I got an error. Help please!

bung...@hotmail.com

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Oct 17, 2017, 8:10:43 AM10/17/17

to Salvus

Hi there,

I've been trying to install Salvus. According to this website (https://salvus.io/installation/), I got to "Install salvus and run the test suite" section and I somehow can't run "cmake ..\" section on my Macbook. Here is what I got:

(salvus) dhcp-10-181-9-64:build bung$ conda --version

conda 4.2.13

(salvus) dhcp-10-181-9-64:build bung$ source activate

(root) dhcp-10-181-9-64:build bung$ conda install -c anaconda conda

Fetching package metadata .............

Solving package specifications: ..........

Package plan for installation in environment /Users/bung/anaconda:

The following packages will be downloaded:

package | build

---------------------------|-----------------

conda-4.3.29 | py36hbf39572_0 511 KB anaconda

The following packages will be UPDATED:

conda: 4.2.13-py36_0 conda-forge --> 4.3.29-py36hbf39572_0 anaconda

Proceed ([y]/n)? y

Fetching packages ...

conda-4.3.29-p 100% |####################################################################| Time: 0:00:01 404.42 kB/s

Extracting packages ...

[ COMPLETE ]|#######################################################################################| 100%

Unlinking packages ...

[ COMPLETE ]|#######################################################################################| 100%

Linking packages ...

[ COMPLETE ]|#######################################################################################| 100%

(root) dhcp-10-181-9-64:build bung$ conda --version

conda 4.3.29

(root) dhcp-10-181-9-64:build bung$ cd /users/bung/src/salvus/

(root) dhcp-10-181-9-64:salvus bung$ source activate salvus

(salvus) dhcp-10-181-9-64:salvus bung$ conda install flake8 h5netcdf pytest-mpl

Fetching package metadata ...............

Solving package specifications: .

Package plan for installation in environment /Users/bung/anaconda/envs/salvus:

The following NEW packages will be INSTALLED:

h5netcdf: 0.4.3-py_0 conda-forge

matplotlib: 2.1.0-py36_0 conda-forge

nose: 1.3.7-py36_2 conda-forge

pip: 9.0.1-py36_0 conda-forge

pytest: 3.2.3-py36_0 conda-forge

pytest-mpl: 0.9-py_0 conda-forge

wheel: 0.30.0-py_1 conda-forge

Proceed ([y]/n)? y

(salvus) dhcp-10-181-9-64:salvus bung$ cmake .. \

> -DPETSC_DIR=/opt/petsc \

> -DEIGEN_INCLUDE=/usr/local/include/eigen3 \

> -DNETCDF_DIR=/usr/local \

> -DHDF5_DIR=/usr/local

CMake Error: The source directory "/users/bung/src" does not appear to contain CMakeLists.txt.

Specify --help for usage, or press the help button on the CMake GUI.

(salvus) dhcp-10-181-9-64:salvus bung$ cd /users/bung/src/salvus/

(salvus) dhcp-10-181-9-64:salvus bung$ cmake .. \

> -DPETSC_DIR=/opt/petsc \

> -DEIGEN_INCLUDE=/usr/local/include/eigen3 \

> -DNETCDF_DIR=/usr/local \

> -DHDF5_DIR=/usr/local

CMake Error: The source directory "/users/bung/src" does not appear to contain CMakeLists.txt.

Specify --help for usage, or press the help button on the CMake GUI.

(salvus) dhcp-10-181-9-64:salvus bung$ pwd

/users/bung/src/salvus

(salvus) dhcp-10-181-9-64:salvus bung$ ls

CMakeLists.txt salvus_examples

README.md salvus_flow

assert_all_python_dependencies_are_installed.py salvus_mesher

build salvus_seismo

pyexodus salvus_wave

(salvus) dhcp-10-181-9-64:salvus bung$ cmake .. \

> -DPETSC_DIR=/opt/petsc \

> -DEIGEN_INCLUDE=/usr/local/include/eigen3 \

> -DNETCDF_DIR=/usr/local \

> -DHDF5_DIR=/usr/local

CMake Error: The source directory "/users/bung/src" does not appear to contain CMakeLists.txt.

Specify --help for usage, or press the help button on the CMake GUI.

(salvus) dhcp-10-181-9-64:salvus bung$ cd build

(salvus) dhcp-10-181-9-64:build bung$ cmake .. \

> -DPETSC_DIR=/opt/petsc \

> -DEIGEN_INCLUDE=/usr/local/include/eigen3 \

> -DNETCDF_DIR=/usr/local \

> -DHDF5_DIR=/usr/local

-- Autogenerating template instantiations

-- Done autogenerating template instantiations

=====================================================================================

The following Python modules/dependencies are not installed in the chosen Python installation.

flake8, h5netcdf, pytest-mpl

Please install them with conda or pip and execute cmake again.

=====================================================================================

CMake Error at CMakeLists.txt:26 (MESSAGE):

-- Configuring incomplete, errors occurred!

See also "/users/bung/src/salvus/build/CMakeFiles/CMakeOutput.log".

(salvus) dhcp-10-181-9-64:build bung$ ls

CMakeCache.txt CMakeFiles CTestCustom.cmake build

(salvus) dhcp-10-181-9-64:build bung$ conda list

# packages in environment at /Users/bung/anaconda/envs/salvus:

#

asn1crypto 0.22.0 py36_0 conda-forge

backports 1.0 py36_1 conda-forge

backports.functools_lru_cache 1.4 py36_1 conda-forge

blas 1.1 openblas conda-forge

ca-certificates 2017.7.27.1 0 conda-forge

certifi 2017.7.27.1 py36_0 conda-forge

cffi 1.10.0 py36_0 conda-forge

chardet 3.0.4 py36_0 conda-forge

cryptography 2.0.3 py36_0 conda-forge

cycler 0.10.0 py36_0 conda-forge

decorator 4.1.2 py36_0 conda-forge

flake8 3.4.1 py36_0 conda-forge

freetype 2.7 1 conda-forge

future 0.16.0 py36_0 conda-forge

h5netcdf 0.4.3 py_0 conda-forge

h5py 2.7.1 py36_1 conda-forge

hdf5 1.8.18 1 conda-forge

icu 58.1 1 conda-forge

idna 2.6 py36_1 conda-forge

jsonschema 2.6.0 py36_0 conda-forge

libffi 3.2.1 3 conda-forge

libgfortran 3.0.0 0 conda-forge

libiconv 1.14 4 conda-forge

libpng 1.6.28 1 conda-forge

libxml2 2.9.5 0 conda-forge

libxslt 1.1.29 5 conda-forge

lxml 4.1.0 py36_0 conda-forge

matplotlib 2.1.0 py36_0 conda-forge

mccabe 0.6.1 py36_0 conda-forge

mkl 2017.0.3 0

ncurses 5.9 10 conda-forge

nose 1.3.7 py36_2 conda-forge

numpy 1.13.3 py36_blas_openblas_200 [blas_openblas] conda-forge

openblas 0.2.19 2 conda-forge

openssl 1.0.2l 0 conda-forge

pip 9.0.1 py36_0 conda-forge

py 1.4.34 py36_0 conda-forge

pycodestyle 2.3.1 py36_0 conda-forge

pycparser 2.18 py36_0 conda-forge

pyflakes 1.5.0 py36_0 conda-forge

pyparsing 2.2.0 py36_0 conda-forge

pysocks 1.6.7 py36_0 conda-forge

pytest 3.2.3 py36_0 conda-forge

pytest-mpl 0.9 py_0 conda-forge

python 3.6.3 0 conda-forge

python-dateutil 2.6.1 py36_0 conda-forge

pytz 2017.2 py36_0 conda-forge

pyyaml 3.12 py36_1 conda-forge

readline 6.2 0 conda-forge

scipy 0.19.1 py36_blas_openblas_202 [blas_openblas] conda-forge

setuptools 36.6.0 py36_1 conda-forge

six 1.11.0 py36_1 conda-forge

sqlalchemy 1.1.13 py36_0 conda-forge

sqlite 3.13.0 1 conda-forge

tk 8.5.19 2 conda-forge

tornado 4.5.2 py36_0 conda-forge

wheel 0.30.0 py_1 conda-forge

xz 5.2.3 0 conda-forge

yaml 0.1.6 0 conda-forge

zlib 1.2.8 3 conda-forge

(salvus) dhcp-10-181-9-64:build bung$

I am in the right directory and the right environment. It told me to install flake8, h5netcdf, pytest-mpl, which I did (as it's shown on the list above)

Sincerely,

Phuripan Jangthongsiri

Lion Krischer

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Oct 17, 2017, 3:14:43 PM10/17/17

to sal...@googlegroups.com

Hi Phuripan,

can you just delete the contents of the `build` directory and run cmake again? Make sure the correct Python environment is active while doing it. Salvus will install its Python packages into the Python installation discovered while you run `cmake` - it is also printed during the cmake run.

I guess at some point it got confused during your installation procedure. If it still does not work, can you send us the produces 'CMakeOutput.log' file?

Cheers!

Lion

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bung...@hotmail.com

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Oct 20, 2017, 7:50:39 AM10/20/17

to Salvus

Hi Lion,

It's still doesn't work. Here is what I got:

(salvus) dhcp-10-181-9-64:build bung$ rm -r build/

(salvus) dhcp-10-181-9-64:build bung$ ls

CMakeCache.txt CMakeFiles CTestCustom.cmake

(salvus) dhcp-10-181-9-64:build bung$ cmake .. \

> -DPETSC_DIR=/opt/petsc \

> -DEIGEN_INCLUDE=/usr/local/include/eigen3 \

> -DNETCDF_DIR=/usr/local \

> -DHDF5_DIR=/usr/local

-- Autogenerating template instantiations

-- Done autogenerating template instantiations

=====================================================================================

The following Python modules/dependencies are not installed in the chosen Python installation.

flake8, h5netcdf, pytest-mpl

Please install them with conda or pip and execute cmake again.

=====================================================================================

CMake Error at CMakeLists.txt:26 (MESSAGE):

-- Configuring incomplete, errors occurred!

See also "/users/bung/src/salvus/build/CMakeFiles/CMakeOutput.log".

(salvus) dhcp-10-181-9-64:build bung$ conda list

# packages in environment at /Users/bung/anaconda/envs/salvus:

#

asn1crypto 0.22.0 py36_0 conda-forge

ca-certificates 2017.7.27.1 0 conda-forge

certifi 2017.7.27.1 py36_0 conda-forge

cffi 1.10.0 py36_0 conda-forge

chardet 3.0.4 py36_0 conda-forge

cryptography 2.0.3 py36_0 conda-forge

cycler 0.10.0 py36_0 conda-forge

decorator 4.1.2 py36_0 conda-forge

flake8 3.4.1 py36_0 conda-forge

freetype 2.7 1 conda-forge

future 0.16.0 py36_0 conda-forge

h5netcdf 0.4.3 py_0 conda-forge

h5py 2.7.1 py36_1 conda-forge

hdf5 1.8.18 1 conda-forge

icu 58.1 1 conda-forge

idna 2.6 py36_1 conda-forge

intel-openmp 2018.0.0 hdd0ccc9_7

jsonschema 2.6.0 py36_0 conda-forge

libcxx 4.0.1 h579ed51_0

libcxxabi 4.0.1 hebd6815_0

libffi 3.2.1 3 conda-forge

libgfortran 3.0.1 h93005f0_2

libiconv 1.14 4 conda-forge

libpng 1.6.28 1 conda-forge

libxml2 2.9.5 0 conda-forge

libxslt 1.1.29 5 conda-forge

lxml 4.1.0 py36_0 conda-forge

matplotlib 1.5.3 np113py36_8 conda-forge

mccabe 0.6.1 py36_0 conda-forge

mkl 2018.0.0 hc285769_4

ncurses 5.9 10 conda-forge

nose 1.3.7 py36_2 conda-forge

numpy 1.13.3 py36h2cdce51_0

obspy 1.0.3 py36_1 conda-forge

openssl 1.0.2l 0 conda-forge

pip 9.0.1 py36_0 conda-forge

py 1.4.34 py36_0 conda-forge

pycodestyle 2.3.1 py36_0 conda-forge

pycparser 2.18 py36_0 conda-forge

pyflakes 1.5.0 py36_0 conda-forge

pyopenssl 17.2.0 py36_0 conda-forge

pyparsing 2.2.0 py36_0 conda-forge

pysocks 1.6.7 py36_0 conda-forge

pytest 3.2.3 py36_0 conda-forge

pytest-mpl 0.9 py_0 conda-forge

python 3.6.3 0 conda-forge

python-dateutil 2.6.1 py36_0 conda-forge

pytz 2017.2 py36_0 conda-forge

pyyaml 3.12 py36_1 conda-forge

readline 6.2 0 conda-forge

requests 2.18.4 py36_1 conda-forge

scipy 0.19.1 py36h3e758e1_3

setuptools 36.6.0 py36_1 conda-forge

six 1.11.0 py36_1 conda-forge

sqlalchemy 1.1.13 py36_0 conda-forge

sqlite 3.13.0 1 conda-forge

tk 8.5.19 2 conda-forge

toml 0.9.3 <pip>

tornado 4.5.2 py36_0 conda-forge

urllib3 1.22 py36_0 conda-forge

wheel 0.30.0 py_1 conda-forge

xz 5.2.3 0 conda-forge

yaml 0.1.6 0 conda-forge

zlib 1.2.8 3 conda-forge

(salvus) dhcp-10-181-9-64:build bung$ source activate salvus

Also, I attached CMakeOutput.log file in this reply. Please let me know if you know what I did wrong.

Sincerely,

Phuripan Jangthongsiri

CMakeOutput.log

Lion Krischer

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Oct 20, 2017, 9:24:21 AM10/20/17

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Hi Phuripan,

please make sure your `build` directory is empty before you run `cmake` again and send the output if it does not work. You tried to delete `build/` while you already were in the build directory.

Cheers!

Lion

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bung...@hotmail.com

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Oct 25, 2017, 8:12:15 AM10/25/17

to Salvus

Hi Lion,

I got the new error. Here is what I got:

(salvus) dhcp-10-181-9-64:salvus bung$ rm -rf /users/bung/src/salvus/build

(salvus) dhcp-10-181-9-64:salvus bung$ mkdir build

(salvus) dhcp-10-181-9-64:salvus bung$ cd build

(salvus) dhcp-10-181-9-64:build bung$ cmake .. \

> -DPETSC_DIR=/opt/petsc \

> -DEIGEN_INCLUDE=/usr/local/include/eigen3 \

> -DNETCDF_DIR=/usr/local \

> -DHDF5_DIR=/usr/local

-- The C compiler identification is AppleClang 9.0.0.9000038

-- The CXX compiler identification is AppleClang 9.0.0.9000038

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Found PythonInterp: /users/bung/anaconda/envs/salvus/bin/python (found version "3.6.3")

-- Autogenerating template instantiations

-- Done autogenerating template instantiations

-- Performing Test COMPILER_SUPPORTS_CXX11

-- Performing Test COMPILER_SUPPORTS_CXX11 - Success

-- Performing Test COMPILER_SUPPORTS_undefined_var_template

-- Performing Test COMPILER_SUPPORTS_undefined_var_template - Success

-- Found MPI_C: /usr/local/Cellar/open-mpi/2.1.1/lib/libmpi.dylib

-- Found MPI_CXX: /usr/local/Cellar/open-mpi/2.1.1/lib/libmpi.dylib

-- salvus_flow will not be installed as some dependencies are missing: redis

-- Configuring done

-- Generating done

-- Build files have been written to: /users/bung/src/salvus/build

(salvus) dhcp-10-181-9-64:build bung$ cd ..

(salvus) dhcp-10-181-9-64:salvus bung$ conda install redis

Fetching package metadata ...............

Solving package specifications: .

# All requested packages already installed.

# packages in environment at /Users/bung/anaconda/envs/salvus:

#

redis 4.0.2 hc28a91c_0

Lion Krischer

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Oct 25, 2017, 8:24:53 AM10/25/17

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Hi,

this is just a warning. SalvusFlow is an optional submodule for running jobs on remote clusters, which is currently still in an experimental phase. SalvusFlow is not needed to create meshes or to run simulations on the same computer on which you are installing Salvus. The missing packages is called `redis-py` on conda but just continue the installation without worrying about SalvusFlow.

Cheers!

Lion

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bung...@hotmail.com

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Oct 25, 2017, 10:23:03 AM10/25/17

to Salvus

Hi again Lion,

Thank you for your help! Once again that I got error. I ran make CTEST_OUTPUT_ON_FAILURE=1 test and got errors (as in an attachment). Please help.

Sincerely,

Phuripan Jangthongsiri

make CTEST_OUTPUT_ON_FAILURE=1 test.rtf

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