step-1 Error

[Scott Ziegler]

Hello,

I tried running the first tutorial on my machine and I am getting an error message I don't understand. The "cmake step-1.cc ." and "make step-1.cc" commands ran fine, but when I try "make run step-1.cc" I get the following error:

Scanning dependencies of target step-1

[ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o

[ 66%] Linking CXX executable step-1

[ 66%] Built target step-1

Scanning dependencies of target run

[100%] Run step-1 with Debug configuration

dyld: Library not loaded: libiomp5.dylib

  Referenced from: /Applications/deal.II-9.0.0.app/Contents/Resources/spack/opt/spack/darwin-highsierra-x86_64/clang-6.0.0/assimp-4.0.1-pdlrx32676yct2pztierxgvynk5gx277/lib/libassimp.4.dylib

  Reason: image not found

make[3]: *** [CMakeFiles/run] Abort trap: 6

make[2]: *** [CMakeFiles/run.dir/all] Error 2

make[1]: *** [CMakeFiles/run.dir/rule] Error 2

make: *** [run] Error 2

I am running an older version of deal.ii (deal.ii.9.0.0) because the latest version wasn't compatible with my laptop. I have a 2012 MacBook Pro running macOS 10.13.6. Any help would be greatly appreciated, thank you.

[Luca Heltai]

The 9.0.0 image contains a spack installation. Can you run "module load dealii" before trying to run?

Luca. 

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[Scott Ziegler]

Thanks for the response! I might be misunderstanding, but in my directory for step-1 I tried running the command exactly as "module load dealii" and I just get "bash: module: command not found" in return. What am I doing wrong?

[Wolfgang Bangerth]

On 9/18/20 3:37 PM, Scott Ziegler wrote:
> Thanks for the response! I might be misunderstanding, but in my directory for
> step-1 I tried running the command exactly as "module load dealii" and I just
> get "bash: module: command not found" in return. What am I doing wrong?

Oh, it doesn't know the 'module' command. It's not that it doesn't know the
module it's trying to load. Can you check how one would install the 'module'
command?

Best
W.

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

[Scott Ziegler]

I've looked and wasn't able to find much. Does anyone know how to install this command on a Mac?

[Luca Heltai]

Are you running the terminal, or the deal.II application?

When you run the deal.II application, you are dropped into a terminal (with instructions) to run deal.II examples. Including how to set up your bashrc (or zshrc) to point to the deal.II 
Installation/the module command. 

Only after you instructed the terminal of the right paths, you’ll be able to run deal.II from the standard terminal. 

Luca

Il giorno 18 set 2020, alle ore 23:37, Scott Ziegler <scot...@rams.colostate.edu> ha scritto:

Thanks for the response! I might be misunderstanding, but in my directory for step-1 I tried running the command exactly as "module load dealii" and I just get "bash: module: command not found" in return. What am I doing wrong?

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6d79eb30-84bf-4419-964b-5747beefb15fn%40googlegroups.com.

[Wolfgang Bangerth]

Hi Luca,

> Are you running the terminal, or the deal.II application?
>
> When you run the deal.II application, you are dropped into a terminal (with
> instructions) to run deal.II examples. Including how to set up your bashrc (or
> zshrc) to point to the deal.II
> Installation/the module command.

He's running in the terminal that shows all of the instructions. The problem
is not that 'module load dealii' doesn't know how to load deal.II, but that
the 'module' command doesn't seem to exist on his system. That's what the

error message says:
bash: module: command not found

I can't seem to find any information (but also don't know where to look) on
how one can install the 'module' command or, more generally, which general
package 'module' would actually come from.

Any ideas?

[luca.heltai]

If he’s running from the deal.II terminal, he should have the module command (it is part of the spack installation).

The deal.II terminal exports the paths so that the module command is there. What version of the deal.II package is he using? On my system, this is the output I get:



bash-3.2$ module avail
------- /Applications/deal.II.app/Contents/Resources/spack/share/spack/modules/darwin-catalina-x86_64 --------
adol-c/2.7.2 hwloc/1.11.11 numdiff/5.9.0 xz/5.2.5
arpack-ng/3.7.0-openblas hypre/2.18.2-openblas oce/0.18.3 zlib/1.2.11
assimp/4.0.1 intel-tbb/2020.2 openblas/0.3.10
autoconf-archive/2019.01.06 libc/1.0 openmpi/3.1.6
autoconf/2.69 libffi/3.3 openssl/1.1.1g
automake/1.16.2 libsigsegv/2.12 p4est/2.2
boost/1.73.0 libtool/2.4.6 parmetis/4.0.3
bzip2/1.0.8 libxml2/2.9.10 perl/5.18.4
cmake/3.17.1 m4/1.4.18 petsc/3.13.1-openblas-py2-py3
dealii/9.2.0-openblas-py2-py3 matio/1.5.13 pkgconf/1.7.3
diffutils/3.7 metis/5.1.0 python/3.7.7
environment-modules/4.5.1 mpc/1.1.0 readline/8.0
expat/2.2.9 mpfr/4.0.2 slepc/3.13.3-openblas-py2-py3
gdbm/1.18.1 mumps/5.2.0-openblas sqlite/3.31.1
gettext/0.20.2 muparser/2.2.6.1 suite-sparse/5.3.0-openblas
ginkgo/1.1.0 nanoflann/1.2.3 sundials/3.2.1
glm/0.9.7.1 ncurses/6.2 superlu-dist/6.3.0-openblas
gmp/6.1.2 netcdf-c/4.7.3 symengine/0.6.0
gmsh/4.5.4-openblas netcdf-cxx/4.2 tar/1.32
googletest/1.10.0 netgen/5.3.1 tcl/8.6.8
gsl/2.5 netlib-scalapack/2.0.2-openblas tetgen/1.5.0
hdf5/1.10.6 ninja/1.10.0-py2-py3 trilinos/12.18.1-openblas
bash-3.2$

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[Scott Ziegler]

I'm using version 9.0.0 of deal.ii. I have an older MacBook and it won't update past iOS 10.13.6. I downloaded the .dmg file and opened it/moved it into my applications but I haven't done anything else besides try to run the first example.

[luca.heltai]

In the documentation of the 9.0.0 package, this is what is installed via spack:

==> 60 installed packages.
-- darwin-highsierra-x86_64 / cl...@6.0.0 -----------------------
adol-c@develop g...@6.1.2 ma...@1.5.9 ni...@1.8.2 readline@7.0
arpa...@3.6.3 gm...@4.0.0 me...@5.1.0 num...@5.9.0 sl...@3.9.2
ass...@4.0.1 gsl@2.3 m...@1.1.0 o...@0.18.3 sql...@3.23.1
auto...@2.69 hd...@1.10.3 mp...@4.0.1 open...@0.3.3 suite-...@5.3.0
auto...@1.16.1 hw...@1.11.9 mu...@5.1.1 ope...@3.1.2 sund...@3.2.0
bo...@1.68.0 hy...@2.14.0 mupa...@2.2.5 ope...@1.0.2o superl...@5.2.2
bz...@1.0.6 intel-tbb@2019 nano...@1.2.3 p4est@2.0 superlu-mt@3.1
cm...@3.12.2 i...@0.19 ncurses@6.1 parm...@4.0.3 t...@8.6.8
environme...@3.2.10 libsi...@2.11 net...@4.6.1 pe...@5.26.2 tet...@1.5.0
g...@8.2.0 lib...@2.4.6 netcdf-cxx@4.2 pe...@3.9.2 tril...@12.12.1
gd...@1.14.1 lib...@2.9.8 net...@5.3.1 pkg...@1.4.2 x...@5.2.4
g...@0.9.7.1 m...@1.4.18 netlib-s...@2.0.2 pyt...@2.7.15 zl...@1.2.11

and includes environme...@3.2.10 (i.e., the module command).

Also, the library is installed in

# deal.II configuration:
# CMAKE_BUILD_TYPE: DebugRelease
# BUILD_SHARED_LIBS: ON
# CMAKE_INSTALL_PREFIX: /Applications/deal.II-9.0.0.app/Contents/Resources
# CMAKE_SOURCE_DIR: /Applications/deal.II-9.0.0.app/Contents/Resources/spack/src/dealii-v9.0.0
# (version 9.0.0)
# CMAKE_BINARY_DIR: /Users/heltai/dealii/build-pack-deal.II-9.0.0
# CMAKE_CXX_COMPILER: Clang 6.0.0 on platform Darwin x86_64
# /Applications/deal.II-9.0.0.app/Contents/Resources/spack/view/bin/mpicxx

Can you try to configure step-1 indicating the paths that you see here directly?

export DEAL_II_DIR=/Applications/deal.II-9.0.0.app/Contents/Resources

Notice that you should have accesso to all libraries and binaries also in

/Applications/deal.II-9.0.0.app/Contents/Resources/spack/view/lib

and

/Applications/deal.II-9.0.0.app/Contents/Resources/spack/view/bin

That is, you can force cmake to look there by adding as option CMAKE_PREFIX_PATH=/Applications/deal.II-9.0.0.app/Contents/Resources/spack/view/

What happens if you try to configure and run step-1 after setting DEAL_II_DIR manually?

L.

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