[deal.II] Installation problem

2023-02-10 Thread ME22D001 Abhishek Nath Thakur 
Hello everyone! I am trying to install 9.4.0 but at the end i am getting 
such error(Given below). I am very new to this and any help would be 
appreciated.


*CMake Error at cmake/scripts/cmake_install.cmake:46 (file): file cannot 
create directory: /usr/local/share/deal.II/scripts. Maybe need 
administrative privileges. Call Stack (most recent call first): 
cmake_install.cmake:47 (include).*


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Re: [deal.II] Installation problem using spack

2022-08-15 Thread Marco Nawijn 
Hi Wolfgang,

No, I didn't check. I was just running a few example programs that were 
compiled during the installation process.
However, I believe it is a good exercise for me to see if I can find the 
bug :). So, I will give it a try and report back if I find anything or get 
stuck.

Marco


On Monday, August 15, 2022 at 4:03:00 PM UTC+2 Wolfgang Bangerth wrote:

> On 8/15/22 00:50, Marco Nawijn wrote:
> > 
> > Just for information, when you run the example with MPI on 1 processor 
> (so -np 
> > 1), the process runs fine. Any value >1 results in this error. The error 
> > itself makes sense because it requests a massive amount of memory (I am 
> > running on a laptop at the moment). A quick fix (based on what I found 
> on the 
> > internet) is to downgrade the version of Metis. However, ideally for 
> Deal-II 
> > newbies using straightforward laptops/workstations, it would be nice to 
> just 
> > run `spack install dealii` and it just works.
> > 
> > If there is anything I can do to help, I am more than willing to.
>
> The question is whether METIS' excessive memory allocation is because of a 
> bug 
> in METIS, or because we call it in a way it doesn't expect. Did your 
> search 
> for the source of the error indicate anything to this effect?
>
> Best
> W.
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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Re: [deal.II] Installation problem using spack

2022-08-15 Thread Wolfgang Bangerth 

On 8/15/22 00:50, Marco Nawijn wrote:


Just for information, when you run the example with MPI on 1 processor (so -np 
1), the process runs fine. Any value >1 results in this error. The error 
itself makes sense because it requests a massive amount of memory (I am 
running on a laptop at the moment). A quick fix (based on what I found on the 
internet) is to downgrade the version of Metis. However, ideally for Deal-II 
newbies using straightforward laptops/workstations, it would be nice to just 
run `spack install dealii` and it just works.


If there is anything I can do to help, I am more than willing to.


The question is whether METIS' excessive memory allocation is because of a bug 
in METIS, or because we call it in a way it doesn't expect. Did your search 
for the source of the error indicate anything to this effect?


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Installation problem using spack

2022-08-15 Thread Marco Nawijn 
Hi Jean-Paul,

I can confirm that the patch works like a charm. Thanks!

I now run into another issue, when running step-17. It fails with the 
following message:
  ***Memory allocation failed for SetupCtrl: maxvwgt. Requested size: 
137438953480 bytes

I did a quick search on the internet and it seems to be related to Metis 
5.1.0.

Just for information, when you run the example with MPI on 1 processor (so 
-np 1), the process runs fine. Any value >1 results in this error. The 
error itself makes sense because it requests a massive amount of memory (I 
am running on a laptop at the moment). A quick fix (based on what I found 
on the internet) is to downgrade the version of Metis. However, ideally for 
Deal-II newbies using straightforward laptops/workstations, it would be 
nice to just run `spack install dealii` and it just works. 

If there is anything I can do to help, I am more than willing to.

Kind regards,

Marco

  

On Thursday, August 11, 2022 at 9:30:41 PM UTC+2 Jean-Paul Pelteret wrote:

> Hi Marco,
>
> I've open a PR in Spack (https://github.com/spack/spack/pull/32079) that 
> backports the patches that we added to the development version to 9.4. Feel 
> free to try it and provide some feedback as to whether or not it works for 
> you.
>
> Best,
> Jean-Paul
>
> On Thursday, August 11, 2022 at 7:50:46 AM UTC+2 marco@colosso.nl 
> wrote:
>
>> Hi Daniel and Timo,
>>
>> Thanks for the feedback. The bug indeed seems to be the problem, since 
>> the spack HDF5 package is definitely build with MPI support. I first 
>> thought it was because by default spack doesn't seem to build HDF5 with C++ 
>> support, but that did not help (of course now I know why).
>>
>> Building without HDF5 would be an option for me for the short term, but I 
>> will first try to see if I can get it working.
>>
>> Again, I am pretty impressed by the spack. It works like a charm and it 
>> provides a lot of flexibility.
>>
>> Kind regards,
>>
>> Marco
>>
>> On Tuesday, August 9, 2022 at 7:27:38 PM UTC+2 Timo Heister wrote:
>>
>>> Your issue might be related to the bug 
>>> https://github.com/dealii/dealii/issues/14065 (see the discussion and 
>>> the linked PR that should solve the problem for deal.II master, but not 9.4)
>>>
>>> On Tuesday, August 9, 2022 at 1:23:55 PM UTC-4 d.arnd...@gmail.com 
>>> wrote:
>>>
 Marco,

 It appears that

 -- Insufficient hdf5 installation found: hdf5 has to be configured with 
 MPI support.

 is the problem. HDF5 has not been compiled with MPI support. Thus, you 
 can either try to make sure that HDF5 is built with MPI support or, in 
 case 
 you are not going to use HDF5 anyway, just disable the dependency.

 Best,
 Daniel

 On Tue, Aug 9, 2022 at 7:41 AM Marco Nawijn  
 wrote:

> Dear All,
>
> I run into an issue when trying to install dealii using spack. The 
> error is as follows:
>
>   Could not find the hdf5 library!
>
>   Insufficient hdf5 installation found!
>
>   hdf5 has to be configured with MPI support.
>
>   Please ensure that a suitable hdf5 library is installed on your 
> computer.
>
>   If the library is not at a default location, either provide some 
> hints for
>   autodetection,
>
> A complete log and additional information is provided in the two 
> attachments.
> I am a little lost at the moment because as far as I can tell, the 
> installation process finds the correct HDF5 folder (I checked the tags). 
> In 
> addition, I installed HDF5 using spack with MPI, C++ and Fortran support 
> (I 
> added the output of `tree` to the attachment). 
>
> I am a little at loss now, because I don't know what dealii is exactly 
> missing from the HDF5 installation.
>
> The system is just a laptop, so nothing cluster like.
>
> Just as a side note. I am pretty impressed with the easy and 
> flexibility of spack. All other dependencies installed without a hitch 
> (petsc, sundials, trilinios etc.).
>
> Does anybody have an idea of what the problem is?
>
> Any help is highly appreciated. 
>
> Marco
> P.S. I am a complete novice with dealii, but otherwise comfortable in 
> the linux eco-system.
>
> -- 
> 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.
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> an email to dealii+un...@googlegroups.com.
> To view this discussion on the web visit 
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>  
>

Re: [deal.II] Installation problem using spack

2022-08-11 Thread Jean-Paul Pelteret 
Hi Marco,

I've open a PR in Spack (https://github.com/spack/spack/pull/32079) that 
backports the patches that we added to the development version to 9.4. Feel 
free to try it and provide some feedback as to whether or not it works for 
you.

Best,
Jean-Paul

On Thursday, August 11, 2022 at 7:50:46 AM UTC+2 marco@colosso.nl wrote:

> Hi Daniel and Timo,
>
> Thanks for the feedback. The bug indeed seems to be the problem, since the 
> spack HDF5 package is definitely build with MPI support. I first thought it 
> was because by default spack doesn't seem to build HDF5 with C++ support, 
> but that did not help (of course now I know why).
>
> Building without HDF5 would be an option for me for the short term, but I 
> will first try to see if I can get it working.
>
> Again, I am pretty impressed by the spack. It works like a charm and it 
> provides a lot of flexibility.
>
> Kind regards,
>
> Marco
>
> On Tuesday, August 9, 2022 at 7:27:38 PM UTC+2 Timo Heister wrote:
>
>> Your issue might be related to the bug 
>> https://github.com/dealii/dealii/issues/14065 (see the discussion and 
>> the linked PR that should solve the problem for deal.II master, but not 9.4)
>>
>> On Tuesday, August 9, 2022 at 1:23:55 PM UTC-4 d.arnd...@gmail.com wrote:
>>
>>> Marco,
>>>
>>> It appears that
>>>
>>> -- Insufficient hdf5 installation found: hdf5 has to be configured with 
>>> MPI support.
>>>
>>> is the problem. HDF5 has not been compiled with MPI support. Thus, you 
>>> can either try to make sure that HDF5 is built with MPI support or, in case 
>>> you are not going to use HDF5 anyway, just disable the dependency.
>>>
>>> Best,
>>> Daniel
>>>
>>> On Tue, Aug 9, 2022 at 7:41 AM Marco Nawijn  
>>> wrote:
>>>
 Dear All,

 I run into an issue when trying to install dealii using spack. The 
 error is as follows:

   Could not find the hdf5 library!

   Insufficient hdf5 installation found!

   hdf5 has to be configured with MPI support.

   Please ensure that a suitable hdf5 library is installed on your 
 computer.

   If the library is not at a default location, either provide some 
 hints for
   autodetection,

 A complete log and additional information is provided in the two 
 attachments.
 I am a little lost at the moment because as far as I can tell, the 
 installation process finds the correct HDF5 folder (I checked the tags). 
 In 
 addition, I installed HDF5 using spack with MPI, C++ and Fortran support 
 (I 
 added the output of `tree` to the attachment). 

 I am a little at loss now, because I don't know what dealii is exactly 
 missing from the HDF5 installation.

 The system is just a laptop, so nothing cluster like.

 Just as a side note. I am pretty impressed with the easy and 
 flexibility of spack. All other dependencies installed without a hitch 
 (petsc, sundials, trilinios etc.).

 Does anybody have an idea of what the problem is?

 Any help is highly appreciated. 

 Marco
 P.S. I am a complete novice with dealii, but otherwise comfortable in 
 the linux eco-system.

 -- 
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 For mailing list/forum options, see 
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 --- 
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 Groups "deal.II User Group" group.
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 .

>>>

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Re: [deal.II] Installation problem using spack

2022-08-10 Thread Marco Nawijn 
Hi Daniel and Timo,

Thanks for the feedback. The bug indeed seems to be the problem, since the 
spack HDF5 package is definitely build with MPI support. I first thought it 
was because by default spack doesn't seem to build HDF5 with C++ support, 
but that did not help (of course now I know why).

Building without HDF5 would be an option for me for the short term, but I 
will first try to see if I can get it working.

Again, I am pretty impressed by the spack. It works like a charm and it 
provides a lot of flexibility.

Kind regards,

Marco

On Tuesday, August 9, 2022 at 7:27:38 PM UTC+2 Timo Heister wrote:

> Your issue might be related to the bug 
> https://github.com/dealii/dealii/issues/14065 (see the discussion and the 
> linked PR that should solve the problem for deal.II master, but not 9.4)
>
> On Tuesday, August 9, 2022 at 1:23:55 PM UTC-4 d.arnd...@gmail.com wrote:
>
>> Marco,
>>
>> It appears that
>>
>> -- Insufficient hdf5 installation found: hdf5 has to be configured with 
>> MPI support.
>>
>> is the problem. HDF5 has not been compiled with MPI support. Thus, you 
>> can either try to make sure that HDF5 is built with MPI support or, in case 
>> you are not going to use HDF5 anyway, just disable the dependency.
>>
>> Best,
>> Daniel
>>
>> On Tue, Aug 9, 2022 at 7:41 AM Marco Nawijn  wrote:
>>
>>> Dear All,
>>>
>>> I run into an issue when trying to install dealii using spack. The error 
>>> is as follows:
>>>
>>>   Could not find the hdf5 library!
>>>
>>>   Insufficient hdf5 installation found!
>>>
>>>   hdf5 has to be configured with MPI support.
>>>
>>>   Please ensure that a suitable hdf5 library is installed on your 
>>> computer.
>>>
>>>   If the library is not at a default location, either provide some hints 
>>> for
>>>   autodetection,
>>>
>>> A complete log and additional information is provided in the two 
>>> attachments.
>>> I am a little lost at the moment because as far as I can tell, the 
>>> installation process finds the correct HDF5 folder (I checked the tags). In 
>>> addition, I installed HDF5 using spack with MPI, C++ and Fortran support (I 
>>> added the output of `tree` to the attachment). 
>>>
>>> I am a little at loss now, because I don't know what dealii is exactly 
>>> missing from the HDF5 installation.
>>>
>>> The system is just a laptop, so nothing cluster like.
>>>
>>> Just as a side note. I am pretty impressed with the easy and flexibility 
>>> of spack. All other dependencies installed without a hitch (petsc, 
>>> sundials, trilinios etc.).
>>>
>>> Does anybody have an idea of what the problem is?
>>>
>>> Any help is highly appreciated. 
>>>
>>> Marco
>>> P.S. I am a complete novice with dealii, but otherwise comfortable in 
>>> the linux eco-system.
>>>
>>> -- 
>>> 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+un...@googlegroups.com.
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/dealii/7383fcc8-af66-438f-b363-3aa1c9032d5en%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>

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Re: [deal.II] Installation problem using spack

2022-08-09 Thread Timo Heister 
Your issue might be related to the 
bug https://github.com/dealii/dealii/issues/14065 (see the discussion and 
the linked PR that should solve the problem for deal.II master, but not 9.4)

On Tuesday, August 9, 2022 at 1:23:55 PM UTC-4 d.arnd...@gmail.com wrote:

> Marco,
>
> It appears that
>
> -- Insufficient hdf5 installation found: hdf5 has to be configured with 
> MPI support.
>
> is the problem. HDF5 has not been compiled with MPI support. Thus, you can 
> either try to make sure that HDF5 is built with MPI support or, in case you 
> are not going to use HDF5 anyway, just disable the dependency.
>
> Best,
> Daniel
>
> On Tue, Aug 9, 2022 at 7:41 AM Marco Nawijn  wrote:
>
>> Dear All,
>>
>> I run into an issue when trying to install dealii using spack. The error 
>> is as follows:
>>
>>   Could not find the hdf5 library!
>>
>>   Insufficient hdf5 installation found!
>>
>>   hdf5 has to be configured with MPI support.
>>
>>   Please ensure that a suitable hdf5 library is installed on your 
>> computer.
>>
>>   If the library is not at a default location, either provide some hints 
>> for
>>   autodetection,
>>
>> A complete log and additional information is provided in the two 
>> attachments.
>> I am a little lost at the moment because as far as I can tell, the 
>> installation process finds the correct HDF5 folder (I checked the tags). In 
>> addition, I installed HDF5 using spack with MPI, C++ and Fortran support (I 
>> added the output of `tree` to the attachment). 
>>
>> I am a little at loss now, because I don't know what dealii is exactly 
>> missing from the HDF5 installation.
>>
>> The system is just a laptop, so nothing cluster like.
>>
>> Just as a side note. I am pretty impressed with the easy and flexibility 
>> of spack. All other dependencies installed without a hitch (petsc, 
>> sundials, trilinios etc.).
>>
>> Does anybody have an idea of what the problem is?
>>
>> Any help is highly appreciated. 
>>
>> Marco
>> P.S. I am a complete novice with dealii, but otherwise comfortable in the 
>> linux eco-system.
>>
>> -- 
>> 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+un...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/dealii/7383fcc8-af66-438f-b363-3aa1c9032d5en%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [deal.II] Installation problem using spack

2022-08-09 Thread Daniel Arndt 
Marco,

It appears that

-- Insufficient hdf5 installation found: hdf5 has to be configured with MPI
support.

is the problem. HDF5 has not been compiled with MPI support. Thus, you can
either try to make sure that HDF5 is built with MPI support or, in case you
are not going to use HDF5 anyway, just disable the dependency.

Best,
Daniel

On Tue, Aug 9, 2022 at 7:41 AM Marco Nawijn  wrote:

> Dear All,
>
> I run into an issue when trying to install dealii using spack. The error
> is as follows:
>
>   Could not find the hdf5 library!
>
>   Insufficient hdf5 installation found!
>
>   hdf5 has to be configured with MPI support.
>
>   Please ensure that a suitable hdf5 library is installed on your computer.
>
>   If the library is not at a default location, either provide some hints
> for
>   autodetection,
>
> A complete log and additional information is provided in the two
> attachments.
> I am a little lost at the moment because as far as I can tell, the
> installation process finds the correct HDF5 folder (I checked the tags). In
> addition, I installed HDF5 using spack with MPI, C++ and Fortran support (I
> added the output of `tree` to the attachment).
>
> I am a little at loss now, because I don't know what dealii is exactly
> missing from the HDF5 installation.
>
> The system is just a laptop, so nothing cluster like.
>
> Just as a side note. I am pretty impressed with the easy and flexibility
> of spack. All other dependencies installed without a hitch (petsc,
> sundials, trilinios etc.).
>
> Does anybody have an idea of what the problem is?
>
> Any help is highly appreciated.
>
> Marco
> P.S. I am a complete novice with dealii, but otherwise comfortable in the
> linux eco-system.
>
> --
> 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.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dealii/7383fcc8-af66-438f-b363-3aa1c9032d5en%40googlegroups.com
> 
> .
>

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[deal.II] Installation problem using spack

2022-08-09 Thread Marco Nawijn 
Dear All,

I run into an issue when trying to install dealii using spack. The error is 
as follows:

  Could not find the hdf5 library!

  Insufficient hdf5 installation found!

  hdf5 has to be configured with MPI support.

  Please ensure that a suitable hdf5 library is installed on your computer.

  If the library is not at a default location, either provide some hints for
  autodetection,

A complete log and additional information is provided in the two 
attachments.
I am a little lost at the moment because as far as I can tell, the 
installation process finds the correct HDF5 folder (I checked the tags). In 
addition, I installed HDF5 using spack with MPI, C++ and Fortran support (I 
added the output of `tree` to the attachment). 

I am a little at loss now, because I don't know what dealii is exactly 
missing from the HDF5 installation.

The system is just a laptop, so nothing cluster like.

Just as a side note. I am pretty impressed with the easy and flexibility of 
spack. All other dependencies installed without a hitch (petsc, sundials, 
trilinios etc.).

Does anybody have an idea of what the problem is?

Any help is highly appreciated. 

Marco
P.S. I am a complete novice with dealii, but otherwise comfortable in the 
linux eco-system.

-- 
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see 
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Installation error: (I stripped the path to the package folders from the output 
so it is
 slightly easier to read; in addition I slightly formatted 
the output,
 again for better reading)

'cmake'
'-G'
'Ninja'
'-DCMAKE_INSTALL_PREFIX:STRING=dealii-9.4.0-pditdv3j4dpps4nc5jx4kfj42kfaphms'
'-DCMAKE_BUILD_TYPE:STRING=DebugRelease'
'-DBUILD_TESTING:BOOL=OFF'
'-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF'
'-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON'
'-DCMAKE_INSTALL_RPATH:STRING=dealii-9.4.0-pditdv3j4dpps4nc5jx4kfj42kfaphms/lib
;dealii-9.4.0-pditdv3j4dpps4nc5jx4kfj42kfaphms/lib64
;arborx-1.1-zbemm6cpbwzbc6k7krso53grucr4fikm/lib
;boost-1.79.0-yulo43tufrk6kqsiigupmm3bktxlosrx/lib
;gsl-2.7.1-6qxuvfmjcopnkiwiqhvfbmngfizuzjy4/lib
;hdf5-1.10.7-v5iwjch4peubuguzhmonjmdg3vxkxdps/lib
;intel-tbb-2020.3-qxolbur3xiql2gma47jkxlvcyexfjpsd/lib
;metis-5.1.0-p7gsmz77yalgrjonfddy35lejrpw6bhf/lib
;netlib-scalapack-2.2.0-2pjpdwlwkht62nb3xwvcc4ug7qunhxus/lib
;oce-0.18.3-3ipfgc77pw27hwrp5bqbcxru2zqvj2vc/lib
;openblas-0.3.20-ih7wyjdf5jdptw3ase6vpwv6ws562jhs/lib
;openmpi-4.1.4-t7algfna2xa4kajv4igfphurkgdggpin/lib
;p4est-2.8-2w57tbexytitual2yrwkvvwg247pb4ct/lib
;petsc-3.17.3-tbou37jct6iwy7dvhz3o7pdvjjnbj7eo/lib
;slepc-3.17.1-ftyxr4kokjjbjs7bw6ea6pnwgcat5hug/lib
;suite-sparse-5.10.1-be64aqdsyjppfvsff3o5pxoiebxqnu32/lib
;symengine-0.9.0-226vwo56e557zv5lgl4lencntm6oinlg/lib
;trilinos-13.0.1-hi6xxic3bbib3dpxde5k3x4cn5f5u44f/lib
;zlib-1.2.12-itsi2i4tzpvkirehmpm4jjffkhtq6ooc/lib
;adol-c-2.7.2-ettinbhhlk2mxftfamwbpw5t44jstkpo/lib64
;arpack-ng-3.8.0-ixbfxtzdlgsbg4srqsxfqttbzs2otwwr/lib64
;assimp-5.2.4-y7f3umvzjviupqd33nmy7x5v3rjtbig4/lib64
;cgal-5.4.1-ikvmqd56pyc6t7vztunay3gyuv4emrpi/lib64
;ginkgo-1.4.0-2li5nizcwch6pc7wq32osy3sb2dafabi/lib64
;muparser-2.2.6.1-zwvhtt2hnul4tpwf7vzgpu4d63fqznqv/lib64
;sundials-6.2.0-wfeuorzp4faj7oluoc4r2upvlomd73kp/lib64
;symengine-0.9.0-226vwo56e557zv5lgl4lencntm6oinlg/lib64'
'-DCMAKE_PREFIX_PATH:STRING=symengine-0.9.0-226vwo56e557zv5lgl4lencntm6oinlg
;mpc-1.2.1-2wfbtlx4n6eetumhkrh7o4oapmemtj4n
;cereal-1.3.2-adcttjetlkihblkiki33v4oejgktdqwi
;sundials-6.2.0-wfeuorzp4faj7oluoc4r2upvlomd73kp
;suite-sparse-5.10.1-be64aqdsyjppfvsff3o5pxoiebxqnu32
;slepc-3.17.1-ftyxr4kokjjbjs7bw6ea6pnwgcat5hug
;petsc-3.17.3-tbou37jct6iwy7dvhz3o7pdvjjnbj7eo
;superlu-dist-7.2.0-s3d5rka6nlilimznjnmkhtiopf6d6ni4
;parmetis-4.0.3-dsixfphfyd7ftl7pf7q2ml3pbq657v6o
;hypre-2.25.0-5dtolxjd5lzm5vfwgfkveztjultvtgjm
;p4est-2.8-2w57tbexytitual2yrwkvvwg247pb4ct
;netlib-scalapack-2.2.0-2pjpdwlwkht62nb3xwvcc4ug7qunhxus
;muparser-2.2.6.1-zwvhtt2hnul4tpwf7vzgpu4d63fqznqv
;metis-5.1.0-p7gsmz77yalgrjonfddy35lejrpw6bhf
;gsl-2.7.1-6qxuvfmjcopnkiwiqhvfbmngfizuzjy4
;gmsh-4.8.4-2o34yusib4chg2ax635pito5czoyapq4
;oce-0.18.3-3ipfgc77pw27hwrp5bqbcxru2zqvj2vc
;intel-tbb-2020.3-qxolbur3xiql2gma47jkxlvcyexfjpsd
;ninja-1.11.0-mx4b5z2d5xs3pr4cunc2fj5hwaneskpm
;hdf5-1.10.7-v5iwjch4peubuguzhmonjmdg3vxkxdps
;ginkgo-1.4.0-2li5nizcwch6pc7wq32osy3sb2dafabi
;cgal-5.4.1-ikvmqd56pyc6t7vztunay3gyuv4emrpi

Re: [deal.II] deal.ii installation problem

2022-06-12 Thread ME20D503 NEWTON 
Thank you so much professor. I successfully installed the deal. ii in my 
system.

On Sunday, June 12, 2022 at 3:59:11 AM UTC+5:30 Wolfgang Bangerth wrote:

>
> > i am facing some problem while installing deal.ii. installation has been 
> > completed upto 100% but in the last i got some error.please find the 
> attachment.
>
> The error message actually says everything you need to know:
> cannot create directory /usr/local/... Maybe you need administrative
> privileges.
>
> What is happening is that you called cmake without saying where you wanted 
> deal.II to be installed (which you would do with the 
> -DCMAKE_INSTALL_PREFIX=... switch). The default for installation is
> /usr/local
> which is a directory only the 'root' user can write to, but not the iittp 
> user 
> you apparently are.
>
> Unless you are a sysadmin, people generally install deal.II into a 
> location in 
> their home directory by specifying -DCMAKE_INSTALL_PREFIX=... when calling 
> cmake -- see also the installation instructions at
> https://dealii.org/developer/readme.html
>
> Best
> W.
>
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

-- 
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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Re: [deal.II] deal.ii installation problem

2022-06-11 Thread Wolfgang Bangerth 



i am facing some problem while installing deal.ii. installation has been 
completed upto 100% but in the last i got some error.please find the attachment.


The error message actually says everything you need to know:
  cannot create directory /usr/local/... Maybe you need administrative
  privileges.

What is happening is that you called cmake without saying where you wanted 
deal.II to be installed (which you would do with the 
-DCMAKE_INSTALL_PREFIX=... switch). The default for installation is

  /usr/local
which is a directory only the 'root' user can write to, but not the iittp user 
you apparently are.


Unless you are a sysadmin, people generally install deal.II into a location in 
their home directory by specifying -DCMAKE_INSTALL_PREFIX=... when calling 
cmake -- see also the installation instructions at

  https://dealii.org/developer/readme.html

Best
 W.


--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

--
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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Re: [deal.II] deal.ii installation problem

2022-06-11 Thread Alexander Kiselyov 
Are you building deal.II manually? The default install path of
manually-built software is /usr/local on Linux. It is usually write-
accessible only by the root user. I recommend to use candi, it will
install deal.II + dependencies in user-accessible locations, it is much
easier than doing it manually. Don't forget to edit candi.cfg to
specify the deal.II version and the needed features. 

Regards,
Alexander

On Fri, 2022-06-10 at 20:18 -0700, ME20D503 NEWTON wrote:
> Dear users,
> i am facing some problem while installing deal.ii. installation has
> been completed upto 100% but in the last i got some error.please find
> the attachment.
> Thank you.
> -- 
> 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.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dealii/466cb4b4-7763-46f7-ac5c-8ad723fdf638n%40googlegroups.com
> .

-- 
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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"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email 
to dealii+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
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Re: [deal.II] Installation problem

2019-03-23 Thread Zhu wenguo 
Dear Paul,
Thank you for your reply! It works now! thank you very much!
Best regards.
wenguo.

On Saturday, March 23, 2019 at 9:59:34 AM UTC+1, Jean-Paul Pelteret wrote:
>
> Dear Wenguo,
>
> It looks like you’re linking deal.II, built as a shared library, against 
> LAPACK, built as a static library. As the error message suggests, you’ll 
> need to build LAPACK with the -fPIC flag in order to do this. As suggested 
> here (
> https://stackoverflow.com/questions/18828730/lapack-linking-error-recompile-with-fpic)
>  
> you should make the following changes to make.inc when building LAPACK:
>
> FORTRAN  = gfortran -m64 -fPIC
> OPTS = -O2 -m64 -fPIC
> DRVOPTS  = $(OPTS)
> NOOPT= -O0 -m64 -fPIC
> LOADER   = gfortran -m64 -fPIC
>
>
> I hope that this helps you resolve your issue.
> Best,
> Jean-Paul
>
> On 23 Mar 2019, at 08:26, Zhu wenguo > 
> wrote:
>
>
> Hello everyone,
>
> I am installing deal ii -9.0.1 using recommended commands. and something 
> went wrong, the error message is as follow:
> has someone ever met this problem?
>
> 
> [ 81%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
> [ 81%] Linking CXX shared library ../lib/libdeal_II.so
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(spotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'spotrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sgetrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dpotrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dgetrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(zpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'zpotrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sladiv2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dladiv2_' which may overflow at 
> runtime; recompile with -fPIC
> collect2: error: ld returned 1 exit status
> source/CMakeFiles/deal_II.dir/build.make:751: recipe for target 
> 'lib/libdeal_II.so.9.0.1' failed
> make[2]: *** [lib/libdeal_II.so.9.0.1] Error 1
> CMakeFiles/Makefile2:871: recipe for target 
> 'source/CMakeFiles/deal_II.dir/all' failed
> make[1]: *** [source/CMakeFiles/deal_II.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(spotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'spotrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sgetrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dpotrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dgetrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(zpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'zpotrf2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sladiv2_' which may overflow at 
> runtime; recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dladiv2_' which may overflow at 
> runtime; recompile with -fPIC
> collect2: error: ld returned 1 exit status
> source/CMakeFiles/deal_II.g.dir/build.make:751: recipe for target 
> 'lib/libdeal_II.g.so.9.0.1' failed
> make[2]: *** [lib/libdeal_II.g.so.9.0.1] Error 1
> CMakeFiles/Makefile2:929: recipe for target 
> 'source/CMakeFiles/deal_II.g.dir/all' failed
> make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2
> Makefile:129: recipe for target 'all' failed
> make: *** [all] Error 2
>
>

Re: [deal.II] Installation problem

2019-03-23 Thread Jean-Paul Pelteret 
Dear Wenguo,

It looks like you’re linking deal.II, built as a shared library, against 
LAPACK, built as a static library. As the error message suggests, you’ll need 
to build LAPACK with the -fPIC flag in order to do this. As suggested here 
(https://stackoverflow.com/questions/18828730/lapack-linking-error-recompile-with-fpic
 
)
 you should make the following changes to make.inc when building LAPACK:

FORTRAN  = gfortran -m64 -fPIC
OPTS = -O2 -m64 -fPIC
DRVOPTS  = $(OPTS)
NOOPT= -O0 -m64 -fPIC
LOADER   = gfortran -m64 -fPIC

I hope that this helps you resolve your issue.
Best,
Jean-Paul

> On 23 Mar 2019, at 08:26, Zhu wenguo  wrote:
> 
> 
> Hello everyone,
> 
> I am installing deal ii -9.0.1 using recommended commands. and something went 
> wrong, the error message is as follow:
> has someone ever met this problem?
> 
> [ 81%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
> [ 81%] Linking CXX shared library ../lib/libdeal_II.so
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(spotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'spotrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sgetrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dpotrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dgetrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(zpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'zpotrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sladiv2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dladiv2_' which may overflow at runtime; 
> recompile with -fPIC
> collect2: error: ld returned 1 exit status
> source/CMakeFiles/deal_II.dir/build.make:751: recipe for target 
> 'lib/libdeal_II.so.9.0.1' failed
> make[2]: *** [lib/libdeal_II.so.9.0.1] Error 1
> CMakeFiles/Makefile2:871: recipe for target 
> 'source/CMakeFiles/deal_II.dir/all' failed
> make[1]: *** [source/CMakeFiles/deal_II.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(spotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'spotrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sgetrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dpotrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dgetrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dgetrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(zpotrf2.o): requires 
> dynamic R_X86_64_PC32 reloc against 'zpotrf2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'sladiv2_' which may overflow at runtime; 
> recompile with -fPIC
> /usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dladiv.o): requires 
> dynamic R_X86_64_PC32 reloc against 'dladiv2_' which may overflow at runtime; 
> recompile with -fPIC
> collect2: error: ld returned 1 exit status
> source/CMakeFiles/deal_II.g.dir/build.make:751: recipe for target 
> 'lib/libdeal_II.g.so.9.0.1' failed
> make[2]: *** [lib/libdeal_II.g.so.9.0.1] Error 1
> CMakeFiles/Makefile2:929: recipe for target 
> 'source/CMakeFiles/deal_II.g.dir/all' failed
> make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2
> Makefile:129: recipe for target 'all' failed
> make: *** [all] Error 2
> -
> thank you!
> Wenguo.
> 
> -- 
> The deal.II project is located at http://www.dealii.org/ 
>

[deal.II] Installation problem

2019-03-23 Thread Zhu wenguo 

Hello everyone,

I am installing deal ii -9.0.1 using recommended commands. and something 
went wrong, the error message is as follow:
has someone ever met this problem?

[ 81%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
[ 81%] Linking CXX shared library ../lib/libdeal_II.so
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(spotrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'spotrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sgetrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'sgetrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dpotrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'dpotrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dgetrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'dgetrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(zpotrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'zpotrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sladiv.o): requires 
dynamic R_X86_64_PC32 reloc against 'sladiv2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dladiv.o): requires 
dynamic R_X86_64_PC32 reloc against 'dladiv2_' which may overflow at 
runtime; recompile with -fPIC
collect2: error: ld returned 1 exit status
source/CMakeFiles/deal_II.dir/build.make:751: recipe for target 
'lib/libdeal_II.so.9.0.1' failed
make[2]: *** [lib/libdeal_II.so.9.0.1] Error 1
CMakeFiles/Makefile2:871: recipe for target 
'source/CMakeFiles/deal_II.dir/all' failed
make[1]: *** [source/CMakeFiles/deal_II.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(spotrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'spotrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sgetrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'sgetrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dpotrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'dpotrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dgetrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'dgetrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(zpotrf2.o): requires 
dynamic R_X86_64_PC32 reloc against 'zpotrf2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(sladiv.o): requires 
dynamic R_X86_64_PC32 reloc against 'sladiv2_' which may overflow at 
runtime; recompile with -fPIC
/usr/bin/ld.gold: error: /usr/local/lib/liblapack.a(dladiv.o): requires 
dynamic R_X86_64_PC32 reloc against 'dladiv2_' which may overflow at 
runtime; recompile with -fPIC
collect2: error: ld returned 1 exit status
source/CMakeFiles/deal_II.g.dir/build.make:751: recipe for target 
'lib/libdeal_II.g.so.9.0.1' failed
make[2]: *** [lib/libdeal_II.g.so.9.0.1] Error 1
CMakeFiles/Makefile2:929: recipe for target 
'source/CMakeFiles/deal_II.g.dir/all' failed
make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
-
thank you!
Wenguo.

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Re: [deal.II] Deal.ii installation problem:- Step 40 runtime error

2018-01-23 Thread RAJAT ARORA 
Hello Professor,

Thanks for the reply. 
I had been struggling with this issue for 5 days now. I raised the ticket 
on XSEDE forum on 18th Jan.
The technical team was expecting everything was fine from their side and 
advised me to reinstall with some different modules loaded. They were also 
expecting mixing of different mpi components.

I actually tried every possible combination (over 20) of modules. When 
nothing worked, I finally decided that to seek help from this forum. I was 
hesitating at first as I was sure that this is not the problem with library 
or its installation but rather it is the problem with the system. I needed 
some guidance to prove this thing.

However, I finally received an email yesterday (after posting this), that 
they made some security update on the system last week which caused the 
issue.  After the change was corrected by them, everything works fine just 
using candi.

Thanks a lot for the help. I really appreciate it.

I am still posting the answers to the questions you asked.

1. It always used to happen at a different position when run with different 
processors on a single node.

2. Even using multiple nodes was giving this error.










On Monday, January 22, 2018 at 11:09:41 PM UTC-5, Wolfgang Bangerth wrote:
>
> On 01/22/2018 08:48 AM, RAJAT ARORA wrote: 
> > 
> > Running with PETSc on 2 MPI rank(s)... 
> > Cycle 0: 
> > Number of active cells:   1024 
> > Number of degrees of freedom: 4225 
> > Solved in 10 iterations. 
> > 
> > 
> > 
> +-+++ 
> > | Total wallclock time elapsed since start| 0.222s |   
>  | 
> > | ||   
>  | 
> > | Section | no. calls |  wall time | % of total 
> | 
> > 
> +-+---+++ 
> > | assembly| 1 | 0.026s |12% 
> | 
> > | output  | 1 |0.0448s |20% 
> | 
> > | setup   | 1 |0.0599s |27% 
> | 
> > | solve   | 1 |0.0176s |   7.9% 
> | 
> > 
> +-+---+++ 
> > 
> > 
> > Cycle 1: 
> > Number of active cells:   1960 
> > Number of degrees of freedom: 8421 
> > r001.pvt.bridges.psc.edu.27927Assertion failure at 
> > 
> /nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.3.3/ptl_am/ptl.c:152:
>  
>
> > nbytes == req->recv_msglen 
> > r001.pvt.bridges.psc.edu.27927step-40: Reading from remote process' 
> memory 
> > failed. Disabling CMA support 
> > [r001:27927] *** Process received signal *** 
>
> These error messages suggest that the first cycle actually worked. So your 
> MPI 
> installation is not completely broken apparently. 
>
> Is the error message reproducible? Is it always in the same place and with 
> the 
> same message? When you run two processes, are they on separate machines or 
> on 
> the same one? 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] Deal.ii installation problem:- Step 40 runtime error

2018-01-22 Thread Wolfgang Bangerth 

On 01/22/2018 08:48 AM, RAJAT ARORA wrote:


Running with PETSc on 2 MPI rank(s)...
Cycle 0:
Number of active cells:   1024
Number of degrees of freedom: 4225
Solved in 10 iterations.


+-+++
| Total wallclock time elapsed since start| 0.222s ||
| |||
| Section | no. calls |  wall time | % of total |
+-+---+++
| assembly| 1 | 0.026s |12% |
| output  | 1 |0.0448s |20% |
| setup   | 1 |0.0599s |27% |
| solve   | 1 |0.0176s |   7.9% |
+-+---+++


Cycle 1:
Number of active cells:   1960
Number of degrees of freedom: 8421
r001.pvt.bridges.psc.edu.27927Assertion failure at 
/nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.3.3/ptl_am/ptl.c:152: 
nbytes == req->recv_msglen
r001.pvt.bridges.psc.edu.27927step-40: Reading from remote process' memory 
failed. Disabling CMA support

[r001:27927] *** Process received signal ***


These error messages suggest that the first cycle actually worked. So your MPI 
installation is not completely broken apparently.


Is the error message reproducible? Is it always in the same place and with the 
same message? When you run two processes, are they on separate machines or on 
the same one?


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Deal.ii installation problem:- Step 40 runtime error

2018-01-22 Thread RAJAT ARORA 
Hello all,

I recently installed deal.ii using candi but after everything successfully 
finishes, I am not able to run step-40 on more than 1 processor. For, 1 
processor it runs fine.


To install everything, I used candi and and loaded following modules.

  1) psc_path/1.1  2) slurm/17.02.5 3) cmake/3.7.2   4) mpi/
gcc_openmpi


I have tried several combinations of the modules in the past week but it is 
not working.
Can someone please help me finding out what is the problem with the 
installation?

I will be able to provide any relevant log file or command output if 
needed. 
Any help will be appreciated.

Here is the error message when I do

mpirun -np 2 ./step-40


Running with PETSc on 2 MPI rank(s)...
Cycle 0:
   Number of active cells:   1024
   Number of degrees of freedom: 4225
   Solved in 10 iterations.


+-+++
| Total wallclock time elapsed since start| 0.222s ||
| |||
| Section | no. calls |  wall time | % of total |
+-+---+++
| assembly| 1 | 0.026s |12% |
| output  | 1 |0.0448s |20% |
| setup   | 1 |0.0599s |27% |
| solve   | 1 |0.0176s |   7.9% |
+-+---+++


Cycle 1:
   Number of active cells:   1960
   Number of degrees of freedom: 8421
r001.pvt.bridges.psc.edu.27927Assertion failure at 
/nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.3.3/ptl_am/ptl.c:152:
 
nbytes == req->recv_msglen
r001.pvt.bridges.psc.edu.27927step-40: Reading from remote process' memory 
failed. Disabling CMA support
[r001:27927] *** Process received signal ***
[r001:27927] Signal: Aborted (6)
[r001:27927] Signal code:  (-6)
[r001:27927] [ 0] /lib64/libpthread.so.0(+0xf370)[0x2b8ccfc72370]
[r001:27927] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b8cd04bf1d7]
[r001:27927] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b8cd04c08c8]
[r001:27927] [ 3] /lib64/libpsm2.so.2(+0x14df8)[0x2b8cda72cdf8]
[r001:27927] [ 4] /lib64/libpsm2.so.2(+0xeb59)[0x2b8cda726b59]
[r001:27927] [ 5] /lib64/libpsm2.so.2(+0x8fcf)[0x2b8cda720fcf]
[r001:27927] [ 6] /lib64/libpsm2.so.2(+0x7b1a)[0x2b8cda71fb1a]
[r001:27927] [ 7] /lib64/libpsm2.so.2(+0x21012)[0x2b8cda739012]
[r001:27927] [ 8] /lib64/libpsm2.so.2(psm2_mq_ipeek2+0xa8)[0x2b8cda734198]
[r001:27927] [ 9] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/openmpi/mca_mtl_psm2.so(ompi_mtl_psm2_progress+0x6b)[0x2b8cdc461d7b]
[r001:27927] [10] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/libopen-pal.so.13(opal_progress+0x2a)[0x2b8cd2e381ea]
[r001:27927] [11] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/libmpi.so.12(ompi_request_default_wait_all+0x225)[0x2b8ccf46f5f5]
[r001:27927] [12] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/libmpi.so.12(PMPI_Waitall+0x9f)[0x2b8ccf49fdff]
[r001:27927] [13] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_MPI_Waitall+0x9)[0x2b8cc6c1c485]
[r001:27927] [14] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_ParCSRCommHandleDestroy+0x3f)[0x2b8cc6ba7664]
[r001:27927] [15] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_ParCSRMatrixExtractBExt+0x48)[0x2b8cc6bab3a7]
[r001:27927] [16] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_BoomerAMGBuildInterp+0x39b)[0x2b8cc6b649b5]
[r001:27927] [17] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_BoomerAMGSetup+0x4056)[0x2b8cc6b507f6]
[r001:27927] [18] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(HYPRE_BoomerAMGSetup+0x9)[0x2b8cc6b470d6]
[r001:27927] [19] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(+0x7ea066)[0x2b8cc67e8066]
[r001:27927] [20] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(PCSetUp+0x551)[0x2b8cc67efcbb]
[r001:27927] [21] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/deal.II-v8.5.1/lib/libdeal_II.g.so.8.5.1(_ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE+0x63)[0x2b8cc1bcf94d]
[r001:27927] [22] 
./step-40(_ZN6Step4014LaplaceProblemILi2EE5solveEv+0x106)[0x42ca38]
[r001:27927] [23] 
./step-40(_ZN6Step4014LaplaceProblemILi2EE3runEv+0x245)[0x42ead1]
[r001:27927] [24] ./step-40(main+0x3c)[0x41d07d]
[r001:27927] [25] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b8cd04abb35]
[r001:27927] [26] ./step-40[0x41cf29]
[r001:27927] *** End of error message ***

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