Questions about installing Aspect on linux ubuntu

When typing cmake… in the build folder.

– ====================================================
– ============ Configuring ASPECT ====================
– ====================================================
– Setting up ASPECT for DebugRelease mode.
CMake Error at CMakeLists.txt:108 (MESSAGE):

*** Could not find a suitably recent version of deal.II. ***

You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake
or set an environment variable “DEAL_II_DIR” that contains a path to a
sufficiently recent version of deal.II.

What should I do

And I can’t find DEAL_II_DIR/examples/step-32

Did you install deal.II? On Linux you can either install system packages (Getting deal.II · dealii/dealii Wiki · GitHub) or compile manually as described here:
Local installation — ASPECT 2.6.0-pre

Thanks for your response

Following the manual
I input “git clone https://github.com/dealii/candi” and“ cd candi ./candi.sh -p INSTALL_PATH ” and I can find folder ‘deal.Ⅱ toolchain’ .

Do I need any other steps to install deal.Ⅱ

By the way I want to install Aspect on HPC through Singularity Is this a feasible way

I input “git clone https://github.com/dealii/candi” and“ cd candi ./candi.sh -p INSTALL_PATH ” .

Did you replace INSTALL_PATH with desired installation folder on your system? INSTALL_PATH is just a placeholder for

and I can find folder ‘deal.Ⅱ toolchain

That folder is not part of the installed library, but rather part of the candi installer package.

Do you by chance have the terminal output saved from when you ran candi? Once it is finished, it will provide information regarding where the libraries were installed.

By the way I want to install Aspect on HPC through Singularity Is this a feasible way

I believe that has been done on at least one HPC system (Frontera), but don’t recall the details. In most cases, we installed deal.II/ASPECT with candi.

Cheers,
John

Thanks for your response

I input “cd candi ./candi.sh -p dellII”

report an error

candi tries now to download, configure, build and install:

Project: deal.II-toolchain
Platform: deal.II-toolchain/platforms/supported/ubuntu.platform

Loading dealii-prepare
Fetching opencascade 0.18.3
Verifying OCE-0.18.3.tar.gz
OCE-0.18.3.tar.gz: OK(sha256)
OCE-0.18.3.tar.gz already downloaded and verified.
./candi.sh: Line 436: cd: dellII/tmp/unpack: There is no file or directory for that
Unpacking OCE-0.18.3.tar.gz
delII/tmp/src/OCE-0.18.3.tar.gz does not exist. Please download first.
ruthless12@ruthless12-Precision-3551:~/ubuntu/candi$

I can find OCE-0.18.3.tar.gz in dellII/tmp/unpack

I don’t know how to solve this problem

In the first error message, it says that the directory does not exist, but you
say that it exists. You have to find out why you get that error message. My
suggestion would be to start the whole process from scratch, in a new and
empty directory.

Best
W.

Thanks for your response

The problem continued after start the whole process.

Whether other plug-ins need to be installed to make ‘Unpacking’ run correctly?

Try running without specifying -p and a path, just “./candi.sh”

Running just “./candi.sh”.The installation process starts. But there is still an error

-- Configuring incomplete, errors occurred!
See also "/home/ruthless12/dealii-candi/tmp/build/symengine-0.8.1/CMakeFiles/CMakeOutput.log".
Failure with exit status: 1
Exit message: There was a problem configuring symengine 0.8.1.

Please follow the instructions at Using candi to compile dependencies — ASPECT 2.6.0-pre about the packages to install. You don’t need symengine.

I can find step-32 and run cmake . && make.

However, something error while running “mpirun -n 2 ./step-32”

ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples$ ls
CMakeCache.txt step-14 step-25 step-36 step-48 step-6 step-71
CMakeFiles step-15 step-26 step-37 step-49 step-60 step-72
cmake_install.cmake step-16 step-27 step-38 step-5 step-61 step-74
CMakeLists.txt step-16b step-28 step-39 step-50 step-62 step-75
doxygen step-17 step-29 step-4 step-51 step-63 step-76
Makefile step-18 step-3 step-40 step-52 step-64 step-77
README.md step-19 step-30 step-41 step-53 step-65 step-78
step-1 step-2 step-31 step-42 step-54 step-66 step-79
step-10 step-20 step-32 step-43 step-55 step-67 step-8
step-11 step-21 step-32.prm step-44 step-56 step-68 step-81
step-12 step-22 step-33 step-45 step-57 step-69 step-82
step-12b step-23 step-34 step-46 step-58 step-7 step-85
step-13 step-24 step-35 step-47 step-59 step-70 step-9
ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples$ mpirun -n 2 ./step-32

Open MPI tried to fork a new process via the “execve” system call but
failed. Open MPI checks many things before attempting to launch a
child process, but nothing is perfect. This error may be indicative
of another problem on the target host, or even something as silly as
having specified a directory for your application. Your job will now
abort.

Local host: ruthless12-Precision-3551
Working dir: /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples
Application name: ./step-32
Error: Permission denied


mpirun was unable to start the specified application as it encountered an
error:

Error code: -125
Error name: The specified application failed to start
Node: ruthless12-Precision-3551

when attempting to start process rank 0.

2 total processes failed to start
[ruthless12-Precision-3551:20895] 1 more process has sent help message help-orte-odls-default.txt / execve error
[ruthless12-Precision-3551:20895] Set MCA parameter “orte_base_help_aggregate” to 0 to see all help / error messages
ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples$ cd step-32
ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples/step-32$ ls
candi.cfg CMakeFiles doc step-32.cc
CMakeCache.txt CMakeLists.txt local.cfg step-32.prm
ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples/step-32$ mpirun -n 2 ./step-32

mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: ./step-32
Node: ruthless12-Precision-3551

while attempting to start process rank 0.

2 total processes failed to start
ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples/step-32$

@leisurely The error message you get actually says what is happening: You are calling mpirun -np 2 ./step-32 in ~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples where step-32 is the name of a sub-directory. But it needs to be the name of an executable. It should work if you do

cd step-32
mpirun -np 2 ./step-32

Best
W.

After cd step-32

“mpirun -np 2 ./step-32” still report an error .There is no executable file named step-32 only step-32.prm

It still have the same error after trying to use “mpirun -np 2 ./step-32” ,"mpirun -np 2 ./step-32.prm"or “mpirun -np 2 ./step-32 step-32.prm”

ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples$ cd step-32

ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples/step-32$ ls
candi.cfg CMakeFiles doc step-32.cc
CMakeCache.txt CMakeLists.txt local.cfg step-32.prm
ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples/step-32$ mpirun -n 2 ./step-32

mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: ./step-32
Node: ruthless12-Precision-3551

while attempting to start process rank 0.

2 total processes failed to start
ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples/step-32$

@leisurely From your directory listing, I can see that you called cmake in this directory. Did that work? If so, when you call make, does that produce an executable?

I will note that you’re doing all of this in the source directory. But you should never touch that. You should be working in the installation directory instead, which is where I would expect the executables to be located.

Best
W.

Unable to “cmake.” success in sub-directory step-32.

ruthless12@ruthless12-Precision-3551:~/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/examples/step-32$ cmake .
– Using the deal.II-9.5.1 build directory found at /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_deal_ii_add_test.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_deal_ii_setup_target.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_shell_escape_option_groups.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_target_compile_flags.cmake
– Include macro /home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1/share/deal.II/macros/macro_target_link_flags.cmake
CMake Error at CMakeLists.txt:44 (message):

Error! This tutorial requires a deal.II library that was configured with
the following options:

  DEAL_II_WITH_MPI = ON
  DEAL_II_WITH_P4EST = ON
  DEAL_II_WITH_TRILINOS = ON

However, the deal.II library found at
/home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1 was
configured with these options:

  DEAL_II_WITH_MPI = OFF
  DEAL_II_WITH_P4EST = OFF
  DEAL_II_WITH_TRILINOS = OFF

This conflicts with the requirements.

– Configuring incomplete, errors occurred!

@leisurely The error message is actually quite informative I believe:

Error! This tutorial requires a deal.II library that was configured with
the following options:

  DEAL_II_WITH_MPI = ON
  DEAL_II_WITH_P4EST = ON
  DEAL_II_WITH_TRILINOS = ON

However, the deal.II library found at
/home/ruthless12/ubuntu2/candi/dealII/tmp/unpack/deal.II-v9.5.1 was
configured with these options:

  DEAL_II_WITH_MPI = OFF
  DEAL_II_WITH_P4EST = OFF
  DEAL_II_WITH_TRILINOS = OFF
This conflicts with the requirements.

In essence, the error message says that in order to run this tutorial, you need to have certain other libraries installed as well on your system, but you don’t.

You seem to be struggling with a lot of relatively basic problems in dealing with installing software, the command line, etc. We can help you with questions on ASPECT, but this problem is too slow in teaching you which directories you need to look into, or how to read error messages. (In addition to the fact that we can not teach everyone these basic skills, within the time we have for user support every day.) Can I suggest that you find someone locally at your university who perhaps has already been using ASPECT, or at least who is experienced in using Linux, with whom you can work and who you can ask for help? I think that will be a better learning experience for you, and will make sure that we can use this forum for questions that are about ASPECT itself.

Best
WB

Ok, thank you all for your help