Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Lev Karatun
Hi Bruno,

that's what I was doing...

Best regards,
Lev Karatun.

2017-04-26 19:48 GMT-04:00 Bruno Turcksin :

> 2017-04-26 18:10 GMT-04:00 Lev Karatun :
> > all tests passed.
> OK Then can you try to configure deal in a new empty directory.
>
> Best
>
> Bruno
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/
> forum/dealii?hl=en
> ---
> You received this message because you are subscribed to a topic in the
> Google Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/
> topic/dealii/p-64i1ahEWM/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> dealii+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Bruno Turcksin
2017-04-26 18:10 GMT-04:00 Lev Karatun :
> all tests passed.
OK Then can you try to configure deal in a new empty directory.

Best

Bruno

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Lev Karatun
Hi Bruno,

all tests passed.

Best regards,
Lev Karatun.

2017-04-26 17:16 GMT-04:00 Bruno Turcksin :

> 2017-04-26 17:10 GMT-04:00 Lev Karatun :
> > [lev@titan FAST]$ make tests
> > make: *** No rule to make target `tests'.  Stop."
> Sorry it was `make check`
>
> Bruno
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/
> forum/dealii?hl=en
> ---
> You received this message because you are subscribed to a topic in the
> Google Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/
> topic/dealii/p-64i1ahEWM/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> dealii+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Bruno Turcksin
2017-04-26 17:10 GMT-04:00 Lev Karatun :
> [lev@titan FAST]$ make tests
> make: *** No rule to make target `tests'.  Stop."
Sorry it was `make check`

Bruno

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Lev Karatun
Doesn't work =(

"[lev@titan FAST]$ pwd
/home/lev/distrib/p4est-build/FAST
[lev@titan FAST]$ l
total 1M
-rw-rw-r--  1 lev lev 1M Apr 26 11:35 config.log
-rw-rw-r--  1 lev lev 1M Apr 26 11:35 config.output
-rw-rw-r--  1 lev lev 1M Apr 26 11:34 _configs.sed
-rwxrwxr-x  1 lev lev 1M Apr 26 11:34 config.status*
drwxrwxr-x 11 lev lev 1M Apr 26 11:34 example/
-rwxrwxr-x  1 lev lev 1M Apr 26 11:35 libtool*
-rw-rw-r--  1 lev lev 1M Apr 26 11:34 Makefile
-rw-rw-r--  1 lev lev 1M Apr 26 11:35 Makefile.p4est.mk
-rw-rw-r--  1 lev lev 1M Apr 26 11:34 Makefile.p4est.pre
-rw-rw-r--  1 lev lev 1M Apr 26 11:35 make.output
drwxrwxr-x  9 lev lev 1M Apr 26 11:35 sc/
drwxrwxr-x  4 lev lev 1M Apr 26 11:35 src/
drwxrwxr-x  3 lev lev 1M Apr 26 11:35 test/
[lev@titan FAST]$ make tests
make: *** No rule to make target `tests'.  Stop."

Best regards,
Lev Karatun.

2017-04-26 12:07 GMT-04:00 Bruno Turcksin :

> Very strange. Can you go in the build directory of p4est (DEBUG or
> FAST it doesn't matter) and run the tests (make tests). Do all the
> tests pass?
>
> Bruno
>
> 2017-04-26 11:43 GMT-04:00 Lev Karatun :
> > Hi Bruno,
> >
> > I don't remember installing zlib, maybe it was installed with the OS? Or
> > maybe it was part of some other packages I installed in the past? I'm not
> > sure. Again, I installed p4est on this machine 2 years ago and haven't
> done
> > anything to it, that's why it seems strange it's not accepted by dealII
> > anymore.
> >
> > Anyway, zlib was indeed not in LD_LIBRARY_PATH:
> >
> >>> rpm -ql zlib-devel.x86_64
> > /usr/include/zconf.h
> > /usr/include/zlib.h
> > /usr/lib64/libz.so
> > /usr/lib64/pkgconfig/zlib.pc
> > /usr/share/doc/zlib-devel-1.2.3
> > /usr/share/doc/zlib-devel-1.2.3/README
> > /usr/share/doc/zlib-devel-1.2.3/algorithm.txt
> > /usr/share/doc/zlib-devel-1.2.3/example.c
> > /usr/share/doc/zlib-devel-1.2.3/minigzip.c
> > /usr/share/man/man3/zlib.3.gz
> >
> > I added it (is it correct now?):
> >
> >>> echo $LD_LIBRARY_PATH
> > /usr/lib64/openmpi/lib:/opt/rh/devtoolset-2/root/usr/
> lib64:/opt/rh/devtoolset-2/root/usr/lib:/usr/share/doc/:/
> usr/include:/usr/lib64
> >
> > Reinstalled p4est, but still getting the same error.
> >
> >
> >
> > Best regards,
> > Lev Karatun.
> >
> > 2017-04-26 10:27 GMT-04:00 Bruno Turcksin :
> >>
> >> Lev,
> >>
> >> 2017-04-26 10:16 GMT-04:00 Lev Karatun :
> >> > it's installed too =(
> >> >
> >> > "Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest
> >> > version
> >> > Nothing to do"
> >>
> >> Maybe it's not in your LD_LIBRARY_PATH? How did you install it?
> >>
> >> Best
> >>
> >> Bruno
> >>
> >> --
> >> The deal.II project is located at http://www.dealii.org/
> >> For mailing list/forum options, see
> >> https://groups.google.com/d/forum/dealii?hl=en
> >> ---
> >> You received this message because you are subscribed to a topic in the
> >> Google Groups "deal.II User Group" group.
> >> To unsubscribe from this topic, visit
> >> https://groups.google.com/d/topic/dealii/p-64i1ahEWM/unsubscribe.
> >> To unsubscribe from this group and all its topics, send an email to
> >> dealii+unsubscr...@googlegroups.com.
> >> For more options, visit https://groups.google.com/d/optout.
> >
> >
> > --
> > The deal.II project is located at http://www.dealii.org/
> > For mailing list/forum options, see
> > https://groups.google.com/d/forum/dealii?hl=en
> > ---
> > You received this message because you are subscribed to a topic in the
> > Google Groups "deal.II User Group" group.
> > To unsubscribe from this topic, visit
> > https://groups.google.com/d/topic/dealii/p-64i1ahEWM/unsubscribe.
> > To unsubscribe from this group and all its topics, send an email to
> > dealii+unsubscr...@googlegroups.com.
> > For more options, visit https://groups.google.com/d/optout.
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/
> forum/dealii?hl=en
> ---
> You received this message because you are subscribed to a topic in the
> Google Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/
> topic/dealii/p-64i1ahEWM/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> dealii+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: How to provide the VectorMemory<BlockVector > for the class SchurMatrix?

2017-04-26 Thread Jean-Paul Pelteret
Dear Jesse,

You can probably just provide an instance of the GrowingVectorMemory 
 
class 
templated on BlockVector< double >. So this would look something like:
GrowingVectorMemory< BlockVector > memory;
const SchurMatrix schur_matrix (A_inv, B, Dt, C, memory);
...

If its of any help to you, and if you have a C++11 compatible compiler, 
then you could alternatively use the (relatively) new LinearOperator 
 
class and the schur_complement 

 
operator. It provides a more flexible framework with which you could 
perform the same operation.

Kind regards,
Jean-Paul

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Lev Karatun
Hi Timo,

it's installed too =(

"Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version
Nothing to do"

Best regards,
Lev Karatun.

2017-04-26 10:09 GMT-04:00 Timo Heister :

> You need the "dev" package too. On my machine it is called zlib1g-dev
>
> On Wed, Apr 26, 2017 at 10:03 AM, Lev Karatun 
> wrote:
> > Hi Bruno,
> >
> > I reinstalled p4est, but zlib didn't get picked up unfortunately. I made
> > sure it is installed on the machine:
> > "Installed Packages
> > Name: zlib
> > Arch: x86_64
> > Version : 1.2.3
> > Release : 29.el6
> > Size: 149 k
> > Repo: installed
> > From repo   : anaconda-CentOS-201410241409.x86_64
> > Summary : The zlib compression and decompression library
> > URL : https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
> gzip.org_zlib_=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=
> 4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_
> PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=uLjZ-nmptzLNBPhgUYKYtMzr6CGUXlu2pzV
> SqPfC5pA=
> > License : zlib and Boost
> > Description : Zlib is a general-purpose, patent-free, lossless data
> > compression
> > : library which is used by many different programs."
> >
> > Best regards,
> > Lev Karatun.
> >
> > 2017-04-26 8:35 GMT-04:00 Bruno Turcksin :
> >>
> >> Lev,
> >>
> >> you need to make sure that zlib is installed on your machine and then
> >> reinstall p4est. zlib should be picked up automatically.
> >>
> >> Best,
> >>
> >> Bruno
> >>
> >> On Tuesday, April 25, 2017 at 7:06:21 PM UTC-4, Lev Karatun wrote:
> >>>
> >>> Hi everyone,
> >>>
> >>> I was updating dealII to the latest version and received the error when
> >>> trying to configure it:
> >>> "  Insufficient p4est installation found!
> >>>   p4est has to be configured with enabled zlib support."
> >>>
> >>> I used the p4est-setup.sh script to install it originally (and haven't
> >>> modified it ever since), could you please let me know how I can modify
> the
> >>> script to include zlib support?
> >>>
> >>> Thanks in advance!
> >>
> >> --
> >> The deal.II project is located at https://urldefense.proofpoint.
> com/v2/url?u=http-3A__www.dealii.org_=DwIBaQ=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmE
> jX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=
> 9Am8pIx4iJmd7fxFLiWvrlI1t2CL0N90F3bMLh8fTTs=
> >> For mailing list/forum options, see
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.
> google.com_d_forum_dealii-3Fhl-3Den=DwIBaQ=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmE
> jX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=
> Ba9AlHxcMubeCXXSitOzI2hsBY8vbHMv-XBJXVe9mTA=
> >> ---
> >> You received this message because you are subscribed to a topic in the
> >> Google Groups "deal.II User Group" group.
> >> To unsubscribe from this topic, visit
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.
> google.com_d_topic_dealii_p-2D64i1ahEWM_unsubscribe=DwIBaQ=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmE
> jX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=
> ha6tA3ZffmCnMyPPWthiGbe7vGXE9OVrfYOK8DsnZjs= .
> >> To unsubscribe from this group and all its topics, send an email to
> >> dealii+unsubscr...@googlegroups.com.
> >> For more options, visit https://urldefense.proofpoint.
> com/v2/url?u=https-3A__groups.google.com_d_optout=DwIBaQ=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmE
> jX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=
> 6WFYfVvDxz9nMWmSbipd5VhagC8OuaDSzZxEzUGV2Eg= .
> >
> >
> > --
> > The deal.II project is located at https://urldefense.proofpoint.
> com/v2/url?u=http-3A__www.dealii.org_=DwIBaQ=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmE
> jX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=
> 9Am8pIx4iJmd7fxFLiWvrlI1t2CL0N90F3bMLh8fTTs=
> > For mailing list/forum options, see
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.
> google.com_d_forum_dealii-3Fhl-3Den=DwIBaQ=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmE
> jX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=
> Ba9AlHxcMubeCXXSitOzI2hsBY8vbHMv-XBJXVe9mTA=
> > ---
> > You received this message because you are subscribed to the Google Groups
> > "deal.II User Group" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to dealii+unsubscr...@googlegroups.com.
> > For more options, visit https://urldefense.proofpoint.
> com/v2/url?u=https-3A__groups.google.com_d_optout=DwIBaQ=Ngd-
> ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmE
> jX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=
> 6WFYfVvDxz9nMWmSbipd5VhagC8OuaDSzZxEzUGV2Eg= .
>
>
>
> --
> Timo Heister
> http://www.math.clemson.edu/~heister/
>
> --
> The 

Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Timo Heister
You need the "dev" package too. On my machine it is called zlib1g-dev

On Wed, Apr 26, 2017 at 10:03 AM, Lev Karatun  wrote:
> Hi Bruno,
>
> I reinstalled p4est, but zlib didn't get picked up unfortunately. I made
> sure it is installed on the machine:
> "Installed Packages
> Name: zlib
> Arch: x86_64
> Version : 1.2.3
> Release : 29.el6
> Size: 149 k
> Repo: installed
> From repo   : anaconda-CentOS-201410241409.x86_64
> Summary : The zlib compression and decompression library
> URL : 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gzip.org_zlib_=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=uLjZ-nmptzLNBPhgUYKYtMzr6CGUXlu2pzVSqPfC5pA=
>  
> License : zlib and Boost
> Description : Zlib is a general-purpose, patent-free, lossless data
> compression
> : library which is used by many different programs."
>
> Best regards,
> Lev Karatun.
>
> 2017-04-26 8:35 GMT-04:00 Bruno Turcksin :
>>
>> Lev,
>>
>> you need to make sure that zlib is installed on your machine and then
>> reinstall p4est. zlib should be picked up automatically.
>>
>> Best,
>>
>> Bruno
>>
>> On Tuesday, April 25, 2017 at 7:06:21 PM UTC-4, Lev Karatun wrote:
>>>
>>> Hi everyone,
>>>
>>> I was updating dealII to the latest version and received the error when
>>> trying to configure it:
>>> "  Insufficient p4est installation found!
>>>   p4est has to be configured with enabled zlib support."
>>>
>>> I used the p4est-setup.sh script to install it originally (and haven't
>>> modified it ever since), could you please let me know how I can modify the
>>> script to include zlib support?
>>>
>>> Thanks in advance!
>>
>> --
>> The deal.II project is located at 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=9Am8pIx4iJmd7fxFLiWvrlI1t2CL0N90F3bMLh8fTTs=
>>  
>> For mailing list/forum options, see
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=Ba9AlHxcMubeCXXSitOzI2hsBY8vbHMv-XBJXVe9mTA=
>>  
>> ---
>> You received this message because you are subscribed to a topic in the
>> Google Groups "deal.II User Group" group.
>> To unsubscribe from this topic, visit
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_topic_dealii_p-2D64i1ahEWM_unsubscribe=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=ha6tA3ZffmCnMyPPWthiGbe7vGXE9OVrfYOK8DsnZjs=
>>  .
>> To unsubscribe from this group and all its topics, send an email to
>> dealii+unsubscr...@googlegroups.com.
>> For more options, visit 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=6WFYfVvDxz9nMWmSbipd5VhagC8OuaDSzZxEzUGV2Eg=
>>  .
>
>
> --
> The deal.II project is located at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=9Am8pIx4iJmd7fxFLiWvrlI1t2CL0N90F3bMLh8fTTs=
>  
> For mailing list/forum options, see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_forum_dealii-3Fhl-3Den=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=Ba9AlHxcMubeCXXSitOzI2hsBY8vbHMv-XBJXVe9mTA=
>  
> ---
> You received this message because you are subscribed to the Google Groups
> "deal.II User Group" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to dealii+unsubscr...@googlegroups.com.
> For more options, visit 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_d_optout=DwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w=6WFYfVvDxz9nMWmSbipd5VhagC8OuaDSzZxEzUGV2Eg=
>  .



-- 
Timo Heister
http://www.math.clemson.edu/~heister/

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Lev Karatun
Hi Bruno,

I reinstalled p4est, but zlib didn't get picked up unfortunately. I made
sure it is installed on the machine:
"Installed Packages
Name: zlib
Arch: x86_64
Version : 1.2.3
Release : 29.el6
Size: 149 k
Repo: installed
>From repo   : anaconda-CentOS-201410241409.x86_64
Summary : The zlib compression and decompression library
URL : http://www.gzip.org/zlib/
License : zlib and Boost
Description : Zlib is a general-purpose, patent-free, lossless data
compression
: library which is used by many different programs."

Best regards,
Lev Karatun.

2017-04-26 8:35 GMT-04:00 Bruno Turcksin :

> Lev,
>
> you need to make sure that zlib is installed on your machine and then
> reinstall p4est. zlib should be picked up automatically.
>
> Best,
>
> Bruno
>
> On Tuesday, April 25, 2017 at 7:06:21 PM UTC-4, Lev Karatun wrote:
>>
>> Hi everyone,
>>
>> I was updating dealII to the latest version and received the error when
>> trying to configure it:
>> "  Insufficient p4est installation found!
>>   p4est has to be configured with enabled zlib support."
>>
>> I used the p4est-setup.sh script to install it originally (and haven't
>> modified it ever since), could you please let me know how I can modify the
>> script to include zlib support?
>>
>> Thanks in advance!
>>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/
> forum/dealii?hl=en
> ---
> You received this message because you are subscribed to a topic in the
> Google Groups "deal.II User Group" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/
> topic/dealii/p-64i1ahEWM/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> dealii+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] How to provide the VectorMemory<BlockVector > for the class SchurMatrix?

2017-04-26 Thread Jesse
Deal all,

I'm using the mixed finite element to solve a Cahn-HIlliard type equation, 
after discretization I obtain a block matrix system. I plan to use the 
class SchurMatrix in deal.ii to obtain the Schur Complement.

The block matrix system is 

* / \ / \ / \ * | A Dt | | u | - | f | * | -B C | | p | - | g | * \ / \ / \ 
/
where A and C are sparse mass matrices, B Dt are sparse stiff matrices. 
But when constructing the SchurMatrix object, I need to provide  'mem'. 
Could someone help me to provide 'mem'?

Thank you in advance.
Jesse 
template

SchurMatrix 
< 
MA_inverse, MB, MDt, MC >::SchurMatrix 
 ( const 
MA_inverse &  Ainv,
const MB &  B,
const MDt &  Dt,
const MC &  C,
VectorMemory 
< 
BlockVector 
< 
double > > &  mem,
const std::vector< types::global_dof_index 

 > 
&  signature = std::vectorhttps://www.dealii.org/8.4.0/doxygen/deal.II/namespacetypes.html#a3bf9e493f1aab00b04933b81856144c4>
>(0) 
)


-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


[deal.II] Re: p4est has to be configured with enabled zlib support

2017-04-26 Thread Bruno Turcksin
Lev,

you need to make sure that zlib is installed on your machine and then 
reinstall p4est. zlib should be picked up automatically.

Best,

Bruno

On Tuesday, April 25, 2017 at 7:06:21 PM UTC-4, Lev Karatun wrote:
>
> Hi everyone,
>
> I was updating dealII to the latest version and received the error when 
> trying to configure it: 
> "  Insufficient p4est installation found!
>   p4est has to be configured with enabled zlib support."
>
> I used the p4est-setup.sh script to install it originally (and haven't 
> modified it ever since), could you please let me know how I can modify the 
> script to include zlib support? 
>
> Thanks in advance!
>

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
https://groups.google.com/d/forum/dealii?hl=en
--- 
You received this message because you are subscribed to the Google Groups 
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.


Re: [deal.II] Refining a hyper_ball with a spherical_manifold produces nan values

2017-04-26 Thread Alexander Gary Zimmerman
Thanks, Luca. The behavior is obvious to me now.

As for the documentation: I indeed missed that detail from 
SphericalManifold; but* there is a very misleading statement in the 
hyper_ball documentation:* "You should attach a SphericalManifold 
 to 
the cells and faces for correct placement of vertices upon refinement and 
to be able to use higher order mappings." I would guess that this could 
lead many people to (at least initially) make my mistake, so maybe a small 
edit to note the pitfall could be made here.

So if I want to have a solid sphere domain with a spherical manifold 
throughout it's entirety, I understand that my best option is to use a 
hyper_shell with a very small inside radius.


On Wednesday, April 26, 2017 at 10:06:00 AM UTC+2, Luca Heltai wrote:
>
> This is actually not a bug. A spherical manifold is undefined on the 
> center of the sphere/ball. You cannot attach set_all_manifold_ids of the 
> spherical manifold and attach a spherical manifold to it, since the central 
> cell (the one where the cell->center() coincides with the ball center) 
> would not know what to do. 
>
> This is documented in the SphericalManfold documentation. See the phrase 
> "In order for this manifold to work correctly, it cannot be attached to 
> cells containing the center of the coordinate system. This point is a 
> singular point of the coordinate transformation, and there taking averages 
> does not make any sense.” 
>
> Best, 
>
> L. 
>
>
> > On 25 Apr 2017, at 13:42, Alexander Gary Zimmerman <
> zimmerma...@gmail.com > wrote: 
> > 
> > When I refine a Triangulation that has been initialized with 
> GridGenerator::hyper_ball, and has a SphericalManifold attached (and having 
> set_all_manifold_ids on the Triangulation), some nan (not a number) values 
> are produced. 
> > 
> > On the other hand, I get the expected behavior when instead using a 
> GridGenerator::hyper_shell. 
> > 
> > I've documented the issue on my repo here: 
> https://github.com/alexanderzimmerman/nsb-pcm/issues/21 
> > 
> > I'm using deal.II-v.8.5.0. I haven't tried reproducing this on any other 
> versions. 
> > 
> > These are in the repo, but here's the test that passes: 
> > 
> > #include  
> > #include  
> > #include  
> > 
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > 
> > using namespace dealii; 
> > 
> > const unsigned int dim = 2; 
> > 
> > 
> > void validate_vertices(Triangulation ) 
> > {   
> > Triangulation::cell_iterator cell; 
> > 
> > unsigned int nv = GeometryInfo::vertices_per_cell; 
> >   
> > for (cell = tria.begin(); cell != tria.end(); ++cell) 
> > { 
> > for (unsigned int v = 0; v < nv; ++v) 
> > { 
> > for (unsigned int i = 0; i < dim; ++i) 
> > { 
> > assert(!numbers::is_nan(cell->vertex(v)[i])); 
> > } 
> > 
> > } 
> > 
> > } 
> > 
> > } 
> > 
> > 
> > int main(int /*argc*/, char** /*argv*/) 
> > { 
> > Triangulation triangulation; 
> > 
> > GridGenerator::hyper_shell(triangulation, Point(), 0.1, 0.5); 
> > 
> > const unsigned int manifold_id = 0; 
> > 
> > triangulation.set_all_manifold_ids(manifold_id); 
> > 
> > SphericalManifold spherical_manifold; 
> > 
> > triangulation.set_manifold(manifold_id, spherical_manifold);   
> > 
> > GridOut grid_writer; 
> > 
> > 
> > for (unsigned int r = 0; r < 2; ++r) 
> > { 
> > std::string file_name = "grid_"+std::to_string(r)+".vtk"; 
> > 
> > std::ofstream file(file_name); 
> > 
> > grid_writer.write_vtk(triangulation, file);   
> > 
> > validate_vertices(triangulation); 
> > 
> > triangulation.refine_global(1); 
> > } 
> > 
> > triangulation.set_manifold(0); 
> > 
> > return 0; 
> > } 
> > 
> > 
> > and here's the test that fails: 
> > 
> > #include  
> > #include  
> > #include  
> > 
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > #include  
> > 
> > 
> > using namespace dealii; 
> > 
> > const unsigned int dim = 2; 
> > 
> > 
> > void validate_vertices(Triangulation ) 
> > {   
> > Triangulation::cell_iterator cell; 
> > 
> > unsigned int nv = GeometryInfo::vertices_per_cell; 
> >   
> > for (cell = tria.begin(); cell != tria.end(); ++cell) 
> > { 
> > for (unsigned int v = 0; v < nv; ++v) 
> > { 
> > for (unsigned int i = 0; i < dim; ++i) 
> > { 
> > assert(!numbers::is_nan(cell->vertex(v)[i])); 
> > } 
> > 
> > } 
> > 
> > } 
> > 
> > } 
> > 
> > 
> > int main(int /*argc*/, char** /*argv*/) 
> > { 
> >

Re: [deal.II] Refining a hyper_ball with a spherical_manifold produces nan values

2017-04-26 Thread luca.heltai
This is actually not a bug. A spherical manifold is undefined on the center of 
the sphere/ball. You cannot attach set_all_manifold_ids of the spherical 
manifold and attach a spherical manifold to it, since the central cell (the one 
where the cell->center() coincides with the ball center) would not know what to 
do.

This is documented in the SphericalManfold documentation. See the phrase "In 
order for this manifold to work correctly, it cannot be attached to cells 
containing the center of the coordinate system. This point is a singular point 
of the coordinate transformation, and there taking averages does not make any 
sense.”

Best,

L.


> On 25 Apr 2017, at 13:42, Alexander Gary Zimmerman 
>  wrote:
> 
> When I refine a Triangulation that has been initialized with 
> GridGenerator::hyper_ball, and has a SphericalManifold attached (and having 
> set_all_manifold_ids on the Triangulation), some nan (not a number) values 
> are produced.
> 
> On the other hand, I get the expected behavior when instead using a 
> GridGenerator::hyper_shell.
> 
> I've documented the issue on my repo here: 
> https://github.com/alexanderzimmerman/nsb-pcm/issues/21
> 
> I'm using deal.II-v.8.5.0. I haven't tried reproducing this on any other 
> versions.
> 
> These are in the repo, but here's the test that passes:
> 
> #include 
> #include 
> #include 
> 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> 
> using namespace dealii;
> 
> const unsigned int dim = 2;
> 
> 
> void validate_vertices(Triangulation )
> {   
> Triangulation::cell_iterator cell;
> 
> unsigned int nv = GeometryInfo::vertices_per_cell;
>   
> for (cell = tria.begin(); cell != tria.end(); ++cell)
> {
> for (unsigned int v = 0; v < nv; ++v)
> {
> for (unsigned int i = 0; i < dim; ++i)
> {
> assert(!numbers::is_nan(cell->vertex(v)[i]));
> }
> 
> }
> 
> }
> 
> }
> 
> 
> int main(int /*argc*/, char** /*argv*/)
> {
> Triangulation triangulation;
> 
> GridGenerator::hyper_shell(triangulation, Point(), 0.1, 0.5);
> 
> const unsigned int manifold_id = 0;
> 
> triangulation.set_all_manifold_ids(manifold_id);
>
> SphericalManifold spherical_manifold;
> 
> triangulation.set_manifold(manifold_id, spherical_manifold);  
>
> GridOut grid_writer;
> 
> 
> for (unsigned int r = 0; r < 2; ++r)
> {
> std::string file_name = "grid_"+std::to_string(r)+".vtk";
> 
> std::ofstream file(file_name);
> 
> grid_writer.write_vtk(triangulation, file);   
> 
> validate_vertices(triangulation);
> 
> triangulation.refine_global(1);
> }
> 
> triangulation.set_manifold(0);
> 
> return 0;
> }
> 
> 
> and here's the test that fails:
> 
> #include 
> #include 
> #include 
> 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> #include 
> 
> 
> using namespace dealii;
> 
> const unsigned int dim = 2;
> 
> 
> void validate_vertices(Triangulation )
> {   
> Triangulation::cell_iterator cell;
> 
> unsigned int nv = GeometryInfo::vertices_per_cell;
>   
> for (cell = tria.begin(); cell != tria.end(); ++cell)
> {
> for (unsigned int v = 0; v < nv; ++v)
> {
> for (unsigned int i = 0; i < dim; ++i)
> {
> assert(!numbers::is_nan(cell->vertex(v)[i]));
> }
> 
> }
> 
> }
> 
> }
> 
> 
> int main(int /*argc*/, char** /*argv*/)
> {
> Triangulation triangulation;
> 
> GridGenerator::hyper_ball(triangulation);
> 
> const unsigned int manifold_id = 0;
> 
> triangulation.set_all_manifold_ids(manifold_id);
>
> SphericalManifold spherical_manifold;
> 
> triangulation.set_manifold(manifold_id, spherical_manifold);  
>
> GridOut grid_writer;
> 
> 
> for (unsigned int r = 0; r < 2; ++r)
> {
> std::string file_name = "grid_"+std::to_string(r)+".vtk";
> 
> std::ofstream file(file_name);
> 
> grid_writer.write_vtk(triangulation, file);   
> 
> validate_vertices(triangulation);
> 
> triangulation.refine_global(1);
> }
> 
> triangulation.set_manifold(0);
> 
> return 0;
> }
> 
> 
> Any ideas?
> 
> Thanks,
> 
> Alex
> 
> P.S. for future reference, if I have an issue formulated like this, should I 
> raise it on the deal.II repo or here in the mailing list?
> 
> -- 
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see 
> https://groups.google.com/d/forum/dealii?hl=en
> --- 
> You received this message because you are subscribed to the Google Groups 
> "deal.II