Segmentation fault when traversing object of type SuffixTreeY

[fclaude]

Segmentation fault when traversing object of type SuffixTreeY

[rcanovas]

Hi I don't know what could it be, but I will try to fixed as soon as I can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the 4th floor of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this DNA
sequence.

The suffix array is constructed successfully (at least I think so) but as
soon as you invoke any methods that requires traversing the tree, a
segmentation fault occurs. For example, invoking the following method call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes a
segmentation fault.

The following methods were invoked to construct the suffix tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820, len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1,
y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1,
y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0, x=1,
y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth (this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child (this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

[rcanovas]

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as soon as I can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the 4th floor of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this DNA
sequence.

The suffix array is constructed successfully (at least I think so) but as
soon as you invoke any methods that requires traversing the tree, a
segmentation fault occurs. For example, invoking the following method call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes a
segmentation fault.

The following methods were invoked to construct the suffix tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820, len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth (this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child (this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

[skuruppu]

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname. Welcome to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll try to
understand it. I wanted to see if I can use it instead of a suffix array in
my RLZ implementation because I need an efficient way to calculate suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want to get a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as soon as I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the 4th floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this DNA
sequence.

The suffix array is constructed successfully (at least I think so) but
as
soon as you invoke any methods that requires traversing the tree, a
segmentation fault occurs. For example, invoking the following method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes a
segmentation fault.

The following methods were invoked to construct the suffix tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820, len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child (this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:
#1 (comment)

[rcanovas]

Every Wednesday I have time (I'm not completely sure if this Wednesday) if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname. Welcome to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll try to
understand it. I wanted to see if I can use it instead of a suffix array in
my RLZ implementation because I need an efficient way to calculate suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want to get a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as soon as I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the 4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this DNA
sequence.

The suffix array is constructed successfully (at least I think so) but
as
soon as you invoke any methods that requires traversing the tree, a
segmentation fault occurs. For example, invoking the following method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes a
segmentation fault.

The following methods were invoked to construct the suffix tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820, len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ (this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:
#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

[skuruppu]

Sure, it would be good to discuss the CST. But first I'd like to read the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this Wednesday) if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname. Welcome to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll try to
understand it. I wanted to see if I can use it instead of a suffix array
in
my RLZ implementation because I need an efficient way to calculate suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want to get a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as soon as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the 4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this DNA
sequence.

The suffix array is constructed successfully (at least I think so)
but
as
soon as you invoke any methods that requires traversing the tree, a
segmentation fault occurs. For example, invoking the following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes a
segmentation fault.

The following methods were invoked to construct the suffix tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:
#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

[rcanovas]

Yes is suppose to be related. Just in case I attach the presentation that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no problem if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be good just to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like to read the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname. Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll try to
understand it. I wanted to see if I can use it instead of a suffix
array
in
my RLZ implementation because I need an efficient way to calculate
suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want to get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the 4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this
DNA
sequence.

The suffix array is constructed successfully (at least I think so)
but
as
soon as you invoke any methods that requires traversing the tree,
a
segmentation fault occurs. For example, invoking the following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes a
segmentation fault.

The following methods were invoked to construct the suffix tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:
#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

[rcanovas]

Are u sure that you have the last libcds version?? because I just try your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the presentation that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no problem if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be good just to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like to read the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname. Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll try
to
understand it. I wanted to see if I can use it instead of a suffix
array
in
my RLZ implementation because I need an efficient way to calculate
suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want to get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the 4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this
DNA
sequence.

The suffix array is constructed successfully (at least I think
so)
but
as
soon as you invoke any methods that requires traversing the tree,
a
segmentation fault occurs. For example, invoking the following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes a
segmentation fault.

The following methods were invoked to construct the suffix tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

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#1 (comment)

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[skuruppu]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's the cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I just try your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the presentation that
I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be good just to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like to read
the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll try
to
understand it. I wanted to see if I can use it instead of a suffix
array
in
my RLZ implementation because I need an efficient way to calculate
suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for this
DNA
sequence.

The suffix array is constructed successfully (at least I think
so)
but
as
soon as you invoke any methods that requires traversing the
tree,
a
segmentation fault occurs. For example, invoking the following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(), causes
a
segmentation fault.

The following methods were invoked to construct the suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698) at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:
#1 (comment)

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#1 (comment)

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[skuruppu]

Yeah I just ran the same code on my laptop which is running 32bit Linux and
the code works fine. The segmentation fault only happens when I run it on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's the cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I just try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be good just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like to read
the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll
try
to
understand it. I wanted to see if I can use it instead of a suffix
array
in
my RLZ implementation because I need an efficient way to calculate
suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for
this
DNA
sequence.

The suffix array is constructed successfully (at least I think
so)
but
as
soon as you invoke any methods that requires traversing the
tree,
a
segmentation fault occurs. For example, invoking the following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct the suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64 (A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:
#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

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[rcanovas]

Did you try running the experiment in 64-bits replacing the suffixtree files
with the ones that I send you?

On Tue, Aug 2, 2011 at 1:04 PM, skuruppu <
[email protected]>wrote:

Yeah I just ran the same code on my laptop which is running 32bit Linux and
the code works fine. The segmentation fault only happens when I run it on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's the
cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I just try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no
problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be good just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like to read
the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but I'll
try
to
understand it. I wanted to see if I can use it instead of a
suffix
array
in
my RLZ implementation because I need an efficient way to
calculate
suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want
to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected] wrote:

Hi I don't know what could it be, but I will try to fixed as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in
the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for
this
DNA
sequence.

The suffix array is constructed successfully (at least I
think
so)
but
as
soon as you invoke any methods that requires traversing the
tree,
a
segmentation fault occurs. For example, invoking the
following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct the suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64
(A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2, argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:

#1 (comment)

Reply to this email directly or view it on GitHub:
#1 (comment)

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[skuruppu]

I haven't been getting any attachments in the emails that you sent. Maybe
you try sending them again? Or let me know where I can download them from.

2011/8/2 rcanovas <
[email protected]>

Did you try running the experiment in 64-bits replacing the suffixtree
files
with the ones that I send you?

On Tue, Aug 2, 2011 at 1:04 PM, skuruppu <
[email protected]>wrote:

Yeah I just ran the same code on my laptop which is running 32bit Linux
and
the code works fine. The segmentation fault only happens when I run it on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's the
cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I just try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no
problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be good
just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like to
read
the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but
I'll
try
to
understand it. I wanted to see if I can use it instead of a
suffix
array
in
my RLZ implementation because I need an efficient way to
calculate
suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you want
to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected]
wrote:

Hi I don't know what could it be, but I will try to fixed
as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a in
the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree for
this
DNA
sequence.

The suffix array is constructed successfully (at least I
think
so)
but
as
soon as you invoke any methods that requires traversing
the
tree,
a
segmentation fault occurs. For example, invoking the
following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl, &next_vr);

where node_vl and node_vr are obtained from cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct the suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64
(A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680) at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2,
argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

Reply to this email directly or view it on GitHub:

#1 (comment)

Reply to this email directly or view it on GitHub:

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[rcanovas]

http://www.dcc.uchile.cl/~rcanovas/downloads/new_cst.zip

On Tue, Aug 2, 2011 at 1:17 PM, skuruppu <
[email protected]>wrote:

I haven't been getting any attachments in the emails that you sent. Maybe
you try sending them again? Or let me know where I can download them from.

2011/8/2 rcanovas <
[email protected]>

Did you try running the experiment in 64-bits replacing the suffixtree
files
with the ones that I send you?

On Tue, Aug 2, 2011 at 1:04 PM, skuruppu <
[email protected]>wrote:

Yeah I just ran the same code on my laptop which is running 32bit Linux
and
the code works fine. The segmentation fault only happens when I run it
on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's the
cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I just
try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the
presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no
problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be good
just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like to
read
the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your
surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but
I'll
try
to
understand it. I wanted to see if I can use it instead of a
suffix
array
in
my RLZ implementation because I need an efficient way to
calculate
suffix
links.

The sequence I used is at
http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access it.

Would be good to see you in any case so let me know if you
want
to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected]
wrote:

Hi I don't know what could it be, but I will try to fixed
as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a
in
the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree
for
this
DNA
sequence.

The suffix array is constructed successfully (at least I
think
so)
but
as
soon as you invoke any methods that requires traversing
the
tree,
a
segmentation fault occurs. For example, invoking the
following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl,
&next_vr);

where node_vl and node_vr are obtained from cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct the
suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64
(A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in
cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at
static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680)
at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2,
argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

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[skuruppu]

Thanks for the link to the new source files but sorry the new code doesn't
compile on a 64 bit machine. I get the following errors:

static/suffixtree/LCP_naive.cpp: In constructor
cds_static::LCP_naive::LCP_naive(cds_static::TextIndex_, char_, size_t):
static/suffixtree/LCP_naive.cpp:44: error: cannot convert unsigned int* to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp:50: error: cannot convert unsigned int_ to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp: In member function virtual size_t
cds_static::LCP_naive::get_LCP(size_t, cds_static::TextIndex_) const:
static/suffixtree/LCP_naive.cpp:57: error: cannot convert unsigned int*
const to size_t* for argument 1 to size_t
cds_utils::get_field_64(size_t*, size_t, size_t)

I noticed that you've changed some of the size_t type variables into
unsigned int types. Unfortunately, g++ and gcc on a 64 bit machine doesn't
allow you to cast anything of type unsigned int into size_t because size_t
is 8 bytes.

It'll probably take a lot of work to make this work in a 64 bit machine so
don't worry about it. I'll just use this library on my laptop for the moment
and keep a look out for a 64 bit version. If I get it to work, I'll send you
a patch. Thanks very much for helping.

2011/8/2 rcanovas <
[email protected]>

http://www.dcc.uchile.cl/~rcanovas/downloads/new_cst.zip

On Tue, Aug 2, 2011 at 1:17 PM, skuruppu <
[email protected]>wrote:

I haven't been getting any attachments in the emails that you sent. Maybe
you try sending them again? Or let me know where I can download them
from.

2011/8/2 rcanovas <
[email protected]>

Did you try running the experiment in 64-bits replacing the suffixtree
files
with the ones that I send you?

On Tue, Aug 2, 2011 at 1:04 PM, skuruppu <
[email protected]>wrote:

Yeah I just ran the same code on my laptop which is running 32bit
Linux
and
the code works fine. The segmentation fault only happens when I run
it
on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's the
cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I just
try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the
presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have no
problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be
good
just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like
to
read
the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your
surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation but
I'll
try
to
understand it. I wanted to see if I can use it instead of a
suffix
array
in
my RLZ implementation because I need an efficient way to
calculate
suffix
links.

The sequence I used is at

http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access
it.

Would be good to see you in any case so let me know if you
want
to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo [email protected]
wrote:

Hi I don't know what could it be, but I will try to
fixed
as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room 4.31a
in
the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix tree
for
this
DNA
sequence.

The suffix array is constructed successfully (at least
I
think
so)
but
as
soon as you invoke any methods that requires
traversing
the
tree,
a
segmentation fault occurs. For example, invoking the
following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl,
&next_vr);

where node_vl and node_vr are obtained from
cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct the
suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64
(A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in
cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at
static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in
cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree (s1=0xfc7680)
at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2,
argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

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#1

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[rcanovas]

Sorry for all the problems, but in this link:
www.dcc.uchile.cl/~rcanovas/downloads/licds.tar
is the last version of the library and at least in my computer (64bits) I
still don't have any
problem =). Please let me know how if it's work.

On Tue, Aug 2, 2011 at 5:47 PM, skuruppu <
[email protected]>wrote:

Thanks for the link to the new source files but sorry the new code doesn't
compile on a 64 bit machine. I get the following errors:

static/suffixtree/LCP_naive.cpp: In constructor
cds_static::LCP_naive::LCP_naive(cds_static::TextIndex_, char_, size_t):
static/suffixtree/LCP_naive.cpp:44: error: cannot convert unsigned int* to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp:50: error: cannot convert unsigned int_ to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp: In member function virtual size_t
cds_static::LCP_naive::get_LCP(size_t, cds_static::TextIndex_) const:
static/suffixtree/LCP_naive.cpp:57: error: cannot convert unsigned int*
const to size_t* for argument 1 to size_t
cds_utils::get_field_64(size_t*, size_t, size_t)

I noticed that you've changed some of the size_t type variables into
unsigned int types. Unfortunately, g++ and gcc on a 64 bit machine doesn't
allow you to cast anything of type unsigned int into size_t because size_t
is 8 bytes.

It'll probably take a lot of work to make this work in a 64 bit machine so
don't worry about it. I'll just use this library on my laptop for the
moment
and keep a look out for a 64 bit version. If I get it to work, I'll send
you
a patch. Thanks very much for helping.

2011/8/2 rcanovas <
[email protected]>

http://www.dcc.uchile.cl/~rcanovas/downloads/new_cst.zip

On Tue, Aug 2, 2011 at 1:17 PM, skuruppu <
[email protected]>wrote:

I haven't been getting any attachments in the emails that you sent.
Maybe
you try sending them again? Or let me know where I can download them
from.

2011/8/2 rcanovas <
[email protected]>

Did you try running the experiment in 64-bits replacing the
suffixtree
files
with the ones that I send you?

On Tue, Aug 2, 2011 at 1:04 PM, skuruppu <
[email protected]>wrote:

Yeah I just ran the same code on my laptop which is running 32bit
Linux
and
the code works fine. The segmentation fault only happens when I run
it
on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's
the
cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I
just
try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected] wrote:

Yes is suppose to be related. Just in case I attach the
presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have
no
problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be
good
just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd like
to
read
the
paper so I'm not too lost. Is this the paper relating to this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if
this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your
surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation
but
I'll
try
to
understand it. I wanted to see if I can use it instead of
a
suffix
array
in
my RLZ implementation because I need an efficient way to
calculate
suffix
links.

The sequence I used is at

http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to access
it.

Would be good to see you in any case so let me know if
you
want
to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you
use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo <[email protected]

wrote:

Hi I don't know what could it be, but I will try to
fixed
as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room
4.31a
in
the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix
tree
for
this
[DNA
sequence](

http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

).

The suffix array is constructed successfully (at
least
I
think
so)
but
as
soon as you invoke any methods that requires
traversing
the
tree,
a
segmentation fault occurs. For example, invoking the
following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl,
&next_vr);

where node_vl and node_vr are obtained from
cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct the
suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR, 32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64
(A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in
cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at
static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in
cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c', child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree
(s1=0xfc7680)
at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2,
argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the problem.

Reply to this email directly or view it on GitHub:
#1

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[skuruppu]

Perfect, it works :) Thank you very much for fixing the problem.

PS: I think the link is meant to be
www.dcc.uchile.cl/~rcanovas/downloads/libcds.tar

Shanika

2011/8/3 rcanovas <
[email protected]>

Sorry for all the problems, but in this link:
www.dcc.uchile.cl/~rcanovas/downloads/licds.tar
is the last version of the library and at least in my computer (64bits) I
still don't have any
problem =). Please let me know how if it's work.

On Tue, Aug 2, 2011 at 5:47 PM, skuruppu <
[email protected]>wrote:

Thanks for the link to the new source files but sorry the new code
doesn't
compile on a 64 bit machine. I get the following errors:

static/suffixtree/LCP_naive.cpp: In constructor
cds_static::LCP_naive::LCP_naive(cds_static::TextIndex_, char_, size_t):
static/suffixtree/LCP_naive.cpp:44: error: cannot convert unsigned int*
to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp:50: error: cannot convert unsigned int_
to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp: In member function virtual size_t
cds_static::LCP_naive::get_LCP(size_t, cds_static::TextIndex_) const:
static/suffixtree/LCP_naive.cpp:57: error: cannot convert unsigned int*
const to size_t* for argument 1 to size_t
cds_utils::get_field_64(size_t*, size_t, size_t)

I noticed that you've changed some of the size_t type variables into
unsigned int types. Unfortunately, g++ and gcc on a 64 bit machine
doesn't
allow you to cast anything of type unsigned int into size_t because
size_t
is 8 bytes.

It'll probably take a lot of work to make this work in a 64 bit machine
so
don't worry about it. I'll just use this library on my laptop for the
moment
and keep a look out for a 64 bit version. If I get it to work, I'll send
you
a patch. Thanks very much for helping.

2011/8/2 rcanovas <
[email protected]>

http://www.dcc.uchile.cl/~rcanovas/downloads/new_cst.zip

On Tue, Aug 2, 2011 at 1:17 PM, skuruppu <
[email protected]>wrote:

I haven't been getting any attachments in the emails that you sent.
Maybe
you try sending them again? Or let me know where I can download them
from.

2011/8/2 rcanovas <
[email protected]>

Did you try running the experiment in 64-bits replacing the
suffixtree
files
with the ones that I send you?

On Tue, Aug 2, 2011 at 1:04 PM, skuruppu <
[email protected]>wrote:

Yeah I just ran the same code on my laptop which is running 32bit
Linux
and
the code works fine. The segmentation fault only happens when I
run
it
on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe that's
the
cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because I
just
try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected]
wrote:

Yes is suppose to be related. Just in case I attach the
presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I have
no
problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could be
good
just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd
like
to
read
the
paper so I'm not too lost. Is this the paper relating to
this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if
this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your
surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree implementation
but
I'll
try
to
understand it. I wanted to see if I can use it instead
of
a
suffix
array
in
my RLZ implementation because I need an efficient way
to
calculate
suffix
links.

The sequence I used is at

http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to
access
it.

Would be good to see you in any case so let me know if
you
want
to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that you
use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo <
[email protected]

wrote:

Hi I don't know what could it be, but I will try to
fixed
as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room
4.31a
in
the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed suffix
tree
for
this
[DNA
sequence](

http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

).

The suffix array is constructed successfully (at
least
I
think
so)
but
as
soon as you invoke any methods that requires
traversing
the
tree,
a
segmentation fault occurs. For example, invoking
the
following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl,
&next_vr);

where node_vl and node_vr are obtained from
cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct
the
suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR,
32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in cds_utils::get_field_64
(A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in
cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at
static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in
cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c',
child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree
(s1=0xfc7680)
at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2,
argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the
problem.

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[rcanovas]

To say the true I fix that problem long time ago, but it seems that with
Francisco Claude we forgot to upload in the new library

On Wed, Aug 3, 2011 at 11:09 AM, skuruppu <
[email protected]>wrote:

Perfect, it works :) Thank you very much for fixing the problem.

PS: I think the link is meant to be
www.dcc.uchile.cl/~rcanovas/downloads/libcds.tar

Shanika

2011/8/3 rcanovas <
[email protected]>

Sorry for all the problems, but in this link:
www.dcc.uchile.cl/~rcanovas/downloads/licds.tar
is the last version of the library and at least in my computer (64bits) I
still don't have any
problem =). Please let me know how if it's work.

On Tue, Aug 2, 2011 at 5:47 PM, skuruppu <
[email protected]>wrote:

Thanks for the link to the new source files but sorry the new code
doesn't
compile on a 64 bit machine. I get the following errors:

static/suffixtree/LCP_naive.cpp: In constructor
cds_static::LCP_naive::LCP_naive(cds_static::TextIndex_, char_,
size_t):
static/suffixtree/LCP_naive.cpp:44: error: cannot convert unsigned int*
to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp:50: error: cannot convert unsigned int_
to
size_t* for argument 1 to void cds_utils::set_field_64(size_t_, size_t,
size_t, size_t)
static/suffixtree/LCP_naive.cpp: In member function virtual size_t
cds_static::LCP_naive::get_LCP(size_t, cds_static::TextIndex_) const:
static/suffixtree/LCP_naive.cpp:57: error: cannot convert unsigned int*
const to size_t* for argument 1 to size_t
cds_utils::get_field_64(size_t*, size_t, size_t)

I noticed that you've changed some of the size_t type variables into
unsigned int types. Unfortunately, g++ and gcc on a 64 bit machine
doesn't
allow you to cast anything of type unsigned int into size_t because
size_t
is 8 bytes.

It'll probably take a lot of work to make this work in a 64 bit machine
so
don't worry about it. I'll just use this library on my laptop for the
moment
and keep a look out for a 64 bit version. If I get it to work, I'll
send
you
a patch. Thanks very much for helping.

2011/8/2 rcanovas <
[email protected]>

http://www.dcc.uchile.cl/~rcanovas/downloads/new_cst.zip

On Tue, Aug 2, 2011 at 1:17 PM, skuruppu <
[email protected]>wrote:

I haven't been getting any attachments in the emails that you sent.
Maybe
you try sending them again? Or let me know where I can download
them
from.

2011/8/2 rcanovas <
[email protected]>

Did you try running the experiment in 64-bits replacing the
suffixtree
files
with the ones that I send you?

On Tue, Aug 2, 2011 at 1:04 PM, skuruppu <
[email protected]>wrote:

Yeah I just ran the same code on my laptop which is running
32bit
Linux
and
the code works fine. The segmentation fault only happens when I
run
it
on
the 64bit Linux machine.

2011/8/2 Shanika Kuruppu [email protected]

I installed version 1.0.8 from
http://libcds.recoded.cl/system/files/libcds-v1.0.8.tgz

This was the only version available from the libcds website.

Are you using it on a 64bit machine? Because I am, maybe
that's
the
cause?

2011/8/2 rcanovas <
[email protected]>

Are u sure that you have the last libcds version?? because
I
just
try
your
problem and its work well

On Tue, Aug 2, 2011 at 10:37 AM, Yigo [email protected]
wrote:

Yes is suppose to be related. Just in case I attach the
presentation
that I
did at SEA... and I also attach my thesis
if you want to read something more specific. Any way I
have
no
problem
if
you prefer to review the thing starting
from zero... It could be easy for you and for me it could
be
good
just
to
review the topic =)... Just let me know.

Best,
Yigo.

On Tue, Aug 2, 2011 at 10:30 AM, skuruppu <
[email protected]>wrote:

Sure, it would be good to discuss the CST. But first I'd
like
to
read
the
paper so I'm not too lost. Is this the paper relating to
this
implementation?

Rodrigo Cnovas and Gonzalo Navarro.
Practical Compressed Suffix Trees.
Proc. SEA'10

Wed next week would be good if you have time.

2011/8/2 rcanovas <
[email protected]>

Every Wednesday I have time (I'm not completely sure if
this
Wednesday)
if
you want to meet
and discuss or if u want me to explain the CST to u.

On Tue, Aug 2, 2011 at 9:59 AM, skuruppu <
[email protected]>wrote:

Hey Rodrigo,

Sorry I didn't realise it was you. I didn't know your
surname.
Welcome
to
Melbourne. Alex told me you were coming.

I don't know much about your suffix tree
implementation
but
I'll
try
to
understand it. I wanted to see if I can use it
instead
of
a
suffix
array
in
my RLZ implementation because I need an efficient way
to
calculate
suffix
links.

The sequence I used is at

http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

I hope I've given the right permissions for you to
access
it.

Would be good to see you in any case so let me know
if
you
want
to
get
a
coffee sometime.

Enjoy the sunshine :)

Shanika

2011/8/2 rcanovas <
[email protected]>

Another thing, Where I can get the data set that
you
use?

On Tue, Aug 2, 2011 at 8:52 AM, Yigo <
[email protected]

wrote:

Hi I don't know what could it be, but I will try
to
fixed
as
soon
as
I
can.
Anyway if you want to discuss about
the implementation, most of the time I'm in room
4.31a
in
the
4th
floor
of
the ICT building.

Best,
Rodrigo

On Mon, Aug 1, 2011 at 9:13 PM, skuruppu <
[email protected]>wrote:

I was attempting to construct a compressed
suffix
tree
for
this
[DNA
sequence](

http://www.csse.unimelb.edu.au/~kuruppu/testdata/REF.raw.gz

).

The suffix array is constructed successfully (at
least
I
think
so)
but
as
soon as you invoke any methods that requires
traversing
the
tree,
a
segmentation fault occurs. For example, invoking
the
following
method
call

cst->Child(node_vl, node_vr, 'c', &next_vl,
&next_vr);

where node_vl and node_vr are obtained from
cst->Root(),
causes a
segmentation fault.

The following methods were invoked to construct
the
suffix
tree.

SuffixTree *cst;
SuffixTreeY csty(text, length, DAC, CN_NPR,
32);
cst = &csty;

The stack trace from gdb is as follows:

#0 0x00000000004086fa in
cds_utils::get_field_64
(A=0xfe2820,
len=6,
index=65836) at ../includes/libcdsTrees.h:26
#1 0x0000000000411354 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11309, r=1, min_r=0x7fffa70200e0)
at static/suffixtree/NPR_CN.cpp:413
#2 0x00000000004112c9 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=361925, r=0, min_r=0x7fffa7020198)
at static/suffixtree/NPR_CN.cpp:408
#3 0x0000000000411793 in
cds_static::NPR_CN::find_RMQ
(this=0xfc77e0,
x=1, y=11581659, csa=0xfe2a60, lcp=0xfc76b0)
at static/suffixtree/NPR_CN.cpp:348
#4 0x0000000000402c39 in
cds_static::SuffixTreeY::SDepth
(this=0xfc7680,
vl=0, vr=11581659) at
static/suffixtree/SuffixTreeY.cpp:91
#5 0x0000000000404eba in
cds_static::SuffixTreeY::Child
(this=0xfc7680,
vl=0, vr=11581659, a=99 'c',
child_l=0x7fffa7020308,
child_r=0x7fffa7020300) at
static/suffixtree/SuffixTreeY.cpp:279
#6 0x00000000004022e9 in testSuffixTree
(s1=0xfc7680)
at
testSuffixTree.cpp:52
#7 0x00000000004024fc in main (argc=2,
argv=0x7fffa7020698)
at
testSuffixTree.cpp:92

Hope this is enough information to fix the
problem.

Reply to this email directly or view it on
GitHub:
#1

Reply to this email directly or view it on GitHub:

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