Re: [deal.II] Re: error while installing dealii using candi

[Ahmad Shahba]

By using the -j1 argument, you are requesting candi to use 1 process for
compilation. If you are interested to engage, say 2 processes, you should
pass -j2 to the candi shell script. Something like

./candi.sh -j2

If you visit the github homepage of candi, you’ll see a whole bunch of
options for controlling the way candi goes about compiling and installing
deal.ii and its dependencies.

On Thu, Jul 21, 2022 at 11:11 AM erkin yildiz  wrote:

> Thank you for your suggestion. JOBS = 1 is the default in candi.sh and
> passing -j1 does not make any difference. Could it be related to the flag
> -std=c++17? How can I impose it?
>
> Thanks for your help
> Erkin
>
> Wolfgang Bangerth , 21 Tem 2022 Per, 16:55
> tarihinde şunu yazdı:
>
>> On 7/21/22 06:00, erkin yildiz wrote:
>> > **
>> >
>> > Can you please suggest me how to use only one or two cores? Please find
>> > attached the log file
>>
>> Use the flag -j1 or -j2 on the command line.
>>
>> 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/
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>> .
>>
>
>
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> .
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Re: [deal.II] Re: error while installing dealii using candi

[erkin yildiz]

Thank you for your suggestion. JOBS = 1 is the default in candi.sh and
passing -j1 does not make any difference. Could it be related to the flag
-std=c++17? How can I impose it?

Thanks for your help
Erkin

Wolfgang Bangerth , 21 Tem 2022 Per, 16:55
tarihinde şunu yazdı:

> On 7/21/22 06:00, erkin yildiz wrote:
> > **
> >
> > Can you please suggest me how to use only one or two cores? Please find
> > attached the log file
>
> Use the flag -j1 or -j2 on the command line.
>
> 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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> .
>

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Re: [deal.II] Re: error while installing dealii using candi

[Wolfgang Bangerth]

On 7/21/22 06:00, erkin yildiz wrote:

**

Can you please suggest me how to use only one or two cores? Please find 
attached the log file


Use the flag -j1 or -j2 on the command line.

Best
 W.

--

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

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[deal.II] Re: error while installing dealii using candi

[Bruno Turcksin]

Hello,

This error often happens when you don't have enough memory to compile the 
program. Try using only one or two cores.

Best,

Bruno

On Wednesday, July 6, 2022 at 4:01:45 AM UTC-4 me20...@iittp.ac.in wrote:

> Dear all,
> please find the error attached.
>
> thank you in advance.[image: PHOTO-2022-07-06-00-19-11.jpg]
>

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Re: [deal.II] Re: Error while installing dealii

[Wolfgang Bangerth]

On 3/15/22 23:26, PUNITH M wrote:


cmake -DTPL_ENABLE_MPI=ON -DMPI_BASE_DIR=/apps/compilers/openmpi/4.1.1 
-DTrilinos_ENABLE_ALL_PACKAGES=ON -DTPL_ENABLE_Boost=OFF 
-DBUILD_SHARED_LIBS=ON -DTPL_ENABLE_Netcdf=OFF 
-DCMAKE_INSTALL_PREFIX=/apps/libs/Trillions-13.2 ../


Is this the same MPI installation as you used for deal.II?

Best
 W.

--

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

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[deal.II] Re: Error while installing dealii

[PUNITH M]

S I did with the following options 

cmake -DTPL_ENABLE_MPI=ON -DMPI_BASE_DIR=/apps/compilers/openmpi/4.1.1 
-DTrilinos_ENABLE_ALL_PACKAGES=ON -DTPL_ENABLE_Boost=OFF 
-DBUILD_SHARED_LIBS=ON -DTPL_ENABLE_Netcdf=OFF 
-DCMAKE_INSTALL_PREFIX=/apps/libs/Trillions-13.2 ../

On Tuesday, March 15, 2022 at 6:05:48 PM UTC+5:30 bruno.t...@gmail.com 
wrote:

> Hello,
>
> Did you configure Trilinos with MPI support?
>
> Best,
>
> Bruno
>
> On Tuesday, March 15, 2022 at 7:09:55 AM UTC-4 punith...@gmail.com wrote:
>
>> I've compiled a deal.ii using CMake with the below options 
>>
>> cmake -DCMAKE_INSTALL_PREFIX=/apps/codes/deal_II/9.3.3 
>> -DHDF5_DIR=/apps/libs/hdf5/gcc/1.12.1 -DP4EST_DIR=/apps/libs/p4est-2.8 
>> -DDEAL_II_WITH_MPI=ON -DTRILINOS_DIR=/apps/libs/Trillions-13.2 ../
>>
>> compile was successful
>> while installing using the command* make --jobs=4 install *I'm getting 
>> the below error
>>
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
>> 'Epetra_MpiComm::Epetra_MpiComm(int)'
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
>> 'Teuchos::details::safeCommFree(int*)'
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [bin/step-10.release] Error 1
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
>> 'Epetra_MpiComm::Epetra_MpiComm(int)'
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
>> 'Teuchos::details::safeCommFree(int*)'
>> make[1]: *** [examples/CMakeFiles/step-10.release.dir/all] Error 2
>> make[1]: *** Waiting for unfinished jobs
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 'collect2: 
>> error: ld returned 1 exit status
>> Epetra_MpiComm::Epetra_MpiComm(int)'
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
>> 'Teuchos::details::safeCommFree(int*)'
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [bin/step-12.release] Error 1
>> make[2]: *** [bin/step-11.release] Error 1
>> make[1]: *** [examples/CMakeFiles/step-12.release.dir/all] Error 2
>> make[1]: *** [examples/CMakeFiles/step-11.release.dir/all] Error 2
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
>> 'Epetra_MpiComm::Epetra_MpiComm(int)'
>> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
>> 'Teuchos::details::safeCommFree(int*)'
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [bin/step-1.release] Error 1
>> make[1]: *** [examples/CMakeFiles/step-1.release.dir/all] Error 2
>> make: *** [all] Error 2
>>
>

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[deal.II] Re: Error while installing dealii

[Bruno Turcksin]

Hello,

Did you configure Trilinos with MPI support?

Best,

Bruno

On Tuesday, March 15, 2022 at 7:09:55 AM UTC-4 punith...@gmail.com wrote:

> I've compiled a deal.ii using CMake with the below options 
>
> cmake -DCMAKE_INSTALL_PREFIX=/apps/codes/deal_II/9.3.3 
> -DHDF5_DIR=/apps/libs/hdf5/gcc/1.12.1 -DP4EST_DIR=/apps/libs/p4est-2.8 
> -DDEAL_II_WITH_MPI=ON -DTRILINOS_DIR=/apps/libs/Trillions-13.2 ../
>
> compile was successful
> while installing using the command* make --jobs=4 install *I'm getting 
> the below error
>
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
> 'Epetra_MpiComm::Epetra_MpiComm(int)'
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
> 'Teuchos::details::safeCommFree(int*)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/step-10.release] Error 1
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
> 'Epetra_MpiComm::Epetra_MpiComm(int)'
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
> 'Teuchos::details::safeCommFree(int*)'
> make[1]: *** [examples/CMakeFiles/step-10.release.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 'collect2: 
> error: ld returned 1 exit status
> Epetra_MpiComm::Epetra_MpiComm(int)'
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
> 'Teuchos::details::safeCommFree(int*)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/step-12.release] Error 1
> make[2]: *** [bin/step-11.release] Error 1
> make[1]: *** [examples/CMakeFiles/step-12.release.dir/all] Error 2
> make[1]: *** [examples/CMakeFiles/step-11.release.dir/all] Error 2
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
> 'Epetra_MpiComm::Epetra_MpiComm(int)'
> ../lib/libdeal_II.so.9.3.3: error: undefined reference to 
> 'Teuchos::details::safeCommFree(int*)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/step-1.release] Error 1
> make[1]: *** [examples/CMakeFiles/step-1.release.dir/all] Error 2
> make: *** [all] Error 2
>

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[deal.II] Re: Error while installing trilinos and dealii with candi on Stampede2

[Jau-Uei Chen]

My apologize to my ignorance. 
I did not realize that we have pre-existing dealii modules on Stampede2 so 
I tired to install it manually. I am happy with using it directly.

Thanks for your prompt response!
Jau-Uei Chen

aadit...@gmail.com 在 2020年11月23日 星期一上午10:56:57 [UTC-6] 的信中寫道：

> Hi,
> There are pre-existing deal.ii modules on Stampede2 about which you 
> can find out by using the *module spider* command :
>
> *module spider dealii*
>
> Output :
>
>
> -
>   dealii:
>
> -
> Description:
>   Portable Extendible Toolkit for Scientific Computing, Numerical 
> library for sparse linear algebra
>
>  Versions:
> dealii/git20170615
> dealii/9.0.0
> dealii/9.1.1
> dealii/9.2.0
>
>
> -
>   For detailed information about a specific "dealii" package (including 
> how to load the modules) use the module's full name.
>   Note that names that have a trailing (E) are extensions provided by 
> other modules.
>   For example:
>
>  $ module spider dealii/9.2.0
>
> -
>
>  Is there a specific reason you want to install it manually?
>
> Best,
> Aaditya
>
> On Monday, November 23, 2020 at 11:28:23 AM UTC-5 jau...@gmail.com wrote:
>
>> Dear dealii community,
>>
>> I am trying to install dealii v9.2.0 with candi on stampede2 by following 
>> instruction shown in here 
>> .
>>  
>> I encounter errors when installing dealii and trilinos.
>>
>> My modules are:
>>   1) git/2.24.1 3) xalt/2.8   5) gcc/7.1.0 7) python/2.7.13   9) 
>> autotools/1.1
>>   2) cmake/3.16.1   4) TACC   6) impi/17.0.3   8) mkl/17.0.4
>>
>> By using the latest version of candi, I only change DEAL_CONFOPTS to
>> DEAL_CONFOPTS="-D DEAL_II_FORCE_BUNDLED_THREADS=ON"
>>
>> and MKL setting to:
>> MKL=ON
>> MKL_DIR=$MKLROOT/lib/intel64
>>
>> However, I got an error when installing trilinos:
>> CMake Error at 
>> cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:1098 
>> (MESSAGE):
>>***
>>*** ERROR: Setting Trilinos_ENABLE_Amesos2=OFF which was 'ON' because 
>> Amesos2 has a required library dependence on disabled package Tpetra!
>>***
>>
>> It seems that it happened when installing trilinos with MKL (see here 
>> )
>>  
>> though it seems to be resolved. I noted that in the post they use "intel" 
>> however, to use MKL, I have to use gcc in stampede2. I also tried to 
>> install the older version of trilinos (v12-10-1) by slightly modifying 
>> "trilinos.package" but it did not work neither. 
>>
>> Out of curiosity, I skip trilinos and install the rest of packages 
>> including dealii. However, I got an error when installing dealii:
>> -- A library with LAPACK API found.
>> -- Performing Test mpifort_LIBRARY
>> -- Performing Test mpifort_LIBRARY - Success
>> -- Performing Test mpi_LIBRARY
>> -- Performing Test mpi_LIBRARY - Success
>> -- Performing Test mpigi_LIBRARY
>> -- Performing Test mpigi_LIBRARY - Success
>> -- Performing Test dl_LIBRARY
>> -- Performing Test dl_LIBRARY - Success
>> -- Performing Test pthread_LIBRARY
>> -- Performing Test pthread_LIBRARY - Success
>> -- Performing Test gfortran_LIBRARY
>> -- Performing Test gfortran_LIBRARY - Success
>> -- Performing Test m_LIBRARY
>> -- Performing Test m_LIBRARY - Success
>> -- Performing Test gcc_s_LIBRARY
>> -- Performing Test gcc_s_LIBRARY - Success
>> -- Performing Test gcc_LIBRARY
>> -- Performing Test gcc_LIBRARY - Success
>> -- Performing Test quadmath_LIBRARY
>> -- Performing Test quadmath_LIBRARY - Success
>> -- Performing Test c_LIBRARY
>> -- Performing Test c_LIBRARY - Success
>> --   LAPACK_LIBRARIES: *** Required variable "_lapack_libraries" empty ***
>> --   LAPACK_LINKER_FLAGS:
>> --   LAPACK_INCLUDE_DIRS:
>> --   LAPACK_USER_INCLUDE_DIRS:
>> -- Could NOT find LAPACK
>> -- DEAL_II_WITH_LAPACK has unmet external dependencies.
>> CMake Error at cmake/macros/macro_configure_feature.cmake:112 (MESSAGE):
>>
>>
>>   Could not find the lapack library!
>>
>>   Please ensure that a suitable lapack library is installed on your 
>> computer.
>>
>>   If the library is not at a default location, either provide some hints 
>> for
>>   autodetection,
>>
>>   $ LAPACK_DIR="..." cmake <...>
>>   $ cmake -DLAPACK_DIR="..." <...>
>>
>

[deal.II] Re: Error while installing trilinos and dealii with candi on Stampede2

[Aaditya Lakshmanan]

Hi,
There are pre-existing deal.ii modules on Stampede2 about which you can 
find out by using the *module spider* command :

*module spider dealii*

Output :

-
  dealii:
-
Description:
  Portable Extendible Toolkit for Scientific Computing, Numerical 
library for sparse linear algebra

 Versions:
dealii/git20170615
dealii/9.0.0
dealii/9.1.1
dealii/9.2.0

-
  For detailed information about a specific "dealii" package (including how 
to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other 
modules.
  For example:

 $ module spider dealii/9.2.0
-

 Is there a specific reason you want to install it manually?

Best,
Aaditya

On Monday, November 23, 2020 at 11:28:23 AM UTC-5 jau...@gmail.com wrote:

> Dear dealii community,
>
> I am trying to install dealii v9.2.0 with candi on stampede2 by following 
> instruction shown in here 
> .
>  
> I encounter errors when installing dealii and trilinos.
>
> My modules are:
>   1) git/2.24.1 3) xalt/2.8   5) gcc/7.1.0 7) python/2.7.13   9) 
> autotools/1.1
>   2) cmake/3.16.1   4) TACC   6) impi/17.0.3   8) mkl/17.0.4
>
> By using the latest version of candi, I only change DEAL_CONFOPTS to
> DEAL_CONFOPTS="-D DEAL_II_FORCE_BUNDLED_THREADS=ON"
>
> and MKL setting to:
> MKL=ON
> MKL_DIR=$MKLROOT/lib/intel64
>
> However, I got an error when installing trilinos:
> CMake Error at 
> cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:1098 
> (MESSAGE):
>***
>*** ERROR: Setting Trilinos_ENABLE_Amesos2=OFF which was 'ON' because 
> Amesos2 has a required library dependence on disabled package Tpetra!
>***
>
> It seems that it happened when installing trilinos with MKL (see here 
> )
>  
> though it seems to be resolved. I noted that in the post they use "intel" 
> however, to use MKL, I have to use gcc in stampede2. I also tried to 
> install the older version of trilinos (v12-10-1) by slightly modifying 
> "trilinos.package" but it did not work neither. 
>
> Out of curiosity, I skip trilinos and install the rest of packages 
> including dealii. However, I got an error when installing dealii:
> -- A library with LAPACK API found.
> -- Performing Test mpifort_LIBRARY
> -- Performing Test mpifort_LIBRARY - Success
> -- Performing Test mpi_LIBRARY
> -- Performing Test mpi_LIBRARY - Success
> -- Performing Test mpigi_LIBRARY
> -- Performing Test mpigi_LIBRARY - Success
> -- Performing Test dl_LIBRARY
> -- Performing Test dl_LIBRARY - Success
> -- Performing Test pthread_LIBRARY
> -- Performing Test pthread_LIBRARY - Success
> -- Performing Test gfortran_LIBRARY
> -- Performing Test gfortran_LIBRARY - Success
> -- Performing Test m_LIBRARY
> -- Performing Test m_LIBRARY - Success
> -- Performing Test gcc_s_LIBRARY
> -- Performing Test gcc_s_LIBRARY - Success
> -- Performing Test gcc_LIBRARY
> -- Performing Test gcc_LIBRARY - Success
> -- Performing Test quadmath_LIBRARY
> -- Performing Test quadmath_LIBRARY - Success
> -- Performing Test c_LIBRARY
> -- Performing Test c_LIBRARY - Success
> --   LAPACK_LIBRARIES: *** Required variable "_lapack_libraries" empty ***
> --   LAPACK_LINKER_FLAGS:
> --   LAPACK_INCLUDE_DIRS:
> --   LAPACK_USER_INCLUDE_DIRS:
> -- Could NOT find LAPACK
> -- DEAL_II_WITH_LAPACK has unmet external dependencies.
> CMake Error at cmake/macros/macro_configure_feature.cmake:112 (MESSAGE):
>
>
>   Could not find the lapack library!
>
>   Please ensure that a suitable lapack library is installed on your 
> computer.
>
>   If the library is not at a default location, either provide some hints 
> for
>   autodetection,
>
>   $ LAPACK_DIR="..." cmake <...>
>   $ cmake -DLAPACK_DIR="..." <...>
>
>   or set the relevant variables by hand in ccmake.
>
> It seems also happened before (see here 
>  and here 
> ). I tried 
> different setting in MKL and DEAL_CONFOPTS that are mentioned in the posts 
> but none of them work for me. (To link Lapack in stampede2, I referent to 
> here .)

[deal.II] Re: Error while installing dealii

[Bruno Turcksin]

Prakash,

How did you configure deal.II?

Best,

Bruno

On Friday, July 3, 2020 at 5:54:23 AM UTC-4, ME20S001 Bardawal Prakash 
wrote:
>
> Hello,
>I got error while installing dealii, can someone help me for 
> solving this issue?
> Here I'm attaching snapshots of that error message
>
> Thanks & Regards,
> Prakash.
>

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Re: [deal.II] Re: Error while installing

[ME20S001 Bardawal Prakash]

I  also run 'sudo make install' command, but again it is showing error that
is 'No rule to make target install'. stop, can you help me to solve this
problem?


On Wed, Jul 1, 2020, 5:15 PM 'peterrum' via deal.II User Group <
dealii@googlegroups.com> wrote:

> The error message already tells you what to do. You need to run the
> commend with admi privileges, i.e., `sudo make install`.
>
> Hope that helps,
> Peter
>
> On Wednesday, 1 July 2020 13:21:12 UTC+2, ME20S001 Bardawal Prakash wrote:
>>
>> Hello,
>> Someone help me solving this issue, here I'm attaching snapshots of
>> that error message. And also the installation files was not created after
>> running 'make install' command.
>>
>> --
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> .
>

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[deal.II] Re: Error while installing

['peterrum' via deal.II User Group]

The error message already tells you what to do. You need to run the commend 
with admi privileges, i.e., `sudo make install`.

Hope that helps,
Peter

On Wednesday, 1 July 2020 13:21:12 UTC+2, ME20S001 Bardawal Prakash wrote:
>
> Hello,
> Someone help me solving this issue, here I'm attaching snapshots of 
> that error message. And also the installation files was not created after 
> running 'make install' command.
>
>

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Re: [deal.II] Re: error while installing dealii

[ME20S001 Bardawal Prakash]

Thanks, I will try with that modification

On Wed, Jun 24, 2020, 5:05 PM simon...@gmail.com 
wrote:

> Hi,
> In your first sceenshot you can see this error message:
>
> "virtual memory exhausted: Cannot allocate memory"
>
> From your other screenshots it looks like you are running ubuntu in a
> virtual box. If that is the case, I would expect that increasing the RAM of
> your virtual machine will fix the problem. If I'm not mistaken, at least
> 3GB is needed to compile dealii, so maybe < 4GB would be a good choice.
>
> Best,
> Simon
>
> On Wednesday, June 24, 2020 at 1:03:16 PM UTC+2 me20...@iittp.ac.in wrote:
>
>>  1. While running *make* command, after 4 to 5 hours i'm getting error
>> like internal compiler error:*killed ( program ccplus ) * or  fatal error
>> :*killed signal terminated program ccplus.*
>> 2.while running the command again it is moving 4 to 5% forward in 3 to 4
>> hours  and again getting the same error.
>> 3.I'm new to start dealii, can you help me for solving  this issue and
>> here  i'm attaching few  snapshots of this error.
>>
>>
>> --
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> 
> .
>

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[deal.II] Re: error while installing dealii

[simon...@gmail.com]

Hi,
In your first sceenshot you can see this error message:

"virtual memory exhausted: Cannot allocate memory"

>From your other screenshots it looks like you are running ubuntu in a 
virtual box. If that is the case, I would expect that increasing the RAM of 
your virtual machine will fix the problem. If I'm not mistaken, at least 
3GB is needed to compile dealii, so maybe < 4GB would be a good choice.

Best,
Simon

On Wednesday, June 24, 2020 at 1:03:16 PM UTC+2 me20...@iittp.ac.in wrote:

>  1. While running *make* command, after 4 to 5 hours i'm getting error 
> like internal compiler error:*killed ( program ccplus ) * or  fatal 
> error:*killed 
> signal terminated program ccplus.*
> 2.while running the command again it is moving 4 to 5% forward in 3 to 4 
> hours  and again getting the same error.
> 3.I'm new to start dealii, can you help me for solving  this issue and 
> here  i'm attaching few  snapshots of this error.
>
>
>

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[deal.II] Re: Error while installing dealii-8.4.1 in Ubuntu

[Bruno Turcksin]

Hi,

you are probably trying to install deal somewhere you shouldn't. Where are 
you building deal and where do you want to install it? You can also use 
candi to install deal https://github.com/dealii/candi

Best,

Bruno

On Thursday, May 26, 2016 at 6:51:08 AM UTC-4, Iniyan Kalaimani wrote:
>
> Hi,
>
> I got this following error while installin dealii-8.4.1 in Ubuntu platform.
>
> *[ 46%] Built target obj_muparser.debug*
> *[ 47%] Built target obj_muparser.release*
> *[ 47%] Built target obj_opencascade.inst*
> *[ 48%] Built target obj_opencascade.release*
> *[ 48%] Generating fe_bdm.inst*
> */bin/sh: 1: ../../bin/expand_instantiations: Permission denied*
> *make[2]: *** [source/fe/fe_bdm.inst] Error 126*
> *make[1]: *** [source/fe/CMakeFiles/obj_fe.inst.dir/all] Error 2*
> *make: *** [all] Error 2*
>
> I even tried to run with "sudo make install" but I got the same error. 
> Could someone please help me on this?
>

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