[deal.II] Re: An issue in compiling on a cluster

[Denis Davydov]

p.s. it's a bit of a learning curve to set things up with Spack, but 
hopefully it does not take too much as there is a lot of documentation.
On the positive side, a lot of developers now give more and more attention 
to Spack and maintain their packages. I know that PETSc and Trilinos guys 
keep an eye on Spack.
Very recently, if I understand right, OpenFOAM developer revised its 
package in Spack and added more things. A developer of quantum mechanics 
code Abinit also contributed
a changes/fixes to their package. So in the ideal world you have a tool to 
build 1000+ packages where package developers are also maintaining some of 
those.

On Tuesday, April 4, 2017 at 8:24:19 PM UTC+2, Alberto Salvadori wrote:
>
> Hi, 
>
> your help in this issue is greatly appreciated.
>
> I installed deal.II on a cluster using the spack distribution, very 
> easily. I also run some examples provided with deal.II with no issues. 
> Great job.
>
> I am now using a library for tensor calculus, that apparently conflicts 
> with the gcc compiler installed with spack. Specifically, the spack 
> configuration uses /gcc-4.9.2 
>
>
> opt/spack/linux-rhel7-x86_64/gcc-4.9.2/openmpi-2.0.2-kupebz5mdlwlfvbkcit3y56cg6r4bxg5/bin/mpic++
>
> while this library needs gcc-6.2.0 or higher. The cluster is equipped 
> with  mpich/3.2-gcc-6.2.0, but I am not sufficiently skilled to edit the 
> configuration or the make files to solve the problem.
> Any help?
>
> Thanks
> Alberto
>

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Re: [deal.II] Re: An issue in compiling on a cluster

[Denis Davydov]

HI Alberto,

On Tuesday, April 4, 2017 at 10:58:39 PM UTC+2, Alberto Salvadori wrote:
>
> Sorry, I am a bit confused.
>
> "you need to make sure that building mpich is set to false." 
>  - where I can set "building mpich" to false? Shall I edit a file  
> ~/.spack/packages.yaml that BTW currently I do not have? 
>  - if so, would this be OK?
>
> *spack providers mpi*
>
> *intel-parallel-studio@cluster:+mpi  mpich@1:  mpich@3:  mvapich2@1.9  
> mvapich2@2.0:  openmpi@1.6.5  openmpi@1.7.5:  openmpi@2.0.0:  spectrum-mpi*
>
> openmpi:
> version: [2.0.0]
> paths:
>   openmpi@2.0.0%gcc@6.2.0: ...SOMEPATH.../m/mpich/3.2/gcc/6.2.0/bin ( the 
> latter is the directory where mpic++ executable is )
> buildable: False
>
> it's almost correct, you need to provide a path to the prefix, i.e. 
without `bin`.
In other words, it's a path to the externally provided MPI package, not to 
the MPI compiler wrappers.
 

> "You need to run something like spack  install@dealii ^mpich %gcc@6.2"
> - sorry, I cannot understand this. I know I am bothering, but can you 
> please explain this a bit further?
>

please have a look at this short 
presentation https://tgamblin.github.io/files/Gamblin-Spack-SC15-Talk.pdf
Essentially it's about adding extra constrains to what you want to build.
If you are a single user, those are generally easier to be added in the 
packages.yaml file as opposed to the command line.

Regards,
Denis.

>

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[deal.II] An issue in compiling on a cluster

[Denis Davydov]

Bruno is right, you definitely don't want compile MPI yourself in a cluster. At 
the very top of the WiKi there is an example of how to configure Spack on a 
cluster with external MPI 
https://github.com/dealii/dealii/wiki/deal.II-in-Spack
Probably you missed this.

I will edit the WiKi to stress this fact.

Regards,
Denis

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Re: [deal.II] Re: An issue in compiling on a cluster

[Alberto Salvadori]

Got it, sorry.
A


*Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto.salvad...@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

On Tue, Apr 4, 2017 at 5:41 PM, Alberto Salvadori <
alberto.salvad...@unibs.it> wrote:

> Ouch ... something went wrong:
>
> asalvad2 *~/.spack/linux* *$* *cd $SPACK_ROOT*
>
> asalvad2 */scratch/asalvad2/spack* *$* *spack install dealii %gcc@6.2*
>
> *==>* Error: : Additional properties are not allowed
> ('openmpi' was unexpected)
>
> asalvad2 */scratch/asalvad2/spack* *$* *module list*
>
> *Currently Loaded Modulefiles:*
>
> *  1) opt_local/1.0  2) gcc/6.2.0  3)
> ompi/2.0.1-gcc-6.2.0*
>
> asalvad2 */scratch/asalvad2/spack* *$* *more
> ~/.spack/linux/packages.yaml *
>
> *openmpi:*
>
> *version: [2.0.1]*
>
> *paths:*
>
> *  openmpi@2.0.1%gcc@6.2.0:
> /opt/crc/o/openmpi/2.0.1/gcc/6.2.0/eth/bin *
>
> *buildable: False*
>
> *Any further help?*
> *Thanks*
> *Alberto*
>
>
>
> *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
> Territorio, Ambiente e di Matematica (DICATAM)
>  Universita` di Brescia, via Branze 43, 25123 Brescia
>  Italy
>  tel 030 3711239
>  fax 030 3711312
>
> e-mail:
>  alberto.salvad...@unibs.it
> web-pages:
>  http://m4lab.unibs.it/faculty.html
>  http://dicata.ing.unibs.it/salvadori
>
> On Tue, Apr 4, 2017 at 5:25 PM, Alberto Salvadori <
> alberto.salvad...@unibs.it> wrote:
>
>> Hi Bruno,
>>
>> I really appreciate your help.
>> I got the right location of my openmpi and just mean to double check
>> before running spack. I shall therefore:
>>
>> 1 - create a file  ~/.spack/linux/packages.yaml as follows:
>>
>> openmpi:
>> version: [2.0.1]
>> paths:
>>   openmpi@2.0.1%gcc@6.2.0: ...SOMEPATH...openmpi/2.0.1/gcc/6.2.0/eth/bin
>> buildable: False
>>
>> 2 - spack install dealii %gcc@6.2
>>
>> Correct?
>> Thanks
>> Alberto
>>
>>
>>
>>
>> *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
>> Territorio, Ambiente e di Matematica (DICATAM)
>>  Universita` di Brescia, via Branze 43, 25123 Brescia
>>  Italy
>>  tel 030 3711239
>>  fax 030 3711312
>>
>> e-mail:
>>  alberto.salvad...@unibs.it
>> web-pages:
>>  http://m4lab.unibs.it/faculty.html
>>  http://dicata.ing.unibs.it/salvadori
>>
>> On Tue, Apr 4, 2017 at 5:11 PM, Bruno Turcksin 
>> wrote:
>>
>>> 2017-04-04 16:58 GMT-04:00 Alberto Salvadori >> >:
>>> > Sorry, I am a bit confused.
>>> >
>>> > "you need to make sure that building mpich is set to false."
>>> >  - where I can set "building mpich" to false? Shall I edit a file
>>> > ~/.spack/packages.yaml that BTW currently I do not have?
>>> Yes, you need to create the file if it doesn't exist.
>>>
>>> >  - if so, would this be OK?
>>> >
>>> > spack providers mpi
>>> >
>>> > intel-parallel-studio@cluster:+mpi  mpich@1:  mpich@3:
>>> mvapich2@1.9
>>> > mvapich2@2.0:  openmpi@1.6.5  openmpi@1.7.5:  openmpi@2.0.0:
>>> spectrum-mpi
>>> >
>>> >
>>> > openmpi:
>>> > version: [2.0.0]
>>> > paths:
>>> >   openmpi@2.0.0%gcc@6.2.0: ...SOMEPATH.../m/mpich/3.2/gcc/6.2.0/bin
>>> (
>>> > the latter is the directory where mpic++ executable is )
>>> > buildable: False
>>> This looks sketchy: you say openmpi but then the path says mpich...
>>> Otherwise it looks good.
>>>
>>> >
>>> > "You need to run something like spack  install dealii ^mpich %gcc@6.2"
>>> > - sorry, I cannot understand this. I know I am bothering, but can you
>>> please
>>> > explain this a bit further?
>>> spack install dealii %gcc@6.2 -> install deal.II with the gcc 6.2
>>> compiler. Because you have more than one compiler on your system, you
>>> need to tell spack which compiler to use.
>>> spack install dealii ^mpich -> I am not sure about this one.  But by
>>> default, spack uses openmpi but your path says that you are using
>>> mpich. Thus, you need to force spack to use mpich instead of openmpi.
>>> I am not sure this is the exact command though that's why I said it
>>> should look like "spack install ^mpich %gcc@6.2"
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see https://groups.google.com/d/fo
>>> rum/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.
>>>
>>
>>
>

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Re: [deal.II] Re: An issue in compiling on a cluster

[Alberto Salvadori]

Ouch ... something went wrong:

asalvad2 *~/.spack/linux* *$* *cd $SPACK_ROOT*

asalvad2 */scratch/asalvad2/spack* *$* *spack install dealii %gcc@6.2*

*==>* Error: : Additional properties are not allowed
('openmpi' was unexpected)

asalvad2 */scratch/asalvad2/spack* *$* *module list*

*Currently Loaded Modulefiles:*

*  1) opt_local/1.0  2) gcc/6.2.0  3)
ompi/2.0.1-gcc-6.2.0*

asalvad2 */scratch/asalvad2/spack* *$* *more ~/.spack/linux/packages.yaml *

*openmpi:*

*version: [2.0.1]*

*paths:*

*  openmpi@2.0.1%gcc@6.2.0: /opt/crc/o/openmpi/2.0.1/gcc/6.2.0/eth/bin *

*buildable: False*

*Any further help?*
*Thanks*
*Alberto*



*Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto.salvad...@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

On Tue, Apr 4, 2017 at 5:25 PM, Alberto Salvadori <
alberto.salvad...@unibs.it> wrote:

> Hi Bruno,
>
> I really appreciate your help.
> I got the right location of my openmpi and just mean to double check
> before running spack. I shall therefore:
>
> 1 - create a file  ~/.spack/linux/packages.yaml as follows:
>
> openmpi:
> version: [2.0.1]
> paths:
>   openmpi@2.0.1%gcc@6.2.0: ...SOMEPATH...openmpi/2.0.1/gcc/6.2.0/eth/bin
> buildable: False
>
> 2 - spack install dealii %gcc@6.2
>
> Correct?
> Thanks
> Alberto
>
>
>
>
> *Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
> Territorio, Ambiente e di Matematica (DICATAM)
>  Universita` di Brescia, via Branze 43, 25123 Brescia
>  Italy
>  tel 030 3711239
>  fax 030 3711312
>
> e-mail:
>  alberto.salvad...@unibs.it
> web-pages:
>  http://m4lab.unibs.it/faculty.html
>  http://dicata.ing.unibs.it/salvadori
>
> On Tue, Apr 4, 2017 at 5:11 PM, Bruno Turcksin 
> wrote:
>
>> 2017-04-04 16:58 GMT-04:00 Alberto Salvadori > >:
>> > Sorry, I am a bit confused.
>> >
>> > "you need to make sure that building mpich is set to false."
>> >  - where I can set "building mpich" to false? Shall I edit a file
>> > ~/.spack/packages.yaml that BTW currently I do not have?
>> Yes, you need to create the file if it doesn't exist.
>>
>> >  - if so, would this be OK?
>> >
>> > spack providers mpi
>> >
>> > intel-parallel-studio@cluster:+mpi  mpich@1:  mpich@3:
>> mvapich2@1.9
>> > mvapich2@2.0:  openmpi@1.6.5  openmpi@1.7.5:  openmpi@2.0.0:
>> spectrum-mpi
>> >
>> >
>> > openmpi:
>> > version: [2.0.0]
>> > paths:
>> >   openmpi@2.0.0%gcc@6.2.0: ...SOMEPATH.../m/mpich/3.2/gcc/6.2.0/bin
>> (
>> > the latter is the directory where mpic++ executable is )
>> > buildable: False
>> This looks sketchy: you say openmpi but then the path says mpich...
>> Otherwise it looks good.
>>
>> >
>> > "You need to run something like spack  install dealii ^mpich %gcc@6.2"
>> > - sorry, I cannot understand this. I know I am bothering, but can you
>> please
>> > explain this a bit further?
>> spack install dealii %gcc@6.2 -> install deal.II with the gcc 6.2
>> compiler. Because you have more than one compiler on your system, you
>> need to tell spack which compiler to use.
>> spack install dealii ^mpich -> I am not sure about this one.  But by
>> default, spack uses openmpi but your path says that you are using
>> mpich. Thus, you need to force spack to use mpich instead of openmpi.
>> I am not sure this is the exact command though that's why I said it
>> should look like "spack install ^mpich %gcc@6.2"
>>
>> Best,
>>
>> Bruno
>>
>> --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see https://groups.google.com/d/fo
>> rum/dealii?hl=en
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "deal.II User Group" group.
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>>
>
>

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Re: [deal.II] Re: An issue in compiling on a cluster

[Bruno Turcksin]

Yeah it looks good.

Bruno

2017-04-04 17:25 GMT-04:00 Alberto Salvadori :
> Hi Bruno,
>
> I really appreciate your help.
> I got the right location of my openmpi and just mean to double check before
> running spack. I shall therefore:
>
> 1 - create a file  ~/.spack/linux/packages.yaml as follows:
>
> openmpi:
> version: [2.0.1]
> paths:
>   openmpi@2.0.1%gcc@6.2.0: ...SOMEPATH...openmpi/2.0.1/gcc/6.2.0/eth/bin
> buildable: False
>
> 2 - spack install dealii %gcc@6.2
>
> Correct?
> Thanks
> Alberto
>
>
>
> Alberto Salvadori
>  Dipartimento di Ingegneria Civile, Architettura, Territorio, Ambiente e di
> Matematica (DICATAM)
>  Universita` di Brescia, via Branze 43, 25123 Brescia
>  Italy
>  tel 030 3711239
>  fax 030 3711312
>
> e-mail:
>  alberto.salvad...@unibs.it
> web-pages:
>  http://m4lab.unibs.it/faculty.html
>  http://dicata.ing.unibs.it/salvadori
>
> On Tue, Apr 4, 2017 at 5:11 PM, Bruno Turcksin 
> wrote:
>>
>> 2017-04-04 16:58 GMT-04:00 Alberto Salvadori :
>> > Sorry, I am a bit confused.
>> >
>> > "you need to make sure that building mpich is set to false."
>> >  - where I can set "building mpich" to false? Shall I edit a file
>> > ~/.spack/packages.yaml that BTW currently I do not have?
>> Yes, you need to create the file if it doesn't exist.
>>
>> >  - if so, would this be OK?
>> >
>> > spack providers mpi
>> >
>> > intel-parallel-studio@cluster:+mpi  mpich@1:  mpich@3:  mvapich2@1.9
>> > mvapich2@2.0:  openmpi@1.6.5  openmpi@1.7.5:  openmpi@2.0.0:
>> > spectrum-mpi
>> >
>> >
>> > openmpi:
>> > version: [2.0.0]
>> > paths:
>> >   openmpi@2.0.0%gcc@6.2.0: ...SOMEPATH.../m/mpich/3.2/gcc/6.2.0/bin
>> > (
>> > the latter is the directory where mpic++ executable is )
>> > buildable: False
>> This looks sketchy: you say openmpi but then the path says mpich...
>> Otherwise it looks good.
>>
>> >
>> > "You need to run something like spack  install dealii ^mpich %gcc@6.2"
>> > - sorry, I cannot understand this. I know I am bothering, but can you
>> > please
>> > explain this a bit further?
>> spack install dealii %gcc@6.2 -> install deal.II with the gcc 6.2
>> compiler. Because you have more than one compiler on your system, you
>> need to tell spack which compiler to use.
>> spack install dealii ^mpich -> I am not sure about this one.  But by
>> default, spack uses openmpi but your path says that you are using
>> mpich. Thus, you need to force spack to use mpich instead of openmpi.
>> I am not sure this is the exact command though that's why I said it
>> should look like "spack install ^mpich %gcc@6.2"
>>
>> 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
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>
>
>
>
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Re: [deal.II] Re: An issue in compiling on a cluster

[Alberto Salvadori]

Hi Bruno,

I really appreciate your help.
I got the right location of my openmpi and just mean to double check before
running spack. I shall therefore:

1 - create a file  ~/.spack/linux/packages.yaml as follows:

openmpi:
version: [2.0.1]
paths:
  openmpi@2.0.1%gcc@6.2.0: ...SOMEPATH...openmpi/2.0.1/gcc/6.2.0/eth/bin
buildable: False

2 - spack install dealii %gcc@6.2

Correct?
Thanks
Alberto




*Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto.salvad...@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

On Tue, Apr 4, 2017 at 5:11 PM, Bruno Turcksin 
wrote:

> 2017-04-04 16:58 GMT-04:00 Alberto Salvadori :
> > Sorry, I am a bit confused.
> >
> > "you need to make sure that building mpich is set to false."
> >  - where I can set "building mpich" to false? Shall I edit a file
> > ~/.spack/packages.yaml that BTW currently I do not have?
> Yes, you need to create the file if it doesn't exist.
>
> >  - if so, would this be OK?
> >
> > spack providers mpi
> >
> > intel-parallel-studio@cluster:+mpi  mpich@1:  mpich@3:  mvapich2@1.9
> > mvapich2@2.0:  openmpi@1.6.5  openmpi@1.7.5:  openmpi@2.0.0:
> spectrum-mpi
> >
> >
> > openmpi:
> > version: [2.0.0]
> > paths:
> >   openmpi@2.0.0%gcc@6.2.0: ...SOMEPATH.../m/mpich/3.2/gcc/6.2.0/bin
> (
> > the latter is the directory where mpic++ executable is )
> > buildable: False
> This looks sketchy: you say openmpi but then the path says mpich...
> Otherwise it looks good.
>
> >
> > "You need to run something like spack  install dealii ^mpich %gcc@6.2"
> > - sorry, I cannot understand this. I know I am bothering, but can you
> please
> > explain this a bit further?
> spack install dealii %gcc@6.2 -> install deal.II with the gcc 6.2
> compiler. Because you have more than one compiler on your system, you
> need to tell spack which compiler to use.
> spack install dealii ^mpich -> I am not sure about this one.  But by
> default, spack uses openmpi but your path says that you are using
> mpich. Thus, you need to force spack to use mpich instead of openmpi.
> I am not sure this is the exact command though that's why I said it
> should look like "spack install ^mpich %gcc@6.2"
>
> Best,
>
> Bruno
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/
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Re: [deal.II] Re: An issue in compiling on a cluster

[Alberto Salvadori]

Sorry, I am a bit confused.

"you need to make sure that building mpich is set to false."
 - where I can set "building mpich" to false? Shall I edit a file
~/.spack/packages.yaml that BTW currently I do not have?
 - if so, would this be OK?

*spack providers mpi*

*intel-parallel-studio@cluster:+mpi  mpich@1:  mpich@3:  mvapich2@1.9
mvapich2@2.0:  openmpi@1.6.5  openmpi@1.7.5:  openmpi@2.0.0:  spectrum-mpi*

openmpi:
version: [2.0.0]
paths:
  openmpi@2.0.0%gcc@6.2.0:
...SOMEPATH.../m/mpich/3.2/gcc/6.2.0/bin ( the latter is the directory
where mpic++ executable is )
buildable: False

"You need to run something like spack  install@dealii ^mpich %gcc@6.2"
- sorry, I cannot understand this. I know I am bothering, but can you
please explain this a bit further?

Thanks
Alberto


*Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto.salvad...@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

On Tue, Apr 4, 2017 at 4:14 PM, Bruno Turcksin 
wrote:

> Alberto,
>
> 2017-04-04 16:04 GMT-04:00 Alberto Salvadori :
> > If I understand well then, I have to add the  mpich/3.2-gcc-6.2.0
> compiler
> > to spack - I did this just now.
> > I checked that the file compilers.yaml includes the compiler and its
> > path.The same file still includes the compiler gcc-4.9.2
> That's good but you also want to make sure that spack will not compile
> its own mpi. So you need to make sure that building mpich is set to
> false.
> > Shall I delete the corresponding section  in the compilers.yaml file?
> No you don't need to
> > Can I just run spack install dealii instead?
> You need to run something like spack  install@dealii ^mpich %gcc@6.2
> You need to make sure that spack will compile using mpich and that it
> won't install it.
>
> Best,
>
> Bruno
>
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Re: [deal.II] Re: An issue in compiling on a cluster

[Bruno Turcksin]

Alberto,

2017-04-04 16:04 GMT-04:00 Alberto Salvadori :
> If I understand well then, I have to add the  mpich/3.2-gcc-6.2.0 compiler
> to spack - I did this just now.
> I checked that the file compilers.yaml includes the compiler and its
> path.The same file still includes the compiler gcc-4.9.2
That's good but you also want to make sure that spack will not compile
its own mpi. So you need to make sure that building mpich is set to
false.
> Shall I delete the corresponding section  in the compilers.yaml file?
No you don't need to
> Can I just run spack install dealii instead?
You need to run something like spack  install@dealii ^mpich %gcc@6.2
You need to make sure that spack will compile using mpich and that it
won't install it.

Best,

Bruno

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Re: [deal.II] Re: An issue in compiling on a cluster

[Alberto Salvadori]

Thanks, Bruno.

If I understand well then, I have to add the  mpich/3.2-gcc-6.2.0 compiler
to spack - I did this just now.
I checked that the file compilers.yaml includes the compiler and its
path.The same file still includes the compiler gcc-4.9.2
Shall I delete the corresponding section  in the compilers.yaml file?
Can I just run spack install dealii instead?

Thanks!
Alberto




*Alberto Salvadori* Dipartimento di Ingegneria Civile, Architettura,
Territorio, Ambiente e di Matematica (DICATAM)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto.salvad...@unibs.it
web-pages:
 http://m4lab.unibs.it/faculty.html
 http://dicata.ing.unibs.it/salvadori

On Tue, Apr 4, 2017 at 3:29 PM, Bruno Turcksin 
wrote:

> Alberto,
>
> you don't want spack to install mpi on a cluster take a look here
> https://spack.readthedocs.io/en/latest/getting_started.
> html#system-packages Also gcc 4.9 and gcc 6.2 are not compatible, so you
> need everything to be compiled by the same compiler, i.e. gcc 6.2.
>
> Best,
>
> Bruno
>
> On Tuesday, April 4, 2017 at 2:24:19 PM UTC-4, Alberto Salvadori wrote:
>>
>> Hi,
>>
>> your help in this issue is greatly appreciated.
>>
>> I installed deal.II on a cluster using the spack distribution, very
>> easily. I also run some examples provided with deal.II with no issues.
>> Great job.
>>
>> I am now using a library for tensor calculus, that apparently conflicts
>> with the gcc compiler installed with spack. Specifically, the spack
>> configuration uses /gcc-4.9.2
>>
>> opt/spack/linux-rhel7-x86_64/gcc-4.9.2/openmpi-2.0.2-kupebz5
>> mdlwlfvbkcit3y56cg6r4bxg5/bin/mpic++
>>
>> while this library needs gcc-6.2.0 or higher. The cluster is equipped
>> with  mpich/3.2-gcc-6.2.0, but I am not sufficiently skilled to edit the
>> configuration or the make files to solve the problem.
>> Any help?
>>
>> Thanks
>> Alberto
>>
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[deal.II] Re: An issue in compiling on a cluster

[Bruno Turcksin]

Alberto,

you don't want spack to install mpi on a cluster take a look here 
https://spack.readthedocs.io/en/latest/getting_started.html#system-packages 
Also gcc 4.9 and gcc 6.2 are not compatible, so you need everything to be 
compiled by the same compiler, i.e. gcc 6.2.

Best,

Bruno

On Tuesday, April 4, 2017 at 2:24:19 PM UTC-4, Alberto Salvadori wrote:
>
> Hi, 
>
> your help in this issue is greatly appreciated.
>
> I installed deal.II on a cluster using the spack distribution, very 
> easily. I also run some examples provided with deal.II with no issues. 
> Great job.
>
> I am now using a library for tensor calculus, that apparently conflicts 
> with the gcc compiler installed with spack. Specifically, the spack 
> configuration uses /gcc-4.9.2 
>
>
> opt/spack/linux-rhel7-x86_64/gcc-4.9.2/openmpi-2.0.2-kupebz5mdlwlfvbkcit3y56cg6r4bxg5/bin/mpic++
>
> while this library needs gcc-6.2.0 or higher. The cluster is equipped 
> with  mpich/3.2-gcc-6.2.0, but I am not sufficiently skilled to edit the 
> configuration or the make files to solve the problem.
> Any help?
>
> Thanks
> Alberto
>

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[deal.II] MappingQ, and minimal test for reproducing Benchmark

[Juan Carlos Araujo Cabarcas]

Dear all,

I'm am trying to reproduce with my implementation, the results in the 
Photonic Crystal computations performed in [1]. Here, the author uses a 
grid with an inner disk with radius R=0.475, and for FEM it is used the 
software Concepts [2] that implements curvilinear elements denoted Blending 
technique, or transfinite interpolation in quadrilaterals [3], [4,p. 144]. 
Exponential convergence was obtained for the p-FEM version.

By using the deal.II SphericalManifold, I can only get with the attached 
code up to R<0.46, before I get the exception: 

"The image of the mapping applied to cell with center [0.446317 -0.206317] 
is distorted. The cell geometry or the mapping are invalid, giving a 
non-positive volume fraction of -0.000129188 in quadrature point 54."

I am attaching a minimal test case (modified from step-10) that reproduces 
the errors:
mesh_test.cc
and the code for the same mesh used in [1], adapted to deal.II standards in:
unit_cell.h

The question is then if it is possible to get this example running for 
R=0.475, in order to reproduce the results in [1]. Is there something I am 
doing wrong that can be improved? Can this behaviour be explained by round 
off's?

Furthermore, is anyone implementing transfinite interpolation [3,4] in 
deal.II?

Thanks in advance, any help is greatly appreciated!

References:
[1] Engström, C.,Spectral approximation of quadratic operator polynomials 
arising in photonic band structure calculations, Numer. Math. (2014) 126: 
413.
[2] Concepts web page: 
http://wiki.math.ethz.ch/Concepts/WebRoot?redirectedfrom=Concepts.WebHome
[3] W. J. Gordon, C. A. Hall, Construction of curvilinear coordinate 
systems and application to mesh generation Int. J. Num. Meth. Eng., Vol. 7 
(1973), pp. 461-477
[4] Pavel Solin, Karel Segeth, Ivo Dolezel, Higher-Order Finite Element 
Methods, Studies in Advanced Mathematics, CRC Press, 2003.


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/* -
 *
 * Copyright (C) 2001 - 2014 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * The deal.II library is free software; you can use it, redistribute
 * it, and/or modify it under the terms of the GNU Lesser General
 * Public License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * The full text of the license can be found in the file LICENSE at
 * the top level of the deal.II distribution.
 *
 * -

 *
 * Authors: Wolfgang Bangerth, Ralf Hartmann, University of Heidelberg, 2001
 */

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#include 

#include 
#include 
#include 

// added lines
#include "unit_cell.h"
#include 

namespace Step10
{
  using namespace dealii;

  const long double pi = 3.141592653589793238462643;

  template 
  void gnuplot_output()
  {
std::cout << "Output of grids into gnuplot files:" << std::endl
  << "===" << std::endl;

Triangulation triangulation;
GridGenerator::hyper_ball (triangulation);
static const SphericalManifold boundary;
triangulation.set_all_manifold_ids_on_boundary(0);
triangulation.set_manifold (0, boundary);

for (unsigned int refinement=0; refinement<2;
 ++refinement, triangulation.refine_global(1))
  {
std::cout << "Refinement level: " << refinement << std::endl;

std::string filename_base = "ball";
filename_base += '0'+refinement;

for (unsigned int degree=1; degree<4; ++degree)
  {
std::cout << "Degree = " << degree << std::endl;

const MappingQ mapping (degree);

GridOut grid_out;
GridOutFlags::Gnuplot gnuplot_flags(false, 30);
grid_out.set_flags(gnuplot_flags);

std::string filename = filename_base+"_mapping_q";
filename += ('0'+degree);
filename += ".dat";
std::ofstream gnuplot_file (filename.c_str());

grid_out.write_gnuplot (triangulation, gnuplot_file, );
  }
std::cout << std::endl;
  }
  }

  template 
  void compute_pi_by_area ()
  {
std::cout << "Computation of Pi by the area:" << std::endl
  << "==" << std::endl;

// const QGauss quadrature(4);
			
		for (double R=0.45; R < 0.5; R += 0.005)
		  for (unsigned int degree=1; degree<11;