Segmentation Fault Problem

[alexandre pedro]

I am using the CIPRES Gateway to run a data set of  1124  taxa and 12573 characters using the dppdiv-pthreads code.

I used this command line:

 

dppdiv-pthreads -T 32 -in infile.txt -tre tree.tre -n 1000000 -pf 100 -hsh 2.0 -pm 3.0 -sf 100 -out testalex -rb 4.0 -urg -ra 2.0

 

When I run it on test data sets 1 and 7, it runs fine. However, with my data sets (produced by RaxML)

I consistently get segmentation fault errors immediately. I have tried running between 1-32 pthreads and get the same result. Also, test data set 7 runs with 32 threads, so it doesn’t seem like an out of memory error.

 

Does anyone have any suggestions for what I might try to resolve this? The CIPRES system manager Mark Miller is aware of such error and is also interested on such suggestions.

Thank you so much,

Alex

[Tomas Flouri]

Hi Alexandre,

I am aware of this problem from Mark, however I did not have much time to check it :( I will check it out today and try to fix it.

Cheers,

Tomas

On 02/05/2013 03:27 AM, alexandre pedro wrote:

I am using the CIPRES Gateway to run a data set of� 1124� taxa and 12573 characters using the dppdiv-pthreads code.

I used this command line:

�

dppdiv-pthreads -T 32 -in infile.txt -tre tree.tre -n 1000000 -pf 100 -hsh 2.0 -pm 3.0 -sf 100 -out testalex -rb 4.0 -urg -ra 2.0

�

When I run it on test data sets 1 and 7, it runs fine. However, with my data sets (produced by RaxML)

I consistently get segmentation fault errors immediately. I have tried running between 1-32 pthreads and get the same result. Also, test data set 7 runs with 32 threads, so it doesn�t seem like an out of memory error.

�

Does anyone have any suggestions for what I might try to resolve this? The CIPRES system manager Mark Miller is aware of such error and is also interested on such suggestions.

Thank you so much,

Alex

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�

[Diego Darriba]

Hi Alexandre.

DPPDiv requires a rooted topology, otherwise it will crash. Is it possible that you are using an unrooted tree?

Best,
Diego D.

[Tomas Flouri]

Hi Diego,

no the problem is with rooted trees also, particularly:
dppdiv -in alignment -tre tree -out out -n 1000 -rnp
will crash.

I'm having a look at it now.

Tomas

[Miller, Mark]

Just to add, I find anything with the –rnp flag crashes with a seg fault in the pthreads version, even the test data sets.

I admit I have not tried the non-pthreads versions yet.

 

Mark

 

 

From: dppdiv...@googlegroups.com [mailto:dppdiv...@googlegroups.com] On Behalf Of Tomas Flouri
Sent: Tuesday, February 05, 2013 12:28 AM
To: dppdiv...@googlegroups.com
Subject: Re: Segmentation Fault Problem

 

Hi Diego,

no the problem is with rooted trees also, particularly:
dppdiv -in alignment -tre tree -out out -n 1000 -rnp
will crash.

I'm having a look at it now.

Tomas

On 02/05/2013 10:26 AM, Diego Darriba wrote:

Hi Alexandre.

DPPDiv requires a rooted topology, otherwise it will crash. Is it possible that you are using an unrooted tree?

Best,
Diego D.

On 02/05/2013 09:05 AM, Tomas Flouri wrote:

Hi Alexandre,

I am aware of this problem from Mark, however I did not have much time to check it :( I will check it out today and try to fix it.

Cheers,

Tomas

On 02/05/2013 03:27 AM, alexandre pedro wrote:

I am using the CIPRES Gateway to run a data set of  1124  taxa and 12573 characters using the dppdiv-pthreads code.

 

I used this command line:

 

dppdiv-pthreads -T 32 -in infile.txt -tre tree.tre -n 1000000 -pf 100 -hsh 2.0 -pm 3.0 -sf 100 -out testalex -rb 4.0 -urg -ra 2.0

 

When I run it on test data sets 1 and 7, it runs fine. However, with my data sets (produced by RaxML)

I consistently get segmentation fault errors immediately. I have tried running between 1-32 pthreads and get the same result. Also, test data set 7 runs with 32 threads, so it doesn’t seem like an out of memory error.

 

Does anyone have any suggestions for what I might try to resolve this? The CIPRES system manager Mark Miller is aware of such error and is also interested on such suggestions.

 

Thank you so much,

 

Alex

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[Tomas Flouri]

Hi Mark,
we just fixed it with Diego. If you get the new version from github it should be ok. The problem was in both single-thread and pthreads versions.

Cheers :)
Tomas

[Tracy Heath]

Hi Alexandre,

If your tree is rooted, you might also want to make sure that it is fully bifurcating. The program requires that the input tree is fully resolved and you'll get the same error.

Cheers,

Tracy

[alexandre pedro]

Thank you, Tracy and Tomas, for the quick a precisa responses. Although I could not find in RAxML manual splicitly, I believe the program's output is a rooted tree (please, correct me if I'm any mistaken, and how to root it properly for DPPDIV).

Thanks a lot, really.

Best

Alex

Alexandre Pedro Selvatti Ferreira Nunes

Laboratório de Biologia Evolutiva Teórica e Aplicada
Departamento de Genética - Instituto de Biologia (UFRJ)
Prédio do CCS, Bloco A, Sala A2-095
Universidade Federal do Rio de Janeiro
Rua Prof. Rodolpho Paulo Rocco, S/N
Cidade Universitaria, Ilha do Fundão
Rio de Janeiro, RJ, Brasil
CEP: 21941-617

[Alexandros Stamatakis]

Hi Alex,

By default RAxML generates an unrooted tree, except if you use the
outgroup option -o, in which case it will generate a rooted tree.

Alexis

On Tue, 2013-02-05 at 16:58 -0200, alexandre pedro wrote:
> Thank you, Tracy and Tomas, for the quick a precisa responses. Although I
> could not find in RAxML manual splicitly, I believe the program's output is
> a rooted tree (please, correct me if I'm any mistaken, and how to root it
> properly for DPPDIV).
>
> Thanks a lot, really.
>
> Best
>
> Alex
>
> On Tue, Feb 5, 2013 at 3:50 PM, Tracy Heath <tra...@gmail.com> wrote:
>
> >
> > Hi Alexandre,
> >
> > If your tree is rooted, you might also want to make sure that it is fully
> > bifurcating. The program requires that the input tree is fully resolved and
> > you'll get the same error.
> >
> > Cheers,
> > Tracy
> >
> > On Tue, Feb 5, 2013 at 6:36 AM, Tomas Flouri <flo...@gmail.com> wrote:
> >

> >> **

> >> Hi Mark,
> >> we just fixed it with Diego. If you get the new version from github it
> >> should be ok. The problem was in both single-thread and pthreads versions.
> >>
> >> Cheers :)
> >> Tomas
> >>
> >>
> >> On 02/05/2013 04:36 PM, Miller, Mark wrote:
> >>
> >> Just to add, I find anything with the –rnp flag crashes with a seg

> >> fault in the pthreads version, even the test data sets.****
> >>
> >> I admit I have not tried the non-pthreads versions yet.****
> >>
> >> ** **
> >>
> >> Mark****
> >>
> >> ** **
> >>
> >> ** **
> >>
> >> *From:* dppdiv...@googlegroups.com [
> >> mailto:dppdiv...@googlegroups.com <dppdiv...@googlegroups.com>] *On
> >> Behalf Of *Tomas Flouri
> >> *Sent:* Tuesday, February 05, 2013 12:28 AM
> >> *To:* dppdiv...@googlegroups.com
> >> *Subject:* Re: Segmentation Fault Problem****
> >>
> >> ** **

> >>
> >> Hi Diego,
> >>
> >> no the problem is with rooted trees also, particularly:
> >> dppdiv -in alignment -tre tree -out out -n 1000 -rnp
> >> will crash.
> >>
> >> I'm having a look at it now.
> >>
> >> Tomas
> >>

> >> On 02/05/2013 10:26 AM, Diego Darriba wrote: ****

> >>
> >> Hi Alexandre.
> >>
> >> DPPDiv requires a rooted topology, otherwise it will crash. Is it
> >> possible that you are using an unrooted tree?
> >>
> >> Best,
> >> Diego D.
> >>

> >> On 02/05/2013 09:05 AM, Tomas Flouri wrote:****

> >>
> >> Hi Alexandre,
> >>
> >> I am aware of this problem from Mark, however I did not have much time to
> >> check it :( I will check it out today and try to fix it.
> >>
> >> Cheers,
> >>
> >> Tomas
> >>

> >> On 02/05/2013 03:27 AM, alexandre pedro wrote: ****

> >>
> >> I am using the CIPRES Gateway to run a data set of 1124 taxa and 12573

> >> characters using the dppdiv-pthreads code.****
> >>
> >> ** **
> >>
> >> I used this command line:****
> >>
> >> ****

> >>
> >> dppdiv-pthreads -T 32 -in infile.txt -tre tree.tre -n 1000000 -pf 100

> >> -hsh 2.0 -pm 3.0 -sf 100 -out testalex -rb 4.0 -urg -ra 2.0****
> >>
> >> ****

> >>
> >> When I run it on test data sets 1 and 7, it runs fine. However, with my

> >> data sets (produced by RaxML)****

> >>
> >> I consistently get segmentation fault errors immediately. I have tried
> >> running between 1-32 pthreads and get the same result. Also, test data set

> >> 7 runs with 32 threads, so it doesn’t seem like an out of memory error.**
> >> **
> >>
> >> ****

> >>
> >> Does anyone have any suggestions for what I might try to resolve this?
> >> The CIPRES system manager Mark Miller is aware of such error and is also

> >> interested on such suggestions.****
> >>
> >> ** **
> >>
> >> Thank you so much,****
> >>
> >> ** **
> >>
> >> Alex****

> >>
> >> --
> >> You received this message because you are subscribed to the Google Groups
> >> "dppdiv-users" group.
> >> To unsubscribe from this group and stop receiving emails from it, send an
> >> email to dppdiv-users...@googlegroups.com.
> >> For more options, visit https://groups.google.com/groups/opt_out.
> >>

> >> ****

> >>
> >>
> >> --
> >> You received this message because you are subscribed to the Google Groups
> >> "dppdiv-users" group.
> >> To unsubscribe from this group and stop receiving emails from it, send an
> >> email to dppdiv-users...@googlegroups.com.
> >> For more options, visit https://groups.google.com/groups/opt_out.
> >>

> >> ****

> >>
> >>
> >> --
> >> You received this message because you are subscribed to the Google Groups
> >> "dppdiv-users" group.
> >> To unsubscribe from this group and stop receiving emails from it, send an
> >> email to dppdiv-users...@googlegroups.com.
> >> For more options, visit https://groups.google.com/groups/opt_out.
> >>

> >> ****
> >>
> >> ** **

> >>
> >> --
> >> You received this message because you are subscribed to the Google Groups
> >> "dppdiv-users" group.
> >> To unsubscribe from this group and stop receiving emails from it, send an
> >> email to dppdiv-users...@googlegroups.com.
> >> For more options, visit https://groups.google.com/groups/opt_out.
> >>

> >> ****

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[alexandre pedro]

Thank you, Alexis. I'm sorry for the silly question, but is it possible to root such output, after the analysis is done, in order to use it as input in dppdiv?

Many thanks,

Alex

[Alexandros Stamatakis]

I guess some tree viewers allow for doing this, but not sure which ones,

alexis

[Tracy Heath]

Hi Alexandre,

You can reroot in PAUP* or a tool like phyutility (http://code.google.com/p/phyutility/). FigTree can do this as well, you can reroot and the export the tree as a newick string. 

Cheers!

Tracy

[alexandre pedro]

Thank you, Alexis and Tracy, got it :)

Cheers!

Alex

[Kevin Lim]

Hi Tomas,

I am getting a similar segmentation fault problem on the latest version of dppdiv. I am sure my tree is rooted because I specified an out group running RAxML. Could I please find out what else could be likely the problem? The program stops after computing the Exponential calibration parameters (contamination model)

Thank you.

Regards,

Kevin

[Alex]

Hello,

I am writing to inquire whether this issue was resolved?  I am currently trying to run an analysis on CIPRES and I am also encountering a segmentation fault error.  The tree is rooted and fully bifurcating.  I can't figure out what else can be causing the error.

Thanks.

[Renato Augusto Corrêa dos Santos]

Hello everyone,

I would like to know if this issue was resolved.

I am having the same problem - after "Exponential calibration parameters":

Rate Group Elements: (0.17719) -> 0 2 3 4 5 6 7 8 9 10 11 12 13 14 15 20 21 22 23 24 25 26 27 28 29 30 32
Rate Group Elements: (0.24467) -> 1 16 31
Rate Group Elements: (0.19424) -> 18 19
Concentration parameter: 0.9681
Root height parameter: 152.9557
Exponential calibration parameters (contamination model):  = [l1 = 0.7644, l2 = 0.0590, eps = 0.0900]

Cheers,

Renato Augusto Corrêa dos Santos.

[Stephanie Loria]

Hi All,

I am having the same problem as everyone else. Cipres is terminating the same way.

Best wishes,
Stephanie