > the popup dialog to enter a name is suppressed by default and this >> > cannot be overridden for some reason. But the worksheet can be renamed >> > later using the File menu. >> >> > 3. Moving to Puppy Linux and VirtualBox was a smart move. They are >> > both better choices that the previous arrangement. >> >> > Thanks for reading! >> >> -- >> William Stein >> Associate Professor of Mathematics >> University of Washingtonhttp://wstein.org > > > -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org --~--~---------~--~----~------------~-------~--~----~ To post to this group, send an email to sage-devel@googlegroups.com To unsubscribe from this group, send an email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---
