[TECH] Ideas for Optimizing Design pattern implementations with Stack Collapsing

One major drawback I guess with all these object oriented systems I guess is performance, since people write the code so that its extensible it always ends up creating deep stack sizes, recently I was looking into (Jmol) this structure visualization tool supports several input format descriptions for the structures (pdb,cif,molxyz....). This is how they hide format details from the display code
JmolAdapter (abstract class)
==> SmarterJmolAdapter (this contains a interface called AtomSetCollection ). So depending on the input file we have several AtomSetCollection readers like PdbAtomSetCollection etc...

Although I came to a conclusion that to implement the structural alignment algorithm into Jmol, I need to implement this AtomSetCollection which structurally aligns the protein structures, but I guess there are several draw backs of the implementation of object oriented java implementation, the cost of creating an extensible design does not come for free it comes at the cost of performance, I found that a simple command execution could end up creating a stack size of 32 this is what concerns me is there a way we can collapse the stack when we know that the intermediate functions on the stack are just delegating the call to the actual instance, I guess this STACK COLLAPSING technique can always be applied when ever the Adapter design pattern is used. For example see the below stack of size 32, its not doing any thing great its just opening a new script file, because of the way the code is written (use of design patterns) the stack size seem to increase a lot and ULTIMATELY ALL THESE PATTERNS ARE JUST DELEGATING A FUNCTION CALL TO TO FUNCTION ON TOP OF THE STACK, I'm think of ways to improve the delegation since at each level of the stack you are doing a look up and it increases linearly with the size of the stack.

  [1] org.jmol.viewer.ScriptManager.addScript (ScriptManager.java:69)
  [2] org.jmol.viewer.ScriptManager.addScript (ScriptManager.java:52)
  [3] org.jmol.viewer.Viewer.evalStringQuiet (Viewer.java:3,152)
  [4] org.jmol.viewer.Viewer.evalString (Viewer.java:3,119)
  [5] org.jmol.viewer.Viewer.openFile (Viewer.java:1,379)
  [6] org.openscience.jmol.app.Jmol$OpenAction.actionPerformed (Jmol.java:1,435)
  [7] javax.swing.AbstractButton.fireActionPerformed (AbstractButton.java:1,849)
  [8] javax.swing.AbstractButton$Handler.actionPerformed (AbstractButton.java:2,169)
  [9] javax.swing.DefaultButtonModel.fireActionPerformed (DefaultButtonModel.java:420)
  [10] javax.swing.DefaultButtonModel.setPressed (DefaultButtonModel.java:258)
  [11] javax.swing.AbstractButton.doClick (AbstractButton.java:302)
  [12] javax.swing.plaf.basic.BasicMenuItemUI.doClick (BasicMenuItemUI.java:1,051)
  [13] javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased (BasicMenuItemUI.java:1,092)
  [14] java.awt.Component.processMouseEvent (Component.java:5,517)
  [15] javax.swing.JComponent.processMouseEvent (JComponent.java:3,135)
  [16] java.awt.Component.processEvent (Component.java:5,282)
  [17] java.awt.Container.processEvent (Container.java:1,966)
  [18] java.awt.Component.dispatchEventImpl (Component.java:3,984)
  [19] java.awt.Container.dispatchEventImpl (Container.java:2,024)
  [20] java.awt.Component.dispatchEvent (Component.java:3,819)
  [21] java.awt.LightweightDispatcher.retargetMouseEvent (Container.java:4,212)
  [22] java.awt.LightweightDispatcher.processMouseEvent (Container.java:3,892)
  [23] java.awt.LightweightDispatcher.dispatchEvent (Container.java:3,822)
  [24] java.awt.Container.dispatchEventImpl (Container.java:2,010)
  [25] java.awt.Window.dispatchEventImpl (Window.java:1,791)
  [26] java.awt.Component.dispatchEvent (Component.java:3,819)
  [27] java.awt.EventQueue.dispatchEvent (EventQueue.java:463)
  [28] java.awt.EventDispatchThread.pumpOneEventForHierarchy (EventDispatchThread.java:242)
  [29] java.awt.EventDispatchThread.pumpEventsForHierarchy (EventDispatchThread.java:163)
  [30] java.awt.EventDispatchThread.pumpEvents (EventDispatchThread.java:157)
  [31] java.awt.EventDispatchThread.pumpEvents (EventDispatchThread.java:149)
  [32] java.awt.EventDispatchThread.run (EventDispatchThread.java:110)

[TECH] Association rules of by Data Mining (TM Algorithm) on Cancer Data.

I have datamined the Cancer data at http://breastscreening.cancer.gov/rfdataset/ using the TM(Transaction Mapping) and FP-Growth algorithm, this is what I have done to mine the association rules.

1. Randomly partition the data into two parts, I partitioned the data into part1 of size = 148458 records, part2 of size = 153897.
2. Used the part1 (148458 records) and found association rules of support >=0.4 and confidence >=0.4 , I got 72 rules from this.
3. For each of the rule (in step 2) I found the support and confidence of each of the rules in part2, it looks like the support and confidence is close to the support and confidence in training data (part1).

The 72 rules of step1 [
http://www.engr.uconn.edu/~vkk06001/CancerDataMining/rules.txt ]

Support and Confidence of each of this rules in part2
[http://www.engr.uconn.edu/~vkk06001/CancerDataMining/training_result.txt ]

I have made the rules human readable removing all the encoding please
see the rules
[
http://www.engr.uconn.edu/~vkk06001/CancerDataMining/human_readable.txt ]

These are in the following format
==============RULE:1=================
SUP:0.402 ,CONF:0.412,TRAIN_SUP:0.404,TRAIN_CONF:0.414
{
Diagnosis of invasive breast cancer within one year of the index
screening mammogram = no,
}
IMPLIES ===>
{
Diagnosis of invasive or ductal carcinoma in situ breast cancer within
one year of the index screening mammogram = no,
menopaus = postmenopausal or age>=55,
hispanic = no,
}
==============RULE:2=================

SUP indicates support of this rule in part2 , CONF indicates confidence of this
rule in part2, TRAIN_SUP indicates the support of this rule in part1 and
TRAIN_CONF indicates the confidence of this rule in part1.

These rules may not make any sense for me but it might make sense for a cancer doctor. There are several useful perl programs for people who want to do some datamining please feel free to use them http://www.engr.uconn.edu/~vkk06001/CancerDataMining , let me know if you have any questions.

[TECH] An observation to merge upper convex hulls in O(log(n)) time rather than O(log^2(n)).

The well known divide and conquer algorithm for finding convex hull for a given set of points, needs to merge smaller hulls H_1 and H_2 for doing this merge the algorithm uses lemma 3.2 (in Book Fundamentals of Computer Algorithms). This lemma essentially finds the tangent line (u,v) in O(log^2(n)) time.

We can in fact merge the hulls in more efficient manner, the observation is based on the fact that any point with maximum y-coordinate should definitely be on the hull. Let p1 and p2 be the points in hulls H_1 and H_2 with maximum y-coordinate, then we can safely state that either p1 or p2 will be on the combined hull of H_1 and H_2, we can determine which of these two points lie on the merged hull by comparing the y-coordinates of p1,p2. Among these two the point with maximum y-coordinate will definitely be on the merged hull so one end of the tangent line (u,v) is fixed, the other end of the tangent line can be probed in O(log(n)) time, this basically saves the extra O(log(n)) time which is spent previously in lemma 3.2 for finding the other end of tangent in H_2

[TECH] Hanging simulation..

I came across a interesting problem in which the entire simulation was hanging just because of an extra non-sensitive always block , in the verilog code the statement "always dummy_reg = in;" was causing both VCS and NC-VERILOG hang. Theoretically speaking irrespective of what I do in my design the simulation should stop after 500 steps because I have a "#500 $finish" in the initial block of the module "TestHangMux", although I got around this problem by removing the "dummy_reg" totally in the multiplexer, but I still don't understand why the simulation was hanging irrespective of the "#500 $finish" statement, is it because we have multiple non-sensitive "always" statement? the LRM(Language Reference Manual) says that all the "always" blocks execute in parallel just like parallel processors in that that the statement "#500 $finish" should have executed in parallel and stop the simulation but why it hangs?

===================================
module HangMux(in,sel,out);
input [1:0]in;
input sel; output out;
reg [1:0]dummy_reg;
reg out;

always @(sel) begin
    case(sel)
        0: out = dummy_reg[0];
        1: out = dummy_reg[1];
    endcase 
end

always dummy_reg = in;


endmodule

module TestHangMux(out_net);
output out_net;
wire out_net;
reg [1:0]in_reg;
reg sel;

initial begin
 in_reg = 2'b01;
 sel = 0;
#500 $finish;
end

always begin
#10 sel = ~sel;
end

HangMux hang_me (in_reg,sel,out_net);
endmodule
==============================

[TECH] Finding frequent itemsets faster than FP-Growth algorithm

I wanted to implement my prime-number mapping intersection algorithm into the TM(Transaction Mapping) Algorithm, I got the FP-Tree implementation from PERL FP Tree and was trying to test this on a data of around 300,000 records, it works till 10,000 records with support and confidence of 0.8 and 0.9 and fails if the number of records > 20,000. I'm not sure if its a perl bug but the following code which is the cause of the problem seems difficult to understand

===================================================================
@association_rules = map $_->[0], (sort {$b->[1] <=> $a->[1]} 
      (map [$_, $_->confidence], @association_rules));      
===================================================================

I tried to bless the reference $_ but it did'nt work. The following is the error it gives.

[vamsik@abadon Tree-FP-0.04]$ !perl
perl test_vamsi.pl
Setting support
Mining rules...
Can't call method "confidence" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/Tree/FP.pm line 397,  line 20001.

I need to fix this and send it to the FPTree maintainer tomorrow. I guess its really a issue to implement the FPTree in perl because of the speed and time especially when the algorithm need to work on huge data just in my case. A good idea is to re-write FPTree in C and extend TM based on that and compare the results.

[TECH] why is ((unsigned long)a_ptr+(unsigned long)b_int) not equals (a_ptr+(unsigned long)b_int)

I was looking at some code today on SGI super computer, and wanted to make sure that there are no 32-64 bit problems in the code since SGI was super computer. I found the following thing to be interesting

<---------------------->
((unsigned long)a_ptr+(unsigned long)b_int)!=
          (a_ptr+(unsigned long)b_int)
<---------------------->

That is if I cast both the operands of binary + to (unsigned long) the value I get from that addition is different from if I cast just one operand of binary + to (unsigned long), whats the compiler doing here? since if both the operands to binary + are unsigned long and the value(no.of bits) could be larger than sizeof(unsigned long) is it the reason why I get different values here?, I couldn't find this in FAQ.

[TECH] Verilog incompatabilities between 'ncverilog' and 'vcs'

Thanksgiving vacation may be fun for some but its really not fun if your IT department is taking a break, our Synopsys License server has been down for last few days all my emails are vain no one responds. I used 'vcs' to compile all my verilog code all these days, now I'm helpless.....how can we solve this problem.
I want to get some synthesis metrics for the Sequence Alignment design, although Synopsys License server is down looks like the Cadence License server is up :). Thats good news but whats equivalent to 'vcs' in Cadence....'NCVERILOG' I found 'ncverilog' and try to compile all my design modules now the in-compatibility, NC-Verilog don't like to see any thing in the module description until all the port list is filled up,but vcs scans the code of the entire declaration list before checking if the port list is filled up (I guess thats the way it should be the algorithm should be very general). I like 'vcs' and not impressed by 'NC-Verilog' but unfortunately I have to live with it for few more days, by porting my verilog code...sounds crazy I have ported code on machines different processors but the way these compilers are build is really crazy....

[TECH] Iso-spectral and Non-Isomorphic Graphs (PINGS)

Having the same spectrum for the adjacency matrix is a Necessary but not sufficient condition for Graph Isomorphism, our recent algorithmic result states a conjecture that every graph is characterized by its Family of Spectra, rather than Spectrum itself.

I have been doing some work on efficient algorithms for generating PINGS (Pair of Isospectral and Non-Isomorphic Graphs), I wrote a program which can search for PINGS in a very efficient manner, I found some interesting results there are no PINGS for n=2,3,4 for n=5 we have one PING (see the picture) it happens that its the only PING for n=5 it has a symmetric spectrum of {-2,0,0,2}. Also I found a very interesting result that there cannot be more than two INGS(Iso-Spectral and non-isomorphic graphs) which share the same spectrum so if INGS exists they exist as PINGS, I was curious if they exist something like XINGS X=P or T or ... but it happens its just P (only a pair). There are 5 PINGS for n=6 for n=7 there are 55 PINGS see the list at http://trinity.engr.uconn.edu/~vamsik/n.7.

[TECH] Design of my first chip (A sequence Aligner O(n) space implementation)

Designing hardware is totally different from writing software, writing verilog code is totally different from writing software 'C' programs, often a software engineer tries to solve the problems using loops,arrays etc.. unfortunately implementing the same algorithm in hardware is totally different. I had my experience in designing a chip (verilog code) for finding edit distance between two strings this has a well known O(n^2) dynamic programming based algorithm. Now the trick is how do you create a hardware which realizes the two for loops in the O(n^2) algorithm, after quite a bit of thinking I came up with a solution which involves just SHIFTERS,MULTIPLEXERS and ADDERS. I'm not aware of any such hardware implementation of edit distance algorithm till now...I'm tempted to share my design diagram on the blog but I cannot do it until it gets published some where....

My design flow is as follows (verilog)->vcs; (libs+verilog)->Design Compiler; and I will use cadence virtuso (ICFB) for my placement and routing and also extraction; Will use HSPICE/Nanosim and spectre for postlayout simulation.

[TECH] A simple O(n^2) time algorithm to construct the Ultra-metric trees.

Given a matrix 'D' which is symmetric an Ultra-metric tree 'T' is a binary tree with internal nodes corresponding to D(i,j) and leaves corresponding to rows in the matrix 'D', and a path from the root to the leaf must be strictly decreasing (Ultra-metric tree). Also D(i,j) is the lowest common ancestor for 'i' and 'j'.
The problem is given 'D' we need to figure out corresponding 'T'.

The well know fact about the Ultra-metric trees is that if we take any 3 leaves i,j,k the maximum is not unique (e.x D(i,j)=5, D(j,k)=6,D(i,k)=5) we have D(i,j) and D(i,k) having same value.
How do we test if D is Ultra-metric?

• A trivial solution is O(n^3).
• The Errata shows construction of Ultra-metric trees in O(n^2) and asks a question if we can check for the Ultra-metric property in O(n^2) ? which my next item answers affirmatively.
• My observation is we can partition the leaves of the ultra-metric tree with out any need of building a complete weighted graph as in Gusfields solution, one fact is that every row in D is going to have a maximum (global) we don't need to spend O(n^2) (comparing all the elements in the matrix D) to find one. The algorithm below we perform such a check if an ultra-metric tree exists and also builds one.

  
  L = {1,2,....n};
  UltraMetricPartition(L){
   i = select_a_random_element_in(L) ;
   max = find_max(D(i,*)); /*Takes linear time*/
   /*max = D(i,q) && q should be in L*/
   Part_q = {};
   Part_i = {};
   foreach(j in L){
      if(j!=i){
          if(D(j,i)<=max && D(j,q)==max){
               Part_i += {j};
          }else if(D(j,q)<=max && D(j,i)==max){
               Part_q += {j};
          }else{
             printf("D is not ultra-metric");
             return 0;
          }
      }
   }
   UltraMetricPartition(Part_i);
   UltraMetricPartition(Part_q);
  
  }
  
  

Running time would be T(n) = T(n-k) + T(k) + O(n), clearly its quadratic O(n^2).

[TECH] Implementing Reliability(FEARLESS) on top of FUSE

FUSE is a user space file system implementation framework, the file system implementation can run as a user process and interact with the VFS of the kernel through a named pipe /dev/fuse, FUSE comes by default with all kernels > 2.6.8

"Any data which persists on just one disk is very unreliable" , I was talking with Rohit couple of days back and he compared disk as an "Electric Bulb", and u know about the filament in the bulb it can go off any time. So what do you think of your laptop how many disk's does it have? JUST ONE.....thats extremely unreliable until and unless your system is not backed up every day. So how can we get the reliability achieved by RAID (Redundant Array of Inexpensive Disks) ? the answer is persist what is called an "ACTIVE DATA" on some thing like FLASH memory and we can integrate this with a backup mechanism to get good reliability for personal storage devices like laptops. FEARLESS is idea which came up with this reliability for personal storage devices, you can read paper by Dr.Chandy.

Our IDEA is now to realize FEARLESS using FUSE and rsync (for backup), so FEARLESS would be just another file system similar to SSHFS but very reliable

Cheers!
Vamsi.

[BDAY] unsigned char age = age++;

Today happened to be my birthday, we just need an unsigned char to represent age, can you tell whats wrong with the code in the title (or below?).

static unsigned char age;

void Birthday(){
  age = age++;
}

Looks like the Standard 'C' says the value in the age is undefined ? because the assignment (=) is not a sequence point where the side effects (++,--) are settled. That can make the age of the person remain the same or increase it by one its ambiguous.

Cheers!
Vamsi. google index this

[TECH] O(n^2/(log(n)^2)) time algorithm for finding edit distance. [How does it feel when you know have reinvented the wheel :(]

Yesterday night during the workout suddenly I thought about what will happen if we encode the t-vector {-1,0,1}in the Four Russian algorithm as an integer.....the idea was a BOOM! I really felt like EUREKA! just like Archimedes thought when he discovered the law of flotation, I felt that suddenly I speedup the edit-distance dynamic programming algorithm which is O(n^2) by a factor of O(log^2(n)), it was really great I spend working on the details all special cases and written up every thing was great till then. I discussed the solution with Dr.Wu and found that it was actually solution to some exercise problem in Gusfield's book which says that in a RAM based computation model the copy of vector 't' can be done in O(log(t)) time.

How do you feel when you know some thing which you are exited just slips from you ? its very painful and its like killing you, but thats the way the world is its full of SMART people and any path which you are taking might have been taken before........

[TECH] Generic Randomized Quicksort algorithm.

Adding to my own collection of generic data structures, today I added a generic Randomized Quicksort algorithm, I need a good sorting routine in the SAPE algorithm for sorting distances. I want to makesure that it can sort any kind array (array of char's,int's,float's,double's and also structures).

/*A generic Randomized Quicksort:
 *The key idea of being generic comes
 *from the fact that you take a memory 
 *block and size of each element and 
 *sort this memory chunk, so we always
 *deal with address's.
 *
 *
 *Sep 20,2007 vamsik@engr.uconn.edu
 **/
#include
#include
#include
#include
#include
#include "RandQsort.h"

/*INPUT: swap_routine,compare_routine
 * swap_routine: The algorithm gives the 
 * (void *)'s swap_routine of two things
 * which need to be swapped.
 *
 * compare_routine: The algorithm gives the
 * (void *)'s to the compare_routine its 
 */
static char QSORT_RAND_SEED=0;
static void (*swap_routine)(void *,void *) = NULL;
static unsigned char (*compare_routine_l)(void *,void *) = NULL;
static unsigned char (*compare_routine_g)(void *,void *) = NULL;
static time_t t_rqsort;
unsigned int GetPivot(void){
 if(!QSORT_RAND_SEED){
  assert(((time_t)-1)!=time(&t_rqsort));
  srand(t_rqsort);
  fprintf(stdout,"Setting RAND_SEED to %d \n",t_rqsort);
  QSORT_RAND_SEED=1;
 }
 return ((unsigned int)rand());
}
/*Avoid loosing the pivot during swaps*/
void UpdatePivot(void **pivot,void **i,void **j){
 if(*i==*pivot){
  *pivot = *j;
 }else if(*j == *pivot){
  *pivot = *i;
 }
}
/*Take a memory address location and size 
of the data items[Inplace partition]*/
static void PartitionWithPivot(void* start,void* end,
unsigned int dsize){
 void *pivot=NULL;
 void* i=start;
 void* j=end;
 unsigned int p_index = GetPivot();
 if(start==end){
  return;
 }
 p_index %= (((unsigned int)(end-start))/dsize);
 pivot=(void *)((unsigned long)start+
  (unsigned long)((p_index)*dsize));
 while(i=start)){
   j-=dsize;
  }
  /*Swap i,j*/
  if(istart){
  swap_routine(pivot,(void *)(i-dsize));
  PartitionWithPivot(start,(void *)(i-(2*dsize)),
  dsize);
 }
 if((i+dsize)<=end){
  PartitionWithPivot(i,end,dsize);
 }
}
/*Call PartitionWithPivot recursively*/
void RandQsort(void *start,void *end,unsigned int dsize,
void_void_fptr sroutine,bool_void_fptr croutine_l){
 swap_routine = sroutine;
 compare_routine_l = croutine_l;
 assert(swap_routine && compare_routine_l);
 PartitionWithPivot(start,end,dsize);
}
#ifdef UNIT_TEST_RQSORT
/*TEST1:Testing for chars*/
unsigned char CharCompare_L(void *a,void *b){
 return ((*((char *)a))<=(*((char *)b)))?1:0;
}
unsigned char CharCompare_G(void *a,void *b){
 return ((*((char *)a))>=(*((char *)b)))?1:0;
}
void CharSwap(void *a,void *b){
 char temp=*((char *)a);
 *((char *)a) = *((char *)b);
 *((char *)b) = temp;
}
void TestCharSort(){
 char *data = malloc(sizeof(char)*10);
 char test_buffer[64];
 unsigned int i,j,k;
 time_t test_time;
 for(i=0;i<10;i++){
  data[9-i] = '0'+i;
 }
 /*Randomize the input data*/
 time(&test_time);
 srand(test_time);
 for(i=0;i<100;i++){
  j=(rand())%10;
  k=(rand())%10;
  test_buffer[63]=data[j];
  data[j]=data[k];
  data[k]=test_buffer[63];
 }
 /*Print the buffer*/
 if(strncpy(test_buffer,data,10)!=test_buffer){
  fprintf(stderr,"SYSTEM_ISSUE:Copy into buffer failed\n");
 }else{
  test_buffer[10]='\0';
  fprintf(stdout,"%s\n",test_buffer);
 }
 RandQsort((void *)data,(void *)(data+9),1,
 CharSwap,CharCompare_L);
 for(i=0;i<10;i++){
  if(data[i]-('0'+i)){
   printf("Test Failed for Chars\n");
   printf("Expecting %d but found %d\n",i,
    ((unsigned int)data[i]-'0'));
   exit(1);
  }
 }
 test_buffer[0]='\0';
 if(strncpy(test_buffer,data,10)!=test_buffer){
  fprintf(stderr,"FAILED_TEST: UNABLE TO COPY BUFFER\n");
  fprintf(stderr,"MAY_BE_SOME_MEMORY_CORRUPTION_DURING_SORT\n");
  exit(1);
 }else{
  fprintf(stdout,"%s\n",data);
 }
 printf("Test Passed For Chars....\n");
}

unsigned char FloatCompare(void *a,void *b){
 int a_int = (int)((*(float *)a)*10000);
 int b_int = (int)((*(float *)b)*10000);
 return (a_int<=b_int)?1:0;
}
void FloatSwap(void *a,void *b){
 float temp;
 temp = *((float *)a);
 *((float *)a) = *((float *)b);
 *((float *)b) = temp;
}

#include
void TestFloatSort(){
 float *data = malloc(sizeof(float)*10);
 float temp;
 unsigned int i,j,k;
 time_t test_time;
 for(i=0;i<10;i++){
  data[9-i] = (float)sin(i);
 }
 /*Randomize the input data*/
 time(&test_time);
 srand(test_time);
 for(i=0;i<100;i++){
  j=(rand())%10;
  k=(rand())%10;
  temp=data[j];
  data[j]=data[k];
  data[k]=temp;
 }
 /*Print the buffer*/
 for(i=0;i<10;i++){
  printf("%f ",data[i]);
 }
 printf("\n");
 printf("The # of elements %d\n",(&data[9]-&data[0])/4);
 RandQsort((void *)&data[0],(void *)&(data[9]),4,
 FloatSwap,FloatCompare);
 for(i=1;i<10;i++){
  if(!FloatCompare((void *)&data[i-1],(void *)&data[i])){
   printf("Test FAILED comparing %f , %f\n",
   data[i-1],data[i]);
   exit(1);
  }
 }
 for(i=0;i<10;i++){
  printf("%f ",data[i]);
 }
 printf("\n");
 printf("Test Passed For Floats....\n");
}

/*Test for floats*/
int main(){
 TestCharSort();
 TestFloatSort();
 exit(0);
}
#endif

[TECH] Perl template toolkit and Bugzilla

I have now done with the customization of Bugzilla for our internal needs, to keep track of things. The core of the idea of templates was simple

• Seperate the presentation from the code

The good thing about using Perl + TTK is that the split (presentation code and actual code) is very wide compared to any other framework which I'm aware at least from my past experience. I have used the following frameworks previously. Its a very useful add on as a skill learn more about http://www.template-toolkit.org

Have few things to fix today, Add code to SAPE_1 with the new Center of Gravity algorithm.

Cheers!
Vamsi

[TECH] Bugzilla Internals

Got back to work today !

Was looking at the Bugzilla's perl code to extend it for some of my internal work, I found that it was a expert level perl code (Object oriented) they are using several things which I never used, It was a good learning experience.

I want extract few concepts from this code

• How do all these websystem's avoid hard coding of HTML inside the code which generate's HTML dynamically (I know its kind of servlet and JSP/ASP situation), I found that these guys have some mechanism based on templates which avoids hard coding of the HTML inside the dynamic HTML generation code

I guess this is the key idea/concept behind all the code which generates HTML dynamically.

I was reading Sriram's "Advanced Perl Programming" I think its a great book the way he build's up the concepts, I was really impressed by a quote by him in the book
"It is indicative of inflexible procedural design if you find yourself using conditional statements to distinguish between object types"

I want to go out to get some lunch today :)
Cheers!
Vamsi

[NON-TECH] The old and cold feeling comes back........

I visited India from Aug10-Aug30 all those 20 days were great most of the time I was in Hyderabad, life was great in India except that there was a lot of pollution especially in Hyderabad and also overcrowded places especially because of the booming IT industry.

Some of the things I noticed have changed in India from the time I left

• The money spending power of people have increased a lot, I heard that the average salary for a undergrad is now around 5.0 lack/annum ($12.5k ), this was a huge increase compared to average of 2.4 lack/annum ($6k) which is more than double.
• The cost of living has gone up from the last year, I remember that I used to eat in a hotel called Kakatiya in Ameerpet a full meal for Rs 26.00/- the same costs Rs 32.00/- now. A bottle of mineral water went up to 13.00/- from 10.00/-
• There have been a lot of malls/multiplexes mushrooming every where in Hyderabad. I saw several existing houses being demolished and new multiplexes and malls are taking their place.
• Looks to me that almost every thing is available in India now. I was shocked to see PSP in Music World, I guess people are now getting into games market and if its true India will be a great market for selling computer games.
• In India cell phone has become a revolution I find that almost every one in the country has a mobile phone, thanks to Reliance which had a vision of making cell phones affordable to every one.

All these things are fine but my old feeling comes back again, I remember all those dilemma which I was having when I just landed in U.S went to riverside and came to UCONN, all those feeling are fresh in my mind. Well that COLD FEELING of missing India comes back again I don't know why but its back.....I feel sorry for myself I don't know what I'm up to in my life.....But I'm transforming my self to be better than what I used to be, and I believe that what ever is happening is just transformation for something better........as usual Connecticut is very lonely very quiet place, I used to go for jogging in India every day around 7-8 a.m in the morning.....

Well its life and lets face it without fear!
Cheer! Vamsi.

[NON-TECH] From Dennis Ritchie's Bio....

Some times there are far too many things for people to decide on what to do? how to excel? what exactly is our strength ? . The problem here is that people tend to be *good* in several things, but being *good* is not enough if a person who is *good* compares to some of the smartest people in the same field. All this thoughts haunt every one I found the following from Dennis Ritchie's biography here
"My undergraduate experience convinced me that I was not smart enough to be a physicist, and that computers were quite neat. My graduate school experience convinced me that I was not smart enough to be an expert in the theory of algorithms and also that I liked procedural languages better than functional ones."
see that line "I was not smart enough to be an expert in the theory of algorithms....." I guess any person at his position would never say that (even though he is not smart), I really felt this guy is TRULY a GREAT GUY, he had to be really modest and humble to say such things......
Cheers!
Vamsi.

[TECH] My Quick VIM tip of the day

To add something to every line in a file with vim
:s/^/something/gc

[TECH] FORTRAN awful stories

Well first time in my life had a chance to look at a messy FORTRAN code. I used some of the CRAY style POINTER(ptr,pointee) stuff and it looked to me its really weird.
There are several crazy things which got me irritated while writing the code

• Can you beleive that when you write FORTRAN code you must make sure that every line is no more than 80 chars, some one told me that FORTRAN had this because of the punch cards whose size limit come from there.
• Really strange that FORTRAN has no concept of global variables, and its a real pain especially when you have SUBROUTINES you will have to make a COMMON block and copy all the definitions into the SUBROUTINE, real big pain, thanks to INCLUDE which saves us.
• I found they there seems to be a huge variations in the standards of FORTRAN, there are several things 'g77' did'nt support, I used 'ifort' intel fortran compiler.
• Really had tough time figuring out the format specifiers equivalent to 'printf' for 'WRITE(6,*)'
• Last but not least FORTRAN dont have a ';' at the end of statement and its really pain when you are a 'C' programmers.
• Last++ IF conditions seems to require THEN , I figured out after writing several lines of code :(, really an Experience of writing programs in legacy languages and a real test for a real programmer.

I forgot I wanted to keep track of this piece of code, to close all the files in a program with calling close(fd) in each of fd's

fp = tmpfile();
fp->_chain = stderr;
fpclose(fp);
fp = NULL;

Take care guys!
Cheers!
Vamsi