Issue with assertion failing on mac
122 views
Skip to first unread message
Rob Lanfear
Aug 25, 2015, 2:03:06 AM8/25/15
to raxml
Hi All,
I am analysing a dataset on a mac, and I get the following error:
Assertion failed: (rate >= RATE_MIN && rate <= RATE_MAX), function setRateModel, file optimizeModel.c, line 123.
The behaviour is a little odd though. Whether or not I get the error depends on the dataset (I get it in <1% of datasets), the machine, and the compiler I used to build RAxML.
I am using the latest version of RAxML:
A dataset to recreate the error (with compiled binaries) is here:
With the dataset provided, I get the error on one machine when I use the .gcc makefile version, but not the .mac makefile version (which compiles with clang on my machine).
But on another (slightly newer) mac, it is the other way around: the gcc version works fine, and the mac version failed.
I have other datasets where it is the other way around - it works fine with the .mac makefile on the older mac, but breaks with the .mac makefile on the newer one.
In short, for any given machine and compiled binary of RAxML, I have datasets that produce the above error.
Any ideas?
Rob
Alexandros Stamatakis
Sep 7, 2015, 4:50:19 AM9/7/15
to ra...@googlegroups.com
just got back from vacations, will try to look at it soonish,
alexis
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.
--
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
alexis
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.
--
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
Rob Lanfear
Sep 7, 2015, 6:41:44 AM9/7/15
to ra...@googlegroups.com
No worries. I understand that this is unlikely to make it to the top of any to-do lists!
In some further analyses, I am pretty sure that this issue is limited to GTR+I+G models, and doesn't occur with GTR+G models. I have only seen it with the former.
Cheers,
Rob
--
You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/OtsJDzHW-Zc/unsubscribe.
To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
Rob Lanfear
School of Biological Sciences,
Macquarie University,
School of Biological Sciences,
Macquarie University,
Alexandros Stamatakis
Sep 29, 2015, 10:38:29 AM9/29/15
to ra...@googlegroups.com
Hi Rob,
Sorry for the late reply, I've been busy with other stuff.
Can you confirm that the error only appears with +I?
I am 99% sure that I know where it comes from if it only happens when +I
is being used.
Cheers,
Alexis
On 07.09.2015 12:41, Rob Lanfear wrote:
> No worries. I understand that this is unlikely to make it to the top of
> any to-do lists!
>
> In some further analyses, I am pretty sure that this issue is limited to
> GTR+I+G models, and doesn't occur with GTR+G models. I have only seen it
> with the former.
>
> Cheers,
>
> Rob
>
> On 7 September 2015 at 18:50, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
Sorry for the late reply, I've been busy with other stuff.
Can you confirm that the error only appears with +I?
I am 99% sure that I know where it comes from if it only happens when +I
is being used.
Cheers,
Alexis
On 07.09.2015 12:41, Rob Lanfear wrote:
> No worries. I understand that this is unlikely to make it to the top of
> any to-do lists!
>
> In some further analyses, I am pretty sure that this issue is limited to
> GTR+I+G models, and doesn't occur with GTR+G models. I have only seen it
> with the former.
>
> Cheers,
>
> Rob
>
> On 7 September 2015 at 18:50, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> 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 <http://www.exelixis-lab.org>
>
>
> --
> 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
>
>
>
> --
> You received this message because you are subscribed to a topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/OtsJDzHW-Zc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>.
>
> --
> You received this message because you are subscribed to a topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/OtsJDzHW-Zc/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> raxml+un...@googlegroups.com
> Rob Lanfear
> School of Biological Sciences,
> Macquarie University,
> Sydney
>
> phone: +61 (0)2 9850 8204
>
> www.robertlanfear.com <http://www.robertlanfear.com>
> School of Biological Sciences,
> Macquarie University,
> Sydney
>
> phone: +61 (0)2 9850 8204
>
Rob Lanfear
Sep 30, 2015, 2:00:13 AM9/30/15
to ra...@googlegroups.com
Hi Alexis,
Yes - on my machine I can only get the error with +I. I never get it for models without +I ('never' is probably in the region of a few million analyses, since I'm running partitionfinder on large datasets, and partitionfinder is calling RAxML a lot).
Cheers,
Rob
To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
Alexandros Stamatakis
Sep 30, 2015, 3:44:00 PM9/30/15
to ra...@googlegroups.com
okay, will try to fix it tomorrow, I know what the problem is, but not
the solution yet,
alexis
On 30.09.2015 07:59, Rob Lanfear wrote:
> Hi Alexis,
>
> Yes - on my machine I can only get the error with +I. I never get it for
> models without +I ('never' is probably in the region of a few million
> analyses, since I'm running partitionfinder on large datasets, and
> partitionfinder is calling RAxML a lot).
>
> Cheers,
>
> Rob
>
> On 30 September 2015 at 00:38, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>>.
> <mailto:raxml%252Buns...@googlegroups.com>>.
>
> www.robertlanfear.com <http://www.robertlanfear.com>
the solution yet,
alexis
On 30.09.2015 07:59, Rob Lanfear wrote:
> Hi Alexis,
>
> Yes - on my machine I can only get the error with +I. I never get it for
> models without +I ('never' is probably in the region of a few million
> analyses, since I'm running partitionfinder on large datasets, and
> partitionfinder is calling RAxML a lot).
>
> Cheers,
>
> Rob
>
> On 30 September 2015 at 00:38, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> Hi Rob,
>
> Sorry for the late reply, I've been busy with other stuff.
>
> Can you confirm that the error only appears with +I?
>
> I am 99% sure that I know where it comes from if it only happens
> when +I is being used.
>
> Cheers,
>
> Alexis
>
>
>
> On 07.09.2015 12 <tel:07.09.2015%2012>:41, Rob Lanfear wrote:
>
> No worries. I understand that this is unlikely to make it to the
> top of
> any to-do lists!
>
> In some further analyses, I am pretty sure that this issue is
> limited to
> GTR+I+G models, and doesn't occur with GTR+G models. I have only
> seen it
> with the former.
>
> Cheers,
>
> Rob
>
> On 7 September 2015 at 18:50, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:alexandros...@gmail.com
>
> Hi Rob,
>
> Sorry for the late reply, I've been busy with other stuff.
>
> Can you confirm that the error only appears with +I?
>
> I am 99% sure that I know where it comes from if it only happens
> when +I is being used.
>
> Cheers,
>
> Alexis
>
>
>
> On 07.09.2015 12 <tel:07.09.2015%2012>:41, Rob Lanfear wrote:
>
> No worries. I understand that this is unlikely to make it to the
> top of
> any to-do lists!
>
> In some further analyses, I am pretty sure that this issue is
> limited to
> GTR+I+G models, and doesn't occur with GTR+G models. I have only
> seen it
> with the former.
>
> Cheers,
>
> Rob
>
> On 7 September 2015 at 18:50, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:raxml%252Buns...@googlegroups.com>>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>>.
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> 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 <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org>
>
>
> --
> You received this message because you are subscribed to a
> topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/OtsJDzHW-Zc/unsubscribe.
> To unsubscribe from this group and all its topics, send an
> email to
> raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
>
>
> --
> 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 <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org>
>
>
> --
> You received this message because you are subscribed to a
> topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/OtsJDzHW-Zc/unsubscribe.
> To unsubscribe from this group and all its topics, send an
> email to
> raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com>>.
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Rob Lanfear
> School of Biological Sciences,
> Macquarie University,
> Sydney
>
> phone: +61 (0)2 9850 8204 <tel:%2B61%20%280%292%209850%208204>
>
>
>
>
> --
> Rob Lanfear
> School of Biological Sciences,
> Macquarie University,
> Sydney
>
>
> www.robertlanfear.com <http://www.robertlanfear.com>
Alexandros Stamatakis
Oct 2, 2015, 9:13:13 AM10/2/15
to ra...@googlegroups.com
Hi Rob,
Just started checking. In fact, it is not as simple as I thought.
The problem seems to be the combination of -U (memory saving) and +I.
Can you maybe run your analyses without -U and tell me if the error
still occurs. It went away when I removed -U. In the meantime, I'll
investigate a bit further.
Alexis
On 30.09.2015 07:59, Rob Lanfear wrote:
> <mailto:raxml%252Buns...@googlegroups.com>>.
Just started checking. In fact, it is not as simple as I thought.
The problem seems to be the combination of -U (memory saving) and +I.
Can you maybe run your analyses without -U and tell me if the error
still occurs. It went away when I removed -U. In the meantime, I'll
investigate a bit further.
Alexis
On 30.09.2015 07:59, Rob Lanfear wrote:
> Hi Alexis,
>
> Yes - on my machine I can only get the error with +I. I never get it for
> models without +I ('never' is probably in the region of a few million
> analyses, since I'm running partitionfinder on large datasets, and
> partitionfinder is calling RAxML a lot).
>
> Cheers,
>
> Rob
>
> On 30 September 2015 at 00:38, Alexandros Stamatakis
> <alexandros...@gmail.com
>
> Yes - on my machine I can only get the error with +I. I never get it for
> models without +I ('never' is probably in the region of a few million
> analyses, since I'm running partitionfinder on large datasets, and
> partitionfinder is calling RAxML a lot).
>
> Cheers,
>
> Rob
>
> On 30 September 2015 at 00:38, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> Hi Rob,
>
> Sorry for the late reply, I've been busy with other stuff.
>
> Can you confirm that the error only appears with +I?
>
> I am 99% sure that I know where it comes from if it only happens
> when +I is being used.
>
> Cheers,
>
> Alexis
>
>
>
> On 07.09.2015 12 <tel:07.09.2015%2012>:41, Rob Lanfear wrote:
>
> No worries. I understand that this is unlikely to make it to the
> top of
> any to-do lists!
>
> In some further analyses, I am pretty sure that this issue is
> limited to
> GTR+I+G models, and doesn't occur with GTR+G models. I have only
> seen it
> with the former.
>
> Cheers,
>
> Rob
>
> On 7 September 2015 at 18:50, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:alexandros...@gmail.com
>
> Hi Rob,
>
> Sorry for the late reply, I've been busy with other stuff.
>
> Can you confirm that the error only appears with +I?
>
> I am 99% sure that I know where it comes from if it only happens
> when +I is being used.
>
> Cheers,
>
> Alexis
>
>
>
> On 07.09.2015 12 <tel:07.09.2015%2012>:41, Rob Lanfear wrote:
>
> No worries. I understand that this is unlikely to make it to the
> top of
> any to-do lists!
>
> In some further analyses, I am pretty sure that this issue is
> limited to
> GTR+I+G models, and doesn't occur with GTR+G models. I have only
> seen it
> with the former.
>
> Cheers,
>
> Rob
>
> On 7 September 2015 at 18:50, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>>.
> <mailto:raxml%252Buns...@googlegroups.com>>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> 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 <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org>
>
>
> --
> You received this message because you are subscribed to a
> topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/OtsJDzHW-Zc/unsubscribe.
> To unsubscribe from this group and all its topics, send an
> email to
> raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
>
>
> --
> 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 <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org>
>
>
> --
> You received this message because you are subscribed to a
> topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/OtsJDzHW-Zc/unsubscribe.
> To unsubscribe from this group and all its topics, send an
> email to
> raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com>>.
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Rob Lanfear
> School of Biological Sciences,
> Macquarie University,
> Sydney
>
>
>
>
>
> --
> Rob Lanfear
> School of Biological Sciences,
> Macquarie University,
> Sydney
>
> phone: +61 (0)2 9850 8204 <tel:%2B61%20%280%292%209850%208204>
>
> www.robertlanfear.com <http://www.robertlanfear.com>
>
> www.robertlanfear.com <http://www.robertlanfear.com>
Alexandros Stamatakis
Oct 2, 2015, 9:47:20 AM10/2/15
to ra...@googlegroups.com
Hi Rob,
So it turned out that the memory saving option -U was never implemented
for GTR+GAMMA+I, thus the error. RAxML version 8.2.4 that I just
commited now will issue an error message and exit when you try to use it
like this.
Alexis
On 25.08.2015 08:03, Rob Lanfear wrote:
So it turned out that the memory saving option -U was never implemented
for GTR+GAMMA+I, thus the error. RAxML version 8.2.4 that I just
commited now will issue an error message and exit when you try to use it
like this.
Alexis
On 25.08.2015 08:03, Rob Lanfear wrote:
Reply all
Reply to author
Forward
0 new messages